MICROBIOLOGY
The following sections define the services and tests which are available through the UMass Memorial Microbiology Laboratories. In order to provide interpretable, clinically relevant data with adequate predictive value, we use standardized or reference methods as described by the National Committee for Clinical Laboratory Standards, Clinical Microbiology Procedures Handbook or the Manual of Clinical Microbiology (American Society for Microbiology Press), whenever possible. The services offered should meet the diagnostic requirements for most patients. We invite consultations to help clinicians develop diagnostic strategies or interpret Microbiologic data.
I. Laboratory Services
The UMMHC Laboratories offers broad service in the areas of Bacteriology, Virology, Mycology, Serology, Mycobacteriology, and Parasitology. Tests not performed in the UMMHC laboratory may be available as "send out" tests through reference laboratories. Tests performed by a reference lab will be so noted in the results. A hard copy of all test results will be sent to the patient's chart when completed. All results are also entered into the computer and can be viewed either through the microbiology module or PCI.
A. Senior Staff:
Michael Mitchell, M.D.
Medical Director:
Phone: 508/ 856-6417
Fax: 508/ 856-1537
beep 8724
michael.mitchell@banyan.ummed.edu
Brenda Brogden-Torres, BS, MT SM(AAM
)Lab Manager:
Phone: 508/ 856 3429
Fax: 508/ 856-1537
beep 3429
brenda.torres@banyan.ummed.edu
Lead Technologist, Memorial Campus: Marge King
Lead Technologist, Bacteriology: Elaine Peterson
Lead Technologist, Quality Assurance: Maureen Jankins
Lead Technologist, Serology: Diane Hunt
Lead Technologist, Virology: Ron St. Amand
Lead Technologist, Parasitology: Lynn Wu
Lead Technologist, Mycology/Mycobacteriology: Judy Westerling
B. Location: Laboratory, University Campus: H2-408, Ext. 62891
C. Laboratory Hours and Coverage:
1. Days and Evenings: The lab is open with full services available Monday - Friday 7:30 am - 4:00 pm. Limited service is available daily 5:30 pm - 8:30am and on weekends and holidays. Specimens should arrive in the lab before 11pm, when possible. Specimens must arrive earlier for some tests if same day results are needed.
2. On call Support: A microbiology Director and Supervisor are on call through the Page Operator at all times to handle special Microbiology problems. The Clinical Pathology Resident is on call for evenings, nights, weekends and holidays.
II. SPECIMEN Transport
A. Specimens should arrive in the laboratory within 2 hours after collection in appropriate sterile, closed containers. Some specimens must be transported more quickly or in special transport media.
B. Swabs - The use of swabs to collect material for microbiological testing is adequate for a very limited number of specimen types. Specifically, they are acceptable for samples taken from skin, mucous membranes, genital sites and anal crypts.
To insure adequate amounts of material for inoculation, one swab should be submitted for each type of culture requested. For example, two swabs should be submitted if a wound culture is sent for bacteriology and mycology. Several swab transport kits are available in this hospital (e.g., bacteria, virus, chlamydia, etc.). For tests other than bacterial or fungal culture, please refer to the specific section of the UMMHC laboratory manuals for details concerning proper specimen collection using swabs. Specimens collected using charcoal swabs are not optimal for Gram stain interpretation because of the charcoal in the transport medium.
Swabs may not be optimal for use in culturing:
1. Surgical specimens - Please send tissue or an aspirate of fluid or pus. Use an Anaerobic Transport kit that accepts swabs in the unusual circumstances in which swabs must be used for intraoperative specimen collection.
2. Pus or exudate - Please send aspirate in anaerobic transport vial.
3. Anaerobic Bacteria
4. Mycobacteria
5. Yeast and Filamentous Fungi - except for sites listed above.
C. Syringes are acceptable if the needle has been removed, the air has been expelled and the lumen tightly capped. Extra care must be exercised during transport to prevent leakage. Hand carry syringes to the laboratory.
D. Tubes, jars and bottles - These must be sterile and tightly capped. A variety of types are available for aerobic and anaerobic transport.
E. Stool transport systems - Stool for enteric culture and O & P may be transported in clean, tightly capped containers that aren't sterile. Carey-Blair transport media or PVA/Formalin kits should be used (for enteric culture or O & P exams, respectively) if the specimen cannot be transported within 30 to 60 minutes of passage or if the specimen will not arrive in the lab between 8:30am and 3:00pm, Mon-Fri. These kits are available from the Lab. Mix stool with the O&P fixatives in a 1:3-5 stool:fixative ratio.
