Microbiology Flashcards
1
Q
This Gram-negative organism grows well on
McConkey’s agar, is often green in color and
is oxidase positive.
A
What is Pseudomonas aeruginosa?
2
Q
This common Gram-negative organism, many cases of which can be prevented by immunization, requires hemin and NAD for growth.
A
What is Haemophilus influenzae ?
Immunization against this organism has greatly reduced the incidence of meningitis in children.
Haemophilus species fail to grow on blood agar unless it is supplemented with X factor (hemin) and V factor (NAD).
3
Q
Errors in Gram stain
- Gram-negative called gram-positive
- Gram-positive called gram-negative
A
- Gram-negative called gram-positive
Acinetobacter
- Gram-positive called gram-negative
Bacillus and Clostridium species typically are – 95% to 100% gram-positive early in their growth phase in broth cultures but become
– 40% to 50% gram-negative in the late growth phase and
– 90% to 95% gram-negative in the stationary phase.
Loss of Gram stain retention associated with aging of the culture most likely accounts for the frequency of misreading for these species.
4
Q
Culture Media – Selective and Differential
A
Hectoin Enteric agar
- Selective for enteric bacteria
- Differential for Salmonella & Shigella
5
Q
16s rRNA Gene Sequencing for Bacteria ID
A
16s rRNA Gene Sequencing
- highly conserved
- about 1,550 bp long variable and conserved regions.
- conserved regions at the beginning of the gene and at either the 540-bp region or at the end of the whole sequence (about the 1,550-bp region)
- variable region used for comparative taxonomy
6
Q
MALDI-TOF for Bacteria ID
A
MALDI-TOF for Bacteria ID
- Matrix-Assisted Laser-Desorption/Ionization Time-of-Flight Mass Spectroscopy.
- Analyzes high-copy proteins in the bacterial cell; mostly ribosomal proteins.
- Sample is spotted onto plate, mixed with matrix, then fed into the instrument.
- Low reagent cost (pennies), extremely fast ID (minutes).
7
Q
What is Mass Spectrometry and TOF?
A
Mass Spectrometry
- Charged molecules are accelerated by an electric field in vacuum.
- Requires generating gas-phase ionized material.
- The acceleration is proportional to the mass/charge ratio: m/z
- The charges may be deflected or flung about in various ways in different instruments.
- They’re detected by the charge passing through another electric field.
- Detect 10-15 to 10-18 molar concentrations.
- Time-of-flight (TOF) instrument
- The target is accelerated a defined amount, and flies linearly, without further acceleration, until it is detected.
8
Q
This Gram-negative organism is best isolated on a selective agar containing cefsoludin, irgasan, and novobiocin?
A
Yersinia enterocolitica
- CIN agar (Yer-CIN-ia) is used to isolate this organism from the stool
9
Q
CSF Major pathogens
- How do you detect pathogens?
- Young adults?
- Old adults?
- Babies?
- Fungal?
- Parasite?
A
CSF Major pathogens:
- Bacteria: cytospin and gram stain
- Young adults:
- N. meningitidis
- Listeria in pregnant women
- Old adults:
- S. pneumoniae
- Antigen in urine
- HSV
- S. pneumoniae
- Babies:
- Listeria
- group B Streptococci
- E. coli
- Fungal:
- Coccidiomycosis
- Cx
- Histoplasma
- Antigen in CSF, BAL, urine
- Cryptococcus (HIV+)
- Antigen in CSF and serum, follow titers
- Candida albicans
- Coccidiomycosis
- Parasite:
- Nagleria
- Look for motility (STAT)
- Nagleria
H. influenzae
in newborns
and newborns
10
Q
Encephalitis and Brain abscesses
A
Encephalitis
- Viral usually; rarely rickettsial, syphilis, Lyme.
Brain abscesses
- Contiguous: from sinusitis or otitis media
- Upper respiratory flora
- Often polymicrobial
- Hematogenous, from bacterial endocarditis
- Usually monomicrobial, BE pathogens
11
Q
Pleural and Peritoneal pathogens
A
Pleural fluid:
Pneumonia bugs
S. pneumoniae
S. aureus
S. pyogenes
Peritoneal fluid:
GI bugs
E. coli and other gram-negatives
mixed GI flora in surgical patients
GI and skin flora in spontaneous bacterial peritonitis in ascites/liver failure
12
Q
Joint pathogens
A
Joints
- Staphylococcus aureus
- Neisseria gonorrhoeae
- Borrelia burgdorferi (Lyme disease)
- Culture / Gram stain for conventional bacteria
- Serology for Lyme
13
Q
Blood pathogens
A
Major Blood pathogens:
- S. aureus
- S. coag neg.
