Old Micro Written Exams Flashcards
What stage of syphilis is the highest risk for Jarisch-Herxheimer reaction?
Secondary
3 clinical manifestations of syphilis that would result in complications if a Jarish-Herxheimer reaction developed?
1) Neurosyphilis
2) Ocular syphilis
3) Cardiovascular syphilis
3 treatments for head lice?
1) 1% Permethrin Topical Thearpy
2) Wet combing
3) Oral Ivermectin
Burkholderia cepacia
- catalase
- oxidase
- motility
- pyoveridin
- polymyxin
Catalase positive Oxidase positive Motility positive Pyoveridin negative Polymyxin R
3 genomovars of Burkhulderia?
I = cepacia II = multivorans III = cenocepacia
Burkholderia genomovar with worst post transplant outcome?
III = cenocepacia
4 antibiotics to test for sus to B. cepacia?
1) TMP-SMX
2) Meropenem
3) Ceftazidime
4) Ticar-Clav
5) Minocycline
6) Levofloxacin
7) Chloramphenicol
Penicillin Resistant corynebacterium?
C. jeikieum
Corynebacterium with yellow pigment?
1) C. aurimucosum
2) C. xerosis
Corynebacterium with reverse CAMP positive?
1) C. ulcerans
2) C. pseudotuberculosis
AST method for Coryne?
Broth microdilution
3 other Gram positive Bacilli same AST guidelines as corynebacterium?
1) Arcanobacterium
2) Microbacterium
3) Dermabacter
4) Leifsonia
5) Cellulomonas
6) Turicella
7) Rothia
8) Oerskovia
9) Brevibacterium
3 antibiotics to report for coryne?
1) Vancomycin
2) Penicillin
3) Erythromycin
4) Gentamycin
3 advantages of MALDITOF?
1) Rapid
2) Decrease cost of consumables
3) Large database
4) Ease of use
5) High throughput
1 organism that requires testing in addition to MALDITOF?
Streptococcus pneumonaie
Neisseria gonorrhoea
Neisseria meningitidis
4 indications for 16S testing?
1) Typing
2) Unknown ID with other methods
3) Confirm the ID of a rarely isolated pathogen
4) Slow to grow organisms
Ecoli 0104- limitations to usual culture method?
It’s a sorbitol fermenter - may not be picked up on SMAC
2 ways to test for shiga toxin
- Advantage and disadvantage of each
1) PCR
Advantage: Differentiate sxt1 from sxt2
Disadvantage: Specialized lab equipment and training
2) EIA
Advantage: Minimal training or special equipment
Disadvantage: No culture for typing
Source of the shiga toxin gene?
Bacteriophage (sxt phages)
3 parasitology fixatives?
1) SAF
2) MIF (merthiolate-iodine formalin)
3) PVA - polyvinyl alcohol
4) Modified PVA - no mercury
5) Schaudinn’s with or without PVA
Concentration of formalin usually used in the lab?
10% for helminth eggs and larvae
5% for protozoa and cysts
1:10 stool to formalin
Lab monitoring to be done with SAF?
3 times to do it
Benefit in terms of safety
Monitor for formaldehyde vapour (can no exceed 0.75 ppm)
Times: 8 hours and 15 minute exposures
No mercury in it
2 parasitology stains
1) Modified trichrome
2) Modified acid fast
1 way to culture strongiloides?
In a petri dish on a lawn of Ecoli
Best concentration technique for Fasciola?
Sedimentation concentration
2 species of bedbugs that infect humans?
1) Cimex lectularis
2) Cimex hemipterus
2 methods to elminate bedbugs?
1) Heat room to 50 celcius for 90 minutes
2) Wash in hot water and dryer max setting for 30 min
Most common mechanism Staph is non susceptible to vancomycin?
- 2 other antibiotics with this mechanism of resistance?
Thickened peptidoglycan layer
1) Teicoplanin
2) Telavancin
3) Oritavancin
2 things to do if Staph MIC to Vancomycin is 8
1) Confirm isolate ID
2) GRD Etest
Gold standard for hVISA?
Population analysis profile
4 things to address in a Biosecurity Plan?
1) Physical security
2) Personnel suitability and reliability
3) Infectious material and toxin accountability
4) Incident and Emergency response
5) Information security
4 vaccines to recommend to lab workers?
1) Neisseria meningititis
2) Hepatitis B
3) Typhoid
4) Influenza
5) Primary polio series
4 tests lab workers should have before beginning employment?
1) TB skin test
2) HBV
3) HIV
4) Hepatitis C
5) Varicella serology
2 tests to differentiate Kingella kingae from other Kingella species?
1) Produces acid from maltose
2) Beta hemolysis (positive for kingae)
1 growth requirement for Neisseria gonorrhoea?
Hemin?
Chocolate agar?
2 Neisseria species that are not cocci?
1) N. elongta
2) N. weaveri
3) N. bacilliformis
3 Neisseria species that produce acid in glucose and maltose?
1) N. meningititis
2) N. lactamica
3) N. sicca
3 mechanisms of pseudomonas carbapenem resistance?
1) Carbapenemase
2) Efflux
3) Porin deletion (OprD)
2 antibiotics to test in pseudomonas resistant to carbapenems?
1) Aztreonam
2) Colistin
How to fix the prozone effect?
Dilute the sample
How to avoid false positives for RF in serology?
Treat the sample with a reducing agent (2-mercaptoethanol or pronase)
3 microscopic features of crypto?
1) Narrow budding
2) Capsule
3) Round shape
4) Variation in size
1 stain to differentiate crypt from blasto?
Mucicarmine
What cryptococcus is in BC?
Cryptococcus neoformans and Cryptococcus gattii
2 methods to distinguish C. neoformans from C. gattii?
1) Molecular methods
2) Capsule typing (A, D, AD = neoformans, B, C = gattii)
Treatment for cryptococcus
Induction phase = Amphotericin B 0.7-1 mg/kg IV daily x 2 weeks + Flucytosine 25 mg/kg q6h po x 2 weeks
Consolidation phase = Fluconazole 400 mg po daily x 8 weeks
Maintenance phase = Fluconazole 200 mg po daily for >=1 year
*(can stop maintenance phase after a minimum of 1 year if: successful introduction of HAART, CD4 >100, and low or nondetectable VL for >3 months)
1 phenotypic test to confirm a KPC?
Modified Hodge Test
or
Disk Inhibition assay with Meropenem with and without Boronic Acid
4 organisms that carry KPC?
1) E. Coli
2) K. pneumoniae
3) Pseudomonas
4) Enterobacter cloacae
Acinetobacter, Kleb oxy, Salmonella, Enterobacter aerogenes, Citrobacter
Clinical situation for Galactomannan testing?
HSCT patients and neutorpenic patients with hematological malignancies
3 false positives for Galactomannan testing?
1) Piptazo
2) Dietary galactomannan
3) Cross reaction with alternaria, paeciliomyces
Aspergillus treatment and dose
Voriconazole 6 mg/kg IV q12h x 1 days, then 4 mg/kg IV q12h x 2 weeks then step down to oral 200 mg q12h
What do you call bacteria that are inhibited by not killed?
Persisters
2 methods for bactericidal testing?
1) Determination of MBC via broth dilution
2) Kinetic Time-kill Assay
3) Serum bacteriocidal in vivo test
2 viruses that can not grow in cell culture?
1) HMPV
2) Norovirus
Cell line for HSV?
HFL, Vero
Cell line for influenza?
RMK
2 false positive for malaria rapid Ag test?
1) Cross reaction with RF
2) Previous positive with HRP2 persistence
3) Cross reaction with Leish or Trypano
2 false negatives for P. falciparum on malaria rapid Ag test?
1) Low parasitemia
2) Prozone effect
3) P. falciparum strain that does not produce the HRP2 Ag
Rabies gold standard for diagnosis?
Tissue biopsy from nape of neck for DFA
Rabies finding on pathology?
Negri bodies (eosinophilic intracytoplasmic inclusions) in cells of CNS
Most feasible way to diagnose rabies?
PCR of saliva
4 times to test neonate for syphilis?
1) Signs or symptoms of congenital syphilis
2) Mother had positive syphilis test in pregnancy and was not treated
3) Mother treated with anything other than Penicillin in pregnancy
4) Mother positive in the last month of pregnancy
5) Mother treated but less than 4 fold decrease in titres
5 times to order HCV PCR?
1) Acute infection
2) Immunosuppressed patient
3) Monitor treatment
4) Positive Hep C Ab test
5) Monitoring chronic patient
4 reasons for HBV isolated core Ab positive?
1) Window period
2) Previous infection with decreased sAb
3) Chronic infection with low levels of sAg
4) False positive
2 mechanisms of CMV resistance?
UL54 polymerase mutation
UL97 mutation - unable to phosphorylation of ganciclovir
2 ways to test for CMV resistance?
1) Phenotypic - culture in presence of the drug
2) Genotypic - sequencing
How many days to do consecutive QC testing for a new antibiotic?
30
How to test proficiency if no external program is available?
1) Interlab samples with another lab
2) Intralab samples with different technologists looking at the same sample
3) Split samples and do with 2 different methods?
Read the CLSI…
2 reasons for internal controls in PCR?
1) Check for inhibitors in the sample
2) Ensure the reaction conditions were such that genetic material could be amplified
MS patient on Natalizumab.
a. What latent CNS pathogen are they at risk for?
b. What infectious complication can occur when its stopped?
a) JC Virus (also HSV and VZV)
b) PML
Elderly woman with encephalitis picture. Lesion in temporal lobe on imaging. CSF reveals 122 WBC (lymphs) and 244 RBC.
a. What is the etiologic agent & syndrome
b. What is best test to confirm diagnosis
c. What is the treatment (dose, duration)
a) HSV, Herpes Encephalitis
b) PCR of the CSF for HSV
c) Acyclovir 10 mg/kg IV q8h x 21 days
Pregnant woman with history and findings consistent with Listeria meningitis. Which infection precautions did she not follow? List 5.
1) Should not eat deli meats while pregnant
2) Should not consume unpasteurized cheeses (especially soft ones) while pregnant
3) Should not consume unpasteurized milk while pregnant
4) Should wash fruits and vegetables thoroughly prior to consumption
5) Thoroughly cook raw meat to safe internal temperature
6) Keep fridge less than 4.4 degrees celcius and freezer less than -17.8
7) Wash hands, knives, cutting boards after handling raw food
8) Do not eat refrigerated pates and meat spreads
9) Do not eat refrigerated smoked seafoods unless it’s been cooked
Duration of antibiotics for different bacterial meningitis:
Neisseria meningititis Haemophilus influenza Streptococcus pneumoniae GBS Aerobic GNB Listeria
Neisseria meningititis = 7 days Haemophilus influenza = 7 days Streptococcus pneumoniae = 10-14 days GBS = 14-21 days Aerobic GNB = 21 days Listeria = 21 days
What are the animal reservoirs postulated for H7N9 and MERS-CoV?
H7N9 = Avian species, especially poultry MERS-CoV = Bats or Camels
What are the incubation periods to monitor contacts of H7N9 and MERS-CoV for?
H7N9 = 10 days MERS-CoV = 14 days
List 8 countries where MERS CoV has been confirmed.
1) Lebanon
2) Saudi Arabia
3) Oman
4) Jordan
5) Kuwait
6) Qatar
7) Yeman
8) United Arab Emerits
9) France
10) Italy
11) Egypt
12) Iran
13) Algeria
HIV+ patient diagnosed with Crypto meningitis. What are the phases of management & specific doses and durations for each phase?
Induction phase = Amphotericin B 0.7-1 mg/kg IV daily x 2 weeks + Flucytosine 25 mg/kg q6h po x 2 weeks
Consolidation phase = Fluconazole 400 mg po daily x 8 weeks
Maintenance phase = Fluconazole 200 mg po daily for >=1 year
*(can stop maintenance phase after a minimum of 1 year if: successful introduction of HAART, CD4 >100, and low or nondetectable VL for >3 months)
List all the major and minor criteria for Modified Duke’s Criteria
Major:
1) Blood culture positive for IE
- VGS, NVS, Strep gallolyticus, HACEK, S. aureus, Enterococcus without focus from 2 separate sets
- Organisms consistent with IE from persistently positive blood culture (>=2 bottles >12 hr apart, all of 3 bottles or majority of >=4 from >1 hr from first to last)
- Single positive culture for Coxiella burnettii or anti Phase I IgG >1:800
2) Evidence of Endocardial Involvement (Echo positive for IE)
a) New or partial dehiscence of a PV
b) Abscess in the tissues surrounding a heart valve
c) New regurgiant murmur
d) intracardiac mass
Minor:
1) Fever (>38)
2) Predisposition (PV, Turbulent or reguritent flow, IVDU)
3) Vascular phenomenon (emboli, ICH, subconjuntival hemorrhages, Janeway lesions)
4) Immunologic phenomenon (GN, Roth’s spots, Osler’s nodes, RF)
5) Positive blood cultures that do not meet defintions of major criteria or serological evidence of active infection with organism consistent with IE
Definitive IE = Pathological/Culture positive OR
2 major OR
1 major and 3 minor OR
5 minor
Possible IE = 1 major and 1 minor OR
3 minor
What are 3 risk factors for invasive aspergillosis?
1) Allogenic Hematopoetic Stem Cell transplant recipient
2) Hematological malignancy with neutropenia
3) Lung Transplant patients
4) Heart Transplant patients
5) GVHD
6) CGD
7) HIV
What is the treatment of choice for CNS aspergillosis?
Voriconazole 6 mg/kg IV q12h x 1 day, then 4 mg/kg q12 h
Clinical history of an allo BMT patient, who had suffered from cGVHD and been on steroids, who became acutely unwell with respiratory failure, infiltrates on CXR and hypoxemia. Patient had BAL performed, which was negative for usual bacterial, and fungal pathogens. Resp virus multiplex negative.
a) What are 2 possible non-viral etiologies of these symptoms?
b) You suspect CMV. What 2 tests would you to confirm & what empiric treatment would you give?
a) PCP (shouldn’t be that acute) Nocardia Legionella NTM (Mycobacterium avium, Mycobacterium kansasii) TB Mycoplasma pneumonia
b)
Tests = PCR for CMV, pp65 antigen assay, shell vial assay with DFA
Treatment = Gancyclovir + CMV immune globulin
Name 2 pathogens associated with handling fish.
1) Erysipilothrix rhusopathiae
2) Streptococcus iniae
Name 3 pathogens associated with SSTIs after water exposure.
1) Aeromonas hydrophila
2) Vibrio vulnificus
3) Mycobacterium marinum
4) Edwardsiella tarda
5) Erysipilothrix rhusopathiae
32M in Amazon on canoeing trip. Got appropriate malaria prophylaxis. Upon return home, developed 20% eosinophilia and cough and pulmonary infiltrates. Name this syndrome & 4 parasites (to genus) which could cause it.
Syndrome = Loeffler’s syndrome Parasites: 1) Nectator 2) Ancyclostoma 3) Ascaris 4) Strongyloides 5) Toxocara
A patient with IBD is going to be started on a biologic. Give 4 suggestions for workup of this patient.
1) TB Skin Test
2) Hepatitis B serology
3) Hepatitis C serology
4) HIV serology
A patient is confirmed to have active pulmonary TB.
a. As infection control officer, what 4 things do you need to do?
b. You are asked to review system for occupational health exposures on the medical ward affected. What metrics would you use to do this?
a)
1) Place the patient on airborne precautions
2) Ensure the staff are fit testing for N95 respirators
3) Notify public health
4) Ensure the patient will have DOT with medication
5) Contact tracing
6) Identify the index case
b)
TB Skin testing results prior to exposure
Follow up TB skin testing
Assess any TB skin test conversions
Name 3 pathogens that require airborne precautions.
1) Mycobacterium tuberculosis
2) Measles virus
3) Varicella virus
4) SARS
5) Smallpox
Confirmed measles case in kid.
a. What type of precautions & for how long?
b. What PEP can be given and in what time frame (2 boxes to fill in)
c. What do you do for the mother?
a) Airborne until day 5 of the rash
b) Measles gamma globulin within 6 days of the exposure
Can also give measles vaccine within 72 hours of the exposure
c) Ask if she has previous had measles, the measles vaccine or if she was born before 1970. Also check if she is pregnant or not.
Mechanism of action of daptomycin
Calcium dependant depolarization of the cell membrane by binding to the cell membrane, causing inhibition of DNA, RNA and protein synthesis
1 contraindication to daptomycin use
Contraindication = Pneumonia
3 organisms not covered by erta that are covered by other carbapenems.
1) Pseudomonas aeruginosa
2) Acinetobacter species (baumannii or calcoaceticus complex)
3) Enterococcus species (especially faecalis)
Best carbapenem for amp-susceptible E. faecalis? Best for E. faecium (not details given)
E. faecalis = Imipenem
E. faecium = Imipenem? Or none?
When is meropenem preferred over imipenem?
When covering for Morganella morganii, Proteus mirabilis, Proteus penneri, Proteus vulgaris, Providencia rettgeri as they can have higher MICs to Imipenem.
Burkholderia cepacia is intrinsically resistant to imipenem but meropenem can have activity.
Also when there is a risk for seizures.
Name 3 infection control requirements for patient on airborne precautions.
1) Negative pressure airflow
2) Single room
3) Air exhausted outdoor or HEPA filtered if recirculated
4) 6-12 air exhanges per hour
5) Patient to remain in room or wear mask when leaving
- Norovirus outbreak in LTCF with 40 beds. You are Infection control officer and are called in to manage outbreak. You plot the epi curve. They gave a propagated epi curve with index case, followed by 2 peaks.
a. Name 6 control measures you would implement.
1) Patient isolation
2) Strict hand hygiene
3) Restrict visitors
4) Close the unit to new patients
5) Increase cleaning and disinfection of the unit
6) Exclude ill employees until 48 hours after symptoms resolved
7) Dedicate equipment to patients
8) No meetings or gatherings in outbreak zone
What are the 5 types of outbreaks based on an epidemiological curve?
