Updated August, 2005

Table of Contents
Critical Values Notification
Stat Testing
Documenting Consultations
I have no idea what to do
Requests for further workup on completed cultures
Requests for additional susceptibility testing
Stool Testing
Requests for routine culture on unacceptable endotracheal aspirate/sputum
Infection Control Issues
Malaria
Chlamydia/GC testing

 PLEASE NOTIFY DR. STEED (14463, cell phone 214-0940) OR LARRY YOUNGBERG, MICROBIOLOGY LAB MANAGER, (B13434) OF ANY CALLS YOU HANDLE AS SOON AS POSSIBLE ON DAY SHIFT, MONDAY-FRIDAY.

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Diagnostic Microbiology                                  Technical Coordinators:  Anne Panerosa (2-2393)

      Intake (specimen processing)                                                            Nancy Wessell

      Aerobic/anaerobic bacteriology                      Weekend team leaders: Celeste, Eileen, Gloria

      Mycobacteriology (AFB)

      Mycology

      Parasitology

      Virology

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Microbiology Critical Values notification policy:              

The following laboratory values are considered critical to patient care as they represent life-threatening infections, or will require immediate infection control intervention.  They must be called immediately to the physician in charge of the inpatient or outpatient at that time.  EXCEPTIONS: STAT TEST;  OR ?PLEASE PAGE/CALL@ WRITTEN ON THE REQUISITION. 

1.  Positive Gram stain from blood culture specimen of bacteria or fungi

2.  Positive Gram stain from CSF specimen of bacteria or fungi

3.  Positive Gram stain from sterile body fluid specimen of bacteria or fungi

4.  Positive blood culture of bacteria or fungi if original smear negative or isolate(s) discrepant from original Gram stain

5.  Positive CSF culture of bacteria or fungi if original smear negative or isolate(s) discrepant from original Gram stain

6.  Positive sterile body fluid culture of bacteria or fungi if original smear negative or isolate(s) discrepant from original Gram stain

7.  Positive DFA smear or PCR for Bordetella pertussis

8.  Positive AFB smear or culture;  positive M. tuberculosis Gen-Probe

9.  Positive fungal smear for hyphae, yeast cells or spherules suggesting Cryptococcus, Blastomyces, Coccidioides, Histoplasma, or Paracoccidioides

10.  Positive motile amoebic trophozoite

11.  Positive blood smear for parasite

12.  Positive viral culture from blood, CSF, sterile body fluid, tissue, or neonatal urine

13.  Pseudomonas species from ophthalmology locations

Positive PCR results from blood, CSF, sterile body fluid, or tissue will continue to be called.

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STAT TESTING

1.  Gram stain

a.  3rd shift in Fast Flow is trained to read Gram stains on CSF (always a STAT), amniotic fluid (always a STAT), and sterile body fluids ordered for STAT gram stain.  Gram stains performed by 3rd shift in Fast Flow are reviewed by Microbiology personnel early in the morning.

b.  Gram stains on other specimens are not deemed STAT by Microbiology. 

(1)  If a surgeon insists that a stat intraoperative Gram stain must be performed, have 3rd shift do it.

(2)  If a physician insists that a stat Gram stain must be performed on a non-OR specimen, determine the clinical relevance and why it cannot wait until 6 am.  If physician still insists, page Larry (B13434).

2.  Cryptococcal antigen test (applies only if testing ordered STAT, otherwise test performed on day shift)

a.  2nd shift is trained to perform STAT cryptococcal antigen tests.  The answer is positive or negative;  positive cyptococcal antigens tests are titered by day shift.  The titer is not required to initiate appropriate treatment, only to demonstrate response to therapy and/or assess prognosis.

b.  3rd shift is NOT trained to perform cryptococcal antigen tests. 

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Documenting consultations

1.  Consult must include name & beeper of physician requesting additional testing; this information must be added to the culture result to document billing issues.

2.  If request approved, call 2-2393 and ask for Larry, Anne, or Nancy (if a weekday) or weekend team leader to make arrangements for appropriate testing.

3.  If request is denied, I will add this information to the culture result to document the consultation. 

 

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I HAVE NO IDEA WHAT TO DO

IF YOU ARE UNCOMFORTABLE MAKING THESE DECISIONS, your options:

1.  Call me (214-0940)

2.  Call 2-2393 and ask for Larry, Anne, or Nancy (weekdays) or the weekend supervisor or the tech working on that type of culture and ask his/her advice on what to do.  Any of them may be able to tell you enough about the culture to resolve the clinician=s concern.  Then call the clinician back with your answer.