- Enterobacteriaciae
- enterococci
- Pseudomonas
- S. pneumoniae
- viridans streptococci
- yeasts
14
Q
Blood culture
A
Typical Media:
- blood culture bottles (aerobic ± anaerobic)
- Incubated in automatic reader which detects CO2 production (BactAlert, Bactek) or pressure change (Trek)
- Usually incubate 5 days, occasionally fewer, more for special pathogens ( Brucella , Legionella )
15
Q
Blood Culture Contamination
A
Blood Culture Contamination
- Skin flora
- Coagulase-negative staph
- Corynebacterium spp.
- Rarely viridans streps
- A cost issue - Several thousand dollars
- QA guidelines suggest getting rate to 2-3%
- Chlorhexidine or iodine skin preps
- Dedicated IV / blood culture teams
16
Q
Bloodstream Infections – Bacterial Endocarditis
A
Bloodstream Infections – Bacterial Endocarditis
Native Valve Endocarditis
- Streptococci, 60-80%
- Viridans streps
- Beta-streps
- Enterococci
- Staphylococci, 20-35%
- S. aureus
- Gram-negatives, 1-5%
- Fungi, others
Prosthetic valve endocarditis
- Coag negative staph
Risk factors – existing valve disease, IVD
17
Q
Bloodstream Infections – Lines
A
Bloodstream Infections – Lines
- Coag-negative staph
- Enterococcus
- S. aureus
- Enterobacteriaciae
- Pseudomonas
- Acinetobacter
Maki roll-plate method
- Catheter tip rolled on BAP
- >15 colonies of a single isolate considered significant
- Should be paired with peripheral culture
18
Q
UTI in Community
- List in order of frequency
- Pathogens and susceptibilities
- Gram + chains?
- Gram + clusters?
A
UTI in Community
- 95% E.coli
- No resistance
- Klebsiella
- Resistant to ampicillin
- Give ciprofloxacin or nitrofurantoin
- Proteus
- Resistant to nitrofurantoin and tetracyclin
- Give fosfomycin (one dose)
- Group B strep
- Gram + in chains
- Give PCN
- If PCN allery give clyndamycin and erythromycin
- Staph saprophyticus
- Gram + in clusters
- Give cefalosporins
19
Q
Interpretation of Urine Cultures
- Quantity
- Purity
A
Interpretation of Urine Cultures
- Quantity important;
- >10^5 significant, >10^4 possibly significant
- 10^2/ml in sterile collection technique
- 10^2/ml in pregnancy
- Purity is important:
- 1 isolate, likely
- 2 isolates, perhaps
- ≥3 isolates, contaminated
- Special populations: spinal cord injury, neurogenic bladder
20
Q
Pneumonia in Community
- Ambulatory
- Older patients
A
Pneumonia in Community
Ambulatory
- Mycoplasma
- Dx serologically (IgM) or by molecular
- Give erythromycin or tetracyclin
- Legionella
- Urine antigen only detects legionella pneumophila type 1
- If negative Cx or DFA bronchoscopy specimen
- Haemophilus influenzae
- Give rocephin or ceftriaxone
Older patients
- Strep pneumoniae
- Urine antigen
- Cx resp specimen
- MRSA
21
Q
Pneumonia in Hospital
A
Pneumonia in Hospital
- Moraxella
- aspiration
- pure Cx
- Give non-Betalactams
- Klebsiella and Pseudomonas
- Gram -
- Water
22
Q
Bronchitis
A
Bronchitis
- Culture results don’t correlate with symptoms
- H. influenzae
- S. pneumoniae
- Moraxella catarrhalis
- Viruses may be important in exacerbations
- influenza
- parainfluenza
- RSV
- human metapneumovirus
23
Q
Lung abscess
A
Lung abscess
- Destruction of lung parenchyma to produce cavities with air-fluid levels
- Usually polymicrobic with anaerobes and upper respiratory tract flora:
- Peptostreptococcus
- Prevotella
- Bacteroides (nonfragilis )
- Fusobacterium
- occasionally
- Clostridium, Actinomyces, alpha-hemolytic Streptococcus, Enterobacteriaceae.
24
Q
Grading Sputum
A
Grading Sputum
- Squamous Screen
- Acceptable: <10 SEC / 10x field
- Unacceptable: >10 SEC / 10x field
- Murray and Washington
- Culture only group 5 ( >25 WBC and <10 SEC)
- And culture if >10 WBC and <10 SEC
25
This oxidase-positive Gram-negative rod associated with bite wounds and endocarditis does not grow on MacConkey agar, and its name reflects the fact that it often eats its way into the agar.