A. Common Source Outbreaks
a. Point Source Outbreak with no Propigation (Summer BBQ)
b. Continuing Source Outbreak (Contaminated Water Supply)
c. Intermittent Outbreaks (Seasonal)
B. Person to Person Spread
a. Index Case with Limited Spread (Returning traveller infects others)
b. Propigated Spread – Disseminated Outbreak originating from an index case with propagated spread
What are 2 features of norovirus that would make it hard to control, despite appropriate standard precautions?
Extended shedding of the virus in stools Can survive for days on surfaces Nonenveloped virus that can resist disinfection Low infectious dose Multiple modes of transmission Short incubation period
List 5 indications for quadrivalent meningococcal vaccination.
1) Travel to an endemic area
2) Microbiology Laboratory workers
3) Outbreaks
4) Close contacts of a positive case of Neisseria meningitis
5) Military personnel
6) Healthy persons aged 12-24 years
7) Functional or anatomical asplenia
8) Congenital immunodeficiency
9) Patients treated with eculizumab
List 6 indications for PCV-13 in adults.
1) Functional or anatomical asplenia
2) Bone marrow transplant recipients
3) Solid organ transplant recipient
4) HIV positive
5) Immunosuppression therapy
6) Sickle cell or other hemoglobinopathies
7) Congenital immunodeficiencies
8) Malignant neoplasms including lymphoma and leukemia
List 6 groups in which treatment with antivirals would be recommended for influenza.
1) Anyone with influenza presenting in the first 48 hours after symptom onset
2) Over 65 years
3) Children aged 1-5
4) Underlying asthma
5) Diabetics
6) COPD
7) Pregnant women and up to 4 weeks post partum
8) <18 on Chronic Aspirin
9) Obesity
10) Nursing Home
11) Malignancy
List 3 contraindications to the rotavirus vaccine
1) Allergy to any components of the vaccine
2) Previous intussceception
3) Immunocompromised
4) Uncorrected congenital abnormality of the GI tract that would predispose to intusseception
32M bit by dog in Nepal. Returns to Canada 10 days later. Wound is healing and looks ok.
a. What 4 interventions would you do in him to prevent rabies?
Instill wound with rabies immunoglobulin
Give rabies vaccine
Wash wound with soap and water (but it’s 10 days old..)
If the wound has been stitched remove the stitches?
Contact
What is the best specimen for diagnosing rabies and would tests should be done on it?
Tissue biopsy from the nape of the neck for DFA or PCR
Can also do PCR from the CSF or saliva
What are the two forms of clinical rabies?
Furious – hydrophobia, delirium, agitation, aerophobia
Paralytic – Ascending paralysis
What are 6 risk factors for CA-MRSA 10/USA300
1) Incarceration
2) Contact with positive individual
3) Owning a dog
4) Skin trauma
5) Cosmetic body shaving
6) IVDU
7) Native and Aboriginal communities
8) MSM
9) Group homes
Name an integrase inhibitor that can cause increased CK.
Raltegravir
Name an integrase inhibitor that can be used in integrase inhibitor experienced patients.
Dolutegravir
Name 4 Health Canada approved antivirals that can be used with PR (PEG interferon with Ribavirin) for treatment of HCV.
Sofosbuvir
Semepravir
Teleprivir
Bocepravir
What are 6 risk factors, except for co-infections, that are associated with increased risk for developing cirrhosis in HBV.
1) Alcohol
2) High Hepatitis B viral load (>2000)
3) eAg positivity
4) sAg >1000 IU/mL (in eAg negatives)
5) Male
6) Prolonged replication phase
7) Hepatitis D superinfection
8) Age >50
MRSA endocarditis
a. Treatment (agents, duration) for native valve & prosthetic valve IE
Native valve = Vancomycin x 6 weeks
Prosthetic valve = Vancomycin x 6 weeks + Rifampin x 6 weeks + Gentamycin x 2 weeks
What 2 measures besides treatment would you take in a case of MRSA IE?
Surgical intervention
Patient decolonization
Repeat blood cultures in 2-4 days
Look for source of seeding infection
Question about debridement & retention strategy for treating prosthetic joint infection.
a. What 4 factors must be considered in this decision?
1) Time since initial surgery (<30 days)
2) Organism
3) Presence of a sinus tract
4) Joint loosening
What is the treatment of choice for a Proprionibacterium infection?
Penicillin
Parvovirus
a. 4 clinical syndrome associated with besides erythema infectiosum
- Pure red cell aplasia
- Transient aplastic crisis
- Fetal hydrops
- Arthropathy
- Papular purpuric gloves and socks syndrome
A women is exposed to her child who has Parvovirus when she’s 18 weeks pregnant.
a) What 2 tests can be offered to her?
b) What treatment can be offered to her
a)
Parvovirus serology
Parvovirus PCR
b) Intrauterine transfusion
2 mechanisms of resistance of candida specie to azoles.
- Mutation in 14-a-demethylase
2. Efflux pump
1 resistance mutations associated with echinocandin resistance.
Mutation in the B 1,3 glucan synthase
1 antifungal that can develop rapid resistance to on monotherapy
Flucytosine
One species of aspergillus that is usually amphoB resistant.
Aspergillus terres
Hepatitis E. 4 extra-hepatic manifestations and complications.
- Pancreatitis
- Kidney Injury
- Hematological Disorder – thrombocytopenia, aplastic anemia
- Neurological Disorder – GBS, Bell’s palsy, Neuralgic amyotrphy, Acute transverse myelitis, Acute meningoencephalitis
- Arthralgias
- Urticarial rashes
- Described clinical scenario of some dude helping out there post-tsunami and coming back and becoming really sick with lung infiltrates. Cultures grew GNB with was growing as LF, safety pin appearance on gram stain.
a. What is the pathogen?
b. What is the treatment?
a) Burkholderia pseudomallei
b)
Meropenem + TMP-SMX x 14 days or
Ceftazidime + TMP-SMX x 14 days
The initial regime then needs to be followed with TMP-SMX for at least 3 months for the eradication phase
Women who went on vacation to Martha’s vineyard, then showed up with conjunctivitis and pre-auricular LAN on the same side.
a. What are 4 bacterial pathogens that could cause this syndrome?
- Bartonella henselae
- Fransicella tularensis
- Chlamydia trachomatis
- Listeria monocytogenes
- Mycbacterium tuberculosis
- Treponema pallidum
Perinodes Ocular Glandular Syndrome
Guy goes to Nantucket to do some outdoors activities. Returns with fever etc and is confirmed to have anaplasmosis.
a. What is the confirmatory finding on peripheral smear?
Morulae (intracytoplasmic inclusions) in neutrophils
What is the treatment for Anaplasma, dose, duration?
Doxycycline 100 mg po bid x 10 days
12yo Kid goes hiking for a week, and returned 2 days ago. Parents have found tick (no details re: what kind) and are curious about lyme prophylaxis. You see tick attached to his thigh.
a. What are 4 considerations in making decision to prophylax?
1) Attached tick identified as Ixoides scapularis adult or nymph
2) Tick estimated to be attached for >=36 hours (degree of engorgement)
3) Prophylaxis can begin within 72 hours of removing tick
4) Local rate of infection of ticks with B. burgdorferi is >=20%
5) Doxycycline is not contraindicated
What is the drug, dose, duration for Lyme Disease prophylaxis?
Doxycycline 200 mg po x 1
Name 4 gram positive pathogens that cause gastroenteritis.
- Listeria monocytogenes
- Bacillus cereus
- Staphylococcus aureus
- Clostridium perfringes
Guy is in Thailand and gets febrile illness. Acute and convalescent Dengue serology performed. Acute: IgM-, IgG+; Convalescent: IgM+, IgG+
a. Explain the serologic findings
He may have already been IgG positive from another flavivirus or previous Dengue. Likely has acute Dengue
According the new 2009 WHO classification of severe Dengue, describe 3 findings that are associated with it.
- Severe Plasma Leakage
a. Shock
b. Fluid accumulation with respiratory distress - Severe bleeding
- Severe Organ Involvement
a. Liver: ALT or AST >1000
b. CNS: Impaired consciousness
c. Failure of heart and other organs
Should the following people receive the Zoster vaccine?
a. 60M actively on chemo for lymphoma
b. 24F RN, with history of chicken pox in past, who was exposed to patient with disseminated zoster.
c. 65M with no history of chicken pox in the past.
d. 62F with history of shingles in V1 dermatome.
a) No
b) No
c) Yes
d) Yes
Clinical vignette re Chagas disease.
a. What are 2 complications of chronic Chagas disease (from different organ systems)
- Myocarditis
- Megaesophagus
- Megacolon
Besides serology, what are 2 ways to confirm a diagnosis of Chagas, and in which phase of the disease would you use each one.
Peripheral blood smear to see the trypomastigoes in the acute stage
Biopsy to see the amastigotes in the later phase
What are 4 ways Chagas can be transmitted?
- Bite of a reduvid bug
- Blood transfusion
- Organ transplant
- Vertical transmission from mother to fetus
- Fidaxamicin
a. What type of antibiotic is it?
Macrocyclic
What are 3 advantages of using Fidaxomycin over Vancomycin?
1) Bactericidal
2) Narrower spectrum
3) Decreased recurrence of C. difficile for non-NAP1 strains
4) Less renal toxicity
4 causes of non-gonoccocal urethritis in men.
- Chlamydia trachomatis
- Mycoplasma genitalium
- Trichomonas vaginalis
- Herpes Simplex Virus
- Ureaplasma urelyticum
- Candida albicans
- Adenovirus
2 genetic tests that can help predict response to treatments for viral infections.
- CCR5 tropism assay for Maraviroc treatment in HIV
2. Il28B polymorphism for Interferon and Hepatitis C
You get a call from a physician regarding a result on a pediatric patient with mild URTI symptoms. Kid has NP sample positive for FluA, FluB, Adenovirus.
a. What is the best explanation for this?
Recently had the intranasal live flu vaccine and has an URTI with Adenovirus
What are 2 disadvantages of using PCR testing for respiratory viruses, instead of culture?
- Unknown if it represents colonization vs infection (the PCR may be too sensitive)
- Only detects virus which the PCR has primers too, cell culture can grow many types of viruses
- Can not type viruses for surveillance
Chronic lymer story given as vignette.
a. Briefly describe the diagnostic algorithm used for Lyme.
Screening ELISA for IgG and IgM antibody to lyme (C6 peptite ELISA)
Nonreactive reported as negative
Reactive or Intermediate then have a western blot done
If there are >=5/10 positive IgG bands or >=2/3 positive IgM bands it is reported as Reactive for IgG or IgM respectively
If there are less bands than that the sample is reported as NonReactive
What are 2 other Borrellia species that cause Lyme and what impact do they have on serologic results?
European lyme:
1) Borrelia garinii
2) Borrelia afzeli
These would give a positive ELISA Ab screen but may be negative on Western blot. Need to request European Lyme serology if questioning these pathogens.
EBV serology:
EBV VCA IgM+ EBV VCA IgG+ EA IgG- EBNA- Interpret
Acute EBV infection
Doctor calls you asking about PCR for a suspected CJD case.
a. What do you say? (4 lines given for answer)
There is no PCR test however can test the CSF for different proteins (14-3-3, tau, SP100). Also with brain material can use immunohistochemistiry stain to detect the abnormally folded prion proteins. If you have frozen tissue can to an analysis for protease resistant forms.
There is an investigational assay called protein misfolding cyclic amplification (PMCA)
What is the gold standard for diagnosis of CJD
Examination of brain material for:
1) neuronal loss
2) reactive gliosis
3) vacuolation of the neuropil (spongiform change)
Doctor orders serum for Meningococcal IgM
a. As the laboratory Dr, what do you do immediately?
Call the ordering physician and ask them to collect blood and CSF samples for culture and/or PCR instead if N. meningititis is suspected
Also treat empirically and call infection control
A laboratory technologist handled the serum sample for meningococcal IgM and is worried. What do you say?
Provided she followed routine micro precautions she is safe
The greatest risk is in disturbing colonies of growth
Furthermore the technologists risks in working with Neisseria meningitis may be reduced if they previously had the vaccine
Patient grows GNB that on TSI is glucose positive, lactose negative, sucrose not given, small amount H2S. Citrate negative. Indole negative. Poly O positive. Group D positive. Vi positive.
a. What is the most likely ID?
Salmonella Typhi
What other 2 Salmonella species are Vi positive?
Salmonella Paratyphi C
Salmonella Dublin
3 reasons why the O can be negative for Salmonella species
1) Vi is blocking it (boil the sample)
2) It is a rough strain and does not make complete O antigens
3) Mucoid and won’t agglutinate the O antisera
Salmonella Typhi and Paratyphi A reactions for: Citrate Lysine H2S O Group Vi Antigen
Salmonella Typhi = Citrate Neg, Lysine Pos, Small H2S, O Group D, Vi Positive
Salmonella Paratyphi A = Citrate Neg, Lysine Neg, H2S Neg, O Group A, Vi Negative
What are the 8 steps in the HIV lifecycle and which ARV works at each step.
- Binding/Attachment to cell receptor – Entry inhibitors
- Fusion/Uncoating – Fusion Inhibitors
- Reverse Transcription – NNRTI, NRTI
- Integration into the host genome – Integrase inhibitors
- Transcription and Translation
- Processing – Protease Inhibitors
- Assembly
- Budding/Release
Which 2 HIV variants are relatively resistant to NNRTIs?
HIV2
HIV1 Group O
An isolate grows from a blood culture and is confirmed as Abiotrophia.
a. What are two ways to allow this organism to grow on BAP?
1) Grow it around a streak of Staphylococcus aureus
2) Add pyridoxal to the agar
3) Use a pryidoxal disk on blood agar for satelitting test
b. A physician calls you regarding using penicillin to treat a patient with Abiotrophia bacteremia. What do you say?
The organism is may have higher MICs to penicillin
Susceptibility testing can be done and there are CLSI criteria
Suggest susceptibility testing and while awaiting results if concerned about endocarditis would add Gentamicin to the treatment.
According to the Canadian Biosafety Standards and Guidelines (CBSG), please give examples of the types of characteristics that should find for surface finishings and flooring
Made from non-absorbent material
Able to withstand disinfectants
Resistant to scratches
Smooth surfaces without cracks and grooves
Flooring should be slip resistant
According to CBSG, what the 3 requirements for a basic laboratory that does very simple and low volume work?
Bench top surfaces
BSLII cabinet
Designated area
Lockable doors
Give 3 advantages and 3 disadvantages to consolidation.
Advantages: Improved technology Standardized procedures May be able to offer extended laboratory hours Cost reductions
Disadvantages:
Transportation logistics for specimens
Doctors do not have an on site laboratory to consult
May delay reporting of certain tests
Physical space required
Give 4 advantages and 2 disadvantages to IGRA testing compared to TST.
Advantages:
- No cross reaction with BCG vaccine
- Patient does not have to return for a second reading
- Less subjectivity in interpreting the test
- Positive result does not cause skin discomfort to the patient
Disadvantages:
- Costly
- Requires specimen to be processed quickly
- Special equipment and technical expertise required
What bacteria is used as a biologic indicator usually and what is the purpose of this?
Geobacillus stearothermophilus – resistant to heat
What other 3 methods are used to ensure sterility is met.
- Chemical indicator (Autoclave tape)
- Mechanical indicator (Print out from the machine which indicates that the correct temperature and pressure were met)
- Biological Indicator
What are 4 immunizations that should be given to laboratory workers before they start their jobs?
- Quadravalent meningococcal vaccine
- Hepatatis B vaccine
- Annual influenza vaccine
- Typhoid vaccine
- Polio
- Hepatitis A vaccine
- Rabies vaccine
- Japenese Encephalitis vaccine
- Yellow Fever Vaccine
- Smallpox
What is the purpose of concentrating stool O&P specimens? What are the 2 methods available to do this?
Increase sensitivity
Sedimentation concentration Floatation concentration (Zinc Sulfate)
An HIV+ patient presents with 3 weeks of diarrhea. Iron haematoxylin negative. What 2 other stains would you do and what organisms would you be looking for?
Modified Acid fast stain for Cyrptosporidium
Modifed Trichrome stain for Microsporidium
47M spends a lot of time in Thailand and presents with weight loss, LAN, unwell, etc. Biopsy of bone yields a yeast that is found intracellularly to be (3x3 um) and extracellularly to be up to 5x5 um. Some internal septations are noticed in the yeast.
What is it?
Penicillium marneffii
What is the acceptable % contamination rate for blood cultures? What are 2 other pre-analytical QIs for blood cultures?
<3%
Pre analytical QI =
Volume of blood per bottle
Number of bottles collected
Specimen Labelling
What are 5 post-analytical QIs?
- Turn around time for gram stain
- Gram correlation to final ID
- Satisfaction of physican with reporting modality
- Time until the patient is put on organism specific antibiotics
- Time until final report is issued to the physician
- Accuracy of the report issued
- Number of corrected and amended reports
What are 4 phenotypic characteristics of Enterobacteriaceae?
- Glucose fermenters
- Gram negative bacilli
- Facultative anaerobes
- Non spore forming
What are 2 phenotypic characteristics of Pseudomonadaceae?
Gram negative bacilli
Catalase positive
Motile
What are 2 functions of MALDI TOF?
Rapid identification of organisms
Strain typing
Antimicrobial resistance
What are 2 reasons for performing extraction on isolates for MALDI TOF.
To increase chance of ID of an organism
Inactivate organism
Improve sample stability
Name 5 hemorrhagic fever viruses.