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REQUEST FOR FURTHER WORK UP on completed culture

Cultures are worked up@ based on (1) specimen source; (2) pathogens expected; (3) number of potential pathogens isolated; and (4) epidemiological relevancy (e.g., methicillin resistant Staph aureus [MRSA] and vancomycin resistant Enterococci [VRE]).

Any culture with 3 or more potential pathogens (“Rule of 3”) is not generally worked up due to lack of clinical relevance.  An ?official dispensation@ may be granted after consultation with beeper 14463.  For example, for an abdominal surgical specimen, infections are usually polymicrobial with organisms from the gastrointestinal tract.  ID and susceptibility testing do not usually provide information the clinician does not--or should not--already know.  For a different example, IV catheters, foley catheters, endotracheal tubes, and any other tubing going from within a patient thru the skin to the outside world becomes colonized with hospital flora (predominantly Gram negative bacilli like E coli and Pseudomonas aeruginosa) and/or the patient=s skin flora within 3 days.  Mixed Gram negative and/or Gram positive flora almost always represents colonization; again, ID and susceptibility testing do not usually provide clinically relevant information.  These cultures are examined for Staph aureus, which is tested for methicillin resistance, enterococci, which are tested for vancomycin resistance, and Pseudomonas aeruginosa (without AST).  Otherwise, nothing should be done with these cultures.

Also, determine the age of the culture.  Susceptibility testing has a short predictive window:

Staph aureus & MRSA           3-5 days

Coag negative staph               5 days

Most Gram negative bacilli     5 days

Citrobacter, Enterobacter, Providencia, Proteus vulgaris, Pseudomonas aeruginosa, Serratia  3 days

If the culture is already beyond that point, do not perform testing on old specimen; agree with clinician what should be done with the new specimen.  If patient has endocarditis or osteomyelitis, an old specimen can still be tested since treatment is 6-8 weeks.  If specimen cannot be recollected, use your best judgement once you have the clinical situation assessed (i.e., infection vs colonization) and you know the clinician understand the limits of our testing.

You may want to speak with the tech working on the culture to determine what’s growing in the culture and their relative proportions.  For example, you might handle differently a culture with 3 Gram negative rods all in light growth compared with a culture with moderate growth of “E coli”, light growth of “Klebsiella” and scant growth of “Pseudomonas”.

1.  If a physician insists on full identification and susceptibility testing on surgically obtained specimen or CT-guided aspirate, ask ?why?@     

a.  because my attending wants it@ is insufficient scientific reason and the answer is ?no@ (unless, of course, the attending calls you directly--then do it). 

b.  to guide therapy@, still ?no@ because combination therapy is appropriate for polymicrobial infections

c.  Susceptibility testing required on Pseudomonas aeruginosa only, approve test  

d.  If the patient has a history of numerous abdominal procedures over several months with numerous courses of antibiotics, e.g., chronic pancreatitis, then approve ID and susceptibility testing.

2.  If a physician insists on full identification and susceptibility testing on any other specimen, ask ?why?@   

a.  because my attending wants it@ is insufficient scientific reason and the answer is ?no@ (unless, of course, the attending calls you directly--then do it). 

b.  “to guide therapy@, still ?no@ because combination therapy is appropriate for polymicrobial infections

c.  Susceptibility testing required on Pseudomonas aeruginosa only, determine role of this organism in the patients current disease process and how susceptibility test will change therapy; if request is reasonable, approve test

d.  If the patient has a complicated medical history with numerous courses of antibiotics, discuss culture with tech working on it first

3.  If a physician insists on full identification of a yeast grown from a bacterial culture:

a.  Yeast isolated from blood, bone marrow, tissue, bone, sterile body fluid (not urine) [critical sites] on routine bacterial culture are identified whether or not a fungal culture is ordered on the same specimen.

