Transcript THE WORLD OF MICROBIOLOGY OR YOU REALLY DON`T SMELL

MICROBIOLOGY
IN A HOSPITAL SETTING
Kathy Beadle, MHCL MT(ASCP)
Microbiology Manager
Wesley Medical Center
OBJECTIVES
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Specimen collection: Good and Bad
Blood cultures
Stool specimens
Respiratory specimens
Urines
Antimicrobial susceptibility testing
Gram stains
Culture reports
You can do that?
If you can collect a specimen -- we can
culture it!
HOWEVER
The results are only as good as the
specimen obtained.
Collecting Quality Specimens
Good Specimens
– Tissue
• In large mouth
sterile container
– Whole fluid
• In original syringe
or container
• NOT on a swab
Bad Specimens
– Any specimen
collected with a
swab
– Tissue or fluid
placed into a
swab tube/device
– Any surface
specimens
FOR QUALITY RESULTS
SEND TISSUE AND FLUIDS
TO MICROBIOLOGY AS
SOON AS POSSIBLE!
Swabs don’t do the job…
• Out of every 100 bacteria absorbed on a
swab, only 3 make it to culture.
• Anaerobes on swabs die upon exposure to
air, but survive in tissues and fluids.
• Swabs hold only 150 microlitres of fluid.
Surgical Specimens
Rules of Thumb
• The best specimens are “collected with
metal”
– Use scalpels, needles and syringes
• Send fluid in its original container or syringe
• Collect and send as much specimen as
possible
• Label specimens accurately and completely
• Reference the anatomical site and describe
the specimen
TYPES OF BLOOD CULTURES
• Bacterial
– Includes yeast
• Fungal*
– Systemic fungi (Histoplasma,
Coccidioides, etc)
• Mycobacterial*
*Requires special collection device
OPTIMAL BLOOD CULTURE
COLLECTION
• Prior to starting antibiotics, if possible
• 2 Separate Venipunctures
– Included in order for 1 blood culture
– Minimal Time Interval
• 15 - 20 mL Blood if possible (in adults)
Catheter-Related
Bloodstream Infection
• Obtain one culture through line and one by
venipuncture
– If only one is positive, may be a
contaminant
• Reported with time to positivity or detection
– Infected line should become positive at
least 2 hours earlier than venipuncture
• Same organism
BLOOD CULTURE
WORK-UP
• Day 0: Culture Drawn
• Day 1: Positive Culture Detected
– Bottle sub-cultured to solid media
– Gram-stained smear read and reported
– Presumptive tests (if any) set and read
BLOOD CULTURE
WORK-UP
• Day 2: Growth on solid media
– Identification and Susceptibility tests set
– Identification usually complete
– Susceptibility test may be complete
• Day 3: Susceptibility test usually complete
BLOOD CULTURES
• Cultures held 5 days before being finaled
as “No growth”
• Most “fastidious” organisms detected
within routine incubation time
– Franciscella tularensis
– Aggretibacter
– Cardiobacterium hominis
STOOL SPECIMENS
• Routine Culture
– Salmonella
– Shigella
– Campylobacter
– Shiga-Toxin producing E coli (not just
O157)
• Notify the laboratory if you suspect an
unusual pathogen
Ova and Parasite Exam
• 1 - 3 Specimens (only 1 per day!)
• Consider ordering specific tests for
Giardia/Cryptosporidium
• Inpatients: < 72 hr since admission
Clostridium difficile-Associated
Diarrhea
• Symptoms include fever, abdominal
cramping and diarrhea
– Formed specimens rejected
• Notify the lab if toxic megacolon
suspected
• 1 Specimen Usually Sufficient
• “Community-acquired” infections
becoming more common
Clostridium difficile
• General rule:
If the stick stands, the test is banned.