Ebola Marburg Crimean-Congo Machupo Dengue virus Lassa Fever Rift Valley Fever Hantaan
What is the vector for and disease caused by:
a. R. prowazeckii
b. B. bacilliformis
c. Leishmania
d. Loa loa
e. Coltivirus – Yes = Colorado Tick Fever Virus, wood tick (Dermacentor andersoni)
f. Lyme - Yes
g. Crimean Congo Hemorrhagic Fever - Yes
h. Babesia microti – Yes
a) Louse, Epidemic typhus
b) Sandfly, Oroya fever and Verruga Peruana
c) Sandfly, Leishmaniasis
d) Chyrsops fly
What is the vector and disease caused by:
e) Coltivirus
f. Lyme
g. Crimean Congo Hemorrhagic Fever
h. Babesia microti
e) Tick, Colorado Tick Fever Virus
f) Tick
g) Tick
h) Tick
Person in the ICU has suspected pulmonary invasive aspergillosis. Galactomannin is requested.
a. What is the best type of sample to be tested for galactomannin in this setting?
BAL
What are 4 causes of false positive galactomannin?
- Piptazo or Amox-Clav
- Dietary Galactomannan
- Paeciliomyces
- Alterneria
- GI gut bacteria (Bifidobacterium)
What is another serum test that is approved for testing for invasive fungal infection?
Test for B-1,3 D glucan
Bronch specimen that grew white fluffy mould after 14 days in culture on BHI agar.
a. What are 3 possible identities of this mould?
Histoplasma capsulatum
Blastomyces dermatitidis
Coccidiodes imitans
What 3 things should be done with a 14 day white, fluffy mould from a safety perspective?
Tape the plates
Specimen should be in a BSC Level II Cabinet
Refer to reference lab equipped to process these specimens
What are 4 phenotypic differences between T. rubrum and T. mentagrophytes
1) Pigment: Rubrum=red, Mentagrophytes=not red
2) Spiral hyphae: T. mentagrophytes=yes, T. rubrum=no
3) Microconidida: T. mentagrophytes=globose, T. rubrum=teardrop (birds on a wire)
4) Urease: T. mentagrophytes=positive, T. rubrum=negative
5) Hair perforation test: T. mentagrophytes=positive, T. rubrum=negative
6) Macroconidia: T. mentagrophytes=cigar shaped, T. rubrum=pencil shaped
Question re: NAP1 strains.
a. Why does this strain produce more toxins?
tcdC which usually inhibits toxin production is mutated (partial deletion) which allows for hyperproduction of toxins
What antibiotic is this NAP-1 C. diff more resistant to than other C. difficile strains?
Cipro
What are 2 rapid assays your laboratory could introduce to quickly test for C. difficile?
Toxin Immunochromographic assay
PCR
What are 3 advantages and disadvantages of the Gene Xpert TB system?
Advantages - Able to detect TB from direct samples - Able to assess for rifampin resistance directly from the sample - Does not require live cultures (safety) - Little training required Disadvantages - Expensive - Limited throughput - Only detect M. tuberculosis - Decreased sensitivity in smear negative - Detects dead and alive organisms - Has to be maintained at 30 degrees
What are 4 phenotypic and 2 genotypic test to differentiate slow growing mycobacteria in culture?
Phenotypic o Pigment o Niacin Accumulation o Nitrate reduction o Colonly morphology o Temperature o Growth Rate
Genotypic
- Line Probe Assay
- 16s rRNA Gene Sequencing
- hsp65
- Accuprobe Assay
What are 4 bacteria that are intrinsically resistant to vancomycin?
- Lactobacillus
- Leuconostoc
- Pediococcus
- Weisiella
- Erysipilothrix
Guy comes back from country where there is a measles outbreak and has fever and rash.
a. What 3 diagnostic specimens should be collected and what is one test that should be performed on each?
b. In what time frame should these specimens be collected?
Throat Swab – PCR or Culture for Measles
NP Swab – PCR or Culture for Measles
Blood – IgG, IgM Serology
Urine – PCR or Culture for Measles
b) Within 7 days of the rash onset (14 days for urine)
What are 3 non-invasive tests for H. pylori and a disadvantage of each test?
Serology – may detect past infection
Urea breath test – Affected by PPI or bismuth, False negative with GI bleeding
Stool antigen test – Affected by PPI or bismuth, False negative with GI bleeding
Your laboratory decides to implement for M100 S23 methods for testing Enterobacteriaceae in terms of ESBL. You now have susceptibility panels that go down low enough to achieve these breakpoints. What 2 major changes will occur by adopting these recommendations?
- There will appear to be more ESBLs due to the lowered break points
- No longer have to confirm ESBL with MAST testing (only for epidemiology or infection control)
You isolate an Acinetobacter baumanii that tests resistant to cephalosporins and FQs, but susceptible to Imipenem by your automated susceptibility system.
a. What are 2 methods you can use to confirm imipenem susceptibility?
MIC Method (ETest)
Microbroth Dilution
Disk Diffusion
Agar Dilution
What are 3 resistance mechanisms to carbapenems in Acinetobacter species?
- Carbapenemase
- Efflux Pump
- Porin mutation
What are 2 side effects of colistin?
Nephrotoxicity
Neurological disturbances
What are 2 phenotypic methods to confirm carbapenemases?
- Modified Hodge Test
2. Disk Inhibition Assay with Meropenem, Boronic Acid, EDTA (Rosco Test)
What are 2 factors that may impact susceptibility testing results with daptomycin? What is one body site where daptomycin shouldn’t be reported?
- Requires calcium in the media
- There are no disk diffusion criteria
- There are only MIC values for susceptible (not intermediate or resistant)
Should not be tested for respiratory tract infections
You design a multiplex PCR for stool pathogens including norovirus, rotavirus, sapovirus, adenovirus, astrovirus.
a. Which are these requires a reverse transcriptase step?
Norovirus and Sapovirus (the Caliciviruses)
What other 2 assays could be done to test for most of the GI viruses?
- Electron microscopy
- Antigen assay
- PCR
What are a selective and a non-selective agar used in culturing Legionella? What are 2 limitations of the Legionella urine antigen test?
Selective = BCYE Agar with antibiotics – Cefamandole, Polymyxin B, Ansiomycin (BMPA) NonSelective = BCYE Agar without antibiotics
Limitations =
- Only detects Legionella pneumonphila serogroup 1
- May be negative in the first day of illness
- May be negative in those with a low burden of disease
What is the difference between acid fast and modified acid fast stain. Be specific.
The decolorizer used in each stain is different
Modified Acid Fast uses 0.5-1% H2SO4
Acid Fast uses 3% Acid Alcohol or HCl
Patient has anti-HCV+, PCR negative. Provide 5 explanations.
- Level of HCV below the lower limit of detection of the test
- Patient cleared the infection in the past
- Successfully treated for HCV
- False positive antibody test
- False negative PCR assay
- Maternal HCV antibodies in babies
- Passively acquired HCV antibodies from transfusion
List 5 requirements for making an antibiogram.
- Only 1 isolate per patient counted in the antibiogram
- Only routinely tested antibiotics included
- Antibiogram is created at least annually
- Presented as percent of isolates susceptible to the given antibiotic
- Only use final, verified results
- Only species with data on >=30 isolates
- Only diagnostic isolates, not surveillance ones
3 most common pathogens in a dog bite to genus level.
- Pasteurella
- Streptococcus
- Staphylococcus
- Capnocytophaga
State 2 recommendations from NACI regarding the use of HPV vaccine in males.
1) Quadravalent HPV vaccine is recommended in males >=9 years old who have sex with men
2) Quadravalent HPV vaccine is recommended in males 9-26 years of age for the prevention of penile, perianal, perineal intraepithelial neoplasias and associated cancers
3) Quadravalent HPV vaccine is recommended in males 9-26 years of age for the prevention of anal intraepithelial neoplasias grade 1, 2, and 3, anal cancer and anogenital warts.
4) Any MSM >27 should be strongly considered
Name 2 antiretroviral therapies that interact with PPIs
1) Rilpilvirine
2) Atazanavir
Name 1 integrase inhibitor that interacts with CYP3A4
Elvitegravir
Name 2 medications that can be used as boosters
1) Ritonavir
2) Cobisistat
Name 1 antiretroviral therapy that can cause complications with long term exposure to NSAIDS
Tenofovir
- A patient is 10 days post op after insertion of a prosthetic knee. She develops a fever post for 24 hours. She has a PICC line in place and the surgeon orders it to be removed. Prior to removal the line is functioning well with no erythema or discharge around the site. Follow up cultures are negative in the urine and blood. Tip culture is positive for MSSA. You are consulted from management of a ‘line related infection’.
a. What 2 things would you advise the surgeon?
Treat for 5-7 days after line removal
If she was bacteremic with the line in then she would need antibitoics for 4-6 weeks
List 4 viruses associated with blood borne transmission (Not HIV or Hepatitis)
West Nile Virus CMV HTLV EBV Rabies
TB questions
a. What are 4 indications for the use of pyridoxine with INH?
Pregnancy Malnutrition Diabetes Seizure Disorder Substance Abuse Renal Failure
Why do you need to counsel women about alternatives to OCP while on antituberculous therapy?
Rifampin induces hepatic microsomal enzymes accelerating the clearance of the OCP.
What is the mechanism of action for pyrazinamide causing hyperuricemia?
Inhibits uric acid excretion
What 2 tests do you need to follow up for patients on ethambutol?
Visual acuity testing
Red-green color perception testing
A patient is presenting with lymphocutaneous ulcers on his forearm. A biopsy was taken and sent to the lab.
a. What treatment would you start if the biopsy showed long gram positive bacilli?
Nocardia:
TMP-SMX 2.5 – 5 mg/kg po of the trimethoprim component twice daily
A patient is presenting with lymphocutaneous ulcers on his forearm. A biopsy was taken and sent to the lab.
b. What treatment would you start if the gram stain showed yeast?
Sporothrix:
Itraconazole 200 mg po daily x 2-4 weeks after lesions are resolved
A patient is presenting with lymphocutaneous ulcers on his forearm. A biopsy was taken and sent to the lab.
After 48 hours there was no growth on the MAC and pinpoints on the chocolate. Preliminary tests oxidase -, weak catalase +, and urease -. What is the organism?
Fransicella tularensis
A pregnant female presents at 12 weeks gestation with a toxoplasma serology positive for IgM.
a. What 2 non-serological test would you perform?
Fetal ultrasound
PCR for Toxo from Amniotic fluid
No amniocentesis before 18 weeks gestation as per SOGC
A pregnant female presents at 12 weeks gestation with a toxoplasma serology positive for IgM.
b. What 1 treatment would you start?
c. If it is now at 24 weeks what would the treatment of choice be?
b) Spiramycin 1 g 18h
c) Spiramycin
For the following organisms list the latest time Ig can be given as PEP?
a. Measles
b. VZV
c. HBV
d. HAV
e. Rabies
a. Measles
6 days after the exposure (immunoglobulin)
Incubation period for measles is 10 days. Vaccine is live, attenuated. Can not give measles vaccine to pregnant women or those with cell mediated immunity deficits. OK to give to asymptomatic HIV infected kids.
b. VZV
10 days following the exposure (VARiZIg)
Incubation period for varicella (chicken pox) is 14 days
c. Hepatitis B
14 days from a sexual exposure, 24 hours from needlestick, ocular, or mucosal exposure??
Newborns – 12 hours if mom known positive
Newborns – 7 days if mom found after delivery
d. Hepatitis A
14 days (Immunoglobulin)
Indicated for persons 40 years, immunocompromised all ages, and patients with chronic liver diseases. All other people should get the vaccine for PEP instead of immunoglobulin. Note that for Hep A (and measles) its just general immunoglobulin, it’s not specific for the virus.
e. Rabies
Anytime
- With respect to rabies immunoglobulin, state whether you would administer it for the following scenarios:
a. A man was bit by a raccoon while he was trying to scare it away from his garbage can. The raccoon could not be recovered.
b. A girl is bit while playing with her uncles dog at a party.
c. A couple noticed that a bat flew into their cottage house while they were sleeping. There is also a 10 year old son in the cottage.
a. A man was bit by a raccoon while he was trying to scare it away from his garbage can. The raccoon could not be recovered.
Provoked raccoon, not recovered = Yes
b. A girl is bit while playing with her uncles dog at a party.
No, dog is available for monitoring, should be monitored for 10 days for any signs of rabies.
c. A couple noticed that a bat flew into their cottage house while they were sleeping. There is also a 10 year old son in the cottage.
No for the adults only if they had evidence of bite or scratch on their skin.
Yes for the kid because he was an unattended child
List 4 scenarios in which you would provide active immunization following a significant exposure.
Hepatitis B – baby born to a known positive mother
Rabies immunization following a bat bite
Hepatits A vaccine if patient is between 12 months and 40 years of age after exposure to hepatitis A
Tetanus immunization along with immunoglobulin
Measles in nonimmune person
Meningococcal within 7 days (daycare, sleeping in same house, respiratory procedures without protection, saliva contact, 8 hours on a plane)
Varicella
A woman inquires about varicella vaccination. What are 3 contraindications.
1) Pregnancy
2) Immunocompromised
3) Anaphylaxsis to any components of the vaccine
4) Active tuberculosis
For each virus what is the animal reservoir? a. Herpes B b. Sin Nombre virus c. Rabies d. Chlamydia psittaci Birds
a. Herpes B Monkey b. Sin Nombre virus Deer Mouse (Hantavirus) c. Rabies Bats d. Chlamydia psittaci Birds
- A HIV positive female is stable and has been managed on tenofovir, emtricitabine and efavrinez.
a. She becomes pregnant, what would you suggest for antiviral therapy during pregnancy?
Continue on the same thearpy
A HIV positive female is stable and has been managed on tenofovir, emtricitabine and efavrinez.
b. In another scenario the patient is now HIV positive but treatment naïve. What would you treat with?
If not already on therapy would start with Zidovudine-Lamivudine + Lopinavir/Ritonavir
Tenofivir-Lamivudine + Lopinavir/r
- An HIV positive man is now not on any ARV. His CD4 is 865 and VL 2000. He would like to resume sexual intercourse but wanted information on how to be as safe as possible.
a. Counsel this patient on methods of safer intercourse (3 things)
Use condoms consistently and correctly
Patient could start ARVs to decrease chance of transmission
Partner could use pre-exposure prophylaxis (PrEP) therapy with Emtricitabine + Tenofovir once daily
No intercourse if active lesions (HSV)
Abstain until viral load is negative
- A person comes to clinic because he has just had sex with an HIV positive female.
a. Provide 2 different regimes for PEP
Non-occupational exposure:
1) Darunavir/r + Tenofovir + Emtricitabine
2) Raltegravir + Tenoforir + Emtricitabine
3) Atazanavir/r + Tenofovir + Emtricitabine
Duration of PEP for HIV
28 days
A patient with AML with deteriorating respiratory disease.
a. What agent would you use to manage aspergillosis?
Voriconazole (6 mg/kg IV q12 hr x 2 doses, then 4 mg/kg IV q12h)
What risk factors will put a patient at highest risk for mould infection?
1) Allogenic Hematopoetic Stem Cell transplant recipient
2) Hematological malignancy with neutropenia
3) Lung Transplant patients
4) Heart Transplant patients
5) GVHD
6) CGD
7) HIV
A patient with ALL and a CVC. Blood cultures grow yeast and they are germ tube negative.
a. What 2 different antifungal agents could you start empirically and give mechanisms of action.
Micafungin: Noncompetitive inhibition of the synthesis of 1-3B-D Glucan
Liposomal Amphotericin B: Disrupts fungal cell wall by binding egosterol which leads to pore formation and leakage of cellular contents
A patient with ALL and a CVC. Blood cultures grow yeast and they are germ tube negative.
b. List 2 things to follow up with in addition to starting antifungals
Daily blood cultures until documented negative
Ophthalmic exam by an ophthalmologist to look for endophthalmitis even if they don’t have any ocular symptoms
Remove the line
Treatment for candidemia is 2 weeks after blood cultures are negative. Also symptoms should have resolved and in neutropenic patients only d/c therapy after the neutropenia has resolved (ANC >500).
2 indications to treat asymptomatic bacteruria
Prior to a transurethral resection of the prostate
Prior to urological procedure that mucosal bleeding is anticipated
Name 2 organisms that are thought to be transmitted by aerosols but are not thought to be transmitted person to person?
Francisella tularensis Coxiella brunettii Hantavirus Leptospirosis Bacillus antrhasis (can be transmitted with direct skin lesions) – instead say pulmonary anthrax LCV
What would you expect serologies to be for a chronic coxiella infection?
Phase II titers for IgG >=200 and for IgM >=50
Or document a 4 fold rise by immunofluorescent antibody testing in anti-phase II IgG between acute serum and convalescent serum 3-6 weeks later
Chronic infections would be suggested with an IgG titer to phase I >800, or the peristance of anti phase I IgG>800 6 months after completion of therapy.
A veterinarian that was previously well primarily cares for small domestic animals. He presents with fever and fatigue. Has an echo that shows a valvular vegetation.
a. Given his occupation there is a high suspicion for Bartonella. What would the recommended treatment for bartonella endocarditis be according to the IDSA?
b. What other infection would you be considering?
a. Ceftriaxone 2g IV daily x 6 weeks + Gentamycin 1 mg/kg per day q8h x 2 weeks + Doxycycline 100 mg po BID x 6 weeks
If culture confirmed then Doxy x 6 weeks + 2 weeks Gent
b. Q fever
A woman travels to Tanzania and climbs Mount Kilimanjaro. She presents with a fever and eschar. List 3 organisms on the differential.
Rickettsia africae
Rickettsia aktari (Rickettsial pox)
Orientia tsutsugamuchi – Scrub typhus
A male returns from a trip from Costa Rica. He has an ulcer on his lower leg that appears to be Leishmaniasis.
a. What are 2 methods of making the diagnosis (not molecular testing)? For each method of testing list what stage of the protozoa you are trying to detect.
Staining of tissue biopsy with Wright-Geimsa: Looks for Amastigotes
Cutlure of tissue with Schniders Drisophila Media: Looks for promastigoes
3 systemic treatments for leishmaniasis?
Amphotericin B x 14 days
Mitefozine x 30 days
Stiboluconate (Antimony derivative) IM
A patient presents with parotitis which appears consistent with mumps.
a. What is the most common cause of bacterial parotitis?
Stapylococcus aureus
b. 2 modalities for diagnosing mumps?
