Infectious Disease Flashcards
Microbiology 101:
What are the four types of microorganisms? And the subtypes within them?
1) Bacteria
a) Gram-positive
b) Gram-negative
c) Other
2) Viruses
3) Fungi
a) Yeasts
b) Moulds
c) Dimorphic
4) Parasites
a) Protozoan
b) Multicellular
What are the two main categories of gram-positive cocci, and name examples?
1) Clusters
- Staph aureus or CNST (coagulase negative STaph)
2) Pairs/chains
- Streptococcus or Enterococcus
What are the three main categories of gram positive bacilli, and name examples?
1) Spore-forming
- Bacillus
- Clostridium
2) Non-spore forming
- Corynebacterium
- Listeria
3) Branching
- Actinomyces
- Norcardia
Name 3 examples of gram negative cocci.
1) Neisseria meningitidis
2) Neisseria gonnorrheae
3) Moraxella
What are the two main categories of gram negative bailli, and name examples?
1) Lactose fermenters
- Klebsiella
- E. coli
- Enterbacter
2) Non-lactose fermenters
- Pseudomonas
- Stenotrophomonas
Name 2 examples of yeast and the type of infection they usually cause.
Yeast
- Candida spp.
- Cryptococcus spp.
Asexual, unicellular organisms
Typically superficial infection, but invasive disease in immunocompromised hosts
Name an example of a Mould.
Aspergillus spp.
Multicellular organisms that have hyphae
Name 3 examples of Dimorphic Fungi.
1) Blastomycosis spp.
2 ) Histoplasmosis spp.
3) Coccidiomycosis spp.
Mould in the cold, yeast in the heat.
Exist as yeast in body temperature, but becomes mould form in room temperature.
High yield antibiotics:
SPICE (HAM) - name the species and treatment (4).
Serrtia
Providencia
Indole-positive Proteus
Citrobacter
Enterobacter
Hafnia
Acinetobacter
Morganella
Rx:
Carbapenem
TMP-SMX
Flurorquinolone (FQ)
Aminoglycoside (AG)
High yield antibiotics:
ESBL - name the species and treatment (4).
E. coli
Klebsiella
Rx:
Carbapenem
TMP-SMX
FQ
AG (if sensitive)
High yield antibiotics:
CPE - name the treatment (3 +/- 2)
Rx:
Colistin
AG
Tigecycline
Call ID (TMP-SMX or FQ if lucky(
High yield antibiotics:
MRSA - name the treatment (7).
Vancomycin
Doxycycline
TMP-SMX
Clindamycin
Linezolid
Daptomycin
Ceftobiprole
High yield antibiotics:
Pseudomonas - name the treatment (10).
Pip/tazo
Ceftazidime
Cefepime
Carbapenems (not Ertapenem)
Ciprofloxacin
AG
Aztreonam
Colistin
Tigecycline
Ceftazidime-Avibactam
Enterococcus - name the treatment (3 +/- 1).
Vanco (not VRE)
Linezolid
Daptomycin
Amp/piperacillin if lucky
Differentiate meningitis vs. encephalitis, based on symptoms and signs.
Meningitis - predominately starts with headache, neck stiffness and fever, and can get altered LOC later into the course
Encephalitis - predominantly starts with altered LOC and fever and can get seizures, focal neurological changes associated
Key guideline for CNS infections:
Tunkel AR, Hartman BJ, Kaplan SL, et al. Practice guidelines for the management
of bacterial meningitis. Clin Infect Dis 2004;39:1267-84.
Does this adult patient have acute meningitis?
Meningitis ruled out (99%) if fever, neck stiffness and altered NS all absent
Joint accentuation - high sensitivity (97% in one study)
Kernig’s and Brudzinski’s signs - high specificity
What are key signs of basal skull meningitis and what are culprit species?
+CN palsies
Long-tract signs
TB
Listeria
Cryptococcus
Syphilis
Lyme
…in the correct host
Bacterial Meningitis:
When to CT and when not to CT?
** I do not understand this question - review at IMR
** I do not understand this question - review at IMR
Meningitis - CSF Parameters
What are the CSF parameters for bacterial, viral, TB and fungal meningitis?