F. Viral, chlamydia, and genital mycoplasma transport media and swabs are available in various outpatient units and from the lab.
III. Specimen acceptability and timing
A. Specimens must be properly labeled and accompanied by a requisition slip. The requisition slips must be completed according to the instructions listed on the top. Relevant clinical data should be included as a comment (e.g., Pathogen suspected, antimicrobial therapy...). The slip should be attached to the outside of the transport bag.
B. Specimens that arrive in containers which are grossly contaminated on the outside by blood, urine, stool or other potentially hazardous material will be rejected and discarded.
C. Specimens from patients to whom radioactive material has been administered for therapeutic or diagnostic reasons should be accompanied by the following information:
a) Radioisotope administered, b) dose, c) site and d) time of administration.
D. In general, only 1 specimen/site/day with a maximum of 3/week are acceptable with the following exceptions.
1. Blood, Tissue and Body Fluids (except urine) - no specific limit.
2. Mycobacterial culture -
Blood, Bone Marrow, Urine & Respiratory specimens:
3 specimens/source/admission
Specimens from the OR: No specific limit
3. Viral culture - For any site: 1 specimen/source/admission or visit
4. Stool specimens -
Bacterial culture: 2 specimen/week
O & P Exam: 3 specimens/admission. Specimens not accepted for patients in-house for more than three days when diarrhea begins.
The tests which are routinely available through the Microbiology Service are listed below. Tests not listed must be arranged with the Director prior to specimen collection.
A. STAT Requests - STAT Gram stain results will be performed only when specifically requested on the requisition slip (except for specimens from the OR, which are routinely performed STAT). STAT requests should be reserved for truly emergency situations. STAT Gram stain results are generally available within 30 minutes after specimen receipt in the laboratory. STAT requests for every other type of test must be arranged by consultation with the Director on call.
B. Test Results which are called to physicians:
Specimens that are likely to have an important clinical impact or epidemiologic importance are phoned to the ordering physician, nursing unit or client location. These include:
1. STAT test results
2. Initial positive results (culture or smear) from BLOOD, CSF, STERILE FLUIDS (except urine), TISSUE/biopsy from the OR.
3. Gram stains from the OR. Any positive AFB smear.
4. Positive bacterial antigen or cryptococcal antigen test.
5. Drug resistant phenotype in M. tuberculosis.
6. Diseases reportable to the State Public Health Service including STDs and enteric infections.
C. Bacteriology
1. Bacterial Cultures - Notify the laboratory if a specific pathogen is suspected. Certain organisms require special procedures of collection or processing for isolation (e.g., Brucella, Legionella). The work-up of greater than three potential pathogens from a culture is seldom clinically useful and will be performed only after consultation with the Director on call. When the isolates of a mixed culture resemble the normal flora expected from that specimen type, they will be reported as such (e.g., light respiratory [or skin, genital or colonic] flora present). Cervical, vaginal and urethral cultures will always include culture for Neisseria gonorrhoeae in addition to other genital pathogens. Swabs of anal crypts, however, will only be cultured for N. gonorrhoeae. Throat cultures will be cultured routinely to rule out Group A Streptococcus only.
2. Anaerobic cultures - Optimal recovery of anaerobic pathogens requires that material be transported to the Microbiology Lab under anaerobic conditions within one hour of collection. Since oxygen diffuses slowly into large pieces of tissue, they may be transported in capped sterile jars. In addition, pus and fluid specimens may be transported in a capped syringe from which the air has been expelled. Specimens should be collected while the laboratory is open and sent immediately for processing. Anaerobic transport vials are available for specimens for which delayed transport is anticipated. In addition, the Operating Rooms are stocked with anaerobic transport sets for intraoperative specimen collection. If infection with actinomyces is suspected, please note this on the requisition slip (i.e., R/O actino).
It should be noted that samples transported under anaerobic conditions are also acceptable for aerobic, fungal and AFB culture provided a sufficient amount of material is submitted. Because of the slow growth rate and fastidious nature of many anaerobic isolates, the identification and sensitivity testing, if performed, for these isolates may be markedly delayed compared to aerobes.
a. Due to the presence of normal anaerobic flora, the following specimens will not be accepted for anaerobic culture:
- Pharyngeal or lower respiratory tract cultures (except for transtracheal aspirates or open lung biopsy.)
