MICROBIOLOGY

1. The quality of the laboratory result is dependent upon the quality of the specimen and the information given to the laboratory.
    
2. Examination of microbiology cultures is not completed until noon. Significant positive results, e.g. first time positive cultures on blood, body fluid, etc., are called to physicians as soon as the results become available. Please first check the computer for results. If results are not yet available in the computer, please wait until after 12-NOON to call the laboratory.
    
3. Information Required on Requisitions and Specimen Containers:
   1. Patient last name, first name.
   2. Date of Birth (D.O.B.)
   3. Patient medical record # and account
   4. Patient's Diagnosis or Chief Complaint (i.e. FUO OR SBE)
   5. Patient location
   6. The ordering physician and code (Please provide full name of physician.)
   7. The ordering physicians phone # and pager #
   8. Specimen type (culture site and collection time)
   9. The tests required - Tests ordered must be individually marked (a line drawn through multiple tests is not acceptable).
   10. Indicate any special handling required
   11. The date and time of specimen collection
       
         Refer to "Laboratory Specimen Identification Policy" and "Laboratory Test Requisition" under General Information on the
         Clinical Laboratory website for more information.
   12. Call the Microbiology Lab (501-686-6880) for special requests (i.e. cultures for Actinomyces, Nocardia, or Aeromonas in stool, etc.), which must be noted on the special instruction area of the requisition.
   13. If a specimen is directly plated on culture media, the culture plates must be labeled with the patient's name, account number, unit number, culture site, date and time of collection, along with a transmittal or Microbiology Request Form.
   14. Duplicate specimens from the same site on the same patient for the same procedure on the same day will not be routinely processed.  (An exception:  Blood Cultures).  Requests for other exceptions should be directed to the Microbiology Director.
   15. The laboratory will only accept routine stool cultures and ova/parasite examinations on outpatients or on in-patients hospitalized three (3) days or less.
            a.  The laboratory will accept routine stool cultures and ova/parasite examinations on patients hospitalized for more than three (3)
                 days IF the patient is immunocompromised or if there was a failure to order appropriate stool testing during the initial period of
                 hospitalization.
            b.  If there is an unusual situation, and the test needs to be performed, contact the Microbiology Director.
        
4. Collection and Delivery of Specimens (see "Specimen Collection Guidelines"):
   1. Collect enough material for the desired studies. If a two (2) swab culturette will be used for the desired studies, collect specimen on both swabs. Collect a (2) swab culturette for each type of culture desired. (Note: Swabs are generally considered suboptimal specimens due to small amount of material available.)
   2. Place swabs in appropriate transport media (e.g. Anaerobic, etc.); place biopsies, aspirates, or fluids in a sterile container that does not include additives or chemicals and bring to the Clinical Laboratory - ASAP
   3. Collect aspirates or wound discharges with a needle and syringe. Transfer to a sterile container.
      1. Do not use a container that includes additives or chemicals (ex. Clot Activator).
      2. Sterile body fluids can be collected in the blood culture vials.  Ensure there is an appropriate volume of specimen.
      3. Syringes with capped needles will not be processed by laboratory personnel. (NOTE: OSHA publications 29 CFR Part 1910.1030 (e)(2)(ii)(J) PROHIBITS RECAPPING NEEDLES or REMOVING NEEDLE FROM SYRINGE).
   4. Avoid contamination from indigenous flora, whenever possible, to ensure a sample representative of the infectious process. There are many sites of infection where the specimen may contain an etiologic agent whose presence in a healthy host would otherwise be considered normal flora. This normal flora from skin, membranes, and the respiratory tract could interfere with the interpretation of culture results as well as overgrow and obscure the true agent of disease. Specimens to be discouraged due to questionable microbial information include:

      Colostomy discharge
      Foley catheter tip
      Gastric aspirates of newborns
      Lochia
      Vomitus
      
      Instead of swabs, tissue or an aspirate is preferred on the following specimen types:
      
      Burns, Wounds
      Decubitus
      Gangrenous lesions
      Periodontal lesions
      Perirectal lesions
      Surgical specimens
       

   5. Duplicate specimens from the same site on the same patient for the same procedure on the same day will not be routinely processed. (An exception: Blood Cultures). Requests for other exceptions should be directed to Microbiology Director or CP Resident On-Call (501-688-2820).
   6. The laboratory will only accept routine stool cultures and ova/parasite examinations on outpatients or on inpatients hospitalized three (3) days or less. The laboratory will accept routine stool cultures and ova/parasite examinations on patients hospitalized for more than three (3) days if the patient is immunocompromised or if there was a failure to order appropriate stool testing during the initial period of hospitalization.  If there is an unusual situation, and the test needs to be performed, contact the Microbiology Director and/or the CP Resident On-Call (501-688-2820).  Routine stool cultures should be sent to the Microbiology Department in Cary-Blair vials.
   7. All specimens must be delivered to the Clinical Laboratory within one (1) hour of collection for optimal isolation of organisms.

II. BACTERIA CULTURE SPECIFIC GUIDELINES:

A list of specimens with volume and transport requirements can be found at the end of the Micro section.

1. Gram Stain (GS)
   A Gram stain smear is included routinely with most specimens processed. Exceptions include, urine, stool, bone, blood, catheter, surface, gastric aspirate, stem cell harvest, burn/graft quantitative culture and bone marrow harvest. If a Gram stained smear is requested from a specimen not routinely Gram stained or in the event a smear only is desired without culturing the specimen, order appropriately in e-chart or state this in the "Special Instructions" box on the requisition.
   
