Microbiology

The Microbiology Laboratory is located at the Specialty Testing Center.  Services are provided from 0600-0030, seven days a week.  The Laboratory has the following sections:

• Bacteriology
• Mycology
• Parasitology
• Infectious Disease Molecular Testing, additional Molecular services provided by the UC Davis Health Molecular Laboratory

Identification and susceptibility testing are performed on significant isolates following current Laboratory Technical procedures.

An alphabetic and detailed list of specific tests can be found online in our Laboratory Test Directory. Lab Directory includes information such as ordering, collection requirements, result interpretation guidance and expected test turn-around time.

Refer to UC Davis Health Policies and Procedures (P&P) 2025: Collection of Clinical Specimens for Microbiological Examinations)

1. All clinical specimens for microbiological examination must be collected in clean, sterile and properly sealed containers. The outer portion of the container must not be contaminated.

2. All specimens must be enclosed in a zip-lock biohazard plastic bag for transport to the lab.

3. Optimal specimens for anaerobic culture are aseptically obtained fresh pus, fluid or tissue that is rapidly and safely transported to the lab. Direct aspiration of pus or body fluids into a syringe followed by immediate placement into Anaerobic Transport Medium (ATM) vial is recommended. If ATM vial is not available and the syringe is submitted, the needle must be removed, discarded in appropriate sharps container and the syringe capped during transport to provide anaerobic conditions. Submit tissues in an ATM vial. Do not use swabs if fluid or tissue can be obtained. Collect enough material for the desired studies.

4. Only swabs submitted in their self-contained transport tube will be accepted.

5. If the container or specimen is inappropriate in any way, a new specimen will be requested by telephone or electronic report. A specimen may be rejected for any of the following reasons:

   1. Specimen mislabeled or unlabeled
   2. Specimen type/source inappropriate for test requested
   3. Specimen collected in inappropriate collection container for test
   4. Specimen container leaking
   5. Specimen improperly handled (temperature requirement)
   6. Specimen exceeds holding time (during transport greater than 12-hour transportation delay on genital specimen collection to receipt in lab for testing)
   7. Duplicate specimens
   8. Quantity insufficient for analysis
   9. Specimen container grossly contaminated on outside
   10. Specimen, other than feces, submitted in nonsterile container
   11. Specimen too old for requested test
   12. Urine bacterial culture specimen greater than 4 mL not submitted in a urine transport tube (Exception: urine from pediatric ED patients is acceptable if submitted on ice)

For specific test information, refer to the Laboratory Test Directory:

                        https://www.testmenu.com/ucdavis

TRANSPORT SWAB, GENERAL USAGE

1. Follow manufacturer guidelines for the collection and use of the swab.

BLOOD CULTURES

1. Patient preparation and collection: refer to UC Davis Medical Center Patient Care Standard (PCS) 13015, Drawing Blood Cultures for complete instructions.
2. Number, time of collection, type of culture and special cases:
   1. Routine adult blood cultures: In most cases when bacteremia is suspected including sepsis or acute septic shock, collect 2-3 blood culture sets (from separate venipuncture sites, two bottles each) immediately before starting antibiotic therapy. It is not necessary or beneficial to separate or delay blood culture collections temporally in such patients.
   2. Special case, suspected classical sub-acute bacterial, endocarditis, chronic febrile illness: In select cases, it may be diagnostically beneficial to space blood culture collections over time. At a minimum, 2 complete blood cultures should be collected within the first 1-2 hours of evaluation with collection of no more than 2 additional cultures within a 24 hour period (limit 4 cultures per 24 hour period); if cultures remain negative 24 hours after collection and clinical suspicion remains, it may be beneficial to obtain 2-3 more sets. This is sufficient in the majority of cases. From patients who have received antimicrobial agents within two weeks prior to admission, obtain two separate blood cultures on each of three successive days.
   3. Special case, pre-existing antimicrobial therapy: Sensitivity of blood cultures is decreased in patients on antimicrobial therapy. For suspected bacteremia in patients already on antimicrobial therapy and, if therapy cannot be suspended for a few days, draw 4-6 cultures within the first 48 hours. Cultures should be preferentially obtained prior to the next dose of antimicrobial agent if the patient is receiving intermittent parenteral therapy.
   4. Special case, fever of unknown origin: For fever of unknown origin (e.g., occult abscess, typhoid fever, or brucellosis), obtain two or three blood cultures initially. Then 24-36 hours later, obtain two more cultures immediately before the expected (usually afternoon) temperature elevation.
   5. Incubation period and organisms detected: Routine blood cultures are continuously monitored and incubated for five days, unless the lab is notified to hold for a longer period. The majority of routine bacteria and yeast are detected. Molds, dimorphic fungi, Legionella, Chlamydia, Mycoplasma and Coxiella are not detected. If Brucellosis, Bartonellosis or Tularemia is suspected, the laboratory should be notified, extended incubation should be requested; additional testing (e.g., serology or Polymerase Chain Reaction [PCR]) and infectious disease consult should be considered. Extended incubation is not necessary for the detection of HACEK (Haemophilus parainfluenzae, Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae) organisms.
   6. Mycobacterial Blood Culture: For suspected Mycobacterial bloodstream infection, collect 7 mL venous blood and submit in a sodium heparin dark green top Vacutainer for Acid-Fast Bacillus (AFB) culture.
   7. Fungal blood cultures: There are limited indications for fungal blood culture and most fungi (yeast) are better detected in routine automated blood cultures or NOT well detected from blood specimen (molds). Suspected Histoplasmosis is the main indication for fungal blood culture. Fungal Blood Cultures can only be ordered by an Infectious Disease physician. Consult with an ID physician is required.  Special “Isolator / lysis-centrifugation” collection tubes are required (available from the Specimen and reporting center [SARC] and the Microbiology laboratory).
   8. Suspected catheter associated bloodstream infection or catheter-related bloodstream infection (CA-BSI or CR-BSI): In general, blood for culture should be collected through peripheral percutaneous venipuncture and not be drawn through an indwelling intravenous or intra-arterial catheter. When blood cannot be obtained by venipuncture or when blood is specifically being drawn to evaluate for potential catheter-related infection, two blood culture sets should be collected: one from the line in question and one via peripheral percutaneous site.
3. Order CULTURE BLOOD, BACTI or when indicated or approved, order CULTURE BLOOD, FUNGAL or CULTURE BLOOD, AFB. Record the site of the blood culture draw on the order as well as the blood culture bottles.