PCR - saliva, throat swab, buccal swab, urine, CSF
Serology
Culture
c. What are 3 complications of mumps?
Oochitis Aseptic Meningits Sensioneural hearing loss Endocardial Fibroelastosis Oophritis Pancreatits
- Patient admitted with fever, headache and meningismus. A CSF was drawn which is neutrophilic, elevated protein and low glucose. Gram stain shows GNDC.
a. What are 2 things to do immediately?
1) Initiate antibiotics with Ceftriaxone 2g IV x 7-10 days
2) Place the patient on respiratory droplet isolation until 24 hours of antibiotics
- Patient admitted with fever, headache and meningismus. A CSF was drawn which is neutrophilic, elevated protein and low glucose. Gram stain shows GNDC.
b. It is confirmed as N. meningititis. What 2 things do you need to follow up with?
1) Prophylaxis for close contacts with rifampin 600 mg PO BID x 2 days or Cipro 500 mg po x 1 or Ceftriaxone 250 mg IM x 1. Household or intimate contact, medical personel with contact with oral secretions
2) Vaccination if appropriate (dormatories, military)
- A patient is put on TNF alpha inhibitor for rheumatoid arthritis. She now presents with signs and symptoms of meningitis. CSF cultures are positive for E. Coli and B. fragilis.
a. Prior to starting the TNF alpha inhibitor what screening test could have been done to prevent this?
b. What bacterial etiology should be screened for before starting this treatment?
c. What are 2 viruses (non-herpesviridae) that can be reactivated on this treatment?
a. Strongyloides serology
b. Tuberculosis
c.
Hepatitis B Virus
JC Virus
HPV
- Patient with chromoblastomycosis.
a. What is the name of the cells classically seen on gram stain of the lesion?
Muriform cells (aka sclerotic, Copper Penny or Medlar bodies)
- Patient with chromoblastomycosis.
b. List 3 etiologies
1) Fonsecaea pedrosoi
2) Cladophilophora carrionii
3) Fonsecaea monophora
4) Philophora verrucosa
c. List 3 treatment options for a patient with Chromoblastomycosis
1) Itraconazole
2) Terbinafine
3) Liquid nitrogen
4) Surgical Excision
- Patient presents with MRSA bacteremia
a. 2 agents that are approved for MRSA bacteremia?
1) Vancomycin
2) Daptomycin
- Patient presents with MRSA bacteremia
b. An echo was performed and the patient has a vegetation on a prosthetic valve. What agent to add?
Vancomycin
- Diabetic foot that has been unresponsive to courses of Keflex, Cipro and Clinda. Presents to the ER with worsening erythema and discharge around the ulcer, as well as increasing pain.
a. 2 diagnostic tests to diagnose osteomyeltits
b. In the ER she was started on Cephalexin. The lesion is worsening with necrotic skin at the edge of the lesion. What are 2 things to do to manage this patient?
a. XRay Bone and Gallium Scan Probe to bone Bone culture
b.
1) Intravenous Antibiotics
2) Debridement
3) Consult Vascular Surgery
- Physician calls you about a patient with chronic fatigue syndrome. He has read articles about Xenotropic murine leukemia virus related virus (XMRV) and it’s links to chronic fatigue syndrome. He wants to start the patient on treatment and asks for your advice on the workup and treatment of XMRV. What would you advice the physician?
No need for work up or treat
- IPAC has made routine investigation in the GI clinic and has found that some of the times the endoscopes are not being brushed off and cleaned prior to disinfection with glutaraldehyde.
a. What are 2 breeches that have occurred in the GI clinic?
The instruments are not being properly pre-cleaned
The scope is not being cleaned prior to disinfection
b. List 3 spaulding criteria and the level of disinfection/sterilization for each class.
1) Critical = Sterilization
2) Semi-Critical = High Level Disinfection
3) Non-Critical = Cleaning with low level disinfection
What are the 3 most common infectious causes for a mycotic aneurysm?
1) Staphylococcus aureus
2) Coagulase negative Staphylococci
3) Salmonella species
4) VGS
Fidaxomycin
a. Mechanism of action
Inhibits protein synthesis by inhibiting the RNA polymerase
b. 2 favorable pharmacodynamics qualities for fidaxomicin
Mainly distributed in the GI tract
Very little excreted by the kidneys
Bacteriocidal
c. What is 1 clinical benefit for fidaxomicin?
Less risk for recurrence of C. difficile in patients with non-NAP1 strains
- Your hospital has an outbreak of KPC producing Klebsiella pneumonia. List 6 measures that can be instituted to control and manage the ongoing outbreak.
1) Cohort patients and staff
2) Increased environmental cleaning
3) Perform active surveillance cultures on patients
4) Ensure high levels of hand hygiene compliance
5) Strictly enforce contact precautions
6) Dedicated nursing
7) Dedicated instruments
8) Communicate frequently with hospital staff
9) Archive all potential isolates for typing
- Rates of surgical site infections have been increasing in your institution. You are part of a committee that has been asked to examine methods to improve rates of surgical site infections. What are 4 recommendations to make as part of your ‘bundle’?
1) Hair removal with clipping or depilatories instead of shaving
2) Ensure timely and appropriate administration of prophylactic antibiotics
3) Redose prophylactic antibiotics for long procedures
4) Maximize diabetes control prior to operation if possible
5) Chloroxidine daily washes
6) Chlorohexidine instead of iodine
7) Wound closer without tension
8) Gental retraction
- A 24 year old male presents with fever, hypotension, worsening respiratory distress. A CT shows bilateral opacities (rounded) with a left sided empyema. A week ago the patient had a sore throat. This has now worsened.
a. List the syndrome and the organism.
Syndrome = Lemierre’s Syndrome Organism = Fusobacterium necrophorum
- HEV. 2 different types of HEV and provide 1 unique clinical and 1 unique epidemiological association for each.
Endemic – fecal-oral transmission
Sporatic – zoonosis
??? Not sure on this one
- Gram stains:
a. Describe the method
First fix the smear with heat or methanol. Then flood the slide with crystal violet and leave for at least 15 seconds, remove crystal violet with water and flood slide with iodine for at least 15 seconds. Remove the iodine with water and then decolorize the slide with acetone-alcohol for 15 seconds, rinse with water and then flood the stain with counterstain of safranin for at least 15 seconds.
4 organisms that don’t stain well
Mycoplasma Chlamydia Treponema Rickettsia Coxiella Legionella Leptospira
b. 2 organisms that tend to overdecolorize
Streptococcus pneumonia
Clostridium clostridiforme
Bacillus species
- What are 2 test that can be done to differentiate a gram positive from a gram negative organism if the stains are equivocal?
1) KOH test using 3% potassium hydroxide
2) Test for cell wall aminopeptidase (in gram negatives) using either GramSure disk or APNA K915 disks.
3) Vancomycin disk diffusion susceptibility testing (Kirby Bauer)
4) CNA plate
- What is the only indication for HPV PCR testing for cervical specimens in Canada?
Women over 30 years of age with ASCUS (atypical squamous cells of undetermined significance) on cytology (until age 69)
- A man on chronic prednisone admitted with fever and worsening cough and SOB. The respirologist decides to do a BAL for work up of possible PCP.
a. Name 2 stains that can be used for PCP (specifically told not to use NAAT or fluorescence)
Methenamine Silver Stain (Grocott) Papanicolaou’s Stain Toluidine blue O Stain Rapid Geimsa-like Stain PAS (Periodic Acid Schiff Stain)
b. The BAL is positive for PCP, however there is an induced sputum that was sent earlier that was reported as negative. What would lead you to believe that the first test was actually a false negative?
The clinical scenario fits with a diagnosis of PCP.
BAL is more sensitive
In HIV negative patients the sputum is less sensitive
- A man returns to clinic for recurrent mucopurulent urethritis. He was initially seen a few days ago and started on appropriate antimicrobial therapy. You suspect Neisseria gonorrhea.
a. What specimen would you send and what test would you ask for?
Urethral swab for culture and ask for susceptibility testing
b. What is the most common mechanism of resistance to 3rd generation cephalosporins for Neisseria gonorrhea?
Alterations in Penicillin Binding Protein 2 (PBP2) encoded by penA gene. Specifically the presence of a mosaic PBP2 in N. gonorrhea resistant to 3rd generation cephalospsorins.
- A lung biopsy is sent from a patient who is immunocompromised. They are concerned about a fungal infection and have sent for fungal culture.
a. How would you process this specimen in the lab?
Sample should be sent in a sterile container and kept moist to prevent drying. Sample should be at room temperature and transported to the laboratory as soon as possible. The tissue should be minced and not ground. Tissues pieces should be pressed into the agar so they are partially embedded. 2-4 pieces of tissue per media and no streaking. A small portion of tissue should be ground for microscopy smears. If suspecting H. capsulatum then the tissue should be ground instead.
- A lung biopsy is sent from a patient who is immunocompromised. They are concerned about a fungal infection and have sent for fungal culture.
b. What are 3 media you would use and provide a rationale for each?
1) Sabarose dextrose agar without antibiotics – supports growth of all fungi, inhibits bacteria
2) Brain Heart Infusion Agar with sheep blood and without antibiotics – Supports the growth of all fungi, and many bacteria. Since this is a sterile site would want an agar without antibiotics as well.
3) Mycosel Agar – contains chloramphenicol, cycloheximide and glucose. Inhibits bacteria and many pathogenic fungi but allows the grows of dimorphic fungi.
Allows growth of all dimorphics and Dermatophytes
Inhibits Cryptococcus, Aspergillus fumigatus, Scedosporium prolificans, Penicillium marneffei, some Candida and most Zygomyces.
c. What are 2 media you could use to enhance sporulation?
1) Potato dextrose agar (PDA)
2) Rapid sporulation agar (RSA)
3) Potato flake agar (PFA)
4) Cornmeal Agar
- What are risk categories for the following:
i. Bacillus anthracis –
ii. Influenza A H2N2 –
iii. Hepatitis B –
iv. Cladophilophora bantania –
v. Herpes B –
\: i. Bacillus anthracis – Risk group 3 ii. Influenza A H2N2 – Risk group 3 Also the 1918 flu strain iii. Hepatitis B – Risk group 2 iv. Cladophilophora bantania – Risk group 3 Because it can cause serious disease, CNS phaeohyphomycosis. Infection can be contracted through inhalation. Handle with extreme care v. Herpes B – Risk group 4
b. As part of schedule 5 of the health promotion and protection act, what organism is banned from use?
Variola virus (Smallpox)
c. A laboratory worker has Shigella dysentery. It is suspected to be lab acquired. What must you do according to this act?
Inform the Minister of Health and provide details of the incident, the pathogen involved and any other information the Minister may require.
- There is a patient with ‘hemorrhagic bullous lesions’ in a peripheral hospital. It has been transported to your lab, nonmotile, nonhemolytic. Gram stain shows large GPB.
a. What 2 things should you do right away?
Alter the treating physician of a possible diagnosis of anthrax
Transfer the organism into level 3 containment facility
b. What 3 tests would you use to identify Bacillus anthracis?
Egg yolk reaction (should be positive)
Penicillin susceptibility (should be penicillin S)
Demonstrate capsule formation with India Ink staining, or McFayden’s stain
It’s also nonmotile and nonhemolytic
c. You wish to send the Bacillus anthracis off to the reference laboratory. What are 3 issues you need to do when transporting specimens?
Category A. Proper packaging Wrapped in absorbant material Primary receptacle that is water proof Secondary container that is waterproof Third container (box) Properly labeled Inform receiving lab
- Expected susceptibilities for the following organisms: (Just say S or R)
a. Staph aureus and penicillin -
b. Morganella and imipenem –
c. Stenotrophomonas and Septra -
d. Burkholderia and colistin -
e. Klebsiella and ampicillin –
a. Staph aureus and penicillin - Resistant
b. Morganella and imipenem – Susceptible (higher MICs)
c. Stenotrophomonas and Septra - Susceptible
d. Burkholderia and colistin - Resistant
e. Klebsiella and ampicillin – Resistant
Antiviral susceptibility testing
a. What is the main difference between phenotypic and genotypic testing?
Phenotypic testing measures viral replication in the presence of antivirals whereas genotypic testing looks for the genes known to cause resistance.
Genotypic is molecular
Phenotypic requires culture
b. What are 2 chronic viral infections that resistance testing can only be done by genotype?
Hepatitis C Virus
???
c. What are 2 chronic viral infections that can be tested genotypically and phenotypically?
HIV
CMV
HSV
- Viral CPE detection. What are 3 methods to detect viral growth if there is no CPE pattern?
Blind passage
DFA
Hemadsorption
A young man presents acutely ill with meningitis. He has recent exposure to fresh water.
a. What are 3 free living amoebas that can cause this syndrome?
b. What is 1 simple test that can be done on CSF to detect the parasite?
a.
Naegleria fowleri
Acanthamoeba
Balamuthia mandrillaris
b. Wet mount of CSF to look for trophozoites
The ED and community travel medicine clinic have approached you as they feel the thin smears done for malaria testing are insensitive.
a. What are 2 issues to discuss with the ED/clinic to improve sensitivity?
Ensure that a thick smear is ordered with each thin smear to improve sensitivity
Have the ED/clinic order 3 sets of smears on patients suspected of having malaria at 12 hour intervals
The ED and community travel medicine clinic have approached you as they feel the thin smears done for malaria testing are insensitive.
b. What are 2 issues in the lab you should look at to improve sensitivity?
Implement a rapid malaria test as well
Ensure training of technologists is adequate
Proficiency testing
c. Name 2 different tests for malaria testing and for each give 1 advantage.
Microscopy with thin smears – Advantage = able to speciate the organism and determine a percent parasitemia
Immunochromographic rapid test – Advantage = fast turn around time, easy to perform, no specialized equipment
Fluorescent DNA/RNA stains – Advantage = rapid
NAAT = Advantage – Increased sensitivity
b. 2 contraindications for IGRA testing
To diagnose Active TB
When serial testing is required (ex Health care setting)
- Chart about implementing a new antimicrobial susceptibility test. Given data from the gold standard and how the new test compares to the gold standard.
a. Calculate very major, major and minor errors. Also categorical agreement.
Very Major = Resistant isolate called sensitive
Major = Sensitive isolate called resistant
Minor = Sensitive or resistant isolate called intermediate or an intermediate isolate called sensitive or resistant.
Categorical agreement = Percentage of agreement between the categories Sensitive, Intermediate, and Resistant between the new test and the gold standard. (Number of categorical matches / Number of samples tested) x 100
b. What are the accepted errors for introducing a new test (%VME, ME)? What is the minimum % categorical agreement required of the new test?
% Very Major Errors = ≤3%
% Major Errors = ≤3%
Minimum categorical agreement required = ≥90%
Combined Major Error and Minor errors should be ≤7%
- Allogenic BMT patient recently treated for bacterial pneumonia. Recently travelled for several months through the United States. Now presenting with meningitis. CSF is sent to the lab for testing.
a. What are 2 reasons for each of the following scenarios?
i. Positive india ink/ Negative cryptococcal Ag test
1) True cryptococcal infection: False negative crytococcal antigen test due to prozone effect
2) True cryptococcal infection: False negative cryptococcal antigen test due to low titers of cryptococcal antigen.
3) False positive india ink due to WBC instead of the antigen.
- Allogenic BMT patient recently treated for bacterial pneumonia. Recently travelled for several months through the United States. Now presenting with meningitis. CSF is sent to the lab for testing.
a. What are 2 reasons for each of the following scenarios?
ii. Negative India ink / Positive cryptococcal Ag test
1) True cryptococcal infection: False negative India ink stain due to low sensitivity of this staining method
2) No cryptococal infection: False positive cryptococcal Ag test due to rheumatoid factor, sinuresis fluid, Trichosporin, Capnocytophaga
- Allogenic BMT patient recently treated for bacterial pneumonia. Recently travelled for several months through the United States. Now presenting with meningitis. CSF is sent to the lab for testing.
b. What antifungal should you not use and give 2 reasons why
An echinocandin (ie micafungin, caspofungin):
1) Cryptococcus and dimorphic fungi are resistant to echinocandins
2) Echinocandins do not get into the CSF
- Allogenic BMT patient recently treated for bacterial pneumonia. Recently travelled for several months through the United States. Now presenting with meningitis. CSF is sent to the lab for testing.
c. In 5 days the lab is growing a white mycelia on culture. 2 possibilities?
Coccidioides immitis
Histoplasma capsulatum
- Brucella melintensis identified in the lab
a. What 4 phenotypic tests are level 2 labs allowed to do for preliminary workup of Brucella (can not use gram stain)?
1) Oxidase - positive
2) Catalase - positive
3) Urease - positive
4) Positive slide agglutination reaction with specific B. abortus and/or B. melitensis antisera
5) Nitrate – positive
b. What are 4 things you can do in the lab to prevent lab acquired transmission of Brucella melintensis?
1) Tape the plates
2) Perform all work on the culture in a Class II or higher biological safety cabinet
3) Label plates as potential Brucella
4) Do not work up the specimen, instead refer to a reference laboratory
5) Slow growing gram negative bacilli should be referred out if suspiction is high
6) Wash hands
7) Avoid any methods that could generate aerosols
- List 4 recommendations for analyzing and preparing antibiograms as per CLSI?
1) Analyse and present a cumulative antibiogram report at least annually
2) Include only final, verified test results
3) Include only species with testing data for ≥30 isolates
4) Eliminate duplicates by including only the first isolate from a patient
5) Report % susceptible and do not include intermediates
6) Only report drugs from routine susceptibility testing, not special requests
hat are 4 antibiotics that are not recommended for routine testing on CSF as per CLSI?
Ciprofloxacin (Fluoroquinolones)
Tetracycline (Tetracylcines)
Azithromycin (Macrolides)
Clindamycin
Cefazolin (1st and 2nd genearation Cephalosporins except Cefuroxime IV)
Cefoxotin, Cefotetan (Cephamycins)
Agents administered only by the oral route
- What is the method described by CLSI to confirm a KPC? What is 1 example of a false positive using this method?