Eikenella corrodens
* pits the agar when it grows
* oxidase-positive
* Gram-negative rod
* bite wounds and endocarditis
* does not grow on MacConkey agar
26
Animal bites (including human)
Animal bites (including human)
* Oral flora; mixed aerobic/anaerobic flora
* Pasturella multocida – cats and dogs
* Eikenella corrodens
* Capnocytophaga canimorsus – dogs
27
Diabetic foot ulcers
Cellulitis
Toxic Shock Syndromes
Diabetic foot ulcers
* Mixed flora, Gram negatives, anaerobes, streps and staphs
Cellulitis
* Staph and Strep
Toxic Shock Syndromes
* toxigenic strains of S. aureus and S. pyogenes
* Skin and soft tissue infections
* vaginal/tampon use for S. aureus
* Desquamating skin rash, shock out of proportion to the infected area
28
Throat pathogens
Throat pathogens
* Group A strep
* other beta-hemolytic strep
* N. gonorrhoeae
* C. diphtheriae
Typical Media: blood agar, selective media for specific pathogens by request
* Tinsdale agar for C. diphtheriae
29
This specimen is used to isolate Streptococcous agalactiae (group B strep) during prenatal screening. It is inoculated into broth enrichment followed by subculture. Be specific about the specimen source.
Streptococcous agalactiae (group B strep)
* The most sensitive specimen is rectovaginal; various culture schemes are most commonly used, but amplification methods are also employed.
30
Stool pathogens
Stool
* Major pathogens:
* Salmonella
* Shigella
* Campylobacter
* E. coli O157 & others
* Yersinia enterocolitica
* Typical Media: MacConkey’s, Hectoin enteric or XLD, Campy, CIN, sorbitol-MacConkey’s
* Antigen tests for Shiga-like toxins or for O157 antigen
* Campylobacter by antigen
* Special media and procedures for Vibrios
31
Hemolytic-Uremic Syndrome
Hemolytic-Uremic Syndrome
* Primarily in children (peak 5-10 y/o)
* 5-10d after diarrhea
* Renal failure + microangiopathic hemolysis
* Other end-organs affected include CNS
* Associated with shiga-like-toxin producing enteric bacteria
* E. coli strains: O:157 H:7 and others
* Shigella species
* No effective therapy, antibiotics NOT recommended
32
Clostridium difficile -- disease and diagnosis
Clostridium difficile -- disease and diagnosis
* Toxin-mediated illness
* Culture for epidemiologic purposes only
* Toxins A and B
* Antigen tests: rapid or conventional EIA
* Kits that detect both A and B are more sensitive
* GDH antigen is more sensitive than toxin, but is unspecific
* PCR for toxin gene
* Cytopathic effect in cell culture
* Labor-intensive, takes a day or two, more sensitive than toxin EIA.
* Toxigenic culture is ‘gold standard’
* Culture in selective broth, assay for toxin in supernatant.
33
This test is used to distinguish a catalase positive gram-positive coccus, whose colonies are often golden-yellow in color, from other members of the same genus.
Coagulase
* Catalase distinguishes between staph (catalase-positive) and strep (catalasenegative)
* Used to separate S. aureus from coagulase negative staphylococci.
34
Bacterial Vaginosis
Bacterial Vaginosis
* Major Etiology
* Overgrowth of mixed anaerobes (e.g. Mobiluncus, Gardnerella )
* Loss of Lactobacillus morphotypes
* Laboratory Diagnosis
* Wet mount for clue cells
* Gram stain for clue cells
* Elevated pH \>=4.5
35
Important Bacterial Diseases Not diagnosed by conventional culture
Important Bacterial Diseases Not diagnosed by conventional culture
* Spirochetal diseases
* Syphilis
* Lyme
* Diseases caused by rickettsia and rickettsia-like organisms
* Rocky Mountain Spotted Fever
* Ehrlichiosis
36
Syphilis
Syphilis
* Primary lesion
* mucosal surface
* Secondary lesions
* mucocutaneous lesions
* Late manifestations
* neurologic, cardiac
Diagnosis
* Non-treponemal tests
* RPR; VDRL
* For screening and following therapy
* Decline after effective treatment
* Specific treponemal tests
* FTA-abs; MHA; EIA
* Confirmatory; positive for life
* Reverse algorithms using automated treponemal test as primary, non-treponemal test as confirmation.
37
Lyme Disease
Lyme Disease
* tick-transmitted disease caused by B. burgdorferi
* Peak ages bimodal: children 5-9 and adults 20-54
* Peak months: May-Oct
* Europe: Ixodes ricinus vector
* Different Borrelia strains
* Different presentation; more neurologic disease, chronic skin lesions
* Early disease: cutaneous, musculoskeletal, menigoencephalitis, cranial nerve palsies, heart block
* Late disease: chronic arthritis, subtle CNS effects
38
Lyme Disease Diagnosis
Lyme Disease Diagnosis
* Early disease: clinical diagnosis by rash; requires up to 4-6 weeks for IgM response to appear
* Lyme serology and Western blot
* DNA probes and PCR investigational
* CSF titers in late CNS disease
39
This large aerobic spore-forming Gram-positive rod is non-motile and nonhemolytic.