URINE CULTURES

Collect urine specimens by the clean-voided midstream technique, by diagnostic catheterization, by suprapubic aspiration or from an indwelling catheter. The first morning specimen is preferred. Urinary catheter tips are not cultured because the tip is contaminated as it is removed from the urethra. A pooled, 24-hour collection is unacceptable for culture, as is more than one specimen within 24 hours.

1. Preparation and collection:
   1. Indwelling catheter:
      • If necessary, clamp the catheter tubing to collect urine in the tube but do not allow the clamp to remain for more than 30 minutes. Urine obtained from the catheter bag is unacceptable for culture.
      • Clean the sampling port (or tubing site if a port is unavailable) with an alcohol wipe for 15-30 secs and allow to dry for 15-30 secs prior to collection.
      • Use a syringe to enter the sampling port or 21-gauge needle and syringe if a needleless urine sampling port is not available. Withdraw approximately 10 mL of urine.
   2. Clean-voided urine:
      • Clear verbal and/or written instructions must be given to the patient to ensure understanding of the procedure.
      • Gather the following supplies for each patient:
        1. Commercially prepared meatal wipes or soap towelette packages
        2. Rinse water
        3. Wide-mouthed sterile covered container (e.g., screw-cap specimen container)
      • Instruct the female patient to:
        1. Remove undergarments.
        2. Wash hands thoroughly with soap and water, rinse and dry.
        3. Sit comfortably on the toilet and swing one knee to the side as far as possible. With one hand, spread the labia and hold continuously apart during cleaning and specimen collection (urination).
        4. Take a prepared meatal wipe, wash the vulva well, passing only from front to back. Discard the used sponge or wipe.
        5. Repeat the front to back wash, discarding the prepared meatal wipe after each use.
        6. Grasp the collection cup on the outer surface only. Fingers should be kept away from the rim and inner surface of the container. Pass a small amount of urine, 20-25 mL, into the toilet, and then move the cup into the urine stream while urinating. Collect at least 15-20 mL or fill the cup half full.
        7. Void remaining urine into the toilet. Securely close the cap.
      • Instruct the male patient to:
        1. Wash hands thoroughly with soap and water, rinse and dry.
        2. Completely retract the foreskin (if uncircumcised) and cleanse the glans penis using packaged meatal wipes. Repeat cleansing the glans penis. Discard each item after use.
        3. Grasp the collection cup on the outer surface only. Fingers should be kept away from the rim and inner surface of the container. Pass a small amount of urine, 20-25 mL into the toilet, and then move the cup into the urine stream while urinating. Collect at least 15-20 mL or fill the cup half full.
        4. Void remaining urine into the toilet. Securely close the cap.
      • For patients unable to cooperate: Attach a plastic bag device after careful skin cleansing and preparation, as above. Check the bag frequently so that the urine specimen can be collected immediately after it is voided. If the patient has not voided within 30 minutes, remove the bag, rescrub the patient and attach a new collection bag. Do not submit urine collected from diapers.
      • For infants: Submit urine specimens collected through a catheter or infant bag.
   3. Immediately after collection, aspirate 4 mL urine from collection cup into the urine culture transport tube, (UTT), ensure that the tube is filled to the fill line. If urinalysis is also desired, fill the separate (bigger) urinalysis tube with approximately 10 mL urine. If the available specimen volume is less than 4 mL, do not place or submit in UTT. Submit the available urine in a sterile container on ice. Urine at or greater than 4 mL not submitted in a urine transport tube will be rejected. Under no circumstances should a urine sample be taken from urinal or bedpan, nor should the specimen be brought from home.
   4. Freshly voided specimens greater than 4 mL from pediatric patients in the Emergency Department will be accepted for culture if they are transported on ice.
2. Ordering: If culture and urinalysis are desired, order URINALYSIS AND CULTURE IF IND. Two separate urine samples must be submitted, one sample submitted in a yellow top Urinalysis tube for the urinalysis and one sample submitted in a gray top Urine Transport Tube (UTT) for the culture. If only culture is desired, order CULTURE URINE, BACTI and submit urine in a gray UTT tube only. Type of collection must be indicated. GRAM STAIN is not routinely performed and must be ordered if desired.
3. Obtaining Urine Culture Specimen from a Catheterized Patient: Refer to Standard Procedure 4 SP4:  Obtaining Urine Culture from a catheterized patient and 9010 Urethral Catheter Insertion, Maintenance, and Removal Policy
4. Transport: Deliver specimens in urine transport tubes (Boric Acid) to the lab at room temperature. Urine samples are stable for up to approximately 24 hours using the urine culture transport tube or if kept refrigerated.