Modified Hodge Test
False positive:
- Different type of carbapenemase other than KPC which would also destroy the ertapenem in the agar and allows the Ecoli to grow
- CTX-M and AmpC hyperproduction
a. What is a chromosomal carbapenemase produced by Enterobacter cloacae that is resistant to carbapenems but susceptible to cephalosporins?
OXA or SME
- 3 nucleic acid amplification methods besides PCR?
1) Strand displacement assay (SDA)
2) Transcription Mediated Amplification (TMA)
3) LAMP (Loop Amplification)
4) NASBA (Nucleic Acid Sequence Based Amplification)
- RNA to cDNA with reverse transciptase, degrade RNA,
add RNA polymerase and make new RNA
- 4 level 3 organisms that are endemic to at least 1 region in Canada? (need to include 1 bacteria, 1 virus, and 1 fungus)
1) Mycobacterium tuberculosis
2) Histoplasma capsulatum
3) Blastomyces dermatitidis
4) West Nile Virus
5) HIV
6) Brucella
7) Coxiella
8) Rabies
- Your lab is using African Green Monkey kidney cells for viral culture. There is a request for enteroviral culture. The sample inoculated with the patients sample is already showing CPE after 1 day. On examination of other uninnoculated cells there is already CPE. On EM it looks like a herpesviridae. What virus is causing the CPE?
Herpes B Virus (came from the monkey cells)
Can be transmitted to lab workers
- A streptococcus pyogenes isolate is tested as resistant to penicillin. What are 5 things you can do to verify this result?
1) Check for transcription errors, contamination, or defective panel, plate or card
2) Check previous reports on the patient to determine if the isolate was encountered or confirmed earlier
3) Repeat organism ID and AST with initial method to confirm they reproduce
4) Confirm organism ID with second method performed in house or at a reference lab
5) Confirm AST with a second method (in house or referecene lab)
- MALDI-TOF
a. 3 bacteria or bacterial groups that the MALDI-TOF has trouble identifying
1) Streptococcus pneumonia
2) Shigella species
3) Neisseria gonorrhea
4) Aeromonas (can’t speciate it)
5) Acinetobacter complex differentiation
- MALDI-TOF
b. 1 way in which these limitations can be improved
To improve it could look at different types of extraction methods, look at a broader range of protein sizes
Use a different matrix
Extraction procedure
- 4 ways to differentiate Staphylococcus and Micrococcus in the lab
- Bacitracin - Micro S, Staph R
- Modified Oxidase - Micro Pos, Staph Neg
- Furazolidone - Micro R, Staph S
- Lysostaphin - Micro R, Staph S
- Strict Aerobe - Micro Yes, Staph No
- Acid from glycerol aerobically - Staph Yes, Micro No
- Administrators tell you that you need to cut costs in the lab by $50,000. You review the urine culture bench in an attempt to streamline work up. The technologists ask you how to work up the following organisms further.
a. GNB, Ox negative, not swarming, beta hemolytic
b. GNB, Ox negative, swarming, Indole positive
c. GPC, catalase negative, PYR positive
a. GNB, Ox negative, not swarming, beta hemolytic
Indole test, if positive call E.Coli
b. GNB, Ox negative, swarming, Indole positive
No further workup, Identify as Proteus vulgaris
c. GPC, catalase negative, PYR positive
If Beta heme and greater than 1 mm, Identify as Enterococcus
- For Staphylococcus aureus what are 2 different ways to test for Beta lacatamse production?
1) Penicillin zone edge test – Use a 10 U penicillin disk with standard disk diffusion procedure. If the edge of growth around the disk is sharp (cliff) it’s B-lactamase positive. If it’s fuzzy (beach) it’s negative.
2) Nitrocefin-based test – Perform the test from growth taken from the zone margin surrounding a penicillin or cefoxitin disk.
- Isolate in the lab that is GNB. On TSI there is an alkaline slant with scant production of H2S. It is citrate negative, lysine positive and urease negative.
a. 3 antigens that you would test and briefly describe each
O Antigen – Heat stable, Somatic antigen
H Antigen – Flagellar antigen
Vi antigen – Heat labile Capsular polysaccharide
b. 2 difficulties with serotyping Salmonella
1) The O antigen may initially test negative if the Vi antigen is positive due to the Vi antigen blocking the binding of antibodies against the O Ag. Need to boil the sample to destroy the Vi antigen so that the O antigen can then test positive with Group D.
2) The strain may be rough and not make complete O antigens
3) The strain may be mucoid and not agglutinate with any O antisera
- There is concern of a patient in the ICU with novel coronavirus. The physician sends a respiratory specimen requesting molecular testing for viruses, including novel coronavirus.
a. 5 routine precautions you can do in the lab to protect the lab workers during the processing/culturing of molecular respiratory samples?
1) Work in a BSC Level II
2) Wear gloves
3) Wear a lab coat
4) Proper waste disposal
5) Hand hygiene
- Current algorithm for intestinal parasites includes direct smears as well as concentration and iron hematoxylin stain. Name 4 clinically significant intestinal parasites that could be missed with this algorithm and 1 stain for each that you would use for them.
Isospora – Acid Fast Stain
Cyclospora – Acid Fast Stain
Microsporidium – Modified Trichrome Stain
Cryptosporidium – Acid Fast Stain
- The center that you are in has decided on a pre-emptive approach to invasive aspergillus. They are currently routinely testing post transplant patients with Galactomannan.
a. What are 2 other fungi that can be positive on the galactomannan assay?
1) Penicillium species
2) Histoplasma capsulatum
3) Blastomyces dermititidis
4) Paeciliomyes
5) Alternaria
6) Fusarium
b. What would be 2 reasons why adding the B-D-glucan with galactomannan would be beneficial?
1) Increase sensivity for Aspergillus
2) Aid in the diagnosis of a fungal infection that is not aspergillus (positive B-D glucan, negative GM)
- A patient is awaiting a kidney transplant. He is EBV negative. A donor kidney is available and the donor’s serology is VCA IgM negative, VCA IgG pos, and EBNA pos.
a. Interpret the serology
Prior infection with EBV
VCA IgM– Appears at clinical presenation, gone in 4-8 weeks
VCA IgG– Appears at clinical presentation, lasts lifelong
EBNA – Appears 3-4 weeks after onset, lasts lifelong
b. What are the clinical implications of transplanting this kidney into an EBV negative host?
EBV positive donor, EBV negative recipient.
The recipient will be at increased risk post transplant lymphoproliferative disorder (PTLD). He will require routine testing for EBV viral load. One regime may be monthly monitoring for 3-6 months then every 3 months for 1 year. If he is found to have an increasing viral load immunosuppression may be decreased or rituximab started.
b. What are 2 clinical indications for the use of CMV PCR to diagnose active infection?
1) To diagnose congenital CMV infection
2) CMV in the CSF to diagnose encephalitis
3) Aqeuous or vitreous humor for CMV retinitis
4) CMV donor positive, recipient negative transplant patients
- There is an MRSA cluster in neonatal nursery.
a. What are 2 outbreak patterns that could be suggestive of common source infection?
1) Point source outbreak – rapid peak with slower decline
2) Continuous common source – slow peak and then plateau with slow decline
b. 2 phenotypic and 2 genotypic methods to type MRSA
Phenotypic: Phage typing Susceptibilities Capsule serotyping MALDITOF
Genotypic: PFGE MLST Ribotyping Single Locus Sequence Typing Multiple Locus Variable Number Tandem Repeat Analysis
- GP recently vaccinated a patient for Hepatitis B. He accidently sends Hepatitis B serology 2 days after. HBsAg pos, HBsAb neg, HBcAb total neg, HBcAb IgM neg. Interpret.
No previous infection with Hepatitis B
Serology consistent with recent vaccination
Patient is not yet immune to hepatitis B virus
- A child was recently vaccinated for influenza (few days ago). He has been well but has had mild rhinorrhea. NPW positive for influenza A, influenza B and adenovirus. You review the controls and both negative controls were OK, and multiple other clinical samples on the run were negative. What is the most likely explanation?
The child received the intranasal live vaccine for influenza that contains both influenza A and influenza B which explains the positive flu A and flu B PCR results. The child is infected with adenovirus. Adenovirus is causing his mild rhinorrhea.
- Name 4 viral etiologies of gastroenteritis and 2 methods to detect them.
1) Rotavirus
2) Norovirus
3) Adenovirus
4) Astrovirus
Detect via electron microscopy or PCR of stool samples. Also could use antigen detection.
- 4 reasons for a patient to have Anti-HCV Ab positive but HCV PCR negative.
1) Completed successful treatment of HCV infection, sustained virological response
2) Currently on HCV treatment, rapid virological response
3) HCV Infection with low levels of HCV RNA
4) False positive Anti-HCV Ab test
5) Maternal Ab if it’s a baby
6) Past infection that cleared spontaneously
- A homeless man is admitted to hospital with fever. Blood and urine cultures negative. Blood film show tiny, thin coiled organisms.
a. What is the organism?
Borrelia recurrensis
b. What are 2 vectors for Borrelia recurrences?
1) Body Louse
2) Head lice
- A Filipino man with peritonitis. Bacterial cultures are negative and you are beginning to suspect TB.
a. What are 2 specimens you would send for work up of TB peritonitis?
Ascites fluid
Peritoneal biopsy
Send the ascites fluid for an Adenosine Deaminase (specific for TB)
b. What are 2 steps in processing normally sterile sites for TB?
Concentrate fluids by centrifugation
Grind tissues then plate directly to media
- Expired reagents – 2 things to do; 4 things to do when starting a new lot of reagents
- Dispose of reagents safely
- Identify if they were used for any testing after expiration date and verify those results
Starting a new lot:
- Visually inspect reagents for any damage or leakage
- Check expiry dates
- Label with contents, concentration, storage requirements, date prepared and expiration date
- QC the reagents
- New test for GBS not approved by Health Canada. Clinician wants you to run it for a woman in labour with ever and unknown GBS – 2 pieces of advice for clinician.
- The lab is not able to give results from unapproved tests
- The test has not been verified or validated in the laboratory, therefore results can not be reported
- Follow protocol for unknown GBS status
Cause and treatment of STI related epididymitis
Cause = Chlamydia trachomatis or Neisseria gonorrhoeae Treatment = Ceftriaxone 250 mg IM x 1 + Doxycylcine 100 mg po BID x 10 days
For other bacteria (enterics), usually older men: Levofloxacin 500 mg PO daily x 10 days
For MSM: Ceftriaxone 250 mg IM x 1 + Levofloxacin 500 mg PO Daily x 10 days
Mechanism of action of antifungals and their intrinsically resistant fungi
Ampho B = binds to egosterol and disrupts fungal cell membrane, leakage of intracellular contents
Echinocinins = Inhibits Beta 1,3 beta-D-glucan synthase (enzyme responsible for polysacc formation of the cell wall
Azoles = interferes with egosterol synthesis, increased cell permeability and leakage of contents
Resistance to polyenes = Candida lustaniae, Aspergillus teres, Scedosporium apiospermum
Vorconazole = Zygomyces, Sporothrix
Itraconazole = Scedosporium, Zygomyces
Fluconazole = C. krusei, Sporothrix, Aspergillus, Scedosporium, Demateacious fungus, Zygomyces
Posaconazole = None
Echinocandins = C. neoformans, Trichosporon, Fusarium, Zygomyces, Dimorphics, Scedosporium
Indication for starting ARVs not related to CD4, symptoms or OI
Pregnancy Decrease risk to negative partner Acute infection HIV associated nephropathy HIV RNA >100,000 Hepatitis B or C Coinfection Age >50 High Cardiovascular risk or Cardiovascular disease
Standard indicators for bacteremia in HD patients
Fever, chills
Purulence at the insertion or exit site
Letheary, altered LOC, hemodynamic instability, hypothermia, acidosis
VZV complications in BMT
Cutaneous dissemination Pneumonitis Meningoencephalitis Hepatitis Pancreatitis
Why add doxy to onchocerciasis
It treats Wolbachia which is an endosymbiotic bacteria that lives within in Oncocercas volvulans. Important in the filaria’s fertility and reproduction. Treating with Doxy decreased the number of wolbachia and microfilaria but has no effect on the adult worms.
What is the treatment for Onchocerciasis?
Rx for Onchocercisis is:
Doxy 200 mg/day x 6 weeks and then
Ivermectin 150 mcg/kg po for a single dose and consider retreatment every 3-6 months until asymptomatic. Ivermectin only kills the microfilaria not the adults.
DEC is contraindicated for the treatment of Onchocerciasis.
Disease with water exposure (fresh water lake, adventerous run, etc)
Leptospira
Others: Aeromonas, Free Living Ameobas, Schistosomiasis
Abx for severe c diff
First episode severe = Vancomycin 125 mg po QID x 10-14 days
Complicated Severe = Vancomycin 500 mg po with Metronidazole 500 mg IV q8h
Severe = Age >60, WBC >15, Increased serum Cr >=1.5 x normal.
No hard fast rules, left up to clinical judgement
Resistant Klebsiella from india – mechanism
Carbapenemase – Metalo-beta-lactamase (NDM1)
Congenital syphilis - 2 early & 2 late symptoms in child.
Early = Low birth weight, HSM, LAN, Snuffles, Rash, Jaundice Late = Facial features (frontal bossing, saddle nose, protuberant mandible), keratitis, sensioneuronal hearing loss, hutchinson's teeth, anterior bowing of the tibia, seizures, intellectual disability
When is maternal treatment inadequate
Maternal treatment is inadequate if mother was treated <4 weeks before birth, or had a treatment with nonpenicillin agent, or evidence of maternal reinfection, inappropriate dose, no documentation of maternal treatment, maternal titres did not decrease 4 fold after treatment for early syphilis or did not remain stable or low for late syphillis
5 AE of nitrofurontoin
a. Hepatic reactions
b. Optic neuritis
c. Peripheral neuropathy
d. Pulmonary toxicity
e. Hemolytic anemia
f. Renal impairment
g. Antibiotic associated diarrhea
4 serotypes covered in new pneumococcal 13 vaccine not found in PCV 7
a. 19A
b. 1
c. 3
d. 5
e. 7F
f. 6A
Treament options for stenotrophomonas
Trimethoprim/Sulfamethoxazole Levofloxacin Ceftazidime Minocyline Chlormaphenicol Ticarcillin/Clavulinate
Complications and treatment for pseudomonas mastoiditis
Sigmoid sinus thrombosis, intracranial abscess, skull based osteo, mastoid abscess
Ceftazidime 2 g IV q8h x 4-6 weeks
Ciprofloxacin 750 mg po BID x 4-6 weeks
3 factors to monitor for when inserting a central line, and 3 for maintaining
To monitor: Hand hygiene, draping the patient
Maintaining: Wipe port with an appropriate aseptic prior to access, use sterile devices to access the port, ???
indications to wash hands
When visilbly soiled
Prior to touching the patient or patients environment
Before putting gloves on
After removing gloves
After touching a patient or patient environment
Before clean/aseptic procedures
treatment of viridans strep IE w/ MIC =1
This is actually intermediate (0.25-2) by the CLSI (>4) but the IDSA calls this resistant (>0.5)
Treat like enterococcus IE:
Native valve = Pen G 18-30 million U q24h IV divided q4h x 6 weeks + Gentamycin 3 mg/kg q24 hours in 1 dose x 6 weeks
4 weeks if native valve and sypmtoms less than 3 months
6 weeks of native valve and symptoms <3 months, or prosthetic valve
6 indications for surgery for IE
a. Persistent vegetation despite systemic antibiotic
b. Anterior mitral valve leaflet vegetation, esp if >10 mm
c. >=1 embolic event in first 2 weeks of therapy
d. Aortic or mitral insufficiency with signs of ventricular failure
e. Heart failure unresponsive to medical Rx
f. Valve perfortation or rupture
g. New heart block
h. Large abscess or extension of abscess despite appropriate antimicrobials
i. Persistently positive blood cultures >5-7 days
j. Infection with a difficult to treat pathogen (fungi, highly resistant)
Treatment for invasive aspergillus and 2x AE
Treatment = Voriconazole 6 mg/kg IV q12h x 1 day, then 4 mg/kg IV q12h
Adverse Events of Voriconazole = Visual toxicity and hallucinations, photosensitivity skin rash, renal impairment
4 types of zygomycetes
a. Mucor
b. Rhizomucor
c. Rhizopus
d. Cunninghamella
e. Absidia (Lichtheimia)
f. Saksenaea
g. Apophysomyces
h. Scencephalastrum
i. Bacidiobolus
2 common HIV resistant mutations –P
a. M184V mutation of the reverse transcriptase – NRTIs (lamivudine, didanuzine, abacavir). Hypersus to AZT, Tenofovir, Stavudine
b. Q151M mutation of the reverse transcriptase – All NRTIs except Tenofovir
c. K103N – NNRTI – Efavrinz, Neverapine
d. K65R – Tenofovir (increased sus to AZT)
e. L90M – All protease inhibitors
f. TAM mutations (Thymadine analogues) – resistance to AZT, Tenofovir, and Stavudine
Which vaccine contains porcine circovirus
Rotavirus vaccine – Rotatrix and Rotateq
indications for RSV monoclonal antibodies
a. <=28+6 weeks gestation who are less than 12 months old at the start of RSV season
Swimming in Lake victoria -> fever HSM eosinophilia -> name
condition and 2 bugs
Schistosomiasis (Katyama Fever)
- Schistosoma mansoni
- Schistosoma japonicum
Yeast w/ arthroconidia in BMT patient. Name bug and treat
Trichosporon
Treatment = azole – Voriconazole 6 mg/kg IV q12h X 1 day, then 4mg/kg q12h.