- Urine (except suprapubic aspirates.)
- Urethral or vaginal exudates
- Skin
- Stool
3. Gram Staining - Detection of organisms by Gram stain is 1 to 2 orders of magnitude less sensitive than appropriate culture but, even so, it is the most useful "rapid diagnostic" test performed by the lab. Gram stains are routinely performed on biopsy/tissue, genital, sputum, wound and sterile fluid specimens. Gram stain testing for other types of specimens must be ordered specifically. Gram stains on throat specimens will be used to rule out thrush only. Therefore, only the presence and quantity of yeast seen will be reported. Organisms will be reported in their order of predominance.
4. Routine Antimicrobial Susceptibility Testing - Significant aerobic isolates will be tested for sensitivity to a variety of oral and parenteral antibiotics except when sensitivity for the drug of choice can be reliably predicted (e.g., Group A Streptococcus is always sensitive to Penicillin). The drugs reported depend on the type of organism tested (e.g., Gram negative rod) and the source of the isolate (e.g., Urine). N.B., Standardized susceptibility testing is not available for all classes of organisms, like Gram positive rods! Routine susceptibility testing is performed by the Vitek automated system. Interpretive reports are based on "breakpoint" MIC values. Microbroth dilution testing is performed when exact MIC values or data for drugs not on Vitek panels are needed. In addition to quantitative results, interpretive results are recorded as S(sensitive), R(resistant), or I(intermediate). These interpretations are based on achievable serum levels in normal patients. These test interpretations should not be used in treating patients with conditions which alter normal drug pharmacokinetics or for infections at sites where drug concentration does not achieve serum levels. A drug for which the isolate is of Intermediate susceptibility may be useful when parenteral administration is used or when the infection is in a site where the drug is concentrated relative to serum (like urine). When two-fold dilution MIC testing is requested, please inform the laboratory which drugs should be reported with the quantitative MIC result.
5. Specialized Susceptibility Testing - The Director on call should be contacted to discuss sensitivity testing of fastidious aerobic or anaerobic isolates, testing drugs not on routine panels and other special antibiotic testing.
D. Chlamydia trachomatis
The Laboratory routinely performs GenProbe testing on urethral specimens for the detection of Chlamydia (and GC). Testing is performed daily Monday through Friday with final results available within 24 hours. Chlamydia culture is also available. Successful culture requires that specimens contain columnar epithelial cells. Chlamydia (viral) transport medium is available in the Micro Lab. Cultures are set-up on Monday, Wednesday and Friday. Results will be available after 48 hours.
SPECIMENS ACCEPTABLE FOR CULTURE |
|
SPECIMENS UNACCEPTABLE FOR CULTURE |
Cervix |
|
Peritoneal Fluid |
Fallopian Tube |
|
Urethral discharge |
Urethra |
|
Urine |
Epididymis |
|
Cul-de-sac fluid |
Ocular |
|
Vagina or vaginal fluid |
Anal |
|
Throat |
Lymph node |
|
|
Respiratory (Neonate) |
|
|
1. Sampling Technique
For cervical specimens, cultures to rule out gonorrhea should be taken first. Excess mucous and discharge should then be removed using a large cleaning swab. The collection swab tip should then be inserted into the cervical os, urethra or other acceptable site until the dacron is just visible or 2-4cm into the urethra and rotated for 5-10 seconds before removal. Place the swab into the transport medium. Culture specimens should be transported to the lab on ice within 2 hours of collection.
E. Clostridium difficile Assay
Disease caused by C. difficile is detected by demonstration of specific cytotoxicity of a stool specimen on cultured eukaryotic cells. The tests are performed daily, except on weekends and holidays. Specimens should arrive in the laboratory before 10:00am. Final results are generally available after 48 hours. The toxins of C. difficile can also be detected by commercially available EIA kits.
G. Fungal Cultures
1. Fungal cultures: The fungi most commonly isolated from urine are Candida species and they will grow within several days. Therefore, urine yeast cultures will be finalized after five days unless another suspected fungal species is indicated. Spinal fluid and pleural fluid is examined for four weeks. Other specimens will be examined for 4 weeks before being discarded as negative. Yeast isolates usually require 3-5 days and mold 7-14 days for identification after isolation.