Bacillus anthracis
* large Gram-positive rod
* aerobic spore-forming group is genus Bacillus
* lack of hemolysis and motility used to screen for isolates suspicious for B. anthracis
40
Rocky Mountain Spotted Fever : Epidemiology
Rocky Mountain Spotted Fever : Epidemiology
* Dermacenter ticks
* US: SE, Midwest, northern Rockies
* Tick is vector and main reservoir
* Animal reservoirs include dogs and wild animals
41
Rocky Mountain Spotted Fever : Clinical
Rocky Mountain Spotted Fever : Clinical
* Incubation 2-14 days, median 7
* Fever, myalgia, headache
* GI symptoms
* Rash
* 90% of patients have the rash
* Can occur up to 5d after fever
* Extremities first, then spreads centrally (“centripetal”)
42
Rocky Mountain Spotted Fever : Diagnosis
Rocky Mountain Spotted Fever : Diagnosis
* Characteristic rash (only present in ~90%)
* Clinical presentation and risk factors
* Laboratory
* Serology only turns positive during recovery
* Immunohistology of skin biopsy
* PCR on skin biopsies possible
43
Ehrlichia & Anaplasma Types
Ehrlichia & Anaplasma Types
* Ehrlichia chaffeensis
* Human monocytic ehrlichiosis (HME)
* Anaplasma (formerly Ehrlichia) phagocytophila
* Human granulocytic ehrlichiosis (HGE)
* Ehrlichia ewingii and other species
* Emerging diseases
* Tick-borne illnesses, first recognized in humans in the 1980s
44
Ehrlichia chaffeensis :
Human monocytic ehrlichiosis (HME)
Ehrlichia chaffeensis :
Human monocytic ehrlichiosis (HME)
* Lone Star tick, Amblyomma americanum
* US: South central, SE states
* Diagnosis
* Laboratory
* leukopenia, thrombocytopenia, elevated LFT
* Morulae seen in \<10%
* Serology
* PCR
45
Anaplasma (formerly Ehrlichia) phagocytophila : Human granulocytic ehrlichiosis (HGE)
Anaplasma (formerly Ehrlichia) phagocytophila : Human granulocytic ehrlichiosis (HGE)
* Spread by Ixodes ticks (like Lyme)
* Northeast and upper Midwest (reported Europe)
* Peak incidence in July and November
* Most infections probably asymptomatic
* Cytopenias
* leukopenia, anemia, thrombocytopenia
* may be associated with clinically significant bleeding or immunosupression
* Morulae seen in 20-80%
* Serology
* PCR
46
Most members of this catalase-negative genus of Gram-positive cocci hydrolyze esculin and PYR.
Enterococcus
* catalase-negative
* Gram-positive cocci
* hydrolyze esculin and PYR
47
Bacteria With Bioweapons Potential
Bacteria With Bioweapons Potential
* Bacillus anthracis (anthrax)
* Francisella tularensis (tularemia)
* Yersinia pestis (plague)
* Others
* Brucella
* Coxiella
48
* What is it?
* Aerobic/Anaerobic?
* Sporeforming?
* Sites of disease?
* Case-fatality rate?
Bacillus anthracis
* Aerobic sporeforming gram-positive rod
* Causes cutaneous, GI, or inhalational disease
* Highly pathogenic, 60% case-fatality rate in inhalation disease in the 2001 outbreak
49
How do you collect B. anthracis specimens?
B. anthracis – Specimens
**Cutaneous** disease
* Wound **swab** for **culture, Gram stain, India ink**
**Inhalation/GI**
* Sputum or stool have poor yield, rarely indicated
* **Blood** is specimen of choice
Nasal swabs
* For investigational and epidemiologic studies ONLY; not for clinical use
50
How do you rule out Anthrax?
* Direct smears?
* From growth on SBA or equivalent media?
* Catalase positive/negative?
* Motile/Nonmotile?
* Hemolytic/Nonhemolytic on SBA?
Anthrax Ruleout
Presumptive identification criteria
* Direct smears from clinical samples, such as blood, CSF, or skin lesion (eschar)
* Encapsulated gram-positive rods
* From growth on SBA or equivalent media:
* Large gram-positive rods (may stain gram-variable after 72 h of culture). Spores may be found in culture, under non-CO2 atmosphere (but not on direct examination). Spores do not swell the cell and are oval-shaped.
* Rapid, aerobic growth, and tenacious colonies on sheep blood agar.
* Catalase positive
* Nonmotile
* Nonhemolytic on SBA, ground-glass appearance of colonies
REFER TO REFERENCE LAB
51
What is it?