b.  Yeast isolated from any other specimen on routine bacterial culture are not identified as the clinician obviously wasn=t thinking fungus in the differential diagnosis.  Most bacterial cultures are held only long enough to detect bacteria (24-48 hours) and yeast usually take 36-72 hours to grow. That=s why the final report states ?No growth of bacteria@ at whatever incubation period.  Lack of growth of yeast on a routine bacterial culture does not mean the patient does not have a fungal infection!  Fungal cultures use larger volumes of specimen and 10-28 days of incubation (depending on the source) to enhance recovery of yeast and molds.   Remind the physician of bacteria & fungus growth rates and recommend that s/he request fungal culture when yeast (or mold) is in the differential diagnosis.  If the physician sees yeast on a urinalysis and is concerned about the yeast, s/he can call the lab the same day the urine is sent for culture and add a fungal culture (we=ll still have the specimen).  S/he will have a result s/he can believe, will automatically get a yeast ID, and we=ll be paid for the extra work. 

c.  The techs are supposed to note in the worksheet if a yeast has ?feet@--yeast with ?feet@ are presumptive Candida albicans. If a physician insists that an ID is required, call 2-2393 and ask for Larry, Anne, Nancy, or weekend team leader.  If the yeast has feet, have the report updated to presumptive C albicans; you can call the physician back with that information.  If the yeast does not have feet, the yeast will have to be sent to our mycology lab for identification.

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REQUESTS FOR ADDITIONAL SUSCEPTIBILITY TESTING

Antibiotic susceptibility testing batteries have been selected based on (1) what agents usually kill an organism; (2) what agents are in our formulary; (3) what agents are on commercially available testing cards or panels; (4) growth requirements of the organism in question; and (5) number of organisms isolated from a given site.

Remember: Susceptibility testing has a short predictive window (generally from the time of collection):

Staph aureus & MRSA           3-5 days

Coag negative staph              5 days

Most Gram negative bacilli     5 days

Citrobacter, Enterobacter, Providencia, Proteus vulgaris, Pseudomonas aeruginosa, Serratia  3 days

If the culture is already beyond that point, do not perform testing on old specimen; agree with clinician what should be done with the new specimen.  If patient has endocarditis or osteomyelitis, an old specimen can still be tested since treatment is 6-8 weeks.  If specimen cannot be recollected, use your best judgement once you have the clinical situation assessed (i.e., infection vs colonization) and you know the clinician understand the limits of our testing.

Call me or call 2-2393 and ask for Larry, Anne, or Nancy (weekdays) or the weekend supervisor or the tech working on that type of culture for current Gram negative and Gram positive susceptibility testing options and methods (MicroScan MIC panels; disk diffusion or E tests [for determination of MICs by a disk diffusion-type method]).

1.  Requests for Rifampin on Staph aureus or methicillin resistant Staph aureus [MRSA]:

a.  Can be requested only by Infectious Disease physicians, fellows, or residents or pharmacy staff doing the ID rotation.  Generally the information is required to optimize therapy for bacteremia/ endocarditis, osteomyelitis, or deep-seated tissue infection. 

b.  Rifampin is part of every Staph susceptibility test, but is never released without approval to avoid inappropriate usage as a single anti-Staph agent (develops resistance too fast).  Ask Larry, Anne, or weekend team leader to get rifampin results from Vitek and email it to the requesting individual.

2.  Vancomycin resistant Enterococci (VRE): applies to VRE faecium or VRE faecalis only

a.   Ask requesting individual how many antibacterial agents are in the report--1 (we looked for vancomycin resistance only) or 3-4 agents (we did a full susceptibility panel).  Additional testing that can be requested include following:

(1) Linezolid (works against  VRE faecium or VRE faecalis) is on the full susceptibility panel & is routinely reported on VRE faecium/faecalis.

(2) Daptomycin (works against VRE faecium or VRE faecalis) requires susceptibility testing separately because it is not on formulary.

3.  AI see methicillin susceptibility [or resistance] for Staph aureus , but is it susceptible to [insert antibiotic name here]?@  Similarly  AI see vancomycin susceptibility [or resistance] for Enterococcus, but is it susceptible to [insert antibiotic name here]?

a.  We look for methicillin resistance on Staph aureus and/or vancomycin resistance on Enterococcus when there are 3 or more potential pathogens in a given site (refer above to section REQUEST FOR FURTHER WORK UP on completed culture). 

b.  For staphylococci or enterococci, call me or call 2-2393 and ask for Larry, Anne, or Nancy (weekdays) or the weekend supervisor or the tech working on that type of culture.  The NCCLS/ CLSI documents will often extrapolate the results of other antibiotics based on a class drug.  Otherwise, the answer is ?can=t tell without performing that specific susceptibility test at additional charge to the patient@.