See table
- Differential may be unreliable in recent symptom onset
- Individual CSF predictors for bacterial meningitis each with >99 % certainty
- Glucose < 1.9 mmol/L
- CSF:blood glucose < 0.23
- protein > 2.2 g/L
- WBC > 2000 cells/mL
- PMNs >1180 cells/mL
- CSF biochemistry & cell count minimally affected at 2 days of antibiotics, but culture yield decreased
Meningitis - Pathogens + Rx
For age 18-50 years, what are the common bacterial pathogens and empiric antimicrobial Rx?
For age > 50 years or immunocompromised, what are the common bacterial pathogens and empiric antimicrobial Rx?
Meningitis - Pathogens + Rx CSF Gram Stains
What species is…
a) Gram-positive diplococci
b) Gram-negative diplococci
c) Gram-positive bacilli
a) Gram-positive diplococci = S. pneumoniae
b) Gram-negative diplococci = N. meningitidis
c) Gram-positive bacilli = L. monocytogenes
Meningitis - Pathogens + Rx
For meningitis, what is the duration of treatment for S. pneumoniae, N. meningitidis, and LIsteria monocytogenes?
Meningitis - Steroids
How would you prescribe steroids in meningitis and what species does it reduce mortality/morbidity in?
Dexamethasone 10 mg IV q6h for 4 days PRIOR TO or WITH first dose of antibioitis
- Led to 50% reduction in mortality/morbidity for pneumococcal meningitis
- Two subsequent negative trials
- Cochrane Review (2015): Steroids associated with reduction in mortality for meningitis secondary to Streptococcus pneumoniae (29.9 vs. 36%) and reduction in hearing loss and neurological sequelae for all bacteria
General approach
a) Administer before or with first dose of empiric antibiotics for suspected bacterial meningitis
b) Stop if CSF is non-turbid OR low cell count OR non-pneumococcal by culture
c) Do not start if antibiotics have already been received
Neisseria Meningitis - CHEMOprophylaxis
Who should get it, when and what (3 options)?
(high yield question)
Who:
- Household contacts
- Persons sharing sleeping arrangements
- Persons who have direct nose/mouse contamination with oral/nasal secretions
- Children and staff in childcare or nursery
- HCWs who have had intensive unprotected contact (without wearing a mask) [e.g., intubating, resuscitating, closely examining oropharynx)
- Airline passengers sitting immediately on either side of the case (but not across the aisle) when total time on aircraft is 8 or more hours
When?
- Within 10 days usually
What?
1) Ciprofloxacin 500 mg PO x 1 dose (increasing resistance conern) OR
2) ceftriaxone 250 mg IM x 1 dose OR
3) Rifampin 600 mg PO BID x 2 days
Neisseria Meningitis - IMMUNOprophylaxis
Who should get it and what (2 options)?
(high yield question)
Who?
- Household contacts of a case of invasive meningococcal disease (IMD)
- Persons sharing sleeping arrangements with a case of IMD
- Persons who have direct nose/mouth contamination with oral/nasal secretions of a case with IMD
- Children and staff in contact with a case of IMD in child care or nursery school facilities
What?
- Depends on serotype of index case and age/underlying conditions of contact
- Men-C-ACYW or 4CMenB can be considered
Infective Endocarditis - what are the Class I Recommendations for diagnostic work-up, switching to oral Abx, and patient with drug use?
1) At least 2 sets of BCx prior to antibiotics
2) Initial TTE for everyone
3) TEE class I indications - TTE nondiagnostic or IE complications suspected or intracardiac leads (TEE widely used, these are just the Class I indications - e.g., consider in staphylcoccal, enterococcal, fungal infections)
- In patients being considered for an early change to oral antibiotic therapy for treatment of stable IE, baseline TEE before switching to ORAL and repeat TEE 1-3 days before completing antibiotics regimen should be performed
- Patients with suspected or confirmed IE related to drug use should be referred to addictions medicine specialist for opioid substitution therapy
Infective Endocarditis:
Diagnosis - Duke Criteria
Name the major criteria, minor criteria, definition of definite IE and definition of possible IE. (insert table)
IE - Treatment
What is the treatment of IE, base on species vs. native or prosthetic valve? What is the duration of treatment?
For the treatment of IE, what are the Class IIb recommendations for transitioning a patients to oral Abx?
In patients with left sided IE caused by Streptococcus, E. faecalis, S. aureus or CNST deemed stable by the multidisciplinary team after initial IV antibiotics, a change to oral Abx therapy may be considered if:
1) TEE before the switch to oral therapy shows no paravalvular infection AND
2) Frequent and appropriate follow-up can be assured by the care team AND
3) If a f/u TEE can be performed 1-3 days before the complete of the Abx course
(See POET trial for evidence)
For IE, what is the most important surgical indication (Class I)?
*High Yield Question
Decisions about surgery should be made by a “multispecialty heart valve team” of cardiologists, cardiovascular surgeons and ID specialists
(Class I Level B)
For IE, what are the Class I early surgical indications and delayed surgery indications?
For IE, what are the Class II, other surgical indications for Endocarditis?
IE - Prophylaxis
What patient populations need prophylaxis and for what specific procedures?
What are the prophylactic options?
BONUS Question: POET trial
Patient Oral vs. IV Antibiotic Treatment for Endocarditis
- 400 adults with IE (S. aureus, Strep, E. faecalis, CNST) randomized to IV Abx for duration or oral transition after at least 10 days IV (average 17 days IV)
- Primary endpoint was composite of all cause mortality, unplanned cardiac surgery, embolic events or relapse of bacteremia within 6 months
- Primary outcome occurred in 24 patients (12.1%) in the IV group and 18 patients (9.1%) in oral group (p=0.4) showing non-inferiority
- Caveat was followed 3 times per week and all had TEE, mostly L sided IE, very few (1%) Persons Who Inject Drugs. Not widely adapted into practice.
CAP - Diagnosis? Who to hospitalize?
*high yield
Diagnosis
- Clinical (fever, productive cough, SOB, signs of consolidation) + Radiographic (infiltrate on CXR)
Who to hospitalize?
Use clinical judgement + assess severity of illness
- PSI/PORT Score (*preferred in IDSA/ATS 2019)
- CURB-65
- confusion
- RR >/= 30/min
- BUN > 7 mmol/L
- sBP <90 or dBP </= 60
- Age >/= 65
Score 0-1 = outpatient
Score >/= 2 = likely needs admission
Insert PSI score stable
CAP Pathogens
a) What are the most common CAP pathogens?
b) Pathogen concerning for severe disease?
c) Pathogens in patients with increasing comorbidities, antibiotics and hospital exposures?
a) Common pathogens
- S. pneumoniae (most common)
- M (mycoplasma). pneumonia
- C (chlamydia). pneumonia
- H (haemophilus). influenzae
- Respiratory viruses (influenza, RSV, parainfluenze, rhinovirus, adenovirus, coronaviruses…)
b) Severe disease
- Legionella pneumophila
c) In patients with increasing comorbidities, antibiotic and hospital exposures:
- increasing gram negatives, e.g., K. pneumoniae, Pseudomonas
- S. aureus (including MRSA)
CAP - Microbial Diagnostics
To culture or not to culture?
- Do not obtain sputum or blood C&S on outpatients
*consider for inpatients if severe CAP / intubated / being treated empirically for MRSA or Pseudomonas - Consider sending urine pneumococcal + legionella Ag +/- lower tract legionella NAAT in severe CAP or when indicated by epidemiological factors (e.g., outbreak)
- Send rapid influenza molecular assay (NAAT) when influenza virus is circulating in community. **not included in 2019 guidelines, but current standing of care would suggest to also send COVID-19 PCR
- Do not send procalcitonin levels to distinguish between viral and bacterial pathogens
CAP - Outpatient Treatment
Healthy outpatients without comorbidities or risk factors vs. outpatients with comorbidities
1) Healthy outpatients without comorbidities or risk factors
- ***Amoxicillin 1 g TID (strong, moderate) - high yield
- doxycycline 100 mg BID (conditional, low)
- Azithromycin 500 mg and then 250 mg (or Clarithromycin) - only in areas with pneumococcal resistance < 25% (conditional, moderate) - not appropriate for majority of Canada
2) Outpatient with comorbidities (chronic heart, lung, liver, renal, DM, alcoholism, malignancy, asplenia)
- amox-clav OR cephalosporin (Cefpodoxime, cefuroxime) PLUS macrolide (strong, moderate) OR doxycycline (conditional, low)
- Resp FQ, e.g., levofloxacin, moxifloxacin (strong, moderate)
- Adds additional coverage for H. flu and M. catarrhalis (both produce beta-lactase frequently) and as well provides coverage for S. aureus and gram negatives, which are particularly high risk in COPD
CAP - Inpatient Treatment
a) Inpatients, non-ICU, without risk factors for MRSA or PsA
b) Inpatients, severe CAP (e.g., ICU), without risk factors for MRSA, PsA
c) Aspiration PNA
a) Inpatients, non-ICU, without risk factors for MRSA or PsA
i. Beta-lactam (amp-sulbactam, cefotaxime, CTX or ceftaroline) PLUS Macrolide (strong, high)
-doxy is a 3rd line option as alternative if unable to give other options (conditional, low)
ii. Resp FQ
iii. insufficient evidence for Omadacycline (tetracycline) as only single trial of non-inferiority to moxifloxacin
b) Inpatients, severe CAP (e.g., ICU), without risk factors for MRSA, PsA
i. Beta-lactam AND Macrolide (strong, moderate)
- Evidence that macrolide containing combination had lower risk of death, and evidence that combination of beta-lactam and Resp FQ had higher mortality (but poor evidence)
ii. *** Beta-lactam AND Resp FQ - high yield
c) Aspiration PNA
i. Recommend AGAINST adding empiric anaerobic coverage unless empyema or abscess present (conditional, low quality)
CAP - when to cover MRSA/Pseudomonas?
- CAP in inpatients - IDSA/ATS recommend abondoning the previous Healthcare Associated Pneumonia (HCAP) terminologu
- Consider MRSA coverage *based upon local risk factors (not as prevelent in Canada)
- Vancomycin 15 mg/kg IV or linezolid 600 mg q12h
- Consider covering* for PsA based on locally validated risk factors
- *Pip-tazo or Cefepime 2 g q8h or Ceftaz 2 g q8h or Aztreoname or Mero 1 g q8h
CAP - other
A) When to transition to PO
B) Duration of Treatment
C) Steroids?
D ) Influenza
A) Transition to PO - when hemodynamically stable, tolerating PO/absorbing from GI tract
B) Duration of Treatment - 5 non-inferior to 10 in well-selected patients
- 5 days of antibiotics therapy OK if afebrile x 48 hours with </= 1 sign of CAP clinical instability ( HR> 100, RR> 24, sBP< 90, paO2 <90%, can take PO, normal mental status)
C) Steroids: No longer recommended unless refractory shock. NB use of steroids for COVID-19 discussed separately - high yield
D ) Influenza: Oseltamivir if symptoms < 48 hours, hospitalized
- consider bactreial superinfection (GAS, S. aureus)
HAP/VAP: what are the core pathogens and how do you diagnose? What are the risk factors for multi-drug resistant pathogens: MDR VAP, MDR HAP, MRSA VAP/HAP, and MDR pseudomonas VAP/HAP?
Microbiology:
- Core pathogens = S. pneumoniae, MSSA, H. influenzae, GNB including Pseudomonas
Diagnosis:
- CPIS score NOT recommended by IDSA
- Clinical gestalt and Sputum/ETT/Blood Cx (non-invasive preferred)
- Tracheobronchitis vs. VAP
See table for MDR RFs
HAP/VAP: what is the empiric treatment?
Infectious Diarrhea: how do you diagnose?
- Stool cultures for Salmonella, Shigella, Campylobacter, Yersinia, STEC (shiga toxin producing E. coli) in patients with diarrhea AND:
- fever
- bloody or mucoid stools
- Severe abdominal pain
- Sepsis
- C. difficle testing in patients with:
- Recent antibiotics
- Work in healthcare/LTC or prison
- Compatible syndrome
- IBD flare
- Blood cultures in patients with:
- immunocompromise
- Sepsis
- Suspicion of entereic fever
- Stool for Ova and Parasites in patients with
- diarrhea ≥ 14 days
- Immunocompromise e.g., HIV
- Travel
- Increased yield if ordered daily x 3 days
- Repeat up to 3x to increase yield if high suspicion
Diarrhea: when do you empirically treat and with what?
- Empiric therapy in adults with bloody diarrhea not recommended UNLESS:
- Sick immunocompetent patients with bacillary dysentery (frequent scant bloody stools, abdominal pain, tenesmus, fevers), suggestive of Shigella
- Recent travel with high fever (≥ 38.5) and/or sepsis
- Sick immunocompromised patients
- Empiric antibiotics choice: ciprofloxacin or azithromycin
- May use loperamide - caution if bloody stool, fever
Diarrhea Treatment: what is the modified treatment for specific pathogens (while awaiting sensitivities)?