Shape?
Gram positive/negative?
How is it spread?
Where is it found?
Francisella tularensis
* A fastidious, poorlystaining Gram negative rod.
* A zoonotic organism, spread to humans from small mammals by direct contact or by insects
* Endemic in US: West, Midwest, Southeast
52
How do you collect Tularemia specimens?
**Tularemia** – Specimens
Pneumonic disease
* Sputum/throat: Poor yield in most cases.
* Bronch/Trach: Better yield
* Blood: rarely positive
* **Serology** and **DFA** are the **tests of choice**
53
Tularemia Ruleout
* Media? Enhance with?
* Colony appearance?
* Oxidase positive/negative?
* Catalase positive/negative?
* Beta-lactamase positive/negative?
* Satellite or XV test positve/negative?
* Urease positive/negative?
Tularemia Ruleout
* Poor growth (colonies \<1mm at 24h) on chocolate or blood
* Pale-staining fastidious Gram-negative rod
* Enhanced growth on cysteine-containing media
* Oxidase negative
* Catalase weakly positive
* Beta-lactamase positive
* Satellite or XV test negative
* Urease negative
* REFER TO REFERENCE LAB
54
What is it?
Where is it?
How is it spread?
Types of infection?
Yersinia pestis
* A gram-negative rod
* Member of the Enterobacteriaceae
* Zoonosis in the US West
* Oriental rat flea (Xenopsylla cheopis)
* Bubonic
Septicemic
Pneumonic
55
Plague (Yersinia pestis) specimen collection
Bubonic?
Septicemic?
Pneumonic?
Plague Diagnosis Specimen selection
* Bubonic - bubo
* lymph node aspirate
* Septicemic - blood
* organisms may be intermittent
* Take three specimens 10-30 minutes apart
* Pneumonic
* Sputum/throat culture
* Bronchial washings
56
Plague (Yersinia pestis) Ruleout
Appearance on Wright-Giemsa?
Media? Temperature?
Colony appearance?
Oxidase positive/negative?
Catalase positive/negative?
Lactose fermenter?
Urease positive/negative?
Plague (Yersinia pestis) Ruleout
* Suspected criteria: Any isolate, from the respiratory tract, blood or lymph node, containing the major characteristics noted below should be suspected as Y. pestis .
* Bipolar staining rod (Wright-Giemsa) on direct smear
* Pinpoint colony at 24 h on SBA
* Non-lactose fermenter, may not be visible on MAC or EMB at 24 h
* Oxidase and urease negative
* Catalase positive
* Growth often better at 28oC
* Commercial biochemical systems can miss these
* REFER TO REFERENCE LAB
57
How bacteria are REALLY classified
How bacteria are REALLY classified
* Normal pyogenic bacteria
* Aerobic and facultative: Gram positive and Gram-negative, grow on the usual media
* Anaerobes; Gram-positive and Gram-negative
* Weirdo bacteria
* Hard to grow: Legionella , Bartonella
* Spirochetes: hard/impossible to grow, serology
* No cell wall / Intracellular / Cell-associated: Mycoplasma , Chlamydia , Rickettsia , Ehrlichia
* Mycobacteria
58
Facultative/Aerobic Gram-positive rods
* Catalase positive
* Catalase negative
Facultative/Aerobic Gram-positive rods
* Catalase positive
* Actinomadura
* Bacillus (some species)
* Corynebacterium
* **Listeria** (tumbling motility, survives cold well)
* **Nocardia** (most partially acid-fast)
* Nocardiolopsis
* Streptomyces
* Catalase negative
* Arcanobacterium
* Erysipelothrix
59
Facultative / Aerobic Gram-positive cocci
* Catalase positive
Facultative / Aerobic Gram-positive cocci
* Catalase positive
* Micrococcus
* **Staphylococcus**
* Coagulase positive: **S. aureus**
* Coagulase negative: many
* Stomatococcus
60
Facultative / Aerobic Gram-positive cocci
* Catalase negative
Facultative / Aerobic Gram-positive cocci
Catalase negative
* Streptococcus
* Alpha-hemolytic
* **S. pneumoniae** (optochin-sensitive, bile soluble)
* ‘Viridans’ streps
* Beta-hemolytic
* Subtypes by Lancefield antigens
* Group A - **S. pyogenes**
* Group B - **S. agalatctiae**
* S. milleri (anginosus) tiny beta-hemolytic colonies
* Nonhemolytic
* **Enterococci** – grow in 5% NaCL, pyr (+), esculin (+)
* Group D streps
* Leuconostoc
* Pediococcus
61
Facultative / Aerobic Gram-negative rods
Non-Fastidious (growth on MacConkey)
Facultative / Aerobic Gram-negative rods
Non-Fastidious (growth on MacConkey)