4 fungi with arthroconidia
Trichosporon, Geotrichum, Coccicioides, Malbrachea, Hormograchiella, Arhrographia, Geomyces, Neoscytalidium
4 VFs of pseudomonas
a. Pili – adhere to cell surfaces, biofilm, motility
b. Pyoveriden – compete with host proteins for iron chelation
c. Pyocyanin – reacts with oxygen to form oxygen radicals causing tissue damage
d. Flagella – motility, biofilm, adherence
e. Quarum sensing molecules – cell to cell communication
f. LPS - Endotoxin
g. Secretory systems
i. Type 1 – alkaline protease (inhibits fibrin formation)
ii. Type 2 – exotoxin A, phospholipase C, protease IV, elastase
iii. Type 3 – Directly injects exotoxin (Exo U, Y, S, T) into cell cytoplam
Acute EBV complications in immunocompetent
Splenic rupture
Airway obstruction from massive lymphoid hyperplasia
Rash following ampicillin, amoxicillin, or penicillin
Hemolytic anemia
Neurologic – Encepahlitis, GBS, transverse myelitis, optic neuritis
treatment options for resistant acinetobacter
Ticarcillin-Clavunlinate Doxycycline Colistin Meropenem Tigecycline (no interpretive criteria) – does not work for Pseudomonas
risk factors to get worse dengue infections
- Previous infection with a different dengue serotype
- Children <1 year old with circulating maternal antibodies
- Elderly
5x nonstrep bacterial causes of pharyngitis
a. Fusobacterium necrophorum
b. Archanobacterium haemolyticum
c. Corynebacterium diptheriticum
d. Neisseria gonorrhoeae
e. Mycoplasma pneumonia
f. Syphillis
indications for starting HBV treatment
- Compensated cirrhosis with Hep B DNA >2000 IU/mL with any ALT
- Decompensated cirrhosis with detectable Hep B DNA with any ALT
- Acute liver failure
- Clinical complications of cirrhosis
- Prevention of reactivation of chronic Hep B during immunosuppression or chemotherapy
- cause of increased alts in HBV/HIV pt
Discontinuation of tenofovir, lamivudine or emtricitabine can result in an acute exacerbation of hepatitis
indications for PCV13 vaccine
Immunization of children 6 weeks – 17 years of age
Adults with HIV, HSCT, Immunosuppressed
>=50 years old (UpToDate, but NACI doesn’t recommend >65)
Splenectomy – First give PCV13 then 8 weeks later give PSV23, with a PSV23 booster 5 years later
- HIV pt w/ MAC: treatment
Clarithromycin 500 mg po BID + Ethambutol 15 mg/kg/day + Rifabutin 300 mg po q24h
PEP treatment for TB exposure
For adults and older children = no treatment, repeat TST in 8 weeks
Child <=5 years = INH 10 mg/kg/day for 3 months then repeat TST, if negative – stop. If positive continue INH for 9 months total
Neonate = INH 10 mg/kg/day for 3 months, then repeat TST. If repeat is negative, CXR is normal and mother is smear negative. If repeat TST positive, or CXR abnormal then INH + RIF for total of 6 months
complications of vori
- Arrythmias/QT prolongation
- Dermatological - Photosensitivity, skin malignancies, Steven Johnsons
- Hepatic toxicity
- Visual effects
- Renal toxicity
- Skeletal effects (fluorosis, periostitis)
- Pancreatitis
4 false-pos of crypto latex, including 2 biological
1) Rheumatoid factor present in the sample
2) Cross reaction with Trichosporon asahii
3) Specimen was placed in an anerobic transport vial
4) Sample was exposed to soap or disinfectant
5) Cross reaction with Capnocytophaga canimorsum
6) Hydrox-Ethyl Startch (from colloids)
7) Malignancy
8) Rothia bacteremia
HBV core Ab positive, and surface ab/ag neg: 4 BIOL reasons and how to resolve
a. Window period between sAg and sAb, do HBV DNA test
b. Undetectable sAb level due to declining levels after years of infection
c. Undetectable sAg level due to low level after years of infection
d. False positive core Ab
How to resolve – repeat the test, Hep C IgM, HepB DNA PCR
3 QI unique for Blood cultures
a. Contamination rate
b. Percent of positive cultures
c. Volume of blood obtained
d. Adequate number of bottles
Strep bovis vs enterococcus, meds for IE
Strep bovis:
Pen G 12-18 million U divided in 4-6 doses x 2 weeks
PLUS
Gentamycin 3 mg/kg q24 hours x 2 weeks,
Enterococcus:
Pen G 18-30 million U/24 hrs divided in 6 doses x 4-6 weeks
PLUS
Gentamycin 3 mg/kg/24hr divided in 3 doses x 4-6 weeks
neg neg pos AFB smear for pt who is on Rx. Rationale
Drug resistance Dead organism Adherence Drug-drug interactions False positive NTM in the smear
whats WHMIS and 3 things the lab does about it
Workplace Hazardous Materials Information System
Canada’s national hazard communication standard
All laboratory employees require WHMIS training
Have MSDS available
hazard signage
Class A = Compressed Gas Class B = Flammable and Combustable material Class C = Oxidizing Material Class D = 1. Materials causing immediate and serious toxic effects 2. Materials causing other toxic effects 3. Biohazardous infectious materials Class E = Corrosive Material Class F = Dangerously Reactive Material
4 reasons for RPR- TPPA+ results
a. Prior syphilis (treated or untreated)
b. Early primary syphilis
c. Prozone effect of RPR (false negative due to high antibody content)
d. Infection with a non-venereal syphilis (endemic syphilis, yaws, pinta)
e. False positive TP-PA result due to nonspecific interactions
f. Tertiary syphilis
5 pediatric GI viral illness, limitations of EM, which ones are non-culturable
a. Rotavirus – Group A is culturable, but difficult.
b. Norovirus (Caliciviridae family) – non culturable
c. Adenovirus - Culturable
d. Astrovirus – Culturable
e. Sapovirus (Caliciviridae family) – non culturable
EM limitations – concentration of virus must exceed 10^6 to 10^7/gram of stool which is the lower level of detection, low viral burden may be missed, requires specialized microscope, requires trained individuals.
2 protoza treatable w/ SXT, and stain used
a. Cyclospora cayetanensis – Modified Acid fast stain
b. Isospora belli – Modified Acid fast stain
c. Toxoplasmosis gondii – Geimsa stain
d. Acanthamoeba – Modified Field’s Stain or Calcoflour white stain with fluorescent microscopy or trichrome stain
- hookworm vs strongyloides
Hookworm - Large buccal cavity, Inconspicuous genital primordium, Tapered tail
Strongiloides - Short buccal cavity, Prominent genital primordium, Notched tail
4 urease positive yeasts
a. Cryptococcus species
b. Trichosporon species
c. Rhodoturula species
d. Sporobolomyces salmonicolor
e. Candida krusei
f. Candida lipolytica
GPC resistant to vancomycin
- Leuconostoc species
- Pediococcus species
- Weissella confusa
gene targets for PCR for MRSA, Cdiff, Flu, VRE
MRSA = mecA gene and nuc gene (the nuc gene looks that it’s Staph aureus)
C. diff = tcdB gene (toxin B)
Flu = matrix gene
VRE = vanA and vanB genes
3 space requirements for a PCR lab
Reagent preparation room
Sample preparation room
Amplification room
2 requirements for PCR pipettes
Designated pipettes for each area of the lab (the 3 different rooms)
Aerosol resistant pipettes
Calibrated 2 times per year
Cleaned every 3 months
precautions for UV & handling ethidium gels
Ethidium gels – gloves, fume hood, face shield, proper disposal
UV – Self contained UV imaging system
2 culture media for campy
- Charcoal cefoperazaone dexoycholate agar
- Charcoal based selective media
- Campylobacter blood agar plate (brucella agar base, sheeps blood, vanco, trimethoprim, polymyxin B, ampho B and cephalothin)
3 incubation conditions for campylobacter
- 42 degrees celcius (to supressed other GI growth and jejuni prefers 42 degrees, fetus only grows at 37 degrees)
- Microaerophilic
- 5-7% O2, 5-10% CO2, 80-90% N2
6 culture neg IE
- Coxsiella brunetii
- Bartonella spp.
- Tropheryma whipelli
- Brucella spp.
- Chlamydia species
- Legionella species
- Non-candida fungi
- Rickettsia
mumps specimen types, max duration, isolation duration,
Specimen types = buccal swab, throat swab, saliva, urine, CSF
Max duration = 9 days for buccal, throat, saliva
14 days urine
Acute serology = 7 days, Conval = 7-10 days post acute
Incubation period of 18 days, short prodromal illness, with parotitis first unilateral then bilateral within 2-3 days, followed by aseptic meningitis. Men can have orchitis 4-10 days after parotitis.
Isolation duration = 5 days after onset of parotitis, droplet isolation
HIV point of care test vs lab comparison of discrepent results and
advantage of POC
POC is rapid
Does not have to be done in a lab setting
Increased access to testing for some patients
Earlier decisions can be made regarding treatment
3 resistant mechanism for MDR pseudomonas against meropenem and drug options
- Porin mutation to decrease uptake of meropenem (OprD)
- Carbapenemase
- Efflux pump
Drug options = aztreonam, colistin, ticarcillin-clavulinic acid
c. diph culture, and findings
Grows within the zone of a fosfomycin disk on blood agar
Selective media = Cystine tellurite blood agar or Tinsdale Agar base medium
CTBA grows gun metal grey
TIN grows with a brown/black halo around the colony
Catalse positive
Nitrate reduction negative, Motility negative, Urea negative, Reverse CAMP negative
Non lipophilic
Neisser or Loeffler’s blue stain – chromatic granules
Confirm toxin production or not – Elek test or modified Elek test – to look for precipitate of toxin with antitoxin. Screen with PCR first and then do Elek test on the ones that are positive.
5 controls used in PCR
Internal control Positive control Negative control Blank control Patient known positive
- List 6 quality indicators for blood cultures.
1) Contamination rates
2) Positivity rates
3) Bottles adequately filled with blood
4) Number of bottles collected
5) Transit time from collection to incubation
6) Reporting time for gram stains of positive cultures
7) Time to positivity
8) Amended reports issued
9) Physician satisfacation
10) Specimen labeling
- Name 4 preanalytical quality indications used for monitoring the handling and transport of specimens coming from the Far North.
1) Shipping temperatures
2) Time from collection to arrival in laboratory
3) Specimens damaged in transit
4) Specimens unlabeled or mislabeled
5) Specimen requisitions
6) Proper transport media
- List 3 postanalytical quality indicators.
1) Time to reporting of results
2) Accuracy of reports issued
3) Client satisfaction audits
4) Reporting of critical results
- Pt. with painless mass at angle of jaw. (classic actinomycosis picture)
a. What would you look for in the pus, macroscopically
b. What would you find on hematoxylin-eosin staining?
c. What is the antimicrobial of choice?
d. What other bacteria is often found (more) in these infections?
a. Sulfur granules
b. Splendor-Hoeppeli phenomena (filaments radiating away from the bacteria with intensely eosinophilic material, asteroid like)
c. Pencillin
d. Eikenella, Fusobacterium, Capnocytophaga, Staphylococcus, Streptococcus
Others that could cause this: Nocardia, Actinomadura, Streptomyces madurae
- Pt. bitten by a cat and develops rapidly progressive cellulitis. Organism grows as GNB, scant on BAP & choc, no growth on MacConkey.
a. What is the most likely etiologic agent?
Pasteurella multocida
b. List 4 phenotypic tests and the expected results for Pastuerella multocida
Oxidase = Positive Catalase = Positive Urease = Negative Ornithine Decarboxylase = Positive Indole = Positive Acid from maltose Nitrate = positive
- Regarding the detection of HPV DNA in women >30 years of age:
a. What are 2 techniques to detect HPV DNA?
Hybrid Capture Assay
Amplicor HPV Test (PCR)
TMA
b.List 2 advantages o HPV DNA tests, complementary to cervical cytology (>30y).
Increase specificity for diagnosing high grade lesions
Decrease amount of individuals requiring colposcopy
c.List 6 genotypes that must be detected in HPV
16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59
d.Why are HPV DNA tests not indicated in women <30y of age?
May detect incident infection that may spontaneously clear in 6-18 months.
Leads to unnecessary colposcopy
Tenover criteria
Identical: 0 genetic events, 0 different bands
closely related: 1 genetic event, 2-3 different bands
possibly related: 2 genetic events, 4-6 different bands
unrelated: >=3 genetic events, >=7 different bands
S. aureus
Micrococcus sp
Rothia mucilaginosa
Strict aerobe?
6.5% NaCl?
Bacitracin?
S.aureus = Not strict, Grows in salt, R to bacitracin Micrococcus = Strict aerobe, Grows in salt, S to bacitracin Rothia = Not strict, No growth in salt, S to bacitractin
Hair perforation and Urease for
T. rubrum
T. mentagrophytes
T. rubrum - Hair perf neg, Urease neg
T. mentagrophytes - Hair perf pos, Urease pos
- List 2 different mechanisms of resistance to aminoglycosides.
1) Decreased uptake (changes in outer membrane permeability, decreased inner membrane transport, or active efflux)
2) Aminoglycoside Modifiying Enzymes (phosphotransferase, modify the drug)
3) Modification of the target site by mutation in ribosomal proteins or 16S RNA or posttranscriptional methylation of 16S RNA
a. Is there a difference in the criteria between S. aureus & S. lugdunensis?
No
b. Describe hVISA and explain what the term means.
Heterogeneous Vancomycin Intermediate Staphylococcus aureus. A subpopulation of S. aureus that have increased MIC to vancomycin (in the intermediate range).
- What are the breakpoints and mechanisms involved in:
a. VISA?
MIC 4-8
Mechanism = Increase in cell wall thickness by accumulation of peptidoglycan precursors which prevent diffusion of the drug into the organism.
What are the breakpoints and mechanisms involved in:
a. VRSA?
MIC >=16
Mechanism = vanA gene conferring vancomycin resistance by altering peptidoglycan cross-linking targets. (D-Ala-D-Ala to D-Ala-D-Lac, or D-Ala-D-Ser)
- For each enzyme, name an indicator that can be used in the laboratory to detect their presence. Indicate ‘none’ where appropriate.
a. β-metallobetalactamase
b. ESBL
c. AmpC
d. TEM-1
a. β-metallobetalactamase - Inhibition assay using meropenem with and without dipicilonic acid, increase in zone diameter with the addition of dipicolinic acid or EDTA
b. ESBL – Disk inhibition assay using cefotaxime and ceftazidime with and without clavulinic acid with a >=5 mm diameter with addition of clavulinic acid. (MAST test)
c. AmpC – MAST test, but with no change in zone diameter and resistance to Cefoxitin. Or cloxacillin
d. TEM-1 – None (or what about the nitrocefin test
- IVDU with acute nodular lymphangitic lesions. Culture positive for GNB growing in 48h on choc, oxidase negative, weak catalase positive, and urea negative.
a. What is the most likely etiologic agent?
Francisella tularensis
b. What are the nutritional needs of Fransicella tularensis?
Cysteine
Thiosulfate
?Iron
- What are 5 microbiological or epidemiological features of an event that lead to the suspicion of bioterrorism or a biocrime?
i. Multiple patients presenting with a similar illness
ii. Patient presenting with an illness consistent with a diagnosis
of an agent of possible bioterrorism
iii. Cultivation of an organism with an unusual drug resistance
iv. Atypical disease presentations
v. Shorter incubation time that usual
vi. Following a specific threat
vii. Recurrence of a rare disease
viii. Disease during an unusual season
- In the CCR5 testing for maraviroc, you are told that there was “inability to amplify”. List two virologic causes to explain this phenomenon.
1) Viral load below the limit of detection for the assay
2) Inhibitors present
- List 5 steps of the Gram stain
1) Fix smear with heat or methanol
2) Flood slide with crystal violet for 30 sec, rinse with water
3) Flood slide with Iodine, let sit for 30 sec, rinse with water
4) Decolorize with Acetone-Alcohol until run off is clear, rinse with water
5) Counterstain with Safranin for 30 sec - 1 minute, rinse with water
What are 2 bacteria that tend to overdecolourize?
1) Clostridium clostridiforme
2) Streptococcus pneumoniae
- What are 4 phenotypic criteria common to Enterobacteriaceae
1) Ferment glucose
2) Gram stain negative
3) Catalase positive
4) Faculative anaerobes
5) Non-sporing
6) Reduce nitrate to nitrite (there are some exceptions)
- What are 3 bacterial genera that do not stain with the Gram stain?
1) Coxiella
2) Mycoplasma
3) Chlamydia
4) Treponema
5) Ureaplasma
- List 4 members of the Mycobacterium tuberculosis complex.
1) Mycobacterium tuberculosis
2) Mycobacterium africanum
3) Mycobacterium bovis
4) Mycobacterium caprae
5) Mycobacterium microti
6) Mycobacterium canettii
7) Mycobacterium pinnipedii
- What are 3 NTM’s that can give a false positive on an IGRA?
1) Mycobacterium marinum
2) Mycobacterium kansasii
3) Mycobacterium szulgai (Can cause adult pulmonary disease)
4) Mycobacterium flavescens (Rapid grower)
- Regarding sputum culture for mycobacteria:
a. What are two agents for decontamination?
1) NALC-NaOH (N-acetyl –L-cysteine Sodium Hydroxide)* most common
2) Oxalic acid
3) HCl
4) Benzalkonium chloride-triodium phosphate
5) Cetylpyridnium chloride
b. What are the minimum and maximum expected rates of contamination for sputum cultures for mycobacteria?
c. If the rate is lower than the minimum, what is the main cause?
Minimum = 2% Maximum = 5%
Too many mycobacteria are lost in the decontamination process
- A GNB is growing on the MacConkey, H2S+. Salmonella is suspected.
a. Name 2 other H2S+ bacteria.
1) Citrobacter freundii
2) Proteus vulgaris
3) Edwardsiella tarda
4) Proteus mirabilis
5) Morganella
6) Erysipilothrix rhusiopathie
- What is the principal mechanism of resistance of Salmonella to the fluoroquinolones?
gyrA gene – altered target for quinolone binding to active site (QRDR of topioisomerase enzyme)
- What are 2 antigens used in rapid diagnostic tests for malaria?
