ID important bacteria

Question 1

Gram + cocci

Answer 1

Staphylococcus, streptococcus, enterococcus

Question 2

Gram + bacilli

Answer 2

bacillus, clostridium, clostridioides, corynebacterium, listeria

Question 3

Gram - cocci

Answer 3

Neisseria, moraxella, haemophilus

Question 4

Gram - bacilli

Answer 4

Escherichia, proteus, pseudomonas, klebsiella, etc

Question 5

Spirochetes

Answer 5

Borrelia, treponema

Question 6

Atypicals

Answer 6

Legionella, francisella, mycoplasma

Question 7

Acid fast

Answer 7

Mycobacterium

Question 8

Staphylococcus

Answer 8

-6 different types to know/where they are found on or in body (coagulase - or +)
Diagnosis:
1. culture with ID, gram + cocci in clusters, coagulase + or -
2. PCR/NAAT: can identify methicillin resistance (mecA gene is common with S. aureus)

Question 9

Streptococcus

Answer 9

-Alpha, beta, gamma hemolytic strep (hemolysis and colonies)
-examples of each

Question 10

Strep diagnosis

Answer 10

1. Culture with ID: gram + cocci, pairs or chains
2. PCR/NAAT
3. Direct antigen testing:
   -strep pyogenes/rapid strep throat swab
   -strep pneumoniae/detection of antigens in serum
4. Serology:
   -evaluating sequela of infx
   -anti-streptolysin O (ASO)
   -anti-DNase B
   -streptozyme (Ab to 5 strep antigens)

Question 11

Enterococcus

Answer 11

GI tract, facultative anaerobe, resistant to cephalosporins and penicillin G
-ex: faecium/faecalis

Question 12

Enterococcus diagnosis

Answer 12

1. Culture with ID: gram + cocci in pairs or short chains
2. PCR/NAAT: evaluate for abx resistance genes (VRE- vancomycin resistant Enterococcus)

Question 13

Bacillus Anthrasis (anthrax)

Answer 13

gram + bacilli, concern for bioterrorism, modes of transmission: skin contact, ingestion, inhalation (know symptoms)
Diagnosis: culture grows readily, can use PCR, immunoassays, serology

Question 14

Clostridium spp

Answer 14

gram + bacilli, 3 variants/types
1. Clostridium tetani: tetanus, clinical diagnosis
2. Clostridium botulinum: botulism, clinical dx but can culture/test for toxin
3. Clostridium perfringens: gas gangrene, clinical diagnosis, can see crepitus on imaging

Question 15

Clostridioides diff (pseudomembranous colitis)

Answer 15

Sx: profuse foul smelling watery diarrhea
Etiology: toxins secreted by bacteria
Typically associated with recent abx use, ppl can be carriers of strains that don’t produce toxins
Dx: 1. culture (gold standard)
2. Most common ELISA for C diff toxins and ELISA for Glutamate dehydrogenase (GDH) antigen
3. PCR

Question 16

Corynebacterium diphtheriae (diphtheria)

Answer 16

Gram + bacilli “club shaped”
Dx: 1. culture
2. additional tests for toxigenic status (immunoprecipitation test-sample grown on agar plate embedded with anti-toxin impregnated filter paper)
3. PCR for tox gene

Question 17

Listeria monocytogenes (listeriosis)

Answer 17

-gram + bacilli
-At risk pop: pregnant, infants, elderly/immunocompromised
self-limited in healthy adults
-Dx: culture of body fluid (blood or CSF)

Question 18

Neisseria spp

Answer 18

Facultative intracellular gram - diplococci

Question 19

Neisseria gonorrhoeae (gonorrhea)

Answer 19

Found in genital tract
Dx: 1. NAAT of urine
2. Gram stain/culture of discharge

Question 20

Neisseria meningitidis (meningitis)

Answer 20

Affects those living in close quarters, found in nasopharynx
Dx: 1. CSF fluid culture/NAAT
2. blood culture/NAAT

Question 21

Moraxella catarrhalis

Answer 21

Aerobic gram - diplococcus
Causative agent for sinusitis, otitis media, bronchitis
Dx: 1. gram stain/culture
2. PCR

Question 22

Haemophilus spp

Answer 22

Gram - coccobacillus

Question 23

Haemophilus influenzae

Answer 23

Causes otitis media, conjunctivitis, epiglottitis, sinusitis, community acquired pneumonia, severe cases can cause meningitis
Dx: 1. Gram stain/culture
2. NAAT on body fluid

Question 24

Haemophilus ducreyi

Answer 24

causes chancroid (STD)
Dx: 1. gram stain/culture
2. no widely accepted PCR

Question 25

Gram - bacilli

Answer 25

Know E. coli, proteus, pseudomonas, klebsiella but be familiar with the rest

Question 26

Salmonella enterica

Answer 26

Consumption of raw/undercooked chicken/eggs Dx: Stool culture/PCR

Question 27

Shigella spp

Answer 27

Shiga toxin, hemolytic uremic syndrome Dx: Stool culture

Question 28

Vibrio cholerae

Answer 28

Cholera, "rice water stool" -Transmitted through water/shellfish Dx: stool culture

Question 29

Campylobacter jejuni

Answer 29

Associated with consumption of raw/undercooked poultry/unpasteurized milk Dx: stool culture, PCR, enzyme immunoassay

Question 30

Bartonella henselae

Answer 30

Dx: serology (IgG and IgM), PCR for bacteria DNA, blood culture less helpful

Question 31

Legionella spp

Answer 31

Legionellosis Transmission through cold/hot water systems, AC units, swimming pools, showers Dx: GOLD STANDARD CULTURE, urine antigen test, PCR

Question 32

Bordetella pertussis

Answer 32

Pertussis/whooping cough Infants<3 mo.: CBC look for lymphocytes predominant leukocytosis Adults w/1-4 wks of Sx: PCR +/- culture, serum sample Adults w/ 4-12 wks of Sx: serology

Question 33

Francisella tularensis

Answer 33

Tularemia Host is rabbits, hares, rodents and transmitted from vector bite (tick/deer fly) Dx: culture from tissue, serology

Question 34

Brucella spp

Answer 34

Brucellosis Transmission from livestock, can cause endocarditis Dx: clinical typically but BONE MARROW CULTURE GOLD STANDARD Confirmatory testing: serology, NAAT/PCR

Question 35

Rickettsia rickettsii

Answer 35

Intracellular bacteria coccobacillus causing Rocky Mtn Spotted Fever (MW, NE, Southern US), tick vector Dx: clinical diagnosis but confirmatory with immunofluorescent antibody testing (GOLD STANDARD)

Question 36

Spirochetes Borrelia burgdorferi

Answer 36

-Causes lyme dz, vector deer tick, common in Midwest/northeastern US -Dx: 1. early localized dz (erythema migrans)= clinical diagnosis 2. early disseminated/late Lyme dz -initial ELISA test with follow up Western Blot if initial test is positive (will stay + for yrs) -PCR if testing CSF due to concern for neurologic symptoms

Question 37

Treponema pallidum

Answer 37

-Causes syphilis, human vector -Dx: 1. gold standard direct detection (darkfield microscopy, NAAT, immunohistopathology) 2. Serological studies: treponemal/non-treponemal testing

Question 38

Mycoplasma pneumoniae

Answer 38

-Pleomorphic bacterium with no cell wall, lacks nucleus and membrane bound organelles -causes "walking pneumonia" Dx: 1. NAAT/PCR 2. Serology 3. Culture (less common bc of prolonged growth time)

Question 39

Mycobacterium TB

Answer 39

-Acid fast bacilli, facultative intracellular -causes TB -Dx: 1. Active dz: obtain CXR, three sputum specimens test for acid fast stain and NAAT, culture (gold standard but takes 1-6 weeks) -acid fast and NAAT+= probable TB -negative NAAT, + acid fast= prob not TB (3 more samples and retest) -acid fast and NAAT- = TB possible but unlikely 2. Latent dz: detect immune response to Tb antigen but no evidence of active dz

Question 40

Latent TB diagnostics

Answer 40

1. Interferon gamma release assay (IGRA)/Quantiferon gold -ELISA test looking at amount of interferon gamma expressed by T cells (preferred method for those that received BCG vaccine given outside US; no false positives) 2.Purified Protein Derivative (PPD) TB skin test -antigens from TB injected into skin, measure diameter of raised area 48-72 hrs later PPD INTERPRETATION AND IMAGING IN TB SLIDES imaging appears as cavitary lesion with walled off area and central area of necrosis/absence of a structure