2. Direct examination of specimens for fungal elements by wet mount is performed after digestion with KOH and staining with calcofluor white. Direct examination for fungi may require consultation with the Director on call. India Ink preparations are not used for detection of Cryptococcus because of the availability of cryptococcal antigen testing. The sensitivity of India Ink preparations in detecting cryptococcal meningitis is only about 50%, so it is only occasionally used to confirm capsule production in fungal isolates.
3. Cryptococcal antigen detection in CSF is routinely available for the diagnosis of cryptococcal meningitis. Approximately 95% of cases of cryptococcal menigitis will be detected by cryptococcal antigen testing of the CSF. On the other hand, Cryptococcal antigen testing of serum, urine and pleural fluid have not been shown to be as sensitive. All specimens submitted for cryptococcal antigen testing should be accompanied by cultures of blood or other potentially infected material for fungal isolation. If positive, two-fold serial dilutions down to endpoint will be prepared.
H. HIV Testing
Human Immunodeficiency Virus, type 1 serology is performed as a sendout test from the Blood Bank. Quantitative RNA detection and HIV genotyping is performed by Specialty Laboratories. HIV p24 antigen testing or HIV culture is not routinely available. Requests for any type of test must be accompanied by a HIV test consent form.
Initial antibody testing using an ELISA assay is performed. These assays have a very high sensitivity. However, to achieve maximum specificity, all specimens repeatedly positive by ELISA have confirmatory testing using the Western blot technique. Positive results are called to the requesting physician. Final results are available after 2 to 5 days.
Quantitative HIV-1 RNA determinations are currently performed using the RT-PCR amplification technique.
I. Legionella
Serological testing should always be performed when specific diagnosis of Legionella infection is needed. Both acute and convalescent serum samples, along with a State Lab Clinical History Form, should be submitted. Legionella culture is available for some specimen types. Sputum, bronchial washes/lavages, transtracheal aspirates or open lung biopsies may be submitted. Please note that the saline solutions used for some specimen collections may be toxic to Legionella strains. Other specimen types are rarely acceptable. Specimens should be transported to the laboratory on ice. Cultures require up to 10 days incubation. Urine Legionella antigen (L. pneumophila, type 1) testing is available for patients in whom the index of suspicion is high.
J. Mycobacteria
1. Culture - Cultures are inspected for growth for 8 weeks. Identifications may require 1-4 weeks after isolation. Mycobacteria that resemble Mtb or MAI or M. gordonae are identified by using rRNA probes. Other isolates are sent to the State Laboratory for identification. Routine susceptibility testing is performed in-house. Genital, upper respiratory tract and stool cultures are generally unacceptable for mycobacteriology culture.
2. Direct examination of most specimen types by Acid-Fast staining (fluorochrome and/or Kinyoun) is performed by the lab. Respriratory specimens are decontaminated and concentrated prior to smear preparation. Positive results are phoned STAT to the requesting physician. AFB stains are performed daily Monday through Friday and as needed on weekends and holidays.
K. Mycoplasma
1. M. pneumoniae is a common cause of atypical pneumonia, usually occurring in children and young adults who have a history of exposure. The diagnosis is generally made clinically and treatment started empirically. Submit acute and convalescent serum samples for anti-M.pneumoniae antibodies when specific diagnosis is needed. In hospitalized patients with atypical pneumonia which is unusually severe or associated with extrapulmonary complications, specific laboratory diagnosis may be attempted using a combination of tests on an unpaired, "early convalescent" serum sample. In these cases, please contact the Microbiology Director. Cold agglutinin tests are non-specific and should not be performed. Culture for M. pneumoniae is not routinely available.
L. Nocardia
Nocardia species are isolated from fungal and mycobacterial cultures. Please notify the laboratory if you suspect a Nocardia infection. Modified acid fast staining for the direct visualization of Nocardia in tissue can be arranged through the Director on call.
M. Ova and Parasite Exams
5ml to 10ml of stool passed into a clean bedpan or onto waxed paper should be placed into a tightly sealed container (plastic is recommended to reduce the possibility of leakage) and submitted to the lab Monday through Friday 8:30am - 3:00pm. For specimens which will arrive at other times or when transport time >30minutes is anticipated, stool should be transported using a PVA/Formalin transport kit. (Follow included directions.) Examination of specimens for motile forms is not possible for specimens submitted in transport fixatives. Up to three specimens, preferably collected every other day, are acceptable per patient admission. Please note:
1. Stool taken from the toilet or submitted on toilet paper are not acceptable.
2. Stool should not be submitted for 10 to 14 days after administration of barium.
3. Special testing for Cryptosporidium, Isospora, Giardia, Cyclospora and/or Microsporidium is available but must be requested specifically (i.e., r/o Cryptosporidium).
4. Specimens of urine or vaginal secretions for Trichomonas vaginalis should be submitted to the laboratory Monday through Friday 8:30am - 3:00pm.
N. Pneumocystis carinii detection
Direct examination of respiratory specimens for P.carinii is performed using fluorescent monoclonal antibody staining. Testing is not performed on weekends and holidays. Specimens for PCP testing must arrive in the laboratory before 2pm if same day results are needed. Acceptable specimens include material obtained by lung biopsy, bronchoalveolar lavage or induced sputum. Sputum induction is appropriate for the following patients:
1. Patients with AIDS or at high risk for HIV infection with an abnormal CXR, hypoxemia and/or a positive respiratory uptake on gallium scan.
2. Other patients who are on the bronchoscopy schedule in whom PCP is in the differential diagnosis.
O. Serological Testing
RPR, H.pylori, Rubella, VZV and CMV antibody and Cryptococcal and Group B Streptococcal antigen tests, among others, are performed by the laboratory. Hepatitis serology is performed in the Core Lab. Serological testing for uncommon infections are usually sent to Specialty Labs, the State Lab, or the CDC. These generally require acute and convalescent sera. Clinical history forms, available in the laboratory, must be submitted with the acute serum sample for testing at the public health laboratories. Acute serum samples will not be sent out for testing until the convalescent sample is received. The results will be available several weeks after the convalescent serum has been submitted. Please contact the Microbiology Laboratory or the Infectious Disease Consult for specific details regarding serological diagnosis of the disease in question.
P. Virology
Specimens for viral culture collected on swabs must be placed into viral transport media, which is available in the Micro laboratory, and transported immediately to the lab on ice. Tissue, stool, fresh voided urine and other fluids may be submitted on ice without transport media. If transport will be delayed for >1hr. after collection, please contact the Microbiology Director on call for proper holding conditions. All attempts should be made to collect specimens so that they will arrive in the lab Monday through Friday 8:30am - 3:00pm.
The following viruses can be cultured by the UMMHC Virology Lab: Herpes Viruses (HSV, CMV, VZV), Enteroviruses (ECHO, Coxsackie, Polio), Adenovirus, Influenza and Parainfluenza, RSV, Measles, and Mumps. Rapid viral detection by the "shell vial" technique is available for Influenza and Parainfluenza viral types, RSV and Adenovirus.
Herpes simplex cultures require 1-14 days incubation. Cultures for other viruses may require up to 28 days incubation.
Submit specimens according to the following clinical conditions:
1. Vesicular rash - Vesicle fluid or swab of ulcer. Recovery is improved when vesicular fluid rather than ulcers are cultured. Submit stool if herpangina or hand-foot-mouth syndrome is present.
2. Aseptic meningitis - Throat swab and stool. CSF culture has low recovery rate except for Enterovirus.
3. Encephalitis - Brain biopsy in addition to "Aseptic meningitis" specimens.
4. Lower Respiratory Tract infection and Croup - Swab, aspirate or washing of nasopharynx, or lung or throat swab. In pneumonia, lung biopsy.
5. Conjunctivitis - Swab of conjunctiva and/or throat. Submit anticoagulated blood specimen as described below if measles suspected.
6. Non-vesicular rash - Throat swab, stool and/or buffy coat.
7. Myocarditis - Throat swab or stool. Pericardial fluid or biopsy.
8. Viremia (CMV or HSV) - Submit 2 (or 3 if the patient is profoundly neutropenic) purple or green topped tubes of blood. The blood must arrive in the lab before 11:00am.
Direct detection for HSV and VZV are available using specific monoclonal antibodies. FA slides are available for specimen collection from the Virology Section. Results are available by 4pm if the specimen arrives in the laboratory before 1pm.
Molecular diagnostic techniques, like HSV PCR for the diagnosis of herpes encephalitis, may be available for some clinical scenarios. CMV antigenemia is available for monitoring HIV and transplant patients for the early detection of emerging CMV infection.
Appendix I shows specimen types which may be submitted for microbiological testing. The availability of commonly ordered tests for each specimen type is also shown. The laboratory should be alerted for specimen types not listed prior to specimen collection. Specific information concerning some of these specimen types is listed below.
A. Anal Swab
Swabs may be used to collect material from anal crypts. These specimens will be cultured for N.gonorrhoeae only. Swabs contaminated by stool should be discarded and another specimen collected.
B. Tissues/Biopsy
Specimens should be transported in sterile containers. Small samples of tissue may be placed in a small amount of non-bacteriostatic saline (e.g., Ringer’s lactate) to prevent drying. Specimens which have been placed in formalin are unacceptable for culture.
C. Blood
The recommendations, summarized below, are designed to optimize the detection of bacteremia while eliminating unnecessary, excessive cultures.
1. General Issues
a. Specimens other than blood or bone marrow harvests should NOT routinely be inoculated into blood culture media!
b. A routine blood culture set consists of a BacT Alert T-Soy aerobic and a FAN aerobic bottle. The BacT Alert system is a continuous monitoring blood culture system. Note that the septa of these bottles are not sterile and must be thoroughly wiped with alcohol prior to inoculation. Each bottle should be inoculated with 10 ml of blood. When less than 10 ml of blood is available for culture, split the blood evenly between the two bottles. In situations where anaerobic sepsis is likely, an anaerobic T-Soy bottle should also be inoculated.
c. The Isolator 10 blood culture system is available for the detection of fungemia (due to dimorphic molds or yeast other than Candida species) or mycobacteremia. Routine blood culture sets should be drawn and submitted with Isolator tubes. Isolator tubes should be inoculated with no less than 5 ml of blood. Isolators may be cultured for fungal or mycobacterial isolation. Isolator tubes are available from the Microbiology Laboratory.
2. No less than 2 and no more than 3 separate blood culture sets should be drawn in any 24 hour period. The sensitivity of 3 blood cultures in a 24 hour period has been shown to be 99.9% for the detection bacteremia.
3. It may be advantageous to space the blood cultures as far apart as possible during the 24 hour period in patients with intermittant bacteremia (e.g., in patients with sepsis associated with a localized infection or abcess). However, in patients with sepsis and endocarditis, no advantage in spacing blood cultures has been demonstrated. Culture sets should be taken from separate, percutaneous venipuncture sites.
4. Specific recommendations for initial cultures.
a. In suspected sepsis obtain 2 separate culture sets before therapy is started.
b. For subacute endocarditis obtain 3 separate culture sets before therapy.
c. For fever of unknown origin (3 weeks of documented fever without obvious cause identified by initial work-up) obtain 2 separate cultures sets initially followed by another 2 sets the following day just prior to the expected fever spike. The yield from more than 4 cultures is extremely low.
5. Except as noted above for FUO, wait at least 72 hours from the time of the first culture before obtaining additional cultures. This will allow time for detection of bacteremia from initial cultures. Nearly all positive results will be recognized at this time. Very few patients will require blood cultures on 2 successive days, especially if antibiotics have already been administered. If blood cultures are still negative after 72 hours and the clinical condition warrants, draw a maximum of 3 more blood cultures over the next 24 hours.
6. In clinical situations in which fever is present, but the likelihood of bacteremia is low, 2 to 3 culture sets at the onset of the febrile episode or hospital admission are sufficient; repetitive culturing is not necessary or appropriate barring any change in the patient's clinical condition.
D. Bone Marrow
Aspirated Bone Marrow should be injected into a Pediatric Isolator 1.5 (available in the Hematology or Microbiology Lab) after careful sterilization into the depression of the stopper. Limited testing is possible when only small volumes are available. Therefore, when less than 1 ml is aspirated, note your priority for testing on the requisition slip. Culture of bone marrow harvest specimens for reinfusion should be submitted in a blood culture set. For viral culture, use viral transport media.
E. Catheter tips
Catheter tips are appropriate for culture in septic patients without other cause. Peripheral blood cultures should always be submitted simultaneously. Complete identification and sensitivity testing will not be performed on cultures yielding only rare growth unless an unusual pathogen is isolated. Foley catheter tips and drainage tubes are unacceptable for culture.
F. Stool
Rectal swabs for enteric culture will be accepted from neonates only. Salmonella, shigella and campylobacter species are the only pathogens isolated by the routine enteric culture procedure. Please alert the Microbiology Lab if another enteric pathogen, like Yersinia or Vibrio, is suspected. A single stool culture is very sensitive in detecting enteric pathogens in normal patients with acute enteritis. Therefore, only one stool specimen per patient per week will be accepted. In patients with enteric fever, suspected carrier states, or patients who will require therapy (e.g., compromised hosts or patients with severe colitis), more frequent culturing can be arranged through the Microbiology Director. See Sections IV.E. and IV.L. for details of testing stool for C. difficile and O&P, respectively.
G. Sterile fluids (dialysis, joint, pericardial, peritoneal, pleural or spinal fluid)
The following minimum volumes of CSF are required:
Routine culture and Gram stain = 1 ml
Fungal culture = 1 ml
Crypotococcal antigen = 0.5 ml
AFB culture and smear = 3 ml
VDRL = 0.5 ml
If the volume of CSF submitted is inadequate for the tests requested and no priority has been assigned by the requesting physician, the following priority will be assigned: 1) Bacterial culture and Gram stain, 2) Fungal culture, 3) Cryptococcal antigen, 4) AFB culture and smear, 5) VDRL.
For sterile fluids other than CSF, please transport the maximum volume possible (up to 50 ml). Blood cultures should be drawn simultaneously for maximum diagnostic efficacy. Material taken from a chronic collection bag is never appropriate for culture.
H. Throat
Group A streptococcus is the only pathogen routinely identified unless otherwise requested (e.g., R/O diphtheria, R/O GC.)
I. Urine
Urine should normally be collected into a sterile container. Urines are cultured quantitatively and, in general, identification and sensitivity testing is performed only on pathogens in quantities > 104 organisms/ml. Cultures containing 3 or more colonial types in comparable quantities are assumed to be contaminated with genital flora and are not worked-up. If, however, a mixed culture contains a potential pathogen which is in clear predominance, complete identification and sensitivity testing will be performed on that organism, though its significance must be interpreted with caution.
J. Wounds
Whenever possible, tissue or aspirated fluid/pus should be submitted for culture of wounds. The use of swabs for wound culture is discouraged because: 1) swabs sample only the surface of a wound rather than deep infected tissue, 2) they can hold only a small amount of material and 3) they are not optimal for Gram stain. Please indicate the site of the wound and whether it is deep, superficial, surgical, traumatic (e.g., bite), etc.
Specimens which may be submitted for microbiologic testing are listed below. See Sections IV & V for additional information concerning these specimens and test types. Submission of other specimen types must be arranged through the Microbiology Director on call. For each specimen type the appropriate transport conditions and the availability of some commonly ordered tests is also shown.
Bacteriology MYcology AFB Viral
Transport Aerobe Anaerobe Gram Stain Culture Wet Mount Culture Smear
SPECIMEN
ABSCESS SY/ANA + + + + C C C C
ANAL SWAB TM +
BILE SY/ANA + + + + C C C
BIOPSY/TISSUE SC/ANA + + + + C + + +
BLOOD,ROUTINE BOTTLES + + + + + +
BLOOD,ISOLATOR TUBE C C C C
BONE MARROW ISOLATOR 1.5 + + + C +
BRONCH:L,W,B SC + C + + C + + +
CATHETER (IV) SC +
CERVIX TM + + +
EYE TM + C + + C C C +
FOREIGN BODY SC + C + + C C C
SPUTUM SC + + + C + + C
STERILE FLUID SY/ANA + + + + C C C C
STOOL CC + + C C +
THROAT TM + + +
URETHRA TM + + C C +
URINE SC + C + C +
VAGINA TM + + + C +
WOUND TM/ANA + + + + C C C C
+
- ROUTINELY AVAILABLE; C - AVAILABLE ONLY WITH PRIOR APPROVAL BY DIRECTOR ON CALL; "BLANK" - TEST NOT AVAILABLEANA - ANAEROBE TRANSPORT; CC - CLEAN CONTAINER ; SC - STERILE CONTAINER; ST - STERILE TUBE; SY - SYRINGE;
TM - Appropriate TRANSPORT MEDIUM