1) Hrp2 (Histine rich protein 2) – P. falciparum
2) Aldolase – All species of Plasmodium
3) Plasmodium Lactate Dehyrodgenase (pLDH) – Antibodies specific to both P. falciparium and all Plasmodium species
In comparing level 3 laboratories against level 2:
a.List 3 operational or administrative characteristics of a level 3 laboratory
1) Restricted access with controlled access system (record of all persons entering and exiting)
2) Full coverage dedicated protective clothing to be worn
3) Routine cleaning to be done by specifically trained staff
4) All specimens to be opened in a BSCII cabinet
5) All material decontaminated prior to removal
b.List 3 layout and design characteristics of a level 3 laboratory
1) Exhaust air Hepa filtered
2) Anteroom with a walk through shower
3) Negative pressure airflow
4) Windows to be nonopening and sealed
5) Mechanism in place so both doors can not be opened at the same time
- Child returns from Mexico; drank lots of raw goat milk. Now has fever & night sweats.
a. What is the most likely diagnosis?
Brucella
b. Name 3 species of Brucella that are pathogenic in humans
Brucella suis (swine) Brucella melitensis (goats/sheep) Brucella abortus (cattle) Brucella canis (canines)
- 16 y.o. patient has 2 weeks of sore throat, fever, and lymphadenopathy.
a. What is the most likely diagnosis?
b. What are 2 other possible diagnoses?
a. EBV
b.
CMV
Acute HIV
Neisseria gonorrhea
Virus family of Bocavirus?
Parvoviridae
Virus family of hMPV?
Paramyxoviridae
- List 4 types of nucleic acid amplification tests.
1) Polymerase Chain Reaction (PCR)
2) Strand displacement assay (SDA)
3) Transcription Mediated Amplification (TMA)
4) Ligase Amplification Reaction (LAR)
5) Nucleic Acid Sequence Based Amplification (NASBA)
6) LAMP
- Name two classes of carbapenemases (Ambler classification) and for each, name an organism that can produce this enzyme.
Class D = Oxa-48 = E. coli, Acinetobacter
Class A = KPC = Klebsiella pneumoniae
Class B = IMP = K. pneumoniae, Pseudomonas, Acinetobacter
- 63 y.o. female, with BAL likely + for Nocardia.
a. Name 2 other GPB that are modified acid-fast +.
1) Rhodococcus equi
2) Gordonia
3) Mycobacterium
4) Tsukamurella
- 63 y.o. female, with BAL likely + for Nocardia.
b. List 4 antibiotics that would be on the primary antibiogram.
1) TMP-SMX
2) Imipenem
3) Ceftriaxone
4) Amoxicillin-Clavulinic Acid
Also criteria for: Amikacin, Cipro, Clarithromycin, Linezolid, Minocycline, Moxifloxacin, Tobramycin
Secondary = Cefepime, Cefotaxime, Doxycycline
- Regarding Giardia lamblia:
a. List 2 advantages of EIA’s
1) Rapid
2) Minimal technical training required
3) More sensitive than O&P
- Regarding Giardia lamblia:
b. List 2 disadvantages of EIA’s.
1) Does not allow for dection of other potential pathogens
2) Can only be used on stool samples
3) Only detects the cysts
c. Name 2 other specimens aside from stool where Giardia can be found.
1) Duodenal aspirates
2) Duodenal biopsy
- Name 2 mechanisms of resistance of S. pyogenes to macrolides and for each, describe the antimicrobial susceptibility phenotype.
1) mef gene – Codes for an efflux pump: Erythromycin R, Clindamycin S
2) erm gene – Ribosomal methylation: Erythromycin R, Clindamycin R. Higher Erythro MIC
- 83 y.o. female, with meningitis. GPB in CSF.
a. What is the most likely organism?
Listeria monocytogenes
b. List 6 tests for Listeria, and the expected results
1) Catalase – positive
2) Bile esculin – positive
3) Room Temperature Tumbling motility – positive
4) CAMP – Positive
5) VP – positive
6) Methyl Red – Positive
7) Beta hemolytic
8) Hippurate – Positive
9) H2S from Glucose – Negative
- CAPD pt. with PD infection. Culture shows GPC, cat -, LAP -, PYR -, and vanco R.
a. What is the most likely organism?
Leuconostoc
b. List 3 other GPC with intrinsic resistance to vancomycin.
1) Pediococcus (LAP+, PYR-, tetrads or clusters)
2) Weissella
3) Enterococcus gallinarum
4) Enterococcus casseliflavus
- Coxiella serology - phase I IgG 1:1600, phase II IgG 1:50. Interpret.
Chronic infection
Phase I >800, and Phase II is <200
- Your laboratory performs a specialized test for which there is no external control. List 2 ways to ensure the results produced are reliable.
1) Use a patients previous positive sample as a control in your test
2) Back it up with another method of testing
- For Neisseria gonorrhoeae:
a. Name 2 commercially available selective agar for isolation of this organism.
1) Thayer Martin Agar
2) Martin Lewis Agar
b.Name 2 rapid tests for presumptive ID when Neisseria gonorrhoea grows on selective agar.
1) Oxidase positive
2) Gram stain to show gram negative diplococci
c.List 4 methods of confirmation Neisseria gonorrhoea
1) Hybridization probes
2) DFA
3) Utilizes glucose, not maltose or lactose or sucrose
4) Chromogenic Enzyme Substrate Tests
5) DNA Sequencing
6) MALDI-TOF
- What is the value of an EIA serology for B. burgdorferi in a pt. with erythema migrans?
Clinical diagnosis, even if EIA was negative could be too early and you should treat anyways.
- Regarding arboviruses:
a. List 4 tests to confirm a suspected infection of WNV:
1) CSF IgM
2) Serum IgG and IgM
3) Blood PCR
4) Plaque Reduction Neutralization Assay
b.What are 3 arboviruses present in Canada?
1) Eastern Equine Encephalitis
2) St. Louis Encephalitis
3) Powassan virus
4) Western Equine Encephalitis
5) WNV
List three tests/characteristics that differentiate B. anthracis and B. cereus, and give the expected results for each.
Hemolysis
Motility
Penicillin Susceptibility
b.Name one test to confirm the ID of Bacillus anthracis
Real time PCR for toxin genes (pXO1, pXO2 and a Bacillus chromosomal target)
Others:
- Demonstration of lysis by y-phage
- Fluorescent Ab detection of the capsule
c.Name 2 virulence factors of B. anthracis.
1) Capule (antiphagocytic, encoded by pXO2)
2) Exotoxins (encoded by pXO1) =
a. Edema toxin (Edema factor + Protective antigen)
b. Lethal toxin (Lethal factor + Protective antigen)
- Name 2 ways to confirm suspicion of a white mould of being Coccidioides.
1) Specific DNA probe
2) Immunodiffusion test for exoantigen
3) Cultivation for spherules in special synthetic Converse medium
4) Animal inoculation for in vivo production of spherules
- Regarding influenza resistance to oseltamivir:
a. What gene would be targeted if a genotypic resistance test was created?
Neuraminidase gene (NA gene)
What is the most frequent mutation of influenza A that causes oseltamivir-R?
H274Y
Influenza Resistance Mutations to NAIs:
Flu A/H3N2 E119V, R292K
Flu A/H1N1 H274Y
Flu B R152K
The H1N1 H274Y resistance mutation is the reason why most H1N1 are resistant to Oseltamivir, but they are still susceptible to Zanamivir. With the pandemic flu (pH1N1) those were now sensitive to Oseltamivir again.
- A technologist breaks a tube containing M. tuberculosis.
a. What are 5 chronological steps that should follow?
1) All personnel to clear the area
2) Hold breath if not in PPE
3) Exit for at least 1 hour
4) Warning signs alerting others
5) Wear proper PPE before going in
6) Clean up spill safely
7) Post exposure follow up of personnel
- List 4 microscopic methods to confirm the presence of P. jiroveci in a BAL:
1) DFA (C&T)
2) Methenamine Silver Stain (C only)
3) Giemsa (C&T)
4) Calcoflour White (C only)
5) Papanicolaou (C only)
6) Toludine Blue O (C +/-T)
7) DiffQuik
- Regarding molecular typing methods in bacteria:
a. List 4 important characteristics for a good molecular typing test.
1) Typability - % of typable isolates among the total number of isolates subtyped (data to lead to the designation of subtypes)
2) Reproducibility
3) Discrimatory Power
4) Convenience Parameters (Rapidity, cost, technical demands, accessiblility, ease of data management)
b. Name 3 common techniques for typing of S. aureus:
1) PFGE (SmaI)
2) MLST – Sequence based
3) Single-Locus Sequence Typing (spaA for S. aureus) – Sequence based
4) Multiple-Locus Variable-Number Tandem-Repeat analysis (MLVA) – Sequence based
5) Ribotyping (RFLP)
6) Repetative Sequence-Based PCR
- List 4 reasons as to why a confirmed strain of S. aureus could give a negative test for free coagulase, after the tube was incubated at 35°C for 4 hours:
1) Too short of an incubation time, re read after 18 hours
2) False negative due to production of staphylokinase (lyses the clot)
3) Plasma used was not sterile
4) Colony tested was not pure
5) Low inoculum
6) Presence of fibrinolysin that can dissolve the clot (activity increased at 37 degrees, that’s why it is kept at room temp after 4 hours)
- List 2 characteristics of superantigens that explain their high pathogenicity, and list 2 organisms that produce them.
Charasteristics:
1) Activate a large number of T-cells (20%) independent of processing and presentation by an antigen presenting cell
2) Does not require a co-receptor
Organisms:
1) Staphylococcus aureus
2) Streptococcus pyogenes
- Name 2 aerotolerant Clostridium species, and name a rapid test that differentiates Clostridium from Bacillus.
1) Clostridium tertium
2) Clostriudium histolyticum
3) Clostridium carnis
4) Clostridium septicum (Pubmed…)
Rapid test = Catalase (Clostridium Neg, Bacillus Pos)
Also, Clostridium sporulate only anaerobically.
Most Clostridium are catalase negative (can’t find which are catalase positive)
- Pt. with breast ca., chemo, and secondary neutropenia. Becomes febrile; broad-spectrum antibiotics administered through central catheter. Still febrile on day 4; blood cultures + for yeast (non-filamentous).
a. List 2 antifungals appropriate for empiric therapy in this infection, and for each, explain the mechanism of action.
1) Amphotericin B – Binds to egosterol and alters cell membrane permeability causing cell contents to leak out
2) Caspofungin – Inhibits 1-3-B-D-glucan synthase, disrupting cell wall synthesis
b. List 2 steps (aside from antifungals) important in this patient with fungemia management
1) Remove the central catheter
2) Repeat blood cultures until negative
- List 4 types of E. coli and explain the mechanism by which they cause diarrhea.
1) ETEC: Enterotoxogenic E. coli
2) EHEC: Enterohemorrhagic E. coli
3) EPEC: Enteropathogenic E. coli
4) EAEC: Enteroaggregative E. coli
5) EIEC: Enteroinvasive E. coli
ETEC Heat stable and heat liable enterotoxins, fimbrial adhesins, secretory diarrhea
EHEC Shiga toxin, intimin-Tir mediated attaching and effacing
EPEC Localized adherence via fundle forming pilus, intimin-Tir mediated attaching and effacing
EAEC Aggregative adherence via several fimbriae, Pet and other toxins, microvillus atrophy
EIEC Cellular invasion, intracellular motility, and cell-to-cell spread
- Young woman, presents with bat bite on neck. Received tetanus vaccine. List 4 steps in her management.
1) Local wound management – cleaning and flushing of wound with soap and water
2) Post exposure prophylaxis with Rabies Ig – into wound
3) Vaccine administration (Day 0, 3, 7, 14. Add day 28 if immunosuppressed)
4) Arrange to have bat tested if available
- Gardener presents with chronic ulcerated lesion on finger and nodules evolving along her forearm.
a. What is the most likely etiologic agent?
Sporothrix schenckii
b. What is the therapy for Sporothrix?
Itraconazole 200 mg po daily
c. List 4 other agents of chronic nodular lymphangitis.
1) Nocardia
2) Cutaneous Leishmaniasis
3) Mycobacterium marinum
4) Mycobacterium chelonae
5) Cryptococcus
6) Francisella tularensis
- Fish farmer injured while handling a fish, develops acute cellulitis w/ lymphangitis. Culture grows β-hemolytic, GPC in chains, PYR+, non-grouping by Lancefield.
a. What is the most likely etiologic agent?
Streptococcus iniae
What is the treatment for Streptococcus iniae?
Penicllin G
- What are 3 contraindications to the varicella vaccine?
1) Anaphylaxis to previous varicella vaccine or immediate hypersensitivity or anaphylaxis to any vaccine components
2) Pregnancy
3) Impaired immune function
4) Active infective with tuberculosis
- Regarding the pandemic (2009) H1N1 influenza A strain:
a. Name 6 groups at risk of complications.
1) Pregnant women
2) Elderly patients
3) Children less than 1 year old
4) Diabetic patients
5) Immunosuppressed patients
6) Patients with chronic lung diseases
7) Cardiac disease
b. What is the adjuvant in the pandemic flu vaccine, and its composition?
MF59 – Oil in water adjuvant
- What are 2 clinical syndromes associated with HHV-6?
1) Roseola Infantum
2) Infectious mononucleosis
3) Infant Febrile Seizures
4) Meningoencephalitis (rare)
- What are 6 pathogens requiring airborne isolation precautions?
1) Tuberculosis
2) SARS
3) Measles
4) Varicella
5) MERS CoV
6) Smallpox
7) Monkeypox
- A pregnant nurse presents with concerns about CMV infection
a. Describe 4 common clinical findings at birth in congenital CMV.
1) Retinitis
2) Microcephaly
3) Intracerebral calcifications
4) Jaundice
5) HSM
6) Purpura
b. What is the main risk factor for development of congenital CMV?
Primary infection during pregnancy
c. What is the diagnostic test to do in the first 2-4 weeks of life to confirm congenital CMV?
Detection of CMV in the urine or saliva (PCR or culture)
- 70 y.o. female presents with chronic cough, hemoptysis, and RUL infiltrate. AFB smear +, DNA probe + for M. TB complex. She takes care of her 2 & 4 y.o. grandchildren. The 4 y.o. has mediastinal lymphadenopathy; the 2 y.o. has a negative PPD.
a. What treatment would you start for the index patient?
b. What are 2 other presentations common in the pediatric population?
How do you manage each child?
Treatment for index person: Rifampin Isoniazid Pyrazinamide Ethambutol
Pediatric presentations = Fever, Growth delay, Weight loss
Management:
4 year old – Can diagnose with a positive TST or IGRA, abnormal chest Xray or physical exam and epi link. Gastric aspirate and then treat
2 year old – Treat for active or latent depending on CXR, history, physical and gastric aspirate
- List 2 effective therapies against lice
1) Permethrin Hair Rinse
2) Pyrethrin Shampoo
3) Lindane Shampoo (poisonous – not for children <2)
4) Topical Ivermectin
- 50 y.o. male with decompensating right-sided CHF, with no valve disease on echo. Previously lived extensively in S. America for many years.
a. What is the most likely etiologic agent?
Trypanosoma cruzi
Trypanosoma cruzi:
b. How is this organism acquired normally?
c. What is the most accessible test?
d. What is the most useful test?
b. How is this organism acquired normally?
Bite of a triatome bug (Rhodnis prolixus)
c. What is the most accessible test?
Blood films
d. What is the most useful test?
PCR
e. Name an effective therapy for T. cruzi?
Acute = Nifurtimox or Benznidazole Chronic = Support therapy
- 18 y.o. male presents with fever, headache, skin lesions (not in shock). Aspiration of a hemorrhagic bulla shows GNDC. Blood & CSF cultures obtained.
a. What are the 2 most likely etiologic agents?
Neisseria meningititis
Neisseria gonorrhea
b. What are 3 elements of management that need to be dealt with immediately for N. meningitis?
Start IV antibiotics with Ceftriaxone
Place patient on Contact and Droplet precautions
Notify treating physician
Notifly infection control
- 20 y.o. male with multiple sexual partners, now with septic arthritis of the knee. What are the 3 most likely pathogens in this context?
1) Neisseria gonorrhea
2) Staphylococcus
3) Streptococcus
- Female hospitalized with PID. Anaphylactic allergy to pen. Cipro resistance 7% in area.
a. What treatment would you begin?
Clindamycin 900 mg IV q8h PLUS
Gentamicin 1.5 mg/kg IV q8h (first give a loading dose of 2 mg/kg IV)
+/- Doxycylcine (if you think it’s CT or GC)
b. What oral treatment would you step down to given allergy to pen for PID?
Clindamycin 450 mg po QID for a total of 14 days OR
Doxycycline 100 mg po BID
What are 2 types of meat that can transmit trichinellosis?
1) Pork
2) Bear meat
3) Wild boar
4) Walrus
- 28 y.o. female travelling to Nepal. Diarrhea with 10 BM’s/d, with malaise & myalgias. Stool cultures negative, Crypto EIA negative. Circular, modified Kinyoun + organism, measuring 10 μm.
a. What is it?
b. What is the treatment?
Cyclospora cayetanensis (used to be called Cryptosporidium grande)
TMP-SMX 1 ds tab BID x 7 days
- Pt. recently dx’d. with HIV, CD4 50. Appears dehydrated. Investigations show Crypto. What are 3 steps to proceed with in his care? Cryptococcal meningitis:
1) Initiate Amphotericin B + Flucytosine
2) LP to determine pressure and repeat LPs to control increased ICP as needed
3) Initiate HAART therapy 2-10 weeks after starting treatment for crypto meningitis
4) Stabilize patient from dehydration
5) Repeat LP at 2 weeks for sterility
- Woman returning from Indonesia. Fever, cough, and chest pain, with diffuse infiltrates on CXR. Eosinophilia. What are 4 parasitic causes to explain her symptoms?