Never, ever approve any of the following drug/bug combinations:

Organism	Antimicrobial agents that will always be resistant in vivo regardless of susceptibility test results
Methicillin-resistant Staph aureus	All cephalosporins Augmentin (amoxicillin/clavulanate) Imipenem Meropenem Unasyn (ampicillin/sulbactam) Zosyn (piperacillin/tazobactam)
Methicillin-resistant coagulase negative Staph	All cephalosporins Augmentin (amoxicillin/clavulanate) Imipenem Meropenem Unasyn (ampicillin/sulbactam) Zosyn (piperacillin/tazobactam)
Enterococcus spp.	Aminoglycosides (except at synergistic concentrations) All cephalosporins Clindamycin Trimethoprim-sulfa
Salmonella spp., Shigella spp.	1st & 2nd generation cephalosporins Aminoglycosides
Listeria monocytogenes	All cephalosporins

4.  FOR ALTERNATIVE ORGANISM susceptibility testing--Corynebacterium, Bacillus, anaerobes, etc.

a.       Organisms not on the NCCLS charts have no standardized susceptibiilty testing method and no correlation between lab results and patient outcome (i.e., no idea what results mean or even if they are relevant).  If physician insists, determine what agents are reasonable to test using the Sanford guide (attached) and the antimicrobial agents available by Pasco MIC broth panels for Gram negative bacilli and Strep pneumoniae and E tests. 

b.       Anaerobes are sent to the reference lab for testing.  Beta-lactamase generally tells a physician how to treat the patient.

5.  Yeast (Candida) susceptibility testing is a send out and takes about a week to get results back.   The reference lab that we send these to routinely tests: amphotericin B, 5-flucytosine (5-FC), fluconazole, itraconazole, ketoconazole, voriconazole. 

Beta-lactamase positive means:

Haemophilus, N. gonorrhoeae--resistance to penicillin, ampicillin, amoxicillin

Staphylococci and Enterococci--resistance to penicillin, ampicillin, ticarcillin, piperacillin

Anaerobes—resistance to penicillin, ampicillin

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STOOLS

Stool specimens unlikely to provide clinically relevant information on most inpatients are rejected using the criteria below.

STOOL REJECTION CRITERIA  (begun January 6, 1997)

* Exception: Stool for C difficile toxin assay submitted on days of admission 1-3 is acceptable on patients with liquid stool (not semi-solid or solid stool), patients that have been on antibiotics within the previous 3 weeks,  patients that were transferred from another hospital, or patients with Hirschprung’s disease or ulcerative colitis.

Routine stool cultures look for Salmonella, Shigella, Campylobacter only.

E coli O157:H7, Yersinia, Aeromonas, Vibrio must be ordered specifically and are included in the rejection policy.

Our most common parasite is Giardia lamblia and the best test to detect that parasite is the Giardia EIA antigen test.  Second most common parasite is Cryptosporidium and the best test to detect this parasite is the EIA antigen (it may or may not be seen on an O & P).

1.  Stool specimens unlikely to provide clinically relevant information on most inpatients are rejected using the criteria below. 

a.  Patients eating hospital food are unlikely to develop diarrhea due to Salmonella, Shigella, Campylobacter or parasites.  Typical incubation periods for these diseases are 24-48 hours for Salmonella and Shigella, 2-4 days for Campylobacter. Same is true for other stool pathogens (E coli O157:H7, Yersinia, Aeromonas, Vibrio).

b.  Patients not on prior (within the previous 3 weeks) or current antibiotics are unlikely to develop diarrhea due to C difficile.

2.  As with all rejected specimens, the floor is notified.  Exceptions for individual patient needs can be made by any physician upon consultation with beeper 14463.

a.  Stool culture:

(1)  If stool cultures x3 are being collected and the first 1 or 2 specimens have arrived in Microbiology on the first 3 days of admission, but the 2nd or 3rd specimen(s) arrive on or after day 4, accept the specimen(s).

(2)     For a single stool specimen, unless the patient has been eating food from outside or a family member having close contact with the patient has diarrhea (and the family member should not have been allowed to have any contact with the patient!), there is no logical reason for any stool culture.