THROAT CULTURES

Routine throat cultures are used to detect Group A Streptococcus and Arcanobacterium haemolyticum as potential causes of pharyngitis. If Neisseria gonorrhoeae is suspected, it must be specifically requested, (CULTURE GC ONLY). If diphtheria is suspected, contact the microbiology laboratory for collection and ordering instructions. Throat cultures are not acceptable for viral respiratory culture.

1. Preparation and collection:
   1. Obtain an appropriate culture swab to use in collecting the specimen.
   2. Using a tongue depressor to hold the tongue down, carefully examine the back of the throat and the tonsillar area for localized areas of inflammation and exudate. Carefully but firmly rub the swab over areas of exudate overlying the tonsils or posterior pharynx. Avoid contacting the palate, uvula, tongue, cheeks or teeth when collecting the specimen or withdrawing the swab.
   3. Place the swab back into the transport tube. Replace cap tightly.
2. Order CULTURE BETA STREP ONLY, or if N. gonorrhoeae is suspected, order CULTURE GC ONLY (gonococcus). If Diphtheria (Corynebacterium diphtheriae) is suspected, contact the Microbiology laboratory for collection and ordering instructions prior to specimen collection. For these cultures, a special culture medium is necessary and must be available Swab of throat exudate or posterior nares may be performed when diphtheria is suspected. For diphtheria, order CULTURE ENT, BACTI and specify disease or organism suspected. Direct specimen stains (Gram or otherwise) are not routinely performed on throat swabs but may be requested when diphtheria, oral candidiasis or ulcerative gingivitis are suspected.
3. Transport swabs at room temperature and deliver to the lab promptly. Specimens for N. gonorrhoeae (GC) must be received within 12 hours of collection due to the fastidious nature of the organism

NASOPHARYNGEAL CULTURES

The primary indication for culture of the nasopharynx is for detection of upper respiratory virus.  Occasionally, nasopharyngeal culture may be performed to diagnose diphtheria or rule out meningococcal carriage. Swabs of the posterior nasopharynx or culture of aspirated nasopharyngeal secretions may be used for this purpose. The disease or organism suspected should be noted, as special culture media are required in each case. Nasal and nasopharyngeal cultures do not predict the etiologic agent of sinus, middle ear or lower respiratory tract infections and should not be submitted to diagnose suspected infections at these sites.