1) Strongyloides stercoralis
2) Hookworm
3) Ascaris lumbricoides
4) Paragonimus westermani
5) Wucheria bancrofti
6) Brugia species
- Woman returning from Philippines, visiting friends/relatives, no malaria proph. Presents with fever, hypotension, acute renal failure (creat 230). Blood smears show intraerythrocytic parasite, parasitemia 2.9%, with multiple equatorial band forms. (photo of schizont of roughly 10 nuclei & band forms)
a. What is the disease?
b. What is the treatment?
P. knowlesi
Chloroquine phosphate (600 mg base po x 1 immediately, then 300 mg base at 6, 24, and 48 hours)
- Pt. w/ HIV, CD4 50, presents with seizures. Imaging reveals hypodense brain lesions, with uptake of contrast and perilesional edema.
a. What are the two most likely diagnoses?
b. What treatment should be started?
Toxoplasmosis
Primary CNS lymphoma
b. What treatment should be started?
Sulfadiazine + Pyrimethamine
Use above for 6 weeks then half the dose of each for maintenance therapy until CD4 is >200 with HAART
- Pt. on steroids, presents with headache & fever. LP shows high WBC (7000) with lymphocytic predominance. Round encapsulated yeasts seen.
a. Cryptococcal latex antigen is negative. Why?
False negative due to prozone effect
Low antigen concentration
- Pt. from Congo, newly dx’d. with HIV, CD4 10. ARV’s started 6 weeks ago. Abdo pain has since developed, and imaging shows multiple enlarge intraabdominal lymph nodes.
a. What is the name of this clinical picture?
b. What are the 2 most likely pathogens?
c. What test should be done?
d. What treatment should be started?
a. What is the name of this clinical picture?
Immune Reconstitution Inflammatory Syndrome (IRIS)
b. What are the 2 most likely pathogens?
Tuberculosis
MAC
c. What test should be done?
Biopsy with pathology, fungal, routine, mycobacterial culture
d. What treatment should be started?
Anti TB treatment?
- 69 y.o. female with total hip replacement 2y ago. Now has hip pain. Joint aspiration + for S. aureus - R to pen, S to all other antibiotics. What antibiotic(s) would you recommend and for how long?
Cefazolin IV or Cloxacillin IV or Ceftriaxone x 6 weeks
+ Rifampin PO x 6 weeks if debride and retention or 1stage exchange
(If 2 stage exchange or permanent ressection then no rifampin)
Then oral therapy with Cipro or Levo + Rifampin for 3 months with a hip, or 6 months with a knee in all patients who have had debridement and retention or 1-stage exchange
Consider chronic suppression in Debride and retention or 1 stage exchange indefinitely with Keflex, Clox, Septra or Minocycline
- Female with infection of external ear after piercing. No response to cefazolin. What are the 2 most likely pathogens.
1) Pseudomonas aeruginosa
2) MRSA
- A neonate, a few days old, presents with meningitis, and CSF + for GNB.
a. What is the most likely organism?
b. Culture + for lactose fermenter on MacConkey, yellow on BAP. Oxidase, DNase, sorbitol negative. What is the most likely organism now?
(Enterobacter cloacae is sorbitol positive, Elizabethkingia is oxidase positive)
c. Baby improves, then worsens after 4-5 d of treatment. 2 possible explanations?
E. coli
b. Culture + for lactose fermenter on MacConkey, yellow on BAP. Oxidase, DNase, sorbitol negative. What is the most likely organism now?
Cronobacter sakazakii
(Enterobacter cloacae is sorbitol positive, Elizabethkingia is oxidase positive)
c. Baby improves, then worsens after 4-5 d of treatment. 2 possible explanations?
Organism has intrinsic AmpC type resistance
Secondary infection with another organism
Abscess
- 6d old neonate with sepsis and marked lymphocytic leukocytosis. Original septic workup is negative, but there is no improvement on antibiotics.
a. What are 2 non-bacterial pathogens that could explain this picture?
b. For each one, please discuss tests and specimens for diagnosis.
c. For each, list measures to prevent further transmission in hospital.
1) HSV
2) CMV
b. For each one, please discuss tests and specimens for diagnosis.
HSV – CSF for PCR
CMV – CSF for PCR or shell vial or culture. Also collect urine and saliva swab for same.
c. For each, list measures to prevent further transmission in hospital.
Contact isolation for HSV if skin lesions
CMV is standard precautions
- 2 mo. old infant with apnea & bradycardia. In the law few days, he has had a runny nose without fever. An aunt came home recently and has been coughing for 3 weeks.
a. What is the most likely pathogen?
Bordetella pertussis
b. What are measures to prevent transmission of B. pertussis, and how long do they need to last?
Droplet isolation until 5 days after effective antibiotic therapy has been initiated or 3 weeks in untreated patient
Chemoprophylaxis for close contacts with Azithromycin x 5 days
(Close contact = household, daycares)
- Patient with MRSA necrotizing pneumonia. It has an MIC of 2 to vancomycin, and is R to erythro, clinda, and TMP-SMX.
a. List 2 reasons to not give vancomycin alone in this context.
Elevated MIC associated with clinical failure
May represent heteroresitant population of vancomycin intermediate isoaltes, giving vancomycin will select for the resistant population?
Necrotizing pneumonia has a PVL toxin and vanco does not reduce the production of toxins.
Patient with MRSA necrotizing pneumonia. It has an MIC of 2 to vancomycin, and is R to erythro, clinda, and TMP-SMX.
b. What are 2 other antibiotics that can be used? (dosing, interval, & duration).
Linezolid 600 mg IV q12h x 14 days
Tigecycline 50 mg IV q12h x 14 days
Telavancin 10 mg/kg IV q24h x 21 days
- Regarding daptomycin:
a. What is the mechanism of action?
b. What are the 2 main indications?
c. What are 2 drugs to be monitored when administered alongside daptomycin?
Binds to the cell membrane and causes rapid depolarization inhibiting DNA, RNA and protein synthesis
b. What are the 2 main indications?
Skin and skin structure infections caused by susceptible isolates
Staphyloccocus aureus bloodstream infections
c. What are 2 drugs to be monitored when administered alongside daptomycin?
HMG-CoA Reductase Inhibitors
1) Atorvastatin
2) Simvastatin
Tobramycin activity is decreased
MOA of Tigecycline
Inhibit protein synthesis by binding to the 30S ribosomal subunit
MOA of Ertapenem
Inhibit cell wall synthesis by binding to penicillin binding proteins
Tigecycline:
3 GNB’s with intrinsically low activity
Morganella
Proteus
Providencia
Pseudomonas aeruginosa
Ertapenem:
3 GNB’s with intrinsically low activity
Pseudomonas aeruginosa
Stenotrophomonas
Burkholderia
Acinetobacter
- In the NNIS classification of surgical site infections, what are the 3 components of the score?
- Type of wound – Contaminated or Dirty
- Duration of surgery
- American Anesthesiology score 3,4, or 5 (Patients comorbidities )
- Identify six elements that are part of a structured antimicrobial stewardship program.
1) Prospective audit with intervention and feedback
2) Formulary restriction and preauthorization requirements for specific agents
3) Education
4) Guidelines and Clinical Pathways
5) Antimicrobial order forms
6) Dose optimization
7) Conversion from parentral to oral formulations
8) De-escalation of therapy
- List 6 factors influencing the transmission of TB from person to person
1) Site of infection (Laryngeal more contagious)
2) Smear positivity
3) Proximity of contacts
4) Duration of exposure
5) Cough
6) Crowding and room ventilation
7) Treatment
8) Cavitary disease
- Elderly male present with 2 months of subacute fever, now has a new murmur. Blood cultures + for GPC in chains.
a. What therapy is appropriate? (dose, interval, duration)
Vancomycin 15-20mg/kg/dose q12h x 6 weeks
+/- Gentamycin 1 mg/kg q8h x 6 weeks
b. What are 4 indications for surgery in infective endocarditis?
Large Abscess despite appropriate antibiotic thearpy
Heart failure unresponsive to medical management
>=1 embolic event during first 2 weeks of antibiotics
Anterior Mitral leaflet vegetation >1 cm
Persistent vegetation after systemic embolization
Increase in vegetation size despite antibiotics
Valve perforation or rupture
New heart block
Fungal IE
List 4 clinical syndromes caused by Coxiella burnettii.
1) Self limited Febrile Illness
2) Endocarditis
3) Post Q fever Fatigue Syndrome
4) Pneumonia
5) Hepatitis
6) Osteomyelitis
7) Q fever in infancy
8) Q fever in the immunocompromised host
9) Q fever in pregnancy
- Regarding foodborne infections:
a. List 4 pathogens commonly associated with unpasteurized dairy products.
1) Brucella abortus
2) Yersinia entercolitica
3) Coxiella burnetii
4) Cryptosporidium parvum (cows)
5) Listeria
b. List 4 pathogens commonly associated with contaminated fruits & vegetables.
1) Shiga toxin producing E.coli (STEC)
2) Shigella
3) Norovirus
4) Cyclospora cayetanensis (Raspberries)
5) Salmonella
6) Bacillus cereus
- Male patient with colon ca., presents with fever and buttock pain. CT shows gas bubbles in the paraspinal and gluteal muscles. Blood culture + with long GPB.
a. What is the infection?
b. What is the etiologic agent? (include species)
Clostridial necrosis
Clostridium septicum
- What are 4 indications for GBS prophylaxis in the intrapartum period?
1) GBS bacturia during the pregnancy
2) Previous infant with GBC infection
3) Positive GBS screen after 36 weeks
4) No GBS screening swab collected prior to labour onset
a.What is the best alternative for GBS prophylaxis if the patient has a non-type I allergy to penicillin?
Cefazolin
- CMV infection (not disease) post-BMT. Ganciclovir started, followed by valganciclovir, while also on cyclosporine and prednisone. During therapy, pulmonary infiltrates develop, and CMV viremia increased by 3 log. CMV culture from BAL is +.
a. What is the cause of deterioration in the patient?
b. What would be the most useful test in the management of the patient?
c. What are 2 steps in the management of this patient that should be undertaken?
CMV pneumonitis
b. What would be the most useful test in the management of the patient?
Resistance testing of CMV isolate
c. What are 2 steps in the management of this patient that should be undertaken?
Decrease immunosuppression
Change therapy to Cidofovir or Foscarnet
If UL97 mutant (activation one) then Cidofovir will work
If the mutation is UL54 (polymerase) then there may be cross resistance to Cidofovir too
- Hemorrhagic cystitis post-BMT, with negative bacterial culture of urine. What are 3 most likely organisms involved?
1) BK virus
2) Adenovirus
3) JC Virus
4) HSV
5) CMV
6) HHV6
- Regarding Burkholderia cepacia in CF patients:
a. What are the two most common genomovars?
II and III (multivorans and cenocepacia)
b. What are 2 clinical features of B. cepacia syndrome?
1) Necrotizing pneumonia
2) Hematogenous dissemination
- Taiwanese patient presents with 5 cm liver abscess. Abscess drainage grows a mucoid lactose fermenter on MacConkey. VP, indole, and lysine +.
a. What is the most likely organism?
b. What are 2 other metastatic foci in patients that have this picture?
Klebsiella oxytoca
1) Meningitis
2) Endophthalmitis
- Patient with orbital cellulitis.
a. Which form of sinusitis is this commonly associated with?
b. What are 3 physical exam findings associated with this infection?
c. What are 2 complications?
d. What is the treatment?
Acute bacterial rhinosinusitis of the ethmoid sinus
Proptosis, ophalmopelegia, pain with eye movements
Brain abscess, orbital abscess, cavernous sinus thrombophlebitis, vision loss
Vancomycin + Ceftriaxone
Need anaerobic coverage if any intracranial extension. Add metronidazole or do Vanco + PipTazo.
- Patient with HCV & HIV coinfection. Treating with pegylated interferon & ribavirin. What 2 NRTI’s should be avoided if possible, and why?
1) Didanosine
2) Zidovudine
3) Atazanavir
- Patient with rheumatoid arthritis is to receive an anti-TNF inhibitor. PPD +, LTBI treatment started with elevation of hepatic transaminases, and INH is stopped. Her hepatic enzymes resolve. She also takes coumadin for atrial fibrillation.
a. What is an alternative regimen for her LTBI?
Rifampin for 4 months duration
What are 3 side effects of Rifampin?
Discoloration of body fluids (orange)
Hepatotoxicity
Drug interations
- A coryneform bacterium is found in sputum.
a. Name 2 factors that suggest a corynebacterium is significant in the sputum?
1 - Growth is pure
2 - Growth of the coryneform is in heavy amounts and exceeds the growth of respiratory flora
b. Which coryneform frequently causes pneumonias?
Corynebacterium pseudodiptheriticum
- In a blood culture, a GPB is found, cat +, beta-hemolytic.
a. Name 4 biochemical tests to confirm diagnosis.
1 – Bile escuin positive 2 – Room temperature tumbling motility positive 3 – CAMP test positive 4 – VP Positiive 5 – Acid production from glucose 6 – Hippurate hydrolysis positive
b. 4 methods of typing of Listeria?
1) PFGE
2) Multilocus variable-number tandem-repeat analysis
3) Multilocus sequence typing
4) Mixed genome DNA microarray
5) Random Amplification of Polymorphic DNA (RAPD)
6) Amplified fragment length polymorphism
7) Ribotyping
8) MALDI-TOF
c. Patient has anaphylaxis to penicillin. What do you give for Listeria?
Trimethoprim-Sulfamethoxazole
Alternative: Moxifloxacin (bacteriocidal)
Drug of choice is Ampicilin + Gentamycin for synergy
- Neutropenic patient has a blood culture that is growing anaerobic GPB, cat -, swarming, indole -.
a. Name the species.
Clostridium septicum
b. What two infections are associated with C. septicum?
Myonecrosis
Neutropenic enterocolitis
- Clinical case of echinococcus. Name confirmational serological test.
Complement Fixation
ELISA
Indirect Hemmaglutination
- Woman w/primary HSV infection gives birth.
a. What is the percent risk of transmission to the baby?
40%
SOGC says 30-50%
b. Name 6 sites to send specimens from for the baby for congenital HSV?
Blood CSF Swab/scrapings of any skin or mucous membrane lesions Conjuntivae Nasopharynx Mouth Rectum
c. List 4 methods of detecting HSV.
Culture
PCR
DFA
EIA
d. Treatment of neonatal herpes (dose & duration).
Acylovir: 60 mg/kg/day divided q8h.
14 days if only skin, eyes, mouth
At least 21 days if disseminated or CNS disease followed by 6 months of oral suppressive
- 6 epidemiologic or microbiologic elements that would make you suspect an act of bioterrorism has been committed.
1) Multiple patients presenting with a similar illness
2) Patient presenting with an illness consistent with a diagnosis of an agent of possible bioterrorism
3) Cultivation of an organism with an unusual drug resistance
4) Atypical disease presentations
5) Shorter incubation time that usual
6) Unusual season
7) Unusual demographics
- Treatment of tularemia.
Moderate to severe disease = Streptomyc in 10 mg/kg q12h IM x 10 days or Gentamicin 1.7 mg/kg q8h IV x 10 days
Mild Disease = Ciprofloxacin 500 mg po BID x 14 days or Doxycycline 100 mg po BID x 14 days
Meningitis = Streptomycin or Gentamicin + Chloramphenicol 20 mg/kg IV q6h or Strep/Gent with Doxycycline 100 mg IV BID x 14-21 days
- Name 6 non pathogenic protozoans in stool.
8) Entamoeba hartmanni
9) Entamoeba coli
10) Entamoeba polecki
11) Entamoeba dispar
12) Endolimax nana
13) Iodamoeba butschii
14) Chilomastix mesnili
15) Entamoeba gingivalis
16) Entamoeba moshkovskii
17) Trichomonas hominis
- Name 3 permanent stains used for protozoa in the stool.
Iron hematoxylin
Modified Trichrome Stain
Modified Kinyoun’s Acid Fast Stain
- Name 4 methods for differentiating C. albicans from C. dublinensis. Is it important to differentiate & why?
1) Colonies on CHROMagar - A is light green, D is dark
2) Growth at 42-45 degrees - A grows, D does not
3) Chlamydospores on Cornmeal Agar - A single, D in clusters
4) Colonies on Staib agar - A is smooth, D is rough
5) Assimilation of sugars - A + for Xyl, MDH, The, D neg for all
- Man sustains wound on a boat. Becomes infected w/ GNB that is ox +. Vitek cannot identify; results are Vibrio fluvialis 50%, Aeromonas caviae 50%.
a. Name 2 special tests to do, and the expected results.
1) Vibrio static disks (O129) Vibrio = Susceptible (except V. cholera 0139) Aeromonas = Resistant 2) Salt Tolerance Vibrio = Growth in presence of 6.5% NaCl Aeromonas = No growth in 6.5% NaCl 3) Growth on TCBS Agar (Thiosulfate-Citrate-Bile Salts-Sucrose) Vibro = Growth Aeromonas = No growth 4) String Test (with 0.5% sodium deoxycholate) Vibrio = Positive Aeromonas = Negative
b. Knowing that this is a soft tissue infection related to fresh water, what antibiotic would you give?
Ciprofloxacin 500 mg PO BID?? + Clinda
Up To Date suggests 1st GC + Levo + Doxy? Seems like overkill…
- Name 4 explanations for isolated anti-HBc +.
3) Acute infection, during the window period
4) Previous HBV exposure with waning sAb titres
5) Chronic HBV infection with sAg below the limit of detection
6) False positive anti-HBc
- Klebsiella w/KPC. Name 4 bacteria with this mechanism of resistance. What is a phenotypic confirmatory test?
1) E.Coli
2) Enterobacter cloacae
3) Serratia marcescens
4) Pseudomonas aeruginosa
5) Salmonella
6) Morganella
Phenotypic confirmatory tests = Disk inhibition assay with a carbapenem with and without boronic acid
- How to confirm production of metallo-beta-lactamases? Of AmpC?
Metallo-beta-lactamase = Disk inhibition assay with a carbapenem with and without EDTA AmpC = Disk based inhibitor test using Cefoxitin with or without cloxacillin