   
2. Abscess/Wound Bacteria Culture (AWCLT)
   1. Requisition: Mark Abscess/Wound Culture [AW]. Specify the collection site. Some of the more common sites include:

      Abscess             Ear             Pus
      Aspirate             Exudate     Sinus
      Conjunctiva        Eye            Ulcer
      Drainage*          Lesion        Wound
      

      *A drainage is ANY specimen collected through an indwelling tube.

   2. E-Chart: Ordered in the Micro Section.
      1. Select the specimen type
      2. Select the source
      3. Specify the Site of collection
      4. Select Abscess/Wound culture
      5. After the specimen has been collected, status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. Gram Stain is included unless:
      1. specimen in submitted pre-plated
      2. one specimen is submitted for Aerobic and Anaerobic culture (exception: tissues and sterile body fluids)
      3. specimen is submitted from the Morgue (exception: brain)
      4. specimen is submitted from a Medical Examiner Autopsy (exception: brain)
      5. Quantity not sufficient (QNS) for gram-stain and culture.
         
         
3. Anaerobic Bacteria Culture (ANCLT)
   1. All Anaerobic Cultures request must accompany an Aerobic Culture request and additional specimen properly collected in appropriate transport media.
   2. Requisitions: Mark Anaerobic Culture [AN]. Specify the collection site.
   3. E-Chart: Ordered in the Micro Section.
      1. Select the specimen Type
      2. Select the Source
      3. Specify the Site of collection
      4. Select Anaerobic culture
      5. After the specimen has been collected, status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   4. Gram stain is included unless:
      1. specimen is submitted pre-plated
      2. one specimen is submitted for Aerobe and Anaerobic culture (exception: tissues and sterile body fluids)
      3. specimen is submitted from the Morgue (exception: brain)
      4. specimen is submitted from the Medical Examiner Autopsy (exception: brain)
      5. Quantity not sufficient (QNS) for gram-stain and culture.
   5. Collect specimen and IMMEDIATELY place in Anaerobic Transport Media. Do not submit swabs for anaerobic culture except in cases where fluid or biopsy material is absolutely unavailable. Swabs are of significantly less value than aspirates of fluid or pus. Anaerobic Vials for fluid/aspirate transport and Anaerobic Gel Tubes for swab collected specimens are available in the Microbiology Department. Biopsy/Tissue specimens should be collected in a sterile cup or tube with few drops of sterile saline to prevent drying. Anaerobic specimens should be transported to the Clinical Laboratory as quickly as possible. It is essential that the anaerobic collection system be properly used to insure optimal recovery of organisms. Directions for use are on the package for each tube. Additional information or advice on their use may be obtained from a technologist in the Clinical Microbiology laboratory (ext. 501-686-5778).
   6. Specimen Selection - Anaerobic Transport: In general, sites normally colonized with anaerobic flora such as skin, mucous membranes or the environment are unacceptable specimens for anaerobic culture. (For exceptions contact the Microbiology Director or CP Resident On-Call (501-688-2820). Specimens should be hand carried to the Microbiology Laboratory within 30 minutes if they have not been transferred to an anaerobic transport media.
   7. Unacceptable-Anaerobic Specimens: The following specimens are NOT suitable for anaerobic culture and will not be accepted by the laboratory. For any unusual circumstances contact the Microbiology Director or CP Resident On-Call (688-2820). Any specimen contaminated with normal commensal flora of mucocutaneous surfaces, skin or the environment are unacceptable including:

      Bronchoscopy aspirates	Colostomy or ileostomy effluent
      Expectorated sputum	Feces (Exception: Bone Marrow Surveillance Patient)
      Fresh wounds (less than 4 hrs old)	Nasotracheal aspirates
      Saliva	Skin swabs
      Superficial wounds	Throat Swabs (including tonsils)
      Tracheotomy sites (unless abscessed)	Urine (Midstream or Clean Catch)
      Vaginal secretions, endocervical

      NOTE: Actinomyces sp. form part of the normal flora of the oral cavity and may be recovered as normal flora from the respiratory specimens described above. These specimens are unsuitable for culture for Actinomyces sp. and will not generally be acceptable. For unusual clinical situations, contact the Microbiology Director of the CP Resident On-Call (501-688-2820).

   8. Acceptable-Anaerobic Specimens: The following specimens are acceptable for anaerobic culture, and should be collected with care to exclude contamination from adjacent mucosal surfaces:
      

      Abscess	Feces (Bone Marrow Surveillance patients only)
      Aspirates	Suprapubic bladder aspirates
      Blood (see Blood Cultures)	Tissues
      Body Fluids	Transtracheal aspirates
      Endometrial	Wounds