(3)     A routine stool culture will not tell if a patient has the normal bacterial constituents of stool.  That assessment needs to be referred directly to me or Larry‑‑on day shift.

(4)     If the physician insists on the culture and the specimen is in Cary‑Blair transport media (vial with a green top), tell the physician I or Larry will have to make the final decision on day shift and that the specimen will not be adversely affected.

(5)     If the physician insists on the culture and the specimen is in a sterile container AND if before 10:30 pm, tell the physician I or Larry will have to make the final decision on day shift, but that you'll ask 2nd shift to inoculate the specimen in case the culture is approved.

b.  Ova & Parasites, Giardia antigen, Cryptosporidium screen:  O & Ps are performed at a reference lab;  Giardia and Cryptosporidium antigens are performed Mon-Fri

(1)     If O & P x3 are being collected and the first 1 or 2 specimens have arrived in Microbiology on the first 4 days of admission, but the 2nd or 3rd specimen(s) arrive on or after day 5, accept the specimen(s).  O & P specimens should be collected 1 every other day.

(2)     For a single O & P specimen, unless the patient has been eating food from outside or a family member having close contact with the patient has diarrhea (and the family member should not have been allowed to have any contact with the patient!), there is no logical reason for any parasitology testing.

(3)     If the physician insists on the parasitology test(s) and the specimen is in PVA (vial with a red top), tell the physician I or Larry will have to make the final decision on day shift and that the specimen will not be adversely affected.

(4)     If the physician insists on the parasitology test(s) and the specimen is in a sterile container AND if before 10:30 pm, tell the physician I or Larry will have to make the final decision on day shift, but that you'll ask 2nd shift to add PVA to the container to try to preserve the quality of the specimen. 

c.  C. difficile toxin assay (CDT):       testing is performed 7 days a week

(1)     See exceptions under the Stool Rejection Criteria box on the previous page.

(2)     Physicians usually know if a patient received antimicrobial therapy at another hospital or as an outpatient.  Please note the antimicrobial agent the patient received.  If the patient was/is currently on metronidazole (Flagyl) or po vancomycin, the patient does not need a CDT as these antibiotics are the drugs of choice for C difficile disease.  Note:  IV vancomycin is not effective against C difficile;  a specimen submitted on a patient receiving IV vancomycin is suitable for testing.

(3)     Patients with Hirschprung=s disease or ulcerative colitis have an increased susceptibility to C difficile and may be tested without record of previous antimicrobial use.  Please note that the patient has Hirschprung=s disease or ulcerative colitis.

Fecal leukocytes/Fecal WBC's. 

1.  The Infectious Diseases literature says that the presence of fecal WBC's indicates a patient has  diarrhea due to Salmonella, Shigella, or Campylobacter; absence of fecal WBC=s indicates a patient has Vibrio, E coli O157:H7, some parasites, or enteric viruses.  However, the microbiology literature does not support this conclusion and the test is performed in many large medical institutions only on trichrome stained smears (as part of an O & P).  As Kathleen Beavis relates, ?An article from the August 23, 1980 Lancet (pp. 413 - 416) reviews Mass. General's experience with 2468 stool cultures in 1977.  Only 27 stools were examined for fecal leukocytes.  There was no association between the presence or absence of fecal leukocytes and positive cultures.  Of the 13 smears from patients with negative cultures, 4 had fecal leukocytes; of the 14 smears from patients with positive cultures, 5 had fecal leukocytes.@

2.  Testing is performed only on day shift.  Specimen should be submitted in formalin or PVA (latter not widely available in‑house) to maintain the integrity of the cells.  Fresh stool is acceptable if examined within 60 minutes (obviously available only on day shift).  Stat requests are usually made only by ER physicians.

3.  If an ER physician insists that stat fecal WBC's must be performed:  stool must be liquid (best) or semi‑formed (i.e., conforms to the interior of the container of its own accord)

a.   If before 10:30 pm, have 2nd shift do a Gram stain of the stool.  Put the ?Snotty Comment@ on the report and have the test repeated on day shift on a properly submitted specimen.

b.   If after 10:30 pm, no one in Fast Flow is qualified to perform the test.  The physician is welcome to come to the lab to make and read his/her own slide, but Larry will not bring in a tech to do this test as it is not a medical emergency.