* Glucose fermenters – **Enterobacteriaciae**
* Lactose fermenters
* E. coli (indole positive), Klebsiella , Enterobacter
* Non lactose fermenters
* Nearly all the rest: Salmonella , Proteus , Serratia , Yersinia , Shigella
* **Vibrios** are glucose fermenters as well (oxidase (+))
* Non-fermenters
* Oxidase positive
* **Pseudomonas**
* Aeromonas
* Oxidase negative
* **Acinetobacter**
* Stenotrophomonas
* Burkholderia
62
Facultative / Aerobic Gram-negative rods
* Fastidious (no growth on MacConkeys)
Facultative / Aerobic Gram-negative rods
Fastidious (no growth on MacConkeys)
* Oral flora-type organisms
* **Haemophilus** – require either X (hemin) or V (NAD) factors for growth except H. aphrophilus
* HACEK organisms (oral flora -- endocarditis): H. aphrophilus, Aggregatibacter (formerly Actinobacillus), Cardiobacterium, Eikenella, Kingella
* Francisella
* Pasturella
* Capnocytophaga
* Bordetella pertussis: whooping cough, requires specialized media (Regan Lowe), DFA, or PCR
* **Campylobacter**: microaerophilic
* **Helicobacter pylori** : associated with ulcer disease,
* **Brucella**: zoonosis, highly infectious, urease (+)
* **Legionella**: usually doesn’t stain with Gram stain
63
This gram-positive coccus often fails to grow when subcultured from blood. Pyridoxine is necessary to support growth on subculture.
Abiotrophia
Related to the streptococci, Abiotrophia are also referred to as ‘nutritionally-variant streptococci’ (NVS).
They are occasional causes of endocarditis, and may not grow on subculture unless supplemented media are used (Pyridoxine)
64
Facultative / Aerobic Gram-negative cocci
Facultative / Aerobic Gram-negative cocci
* Neisseria sp and Moraxella catarrhalis
* Oxidase positive
* CTA sugar fermentations for identification
* N. gonnorhoeae Gluc+ Mal- Lac-Suc-
* N. meningitidis Gluc+ Mal+ Lac- Suc-
* N. lactamica Gluc+ Mal+ Lac+ Suc-
* M. catarrhalis all negative, DNAse+
65
Anaerobic Culture Methods
* Use ____ media to enhance recovery.
* 3 types?
Anaerobic Culture Methods
* Use prereduced media to enhance recovery
* Brucella-base sheep blood agar
* Kanamycin-vancomycin laked sheep blood agar (KVLB)
* Bacteroides bile esculin (BBE)
66
Anaerobic Gram-positive Rods
Anaerobic Gram-positive Rods
Large, spore-forming
* Clostridium
* **C. perfringens**: associated with severe soft-tissue infections and in vivo hemolysis; double-zone hemolysis
Nonsporeformers
* **Actinomyces** (filamentous, often branching, sulfur granules)
* Eubacterium
* Bifidobacterium
* Proprionibacterium
67
Anaerobic Gram-positive and Gram-negative cocci
Anaerobic Gram-positive and Gram-negative cocci
* Gram-positive
* Peptococcus
* Peptostreptococcus
* Gram-negative
* Veilonella
* All mostly oral flora, associated with polymicrobial infections of contiguous structures.
68
Anaerobic Gram-negative Rods
Anaerobic Gram-negative Rods
* Gram-negative nonsporeformers: Bacteroides ; Prevotella ; Porphyromonas , Fusobacterium
* **Bacteroides fragilis** group
* growth in the presence of bile
* esculin positive
* main organism in human bowel
* pleomorphic gram negative rod
* typically beta-lactamase positive
* Non B. fragilis group
* sensitive to bile
* Oropharynx, GI tract, urogenital tract, skin
* Includes Prevotella , Porphyromonas
* **Fusobacterium**
* Fusiform gram negative bacilli, spindle shaped with pointed ends
* Associated with mouth and respiratory tract abscesses
69
Presumptive Grouping of Anaerobic Gram-negative rods
Presumptive Grouping of Anaerobic Gram-negative rods
* Disk testing plus a few biochemicals
* 10 mm zone is susceptible
* B. fragilis group:
* unpigmented, resistant to vancomycin, kanamycin, and colistin and bile
* Bilophila is also isolated on BBE, is kanamycin and colistin susceptible, doesn’t grow on KVLB.
* Pigmented group
* exhibits black pigment or brick-red fluorescence
* all VKC resistant except:
* Porphyromonas is vanco-susceptible
* Prevotella is colistin-variable
* Fusobacterium
* vanco-resistant but kanamycin and colistin susceptible.
* Most are rapid-indole positive.
70
* Pyelonephritis
* UTI – Pregnancy
Pyelonephritis
* Ascending from cystitis
* descending from endocarditis/sepsis
* Pathogens as per source
UTI – Pregnancy
* Prevalence of bacteriuria 4-7%
* 20-40% develop pyelonephritis if untreated
* Routine screening as part of prenatal care
71
UTI in Hospital
* Pathogen and susceptibility?
* Subtype?
UTI in Hospital
* Enterococcus
* Gram + cocci in pairs
* VRE
* Likely faecium, *vanA*
* *vanA-E* genes contribute to resistance
* *vanC* intrinsic resistance to vanc
* no isolation required
72
Chronic UTI
* Pathogens and detection methods?
* Pre-pubescent females?
Chronic UTI
* Candida
* Albicans--\> fluconazole S
* Glabrata--\> fluconazole R
* TB
* AFB Cx
* Don't do AFB stain (false +)
* Rule out BCG
* Bovis vs. TB important
* Bovis--\> pyrazinamide R
* STD's
* GC and chlamydia
* Molecular test
* Males urine as sensitive as urethral
* Females cervical swab is better
* Ureaplasma urealyticum and Mycoplasma hominis
* Cx
* Pre-pubescent females?
* Alpha-hemolytic strep
73
Atypical pneumonia
Aspiration pneumonia
Nosocomial pneumonia
Atypical pneumonia
* Less abrupt onset, productive cough less likely, CXR findings less discrete and specific
* Mycoplasma: diagnosed serologically (IgM) or by molecular techniques
* Legionella: diagnosed by urinary antigen, DFA of bronch specimen, culture.
* Chlamydophilia: diagnosed serologically
* Except for Legionella, usually treated empirically without ID
Aspiration pneumonia
* upper respiratory mixed flora
Nosocomial pneumonia:
* MRSA, Enterobactereiaciae, Pseudomonas .
* Enterococcus and yeasts are uncommon respiratory pathogens, but frequent isolates
74
Wound Infections
* Subcutaneous cut/abscess?
* Stepped on something in fresh water?
* Cut in salt water?
* Immunocompromised (transplant)?
* West TX thorn?
Wound infections
* Subcutaneous cut/abscess?
* Cx for MRSA/MSSA
* Stepped on something in fresh water?
* Pseudomonas
* Aeromonas
* Cut in salt water?
* Vibrio
* M. marinum
* Immunocompromised (transplant)?
* AFB
* Nocardia
* Fungi
* West TX thorn?
* Coccidiomycosis
* meningitis
* osteomyelitis
75
PNA: Host factor/Agents suggested
76
Syndrome/Causative Agent
77
Syndrome/Causative Agent
78
Syndrome/Causative Agent
79
Syndrome/Causative Agent
80
Syndrome/Causative Agent
81
Syndrome/Causative Agent
82
Syndrome/Causative Agent
83
Syndrome/Causative Agent
84
Syndrome/Causative Agent
85
Syndrome/Causative Agent
86
3 causes of culture negative urinary tract infections?
3 causes of culture negative urinary tract infections?
* Ureaplasma urealyticum
* Chlamydia spp
* Mycoplasma hominis
87
What organism is most commonly associated with hemorrhagic cystitis in bone marrow transplant patients?
Adenovirus, especially serotype 11 is associated with the hemorrhagic cystitis that can be seen in immunosuppressed patients, especially those post-bone marrow transplant.
88
Which organism should be at the top of the differential diagnosis of bloody diarrhea without fecal neutrophils?
E. coli O157:H7, or enterohemorrhagic E. coli (EHEC), should be considered in the presentation of bloody diarrhea without neutrophils. The presence of neutrophils with bloody diarrhea suggests other causes, such as Clostridium difficile, Salmonella, Campylobacter, and Shigella.
89
Which serotypes of Vibrio cholerae are responsible for the majority of cases of epidemic cholera?
O1 and O139 cause epidemic cholera (voluminous rice water stools)
90
Which Vibrio species are the most common and second most common cause of food-borne diarrhea in Japan?
Both V. parahaemolyticus and V. vulnificus are associated with exposure to contaminated seafood or seawater. A common history of eating seafood or getting cut while either swimming in the sea or cleaning a fish tank is often seen.
V. parahaemolyticus is much more common than V. vulnificus.
91
Which plasmid is associated with pathogenicity in Yersinia enterocolitica and can be detected with DNA-based assays?
pYV
Yersinia, like Campylobacter, infections can be seen in a higher percentage of patients expressing the HLA-B27 allele and the associated reactive arthropathy.
92
Which test for Entamoeba histolytica has the highest sensitivity and specificity?
STOOL EIA
93
Which test can act as a substitute for microscopic leukocyte detection?
STOOL LACTOFERRIN
94
Acceptable diagnostic tools for pneumococcal pneumonia?
bronchoscopic biopsy
bronchoalveolar lavage
blood culture
95
Which electrolyte abnormality is associated with Legionella pneumophila infection?