1. Preparation and collection:
   1. For viral culture, obtain viral respiratory collection kit with instructions. For C. diphtheria or N. meningitidis culture, call microbiology for instructions.
   2. Prior to specimen collection, use tissue or gauze to remove excess secretions or exudate from the anterior nares.
   3. Collection is most successful if the patient is lying down. Sitting patients tend to recoil. Remove the swab and gently insert into either nares.
   4. Continue to insert the swab posteriorly until light to moderate resistance is felt. Gently rotate the swab over adjacent nasopharyngeal surfaces for 15-30 seconds.
   5. Withdraw the swab and place it in the transport tube.
   6. For a nasopharyngeal aspirate, attach a sterile suction catheter to a Lukens trap and introduce the end of the catheter into the nasopharynx until mild to moderate resistance is encountered. Withdraw the catheter 1-2 cm and apply suction to aspirate a sample. Cap the trap with aspirated contents.
   7. Nasopharyngeal swabs are tested for respiratory viruses by PCR at the UC Davis Medical Center Molecular laboratory.
2. Order CULTURE ENT, VIRAL. For diphtheria or to detect meningococcal carriage, order CULTURE ENT, BACTI, and specify disease or organism suspected (e.g. meningococcus). Notify the Microbiology lab if Corynebacterium diphtheriae is suspected as a special culture medium is prepared for this request.
3. Transport: Send to the lab at room temperature immediately.

NASAL (ANTERIOR NARES) CULTURES AND MRSA SURVEILLANCE CULTURES

Anterior nares cultures may be submitted for Staphylococcus aureus or MRSA (Methicillin Resistant S. aureus) screening only. Nasal cultures do not predict the etiologic agent of sinus, middle ear or lower respiratory tract infections and should not be submitted to diagnose suspected infections at these sites. Bacteria other than S. aureus are not identified.

1. Preparation and collection:
   1. Obtain a swab. A nasal speculum may be needed for some patients.
   2. Carefully insert the swab at least 1cm into the nares.
   3. Thoroughly sample both anterior nares by rotating the swab across inner surface of one and then the other nostril for 15-30 seconds.
   4. Withdraw the swab and place it in the transport tube.
2. Order CULTURE ENT, BACTI, or CULTURE SURVEILLANCE, MRSA as desired.
3. Transport: Send to the lab at room temperature immediately.

EXPECTORATED SPUTUM

When not contaminated by oropharyngeal surfaces, expectorated sputum provides a surrogate sample of lower respiratory tract secretions. Such specimens may aid in the diagnosis of lower respiratory tract bacterial infection and/or colonization in patients with Cystic Fibrosis. Routine sputum culture specimens (non-Cystic Fibrosis specimens) are microscopically screened by scored direct specimen Gram stain for number of squamous epithelial cells (indication of oropharyngeal contamination) and polymorphonuclear leukocytes (indicating presence of inflammatory response). Specimens demonstrating absence of inflammation or excess epithelial contamination provide misleading results and are rejected as poor quality and unsatisfactory for culture. Careful attention to the instructions greatly reduces the number of unsatisfactory specimens. The first early morning specimen is preferred. Pooled samples are not accepted. In addition to sputum for respiratory culture, blood culture should be considered in patients with suspected moderate to severe bacterial pneumonia. Sputum samples may also be submitted for Mycobacterial (AFB) or Fungal culture but are not acceptable for viral culture.

1. Preparation and collection:
   1. For patients with dentures, remove the dentures first.
   2. Instruct the patient as to the difference between sputum and spit. Sputum should be produced during coughing episode, originate from deep in the lungs and be expectorated as a single bolus into a wide-mouthed sterile container. This should be done under direct supervision, preferably when the patient first awakens in the morning.
   3. Saline nebulization with 10% saline, hydration, chest physiotherapy or postural drainage may be used to facilitate acquiring an adequate specimen from patients with nonproductive coughs. Prior to procedure, brush the buccal mucosa, tongue, and gums with a wet toothbrush for 5-10 minutes then rinse with sterile water or saline.
2. Order CULTURE RESPIRATORY (INCLUDES GS), BACTI or CULTURE CYSTIC FIBROSIS RESP, BACTI as appropriate. Gram stain is not performed on Cystic Fibrosis specimens. In addition, order CULTURE RESPIRATORY, FUNGAL, and/or CULTURE RESPIRATORY, AFB when these agents are suspected.
3. Transport: Carefully and tightly affix the specimen cap. Leaking samples will not be processed. Transport on ice is recommended. Specimens received more than 24 hours after collection will be rejected for culture.

BRONCHOSCOPY, ENDOTRACHEAL and NASOTRACHEAL SPECIMENS

Endotracheal aspirates and bronchoscopic alveolar lavage specimens may be submitted for routine bacterial, fungal, mycobacterial or viral respiratory culture. Bronchial brush specimens may be submitted for bacterial culture only.

1. Preparation and collection:
   1. Collect specimens, in a sterile container, according to protocol. Specimens include brushings (Bartlett protected brush), transbronchial biopsies or bronchial secretions that are aspirated through the inner channel of the bronchoscope with or without an irrigating solution. Refer to PCS 17027 “Non-Bronchoