Micro: Microbial Diagnostics

Question 1

What are important things to do in the pre-analytical phase?

Answer 1

avoid contamination from indigenous flora
select correct anatomic site
optimize capture of pathogens by submitting tissue or needle aspirations
collect adequate volumes to avoid FNs

Question 2

What are important things to do during specimen collection?

Answer 2

place in container designed to promote survival of suspected agent, and to eliminate leakage and potential safety hazards
try to collect before giving antimicrobials
request direct smears when appropriate (in addition to cultures)
label each container w pt name, source, MR, specific site, date, time of collection, initials of collector
designations of wound or abscess acceptable as long as exact anatomic location also stated

Question 3

What are important things to do during specimen transport?

Answer 3

preferably to lab w/i 2 hrs, some can be refrigerated if not possible (urine, stool, sputum)
never refrigerate CSF, genital, eye, internal ear specimens or specimens for anaerobes

Question 4

What are environmentally sensitive organisms?

Answer 4

n. gonorrhea and n. meningitidis
h. flu
anaerobes
don’t refrigerate

Question 5

What is the 3 day rule of hospital diarrhea?

Answer 5

pts who develop diarrhea >72 hrs after admission rarely have bacterial pathogens like salmonella, shigella, or campy
parasites and viruses also unlikely
at parkland, it is a 5 day rule

Question 6

Swabs are usually inferior ways to collect most specimens: when can they be used?

Answer 6

culturing mucous membranes for strep throat
s. aureus nasal carriage
nasopharyngeal specimens for resp viruses or bordetella pertussis
no place in the OR

Question 7

What are some common reasons to reject a specimen?

Answer 7

labels don't match or it's unlabeled
prolonged transport (>24 hrs)
improper or leaking container
unsuitable for request
duplicate specimens on same day for same request (except sterile fluids, tissues, or blood)
plated on outdated or dried media
sputum has oropharyngeal secretions
routine bacterial stool cultures on pts in house >5 days
rotavirus requests during summer

Question 8

How can blood culture contamination rates be minimized?

Answer 8

strict adherence to aseptic collection technique

when possible take peripheral blood via venipuncture rather than indwelling catheters

Question 9

How many blood culture specimens are typically needed?

Answer 9

2-3 will detect virtually all septic episodes, drawn simultaneously from different venipuncture sites
3-4 for pts w suspected inf endocarditis
20-30 mL for each culture

Question 10

What are the general diagnostic methods used in the lab?

Answer 10

combo of direct microscopic exam w culture
serologic studies for non-cultivable or hard-to-culture
molecular techniques

Question 11

What are the four aims of the gram stain?

Answer 11

separating major groups of bacteria
determining quality of specimen
presumptive dx and clinical decision making
direction for further investigation

Question 12

Which organisms is DFA commonly used to detect?

Answer 12

respiratory viruses in nasopharyngeal specimens
herpes simplex and varicella zoster from skin or mucous membrane lesions
pneumocystic j. in BAL specimens
cryptosporidium and giardia in stools

Question 13

What are fluorochrome stains?

Answer 13

directly bind to organism rather than antibody to organism antigen

Question 14

Which organisms cannot be cultivated on routine media?

Answer 14

t. pallidum and m. leprae - only cultivated in living animals
rickettsia and coxiella - serology
chlamydia and viruses - living cell lines, molecular assays
cultures still useful for HSV from mucosal and skin lesions, urine for CMV on neonates, and chlamyida in cases of suspected sexual abuse

Question 15

What are the primary characteristics for the presumptive identification of a cultured isolate?

Answer 15

gram reaction, cell morphology
cultural characteristics (when it can grow), hemolysis on blood agar, colony morphology, motility
growth requirements: simple or fastidious
selective media: growth?

Question 16

What can be looked for on rapid biochemical tests?

Answer 16

ability to produce important enzymes (catalase, oxidase, coagulase)
motile or nonmotile
ability to produce pigments

Question 17

What are some common tests for final species identification?

Answer 17

ability to metabolize sugars, ferment or oxidatively
ability to use range of substrates for growth
other enzymatic activities
also gene sequencing, mass spec, molecular techniques, MALDI-TOF

Question 18

What are some situations where susceptibility testing is not performed?

Answer 18

isolation of mixed flora
isolation of organism w predictable susceptibility (group A strep uniformly penicillin susceptible)
isolation of organism that won’t grow in testing system
most fungi
mycobacteria other than m. tb
anaerobes

Question 19

When are antigen detection tests clinically useful?

Answer 19

crypto antigen on CSF and serum
giardia/cryptosporidium on stool
rotavirus on stool
histo urinary antigen in disseminated
legionella, serogroup 1 urinary antigen
respiratory viruses from nasopharyngeal secretions

Question 20

Other than hard to culture organisms, what else can serology be useful for?

Answer 20

fungal inf (histo, cocci, blasto)
pre transplant screening

Question 21

What are the different types of molecular testing?

Answer 21

nonamplified - use defined oligonucleotide primers w attached detection molecule that are complementary to segment of genome of suspected organism (fungi and mycobacteria from culture, not directly from specimen)
amplified - directly on specimens, PCR most common

Question 22

When is serology commonly used?

Answer 22

esp for viral and m. tb - ordered on spinal fluid if suspected meningitis/encephalitis
if CSF indices and imaging normal, not necessary - probably not infectious