HYPONATREMIA
96
What is the most common way to diagnose Chlamydia pneumoniae pneumonia?
Serology
97
Causes of blood culture-negative endocarditis (BCNE)?
prior antibiotic therapy
Libman-Sacks endocarditis
marantic endocarditis
Coxiella burnetti
98
Included in the Austrian syndrome?
Austrian syndrome refers to the triad of endocarditis, typically caused by S. pneumoniae, with pneumonia and meningitis. The syndrome was first described by Robert Austrian in 1957 and has been shown to be most closely associated with alcoholism.
99
Most common cause of fungal endocarditis?
Candida spp
100
How does antibiotic therapy most commonly affect the diagnosis of bacterial endocarditis on valvular material?
Often, antibiotic therapy leads to a change in the morphology of bacteria, including their gram stain characteristics (positive, negative), which makes identification difficult.
101
What is the animal reservoir of West Nile virus?
Birds
102
Most common cause of winter viral encephalitis?
LYMPHOCYTIC CHORIOMENINGITIS VIRUS
103
Patients with complement deficiencies are at an increased risk for meningitis caused by this infectious agent?
N. meningitidis
104
Organism/Vector
105
Organism/Vector
106
Organism/Vector
107
Organism/Vector
108
Organism/Vector
109
Which virus is assayed by injection into suckling mice and observation for flaccid paralysis?
Coxsackie A virus
110
Ramsay-Hunt syndrome is an infection of the facial nerve as caused by which virus?
VZV
111
Which virus is responsible for the most common congenital infection in the United States?
CMV
Passed transplacentally, the risk of in utero infection is greatest when the mother acquires a primary CMV infection while pregnant. The effects from in utero infection can range from severe to mild, with the most common manifestation of sensorineural hearing loss.
112
Which cell surface antigen is the receptor for the Epstein-Barr virus?
CD21.
The C3d receptor, or CD21, functions as the target for EBV cell entry.
P antigen (associated with Donath-Landsteiner ab), paroxysmal nocturnal hemoglobinuria, neutralized by pigeon egg and hydatid cyst fluid) is the parvovirus receptor.
Insulin-degrading enzyme is the putative receptor for varicella-zoster virus
CD4 is the receptor for HIV.
Recent studies suggest that CD81 may have a role as a receptor for HCV.
113
Which disorder, also known as Duncan disease, is characterized by hepatic necrosis with a profound NK/T cell infiltrate?
X-LINKED LYMPHOPROLIFERATIVE DISORDER.
As an X-linked disorder, primarily men are affected. The range that disease can manifest extends from the previously mentioned hepatic necrosis and death to less severe agammaglobulinemia or B-cell lymphoma. The disorder is due to a defect in the SAP gene, which leads to uncontrolled NK/T cell activation.
114
Human Herpes Virus - Latency, Clinical
115
Viral classification
116
Viral Cell Culture
117
Viral Cell Culture
118
EBV Serology
119
EBV Serology
120
Orthomyxovirus
Orthomyxovirus
* virions have a lipid envelope containing several surface antigens
* dominant antigen is hemagglutinin
* binds to sialic acid-containing receptors on respiratory epithelial cells and becomes expressed on the surface of infected cells
* this expression forms the basis for the hemadsorption test
* Only influenza A & B viruses and parainfluenza viruses are hemadsorption positive
* “hemagglutinating viruses”
* Hemagglutinin (H) and neuraminidase (N) glycoprotein antigens form the basis for influenza virus identification
* H1N1, for example
* H and N undergo periodic major antigenic changes and more frequent minor changes, while the other antigens are stable
* 15 H subtypes and 9 N subtypes
* major strains in circulation:
* influenza A (H1N1)
* influenza A (H3N2)
* influenza B
* Birds, especially aquatic birds, serve as reservoirs for all subtypes.
121
Avian influenza (H5N1)
Avian influenza (H5N1)
* responsible for scattered pandemics in chickens, most recently in Southeast Asia
* Hundreds of humans have become infected with H5N1, with a roughly 50% mortality rat
* predominantly children and young adults, median 15 years
* patchy then diffuse lung opacity and an increased oxygen requirement
* histologic findings of acute and organizing DAD have been found in autopsies
* Lymphopenia is characteristic, without significant changes in the neutrophil count, erythrocytes, or platelets
* The high mortality rate seems to be related to complete naivety to the H5 antigen and its tropism for non-ciliated epithelial cells of the lower respiratory tract.
* Tropism for the distal airways leads to an ARDS/DAD-like clinicopathologic picture and may explain the low rate of human-to-human transmission.
* Almost all human cases appear to result from exposure to sick birds (epizoonotic).