Respiratory Specimens
for Bacterial Culture
• Tracheal Aspirate
• Sputum
– Evaluated by gram stain for adequacy
• Bronchial Alveolar Lavage (BAL)
Respiratory Specimens
for Bacterial Culture
• Mini-BAL
– Patient on ventilator
– Obtained by RT using special catheter
– Cultured quantitatively to guide
interpretation
• Potential pathogens present in
>10,000 col/mL reported
Respiratory Specimens for Virus
• Best specimen: Nasopharyngeal aspirate
• 2nd Best: Nasopharyngeal swab
• Rapid assays:
– Restricted offering
– These tests are not the best for diagnosis
– A negative result does not mean the
patient does not have influenza or RSV
Respiratory Specimens for
Pertussis
• Nasopharyngeal specimens only
• PCR is performed daily on 1st shift at VC
– Specimens from Wesley are sent to VC
Urine Cultures
• Specimens
– Clean-catch (voided)
– Urinary Catheter
• Culture Work-up
– Reflex Cultures
• VC: Urinalysis specimens that contain >5 WBC
• WMC: Urinalysis specimens that contain >20 WBC
– Single organism at >10,000 colonies/mL
Urine for Legionella antigen
• Tests are run throughout the day and night
• Legionella antigen test is only for
Serogroup 1
– Only 70% of Legionella infections are
Serogroup 1
Streptococcus pneumonia
antigen
• Specimen type may be either urine or CSF
• Urine for Streptococcus pneumonia
antigen may give a false positive if the
patient has been vaccinated within 5 days
prior for pneumococcus.
– WMC: A comment will appear on positive
Strep pneumo antigens
ANTIMICROBIAL
SUSCEPTIBILITY TESTING
• Synonyms:
– AST = Antimicrobial susceptibility testing
– Sensitivity
• MIC = Minimum inhibitory concentration
• Vitek = automated method
• E Test = manual method
• Microscan = manual method
• Kirby Bauer = manual method
VITEK 2
KIRBY BAUER
E-TEST
MICROSCAN PLATE
ANTIMICROBIAL
SUSCEPTIBILITY TESTING
• Standardized Tests Defined by
Clinical and Laboratory Standards Institute
– Bacteria
– Fungi
– Mycobacteria
• Research Procedures or Not Available:
– Viruses
– Parasites
ANTIMICROBIAL
SUSCEPTIBILITY TESTING
• Qualitative: (Kirby Bauer)
– Disk Diffusion (S, I, or R)
• Quantitative: (Vitek, E test, Microscan)
– Minimum Inhibitory Concentration (MIC)
Antimicrobial
Susceptibility Reporting
• MIC value
– Based on 2-fold dilution of antibiotic
– Antibiotic with lowest number not
necessarily best
Antimicrobial
Susceptibility Reporting
• Interpretation
– S, I or R
– Based on achievable levels of antibiotic
• Does not consider concentration of
antibiotics in urine or other body fluids
• Does not consider penetration into
tissues or cells
AST NOT ROUTINELY
PERFORMED
• Bacteria that are rarely significant
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Bacillus species
Corynebacteria
Gardnerella vaginalis
Lactobacillus species
AST NOT ROUTINELY
PERFORMED
• Bacteria with Predictable Susceptibility
Patterns
• Except from Blood or CSF cultures
– Groups A and B Streptococci
– Haemophilus species
• β-lactamase tested and reported routinely
– Stenotrophomonas maltophilia
• Trimethoprim/sulfamethoxazole
usually used
– Moraxella
Exception: Group B Strep
at WMC
• Patient with a listed penicillin allergy and
growth of Group B Strep (GBS):
– MIC is set and reported
– D-Test for inducible clindamycin resistance is
set at the same time
– Clindamycin will only be reported as
susceptible if there is no inducible resistance
D Test to Detect Clindamycin
Resistance
AST NOT ROUTINELY
PERFORMED
Bacteria Requiring Special or Nonstandard
Testing Conditions
• Fastidious Gram Negative Rods
– eg. Eikenella, Campylobacter
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Anaerobes from Mixed Cultures
Anaerobes usually susceptible to:
Beta-Lactam/Inhibitor Combinations
Metronidazole
Carbapenems
Additional Resistance
Screening
• Enteric Gram negative bacteria
– ESBL: extended-spectrum β lactamase
• Resistant against all β-Lactam antibiotics
• Streptococci and Staphylococci
– D test for Clindamycin resistance where
appropriate
Screens for
Antimicrobial Resistance
• Streptococcus pneumoniae: Penicillin
• Enterococcus species: Vancomycin
• Staphylococcus aureus: Oxacillin
Streptococcus pneumoniae
Ceftriaxone Interpretation
• Separate breakpoints based on site of
infection
– Meningitis
• Based on achievable CSF levels
• S: < 0.5
I: 1
R: > 2 mcg/mL
– Nonmeningitis
• Based on achievable serum levels
• S: < 1
I: 2
R: > 4 mcg/mL
Streptococcus pneumoniae
Penicillin Interpretation
• Separate breakpoints based on site of
infection
At this time the breakpoint interpretations for
penicillin are reported below the MIC
– Non-meningitis pneumococcal isolates with a penicillin
MIC <=0.06 can be considered to be sensitive to oral
penicillins
– Non-meningitis pneumococcal isolates with penicillin
MIC 0.12 - 2.0 can be considered to be sensitive to IV
penicillin or oral ampicillin
– Pneumococcal Meningitis should not be treated with
penicillin unless the MIC <=0.06
Antibiotics and Susceptibility
Testing
• Don’t hesitate to contact the Microbiology
Laboratory with questions
– Best time to call: 1st Shift (7am-2:30pm)!
– Appropriate antibiotics usually reported
– Do not ask the Laboratory to recommend an
antibiotic to treat a specific patient
• Contact the Pharmacy for questions about
dosing and pharmacology
GRAM STAINS
• Gram stains are preliminary tests
• What we see may not grow, and what grows
we may not see on the gram stain
• Gram positive cocci resembling
staphylococcus
• What we cannot tell you from the gram stain:
Staph aureus vs Staph epi
• Gram positive cocci resembling streptococcus
• Sometimes we can tell you if it looks like
Strep pneumo
• We cannot tell you if it is enterococcus
GRAM STAINS
• Gram negative rods:
– Sometimes we can tell if it looks like an
enteric, pseudomonas, or Haemophilus
– What we cannot tell you is which enteric gram
negative rod. (E.coli, Kleb, Proteus, etc)
CULTURE REPORTS
• First day of growth of Staph aureus
– We cannot tell you if it is Methicillin Resistant
Staph aureus. (MRSA)
• First day of growth of gram negative bacilli
– We cannot tell you the organism name-but we
might be able to give you a good idea. Just
remember, we might be wrong.
CULTURE REPORTS
• Streptococcus on plate media may be
alpha, beta, or gamma in appearance.
• Alpha strep:
– Streptococcus pneumonia
– Streptococcus viridans
– Enterococcus
CULTURE REPORTS
• Beta strep: Groups A,B,C,D,F,G and nongroupable.
– Group A = Streptococus pyogenes
– Group B = Streptococcus agalactiae
– Group D = Enterococcus
CULTURE REPORTS
• Gamma strep: Streptococcus viridans or
enterococcus
– Streptococcus viridans: frequently part of
the normal body flora, rarely a pathogen
– Enterococcus: species, faecalis, or
faecium
• Enterococcus antibiotic screen
– If sensitive to gentamicin, vancomycin, and
ampicillin no further ID/MIC is done
– Exception: blood cultures; CSF
CULTURE REPORTS
• Sterile sites: blood, tissue, body fluid
– Organisms from these sites will be considered
likely pathogens
• Non-sterile sites: gastrointestinal tract,
respiratory tract
– Organisms from these sites will be evaluated
for normal flora and pathogenic flora
CULTURE REPORTS
• Microbiology is not a CSI television show
– There is no piece of equipment we can shoot
the specimen into and get an answer within 45
minutes
• Bacteria have their own timetable for
growth and some have special nutritional
needs or restrictions
• Sometimes an MIC takes more than one try
and more than one method to get an
answer
CULTURE REPORTS
• Cultures that are reported as No Growth
will NOT have a sensitivity
• Non-approved or Non-validated testing will
most likely be rejected
• Write clear and concise orders for your
culture specimens and sign your name
– If we have a question we know who to page
CULTURE REPORTS
• We call critical results to the nurse taking
care of the patient and they notify the
physician
• We will tell you as much as we can as
soon as we know
WE ARE JUST A PHONE CALL
AWAY
• Don’t hesitate to contact the Microbiology
Laboratory with questions
– Best time to call: 1st Shift (7am-2:30pm)
– Best time to visit:1st Shift (7am-2:30pm)