4. Blood Cultures (BCLT)
   1. Requisition: Prepare one Microbiology requisition for each blood culture set to be drawn. Mark Blood Culture [BC]. Specify the site of collection and time drawn.
   2. E-Chart: Ordered in the Micro Section.
      1. Select the Specimen type - Blood
      2. Select the Culture Type
      3. Select the Method of collection
      4. Select the Amount of sets to be drawn
      5. Indicate on both bottles the Site and Time of collection 
      6. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. Collection Procedure:
      1. Locate vein to be used, remove the chlora prep ampule from the kit and break the ampule to release the chlora prep. Rub vigorously for 30 seconds, allow to air dry.
      2. Next, swab site with tincture of iodine. Swab concentrically starting at the center and working outwards. Allow iodine to dry.
      3. Remove plastic guards and disinfect tops of bottles with chlora prep. Each blood culture consists of TWO bottles - one aerobic (blue top) and one anaerobic (purple top).
      4. Collect a full 20 ml of blood
      5. Place 10 ml of blood into each bottle, starting with the aerobic (blue top) bottle. Immediately after collection, mix bottles well to avoid clotting.
      6. Any blood on the outside of the blood culture bottles must be cleaned off. Contaminated containers are a Serious Health Hazard and subject to rejection by the lab.
      7. Label the bottle, including the time the blood was drawn and the site from which it was drawn (Right arm, art line, CVL line, etc). Blood for culture should generally not be drawn through an intravenous or interarterial catheter unless it cannot be obtained by venipuncture.
   4. Specific recommendations are outlined below for obtaining blood cultures.
      1. In suspected acute sepsis, meningitis, osteomyelitis, arthritis, or acute untreated bacterial pneumonia, obtain two blood cultures (from two separate venipuncture sites) before starting therapy.
      2. For fever of unknown origin - FUO (e.g., occult abscess, typhoid fever, or brucellosis), obtain two (2) separate blood cultures initially; and then 24 to 36 hours later, obtain two more just before the expected (usually afternoon) temperature elevation. The yield beyond four (4) cultures is virtually nil.
      3. For suspected infective endocarditis:
         1. Acute - Obtain three blood cultures with three separate venipunctures during the first 1 to 2 hours of evaluation, and begin therapy.
         2. Sub-acute - Obtain three blood cultures in 1 day (ideally 15 minutes or more) apart. If all are negative 24 hours later, obtain three (3) more.
      4. For AFB BLOOD CULTURES for Histoplasma, obtain special (Isolator) tube from Omnicell Lab. Requires 10 ml of blood. See Mycology or Mycobacteriology sections.
   5. Results of first time positive blood cultures, when apparent, will be telephoned to the physician/nurse caring for the patient on the day the culture turns positive. Thereafter results will be issued through the computer reporting system. Any questions may be directed to the Microbiology Lab (ext. 501-686-5778).
   6. Blood cultures are routinely checked for 5 days. If an unusual isolate (e.g., Brucella sp.) is suspected, please notify the laboratory BEFORE drawing cultures (686-5778). Special request blood cultures are held longer than 5 days.
      
      
5. Body Fluid Bacteria Culture - Sterile Body Fluids (BFCLT)
   1. Requisition: Mark Body Fluid Culture [BF]. Specify the collection site. Some of the more common sites include:

      Amniotic	Dialysate*	Peritoneal
      Ascities	Hematoma	Pleural
      Bile (Gall Bladder)	Joint Fluid Aspirate	Seroma
      Bone Marrow Aspirate	Lymphocele	Synovial
      Bone Marrow Core	Paracentesis	Thoracentesis
      CSF (Tube #2)	Pericardial	Vitreous

      *If Dialysate or any body fluid is collected in Blood Culture bottles, order as a Blood Culture request. If Dialysate is collected in a sterile, no-additive tube, order as a Body Fluid Culture.  If specimen is collected in a blood culture bottle, also provide a separate specimen for gram stain in a sterile tube/container.
       

   2. E-Chart: Ordered in the Micro Section
      1. Select Body Fluids
      2. Select the Source
      3. Specify the Site of collection
      4. Select Body Fluid culture
      5. After the specimen has been collected, status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. Gram stain is included unless:
      1. specimen is submitted pre-plated
      2. one specimen is submitted for Aerobe and Anaerobic culture (ex. tissues and sterile body fluids)
      3. specimen is submitted from the Morgue
      4. specimen is submitted from the Medical Examiner Autopsy (MEA)
      5. Quantity not sufficient (QNS) for gram-stain
         
         
6. GC Culture Only (GCCLT)
   SPECIMENS: Genital tract, rectal, throat. A "GC" culture is a screen for the presence or absence of Neisseria gonorrhoeae from specimens of the genital tract, rectal area, or respiratory tract (e.g. throat) where contamination with commensal flora is usually found. If N. gonorrhoeae is suspected from other sites (e.g. joint, eye, blood) a routine culture is more suitable for the optimal recovery of the organism.

   1. Requisition: Mark Gonorrhoeae (GC) culture. Indicate the site (e.g. endo-cervical, urethral, etc.).

   2. E-Chart: Ordered in the Micro Section.
      1. Select appropriate gender under Urogenital
      2. Select the Source
      3. Specify the Site of collection
      4. Select GC culture
      5. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. N. gonorrhoeae is a fragile organism, transfer specimens to the lab immediately.
   4. No Gram Stain performed.
      
      
7. Genital Tract Culture: (GNCLT)
   A routine genital tract culture includes a screen for Neisseria gonorrhoeae as well as other bacterial pathogens. Gram Stain is included.
   1. Requisition: Mark Genital Culture [GEN]. Specify the collection site. Some of the more common selections:

      Bartholin gland/cyst	Inguinal	Semen
      Cervical	IUD	Urethral
      Cul-de-Sac	Labia	Uterine
      Endometrial	Lochia - NOT PROCESSED	Vagina
      Fetus	Placenta	Vulva

   2. E-Chart: Ordered in the Micro Section.
      1. Select appropriate gender under Urogenital
      2. Select the Source
      3. Specify the Site of collection
      4. Select Genital culture
      5. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. N. gonorrhoeae is a fragile organism, transfer specimens to the lab immediately.
      
      
8. Gastrointestinal Tract Culture (ITCLT)
   Intestinal Tract specimens are routinely cultured for Salmonella species, Shigella species and Campylobacter jejuni.
   1. Requisition: Mark Stool/Intestinal Tract Culture [ITC]. Specify the specimen type. Here are some of the more common specimens:

      Colon	Gastric Aspirate (Adult)	Sigmoid Aspirate
      Colostomy	Ileostomy Stool	Stool
      Duodenal Aspirate	Rectal Swab - SPECIAL CASE

   2. E-Chart: Ordered in the Micro Section.
      1. Select Gastrointestinal
      2. Select the Source
      3. Select "Other Cultures"
      4. Select the appropriate culture
      5. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. This test is not performed on patients in-house >3 days, unless the patient is immunocompromised.
   4. Cultures for Yersinia enterocolitica and Vibrio species are performed only on specific requests. Choose "Yersinia Culture" when ordering in E-Chart. Yersinia Culture includes a routine Intestinal Tract Culture. Turnaround time is 3 days.
   5. Upon special request, the laboratory will also culture for Plesiomonas or Aeromonas.
   6. Upon request, specimens will be sent to a reference laboratory for detection of E. coli "shiga like toxin."
      
      
      
9. Clostridium Difficile Toxin (CDIF)
   Enzyme ImmunoAssay for the detection of Clostridium difficile toxin A or B in human stool. Turnaround time < 24 hours.
   1. Requisition: Write "C. difficile" in the Special Instructions box.
   2. E-Chart: Ordered in the Micro Section.
      1. Select Gastrointestinal
      2. Select the Source
      3. Select C. difficile
      4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. Performed for detection of C. difficile toxin A or B only on  loose or watery stool.
      
      
10. Respiratory Culture (RSCLT)
    Bacteria culture performed on specimens from the Respiratory tract. Includes a Gram Stain.
    1. Requisition: Mark Respiratory Culture [RES]. Specify the specimen type. Some of the more common specimens:

       Bronchial Brush	Nose
       Bronchial Wash	Nasopharyngeal
       Bronchoalveolar Lavage (BAL) -   (see Bronchoalveolar lavage/brush    culture for these specimens)	Sputum
       Endotracheal Tubing	Tracheal
       Lung Aspirate	Tracheal Aspirate
       Mouth for Thrush	Transtracheal Aspirate

    2. E-Chart: Ordered in the Micro Section.
       1. Select Respiratory
       2. Select the Source
       3. Select Respiratory culture or appropriate culture
       4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
    3. Nose swabs are ordered as "Nose/Throat Culture" after selecting the source. This culture request is a screen for Staphylococcus aureus.
    4. Throat swabs are ordered as "Nose/Throat Culture". This culture request is a screen for Group A Strep. The Group A Strep Antigen detection is available only to patients in the ER or Outpatient clinics.
       
       
11. Urine Culture (URCLT)
    Specimens collected for Urine Culture are divided into two categories based upon the collection method: Routine or Special.  They are sent to the laboratory in a: BD urine C & S preservative plus plastic tube (gray top, yellow label).

    1. Urine Culture: Routine

       1. Requisition: Mark Urine Culture[UC]. Specify the method of collection. If a patient is a transplant patient, please be sure that is indicated on the requisition. Here are some of the more common routine collection methods:
          Clean Catch
          Catheterized
          Nephrostomy
          
       2. E-Chart: Ordered in the Micro Section.
          1. Select Urine
          2. Select the Method of collection
          3. Select Urine culture
          4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to tha Clinical Lab.
    2. Urine Culture: Special  - Special Urine Cultures are reserved for specimens collected with a sterile method or an invasive procedure. Special urine cultures include a Gram stain.
       1. Requisition: Mark Urine Culture [UC]. Specify the method of collection. These are the following specimens for special urine culture:
           

          Bladder Tap	Kidney
          Bladder Wash	Suprapubic Aspirate
          Cytoscopic	Ureter

       2. E-Chart: Ordered in the Micro Section.
          1. Select Urine
          2. Select the Method of collection
          3. Select Urine culture - Special
          4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
    3. All urinary tract specimens should be processed within 2 hours. Specimens should be refrigerated if transportation will be delayed.
       
       

III.     SUSCEPTIBILITY TESTING

1. Aerobic Organisms:
   1. Results are reported as S (susceptible), I (intermediate), or R (resistant) based upon achievable blood levels. MIC (Minimum Inhibitory Concentration) value are also reported depending on the procedural method. The MIC values are reported in ug/ml..
   2. Interpretations: The interpretive reporting terms are based upon blood levels which are achieved with the usual recommended drug dosage, and are not based upon antibiotic levels which may be reached in urine or other body fluids.
   3. Note: Susceptibility results for certain specific antibiotics denote susceptibility to antibiotics of the same class.
   4. Enterococcal Susceptibility Testing: Enterococci cannot be tested for antimicrobial susceptibilities in the same manner in which we normally test other bacteria.
      1. Enterococcal urinary tract infections typically respond to penicillin, ampicillin or vancomycin. (Special high level aminoglycoside testing is only performed on sources other than sterile body fluids when cleared through the Microbiology Director or Pathology Resident (501-688-2820).
      2. Serious enterococcal infections (isolates from normally sterile body fluids) may require penicillin, ampicillin, or vancomycin in combination with a high-level aminoglycoside. The laboratory tests for resistance to penicillin, ampicillin, and vancomycin as well as to gentamicin and streptomycin on isolates from normally sterile body fluids. If there is resistance to gentamicin sometimes the organism will not be resistant to streptomycin. If resistance to both drugs is present, then the organism will be resistant to all synergistic combinations containing currently available aminoglycosides. Please consult with the Infectious Disease department.
   5. Beta Lactamase Testing: will be performed on the following organisms isolated from sterile body sites or organisms which are predominant in respiratory specimens:

      Haemophilus species
      Neisseria gonorrhea
      Neisseria meningitidis
      Moraxella catarrhalis

      These organisms will not routinely have other antibiotic sensitivities performed in this lab. If this is clinically indicated, please call Microbiology (501-686-5778) to arrange for these tests to be sent to a reference lab.
       

2. Anaerobes: Antimicrobial susceptibility testing is routinely not performed. Organisms are sent to a reference laboratory to obtain MIC values, and results are reported in µg/ml
    

IV.     ANTIGEN/ANTIBODY DETECTION

1. Cryptococcal Antigen (CRYP)
   SPECIMENS: CSF, Serum
   1. Requisition: Mark Cryptococcus [CRYP] in Antigen Detection section
   2. E-Chart: Ordered in the Micro Section
      1. Select CSF or Body Fluids for Serum
      2. Select the Method of collection if requested
      3. Select Cryptococcal Antigen
      4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
   3. Can be ordered without a Fungal Culture.
   4. Requires 0.5 - 1 ml specimen.
   5. All first time positives are reported by phone to requesting physician.
   6. Tube titer automatically performed on first positive screens. Known positive patients are titered only if >7 days since the last titer; or unless as requested by Physician.
       
2. 1. Group A Strep Throat Screen
      SPECIMEN: Throat, Pharynx: Only performed on Clinic and ER patients.
      1. Requisition: Mark Group A Strep - Throat [STRA] in the Antigen Detection Section.
      2. E-Chart: Ordered in Micro Section.
         1. Select Respiratory
         2. Select Throat
         3. Select Strep-A Antigen
         4. After the specimen has been collected, status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
      3. Requires throat swab specimens. (NO GEL)
      4. All positives are reported by phone to the requesting physician.
      5. All negative screens are confirmed by a culture.

V.     MYCOBACTERIOLOGY (AFB) CULTURE  (AFCLT)

1. Ordering:
   1. Requisition: Mark Acid Fast Bacilli [AFB]. Specify the specimen type.
   2. E-Chart: Ordered in the Micro Section.
      1. Select the specimen type
      2. Select the Source
      3. Select AFB Culture
      4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place your name, unit, date and time on the transmittal and send with the specimen to the Clinical Lab.
2. Specimen Collection Notes:
   1. Sputum - Three to five specimens collected on separate days, will be accepted for AFB culture. First morning sputums are preferred. (5 ml minimum).
   2. Swabs - Swabs are inferior specimens for AFB culture and will be rejected.
   3. Atypical Mycobacteria - These specimens require special handling and procedures. Please consult Microbiology BEFORE sending the specimen.
3. AFB Smears: All specimens (Except blood, bone marrow cores, stem cell harvest and bone marrow harvest, will be examined microscopically by the fluorochrome acid-fast technique. All first time positive smear results will be confirmed by Kinyoun technique and, promptly reported by telephone to the requesting physician. Any STAT requests for AFB smears will be made and stained by the Kinyoun technique. When the specimen is routinely processed and concentrated for culture, a smear of the concentrated specimen will be stained by the fluorochrome method which is more sensitive for AFB organisms.
4. AFB Cultures: Cultures are incubated for 6 weeks.
   1. Results: Preliminary reports are issued after 1 week incubation. Final results are issued after 6 weeks.
   2. Positives: First time positives are telephoned to the requesting physicians. Positives are sent to the Arkansas Department of Health and Human Services, Division of Health (ADHHSDOH) for identification and susceptibilities when warranted. Physicians are notified by telephone when the identification has been determined.
5. Susceptibility Testing: Susceptibility testing is routinely performed on M.tuberculosis. Cultures positive for mycobacteria other than M. tuberculosis will be tested for sensitivity to antituberculous drugs when appropriate and at the physician's request. The susceptibility for AFB other than MTB is sent to a reference lab.

VI.     MYCOLOGY (FUNGUS) CULTURE (FNCLT)

1. Ordering:
   1. Requisition: Mark Fungus Culture [FUN]. Specify the specimen type.
   2. E-Chart: Ordered in the Micro Section.
      1. Select the Specimen type
      2. Select the Source
      3. Select Fungal Culture
      4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place label and your name, unit, date and time on the transmittal and send with the labeled specimen to the Clinical Lab.
2. Specimen Collection Notes:
   1. Sputum - Three to five specimens, collected on separate days, will be accepted for Fungal culture. First morning sputum is preferred.
   2. Swabs - Swabs are inferior specimens for Fungal culture and will be rejected.
3. Significant Fungi and aerobic actinomycetes recovered in the Bacteriology Lab can be referred to the Mycology Laboratory for identification. This requires submission of new orders by Requisition or E-Chart or it will not be processed.
4. Microscopic Examination: A potassium hydroxide (KOH) preparation is made for all specimens, except CSF, bone, stem cell harvest/transplant, and bone marrow harvest/transplant. All significant positive smear results will be reported by phone to the requesting physician. The latex agglutination test for the detection of cryptococcal polysaccharide antigen has replaced the india ink procedure. All CSF samples sent for fungus culture will, routinely be tested for cryptococcal antigen.
5. Fungal Culture: Fungal cultures are incubated for 4 weeks.
   1. Results: Preliminary reports are issued after 1 week incubation, and final result at 4 weeks.
   2. Positives: First time positives are telephoned to the requesting physicians. Physicians are notified by telephone with clinically significant results.
6. Silver Stain: Used to look for the presence of Pneumocystis sp. in Respiratory specimens.
   1. Requisition: Write "Silver Stain" in Special Instructions section.
   2. E-Chart: Ordered in the Micro Section.
      1. Select the Specimen type
      2. Select the Source
      3. Select Silver Stain
      4. After the specimen has been collected, Status the order in E-Chart as "Collected". Place label and your name, unit, date and time on the transmittal and send with the labeled specimen to the Clinical Lab.
7. Antifungal Serum and Fluid Level Determinations: Amphotericin B, 5-fluorocytosine, miconazole and ketoconazole level determinations are available through reference lab.
8. Antifungal Susceptibility Determinations: Fungal susceptibility determinations to amphotericin B, 5-fluorocytosine, miconazole, and ketoconazole are available through referral labs. These are not routine procedures and must be requested through Microbiology lab.

VII.     PARASITOLOGY SECTION

1. All Parasitology exams are performed by Reference Labs except blood parasites. See special instructions on collection of blood for parasites.
2. The laboratory only accepts requests for fecal examination for ova and parasites on outpatients or patients hospitalized for three (3) days or less. If there is an unusual situation and the tests need to be performed, contact the Microbiology Director or the CP Resident On-Call (501-688-2820).
3. Only one stool specimen will be accepted for each patient per day. Three specimens collected over a week is optimal.
4. Fecal specimens should be at least 50 gms (walnut sized) if solid, 20 ml feces if fluid.
5. No swabs will be accepted for examination.
6. Stools/duodenal aspirates should be submitted to the laboratory as soon as possible after collection. Soft or liquid stools must be received in the Microbiology Laboratory within one (1) hour of passage. There is no delivery time limit for stool specimens submitted in Formalin/PVA transport media (available in Micro 501-688-5778).
7. Specimens should be in Formalin/PVA transport media. Only natural or saline purged specimens will be accepted. Stool specimens should not be collected following the administration of barium, bismuth, or oil.
8. Outpatients should submit specimens in Formalin/PVA transport vials containing preservatives. These containers are available from the Microbiology Department (501-686-5778).
9. The following summary is a guide to the types of specimens which may be helpful in specific situations:

SUMMARY GUIDE - PARASITOLOGY

Routine exam for Ova and Parasites	Eggs of roundworms, tapeworms, and flukes and trophozoites and cysts of protozoans. Normally passed specimen Submit specimen x3 (1 per day).
Ameobiasis	Loose, watery, mucoid or blood stools for Entamoeba histolytica require immediate examination. Promptness is important because amoeba trophozoites lose motility progressively and degenerate within a short time. no specimen older than 2 hours will be examined for amoeba. Submit specimen x3 (1 per day). Examination from liver abscess requires material from margin of abscess. Please notify the CP Resident On-Call (501-688-2820) prior to collection. Submit to laboratory immediately. Serology test available through a reference lab. Please call CP Resident (501-688-2820).
Cryptosporidium exam	Submit stool for examination. Send to the laboratory immediately and indicate Cryptosporidium examination on requisition. This is a special procedure that can be ordered by itself or in addition to a routine exam for ova and parasites.
Duodenal aspirate	For giardiasis or strongyloidiasis Send to the laboratory immediately. Prior notification required.
Sigmoidoscopic material	Collect in tube with moist applicator stick or pipette. Add drop of saline to prevent desiccation. Submit to laboratory immediately. Swabs are not acceptable.
Schistosomiasis	Contact Microbiology Director or CP Resident On-Call (501-688-2820).
Pinworm	Submit sticky paddle or scotch tape prep (clear tape only) connected first thing in the morning, before urination or defecation. Do not submit fecal specimen.
Trichomonas vaginalis	Collect vaginal secretions with swab: place swab in 2-3 ml saline. Keep specimen at room temperature and deliver to laboratory immediately.
Malaria or Haemoflagellates	Draw blood in purple top tube; send to the laboratory within 30 minutes. Must obtain pathology approval BEFORE collection. Pathology must be provided with patient history. Pathology Resident (501-688-2820).
Pneumocytstis carinii	Bronchoalveolar lavage. Sputum accepted from AIDS patients or immunosuppressed patients - BONE MARROW
Leishmaniasis	Consult Clinical Pathology Resident (501-688-2820).
Echinococcosis	Cyst fluid for examination. Consultation required with CP Resident (501-688-2820).
Worm Identification	Submit entire specimen - roundworms, tapeworms, proglottids, etc.
Ectoparasites	Submit suspected lice, mites, ticks in small vial for identification.

 

IX.     SPECIAL REQUESTS

Tests or procedures not routinely performed. In most cases, prior notification is required to prepare or obtain media for the request. (Micro 501-686-5778). All special request should be specified on the requisition or transmittal.

Acanthamoeba Culture	Performed on CSF, tissue and corneal scrapings. Transport: CSF-sterile container, tissue/scrapings-Page's amoeba saline. The laboratory must receive 24 hour notice before collection. Do not freeze. Do not refrigerate
Actinomyces	Add routine Anaerobic Culture for specimen
Bartonella	Should be received in isolator tube. Held for 2 weeks
Bordetella	Physician must notify Clinical Microbiology Lab before specimen collection so that appropriate transport media (Casamino Acid broth) can be obtained from Children's Hospital. Specimen is collected at bedside: 1 smear (for DFA) swabs put in Casamino Acid (for culture) NOTE: After collection, specimen must be delivered to Clinical Lab and sent to a reference laboratory (ARUP) WITHIN 2 HOURS.
Brucella	Should be received in Blood Culture bottles. Held for 4 weeks.
Chanchroid	(Haemophilus ducreyii)
Chlamydia	Chlamydia cultures are performed at ACH. Transport media and requisitions are available through Receiving. Specimen must be put on ice immediately after collection and sent to the lab. Additional information is available from Central Processing. Chlamydia by PCR is done in the Molecular Diagnostics Lab (501-526-6439).
Diptheria	Requires prior notification to ADHHSDOH. Throat and nasopharyngeal swab specimens in transport media. Specimen sent to ADHHSDOH Microbiology.
Ehrlichia	(Leukocytic rickettsiae) Central Processing sends serum to Arkansas Health Department for serology testing.
Gardnerella vaginalis	A presumptive identification of G. vaginalis can be made based on the typical cell morphology on the gram stain. The presence of clue cells (vaginal epithelial cells covered by small gram negative rods) correlates well with the diagnosis of bacterial vaginosis caused by G. vaginalis. G. vaginalis culture requires special media - HBT agar (human blood) not available at UAMS. If deemed clinically necessary, culture must be sent to ARUP Laboratories.
Giardia Antigen	This alternative to the routine ova/parasite exam is available at Arkansas Children's Hospital. The test is performed Monday, Wednesday, and Friday on the day shift. Stool specimens in 10% formalin are stable at room temperature, but stool specimens on swabs (100 µl minimum specimen) must be kept at 2-8oC until Central Processing can arrange transportation to ACH.
Helicobactor	(H. pylori) Requires a gastric biopsy specimen <1 hour old delivered to the lab. If Warthin-Starry silver stain is requested, send to Histology.
Legionella	Performed on specimens less than 2 hours old. Legionella Culture performed in house.  Legionella Antigen, Urine only, performed in house.
Malaria	Requires Pre-Approval by CP Resident (501-688-2820). Performed on blood in an EDTA tube (purple top).
Malassezia furfur	M. furfur can be isolated from skin scrapings or other specimens using routine Fungus culture specifying your request.
Microsporidia	Requires 10 ml of refrigerated stool. Formalin fixed and sent to Mayo Clinic.
MOTT (Mycobacteria other than tuberculosis)	Acceptable specimens:  blood in ACD tube, CSF, sputum, tissue-no formalin.  Specimens must be kept refrigerated (4°C).  Needs a VA requisition.  Send out to VA.
Mycoplasma	Mycoplasma hominis cultures are performed by a Reference Laboratory. Special transport media, requisitions and additional information are available from Central Processing.
QHIV by PCR	Obtain a Plasma Preparation Tube [PPT] pearl top. Collect 5 ml blood. needs to be sent to the lab with a VA requisition within 2 hours. Sent to the VA. Request is handled by CP.
TB by PCR	Acceptable specimens include: CSF, sputum, tissue (no formalin). Specimens must be kept refrigerated (4ºC). Needs a VA requisition. Send out to the VA.
Viral Cultures	Viral cultures are performed at ACH. Special transport media (blue cap bullet tube with pink media) and requisitions are available through Central Processing. Specimens must be placed on ice. Additional information is available from Reference personnel.
Yersinia	Order a routine Yersinia Culture and specify your request.
Ureaplasma	Ureaplama urealyticum cultures are performed by a ARUP Laboratory. Special transport media and requisitions and additional information are available from Central Processing.

 

X.     SPECIMEN COLLECTION GUIDELINES BY SPECIMEN TYPE OR SITE

The following is a list of common specimens with the recommended method of collection and transport. If there are any questions, contact the Microbiology Laboratory (501)-686-5778.

NOTE: Swabs are generally considered supoptimal specimens due to small amount of material available. Submit one swab transport for EACH culture type requested.

NOTE: DISPOSE OF NEEDLE AND SYRINGE PROPERLY PRIOR TO DISPATCH TO LAB.

Specimen Type or Site	Volume or Method of Collection	Container or Transport
Abscess Bacteria, Fungal, AFB	1-5 ml aspirate swab 1-5 ml aspirate	Sterile No-Additive tube Culturette transport medium Sterile No-Additive tube
Autopsy - see Biopsy
Biopsy (not in Formalin)	1-2 gm of tissue - optimal	Sterile, screw-capped container with a few drops of sterile saline to keep it moist
Blood Bacteria (1 culture=1 set) Adult Peds/short draw Fungal AFB	10 ml 10 ml 1-3 ml 8 ml 10 ml - Adult 1.5 ml - Infant 10 ml	Aerobe (Silver Top Bottle) Anaerobe (Purple Top Bottle) Aerobe (Blue Top Bottle) Isolator Tube (obtain from CSS) Isolator Tube (obtain from CSS) (can combine with Fungal request)
Body Fluids (Sterile Body Fluids): Joint, Pericardial, Peritoneal, Pleural, Vitreous, etc. Bacteria Fungal, AFB	5 ml - optimal 1 ml minimum	Sterile No-Additive tube Sterile No-Additive tube
Bone Marrow Aspirate (Obtain SPS Tube from Bone Marrow tech in Hematology Lab) Bacteria, Fungal, AFB	0.5 ml	Special SPS tube
Bronchial Brush without sheath, in sterile tube with 1 ml saline. (obtain from Microbiology)
Bronchial Washing Bacteria, Fungal, AFB	1 - 5 ml	Sterile container
Bronchoalveolar Lavage (BAL) - Bacterial; AFB, FUN	15 ml - minimum	Sterile container
Cervix Bacteria, Fungal, AFB	Swab	Transport medium
CSF (Spinal Fluid) Bacteria Fungal (includes Cryptococcal Antigen) AFB	0.5 ml minimum 2 ml minimum 1 ml minimum	Sterile No-Additive tube Sterile No-Additive tube Sterile No-Additive tube
Cyst Fluid Bacteria, Fungal, AFB	1-5 ml aspirate optimal, Swab	Sterile tube. Transport medium
Dialysis Fluid Bacteria	1 ml minimum for gram stain 10 ml per blood culture bottle	Sterile No-Additive tube. 1 aerobic (silver top) and  1 anaerobic (purple top)
Ear Bacteria, Fungal, AFB	Swab	Transport medium
Exudate (pus) Bacteria, Fungal, AFB Fungal, AFB	Aspirate optimal - Swab Aspirate, tissue, bone, pus, aspirated fluid	Sterile No-Additive Transport medium
Eye Bacteria, Fungal, AFB	Swab, ocular specimen	Transport medium
Gonococci Only	Swab Inoculate MTM at bedside	Transport medium Plate to Micro Lab ASAP
Hair	Hair shaft and base	Dry, sterile container
Nail	Nail shavings and debris	Dry, sterile container
Pus	See Exudate
Skin Scrapings	Edge of lesion	Dry, sterile container
Sinus Bacteria, Fungal, AFB Fungal, AFB	Aspirate optimal - Swab Aspirate, tissue, pus, bone	Sterile tube. Transport medium
Spinal Fluid - See CSF
Sputum: Three to five specimens, collected on separate days, will be accepted for culture (preferably first morning sputum). Additional specimens submitted after bronchoscopy or after therapy is initiated will be accepted Bacteria, Fungal AFB	5 ml 5 ml - minimum	Sterile screw-capped Sterile screw-capped
Stool Bacteria [ITC]   Ova & Parasite C. difficile toxin FWBC, Occult, Fecal Fat	10 gm - minimum If delivery will be delayed   10 gm - minimum If Delivery will be delayed 10 gm - minimum 10 gm - minimum	Container with sterile, leak-proof lid. Deliver to lab within 1 hour Cary Blair Transport (Not suitable if looking for Yeast) Container with sterile, leak-proof lid. Deliver to lab within 1 hour Formalin/PVA Vials Container with sterile, leak-proof lid. Deliver to lab within 1 hour Container with sterile, leak-proof lid. Deliver to lab within 1 hour
Throat Bacteria, Fungal	Swab	Transport medium
Tissue - See Biopsy
Tracheal Aspirate Bacteria, Fungal, AFB	5 ml - minimum	Sterile screw-capped container
Transtracheal	As much as possible	Sterile tube or container. Deliver to lab immediately
Ulcer Bacteria, Fungal, AFB Fungal, AFB	Aspirate optimal - Swab Aspirate, pus, tissue	Sterile tube. Transport medium
Urethral cultures Bacteria, Fungal, AFB	Exudate or drainage - Swab	Sterile tube. Transport medium
Urine Bacteria, Fungal	10 ml - minimum	Urine Specific Vacutainer Tube or a sterile screw-capped container
Uterine Cultures Bacteria, Fungal	Exudate or drainage - Swab	BD vacutainer urine C & S Preservative Plus plastic tube
Vaginal Bacteria Fungal	Swab Tissue, pus, aspirate	Transport medium
Wound Bacteria Fungal, AFB	Aspirate optimal - Swab Aspirated fluid, pus, tissue, bone, ocular specimens	Sterile tube. Transport medium

MICROBIOLOGY "CRITICAL VALUE" CALL BACK

1.0    PRINCIPLE

To assure that patient results deemed to be "critical" are phoned to the patient's physician or nurse or CDF (and infection control if applicable) and documented by the technologist.

All critical values are reported and documented in the SOFT/SOFTMIC system.

2.0    PROCEDURE

2.1    Critical Values:

The following tests values are considered CRITICAL and will be phoned to the requesting physician, nurse in charge, or CDF of the patient on the unit when such results are obtained.

• Positive gram stain or culture from a sterile body fluid
• Positive gram stain or culture from a brain abscess
• Positive culture from a corneal ulcer
• Enteric isolates: Shigella sp., Salmonella sp., Campylobacter sp., Yersinia sp., and Vibrio sp..
• Positive blood cultures by gram stain
• Positive gram stain or culture of gram positive branching filaments
• Oxacillin resistant Staph aureus
• Vancomycin resistant Enterococci
• Penicillin resistant Streptococcus pneumoniae
• Positive AFB smear or culture
• Positive KOH or fungal culture
• All positive bacterial antigen tests: Cryptococcal Antigen, Group A
  Streptococcus antigen (From ER and Clinic only), Tularemia antigen titer > 1:160
• Positive Silver Stain smears for pneumocystis, histoplasma, etc.
• Positive Ova and Parasites (including blood parasites)
• Positive culture for Neisseria Gonorrhea from genital culture
• Positive C. difficile
• Positive cultures from Ophthalmology
• Positive bone cultures
• Positive Legionella cultures

2.2 Critical Values to be called to Infection Control Coordinator:

• Oxacillin resistant Staph aureus
• Vancomycin resistant Enterococci
• Gram negative bacilli resistant to all three aminoglycosides (gentamicin,
            tobramycin, and amikacin)
• Enteric isolates: Shigella sp., Salmonella sp, Campylobacter sp.
• Neisseria meningitidis

2.3 STAT Tests:

All tests requisitioned as STAT will be called to the physician or nurse in charge of patient as soon as possible.

2.3.1    STAT smears:

1. Gram Stain
2. KOH
3. AFB (Kinyoun)
4. Pneumocystis
5. Giemsa stains for Malaria

2.4 Documentation:

2.4.1    Day and Evening Shifts:

1. Call results to physician or nurse in charge of patient (and infection control coordinator if applicable).
2. Document in SOFT system

2.4.2   3rd Shift:

1. Call to physician or nurse in charge of patient
2. Document results in "night shift" communication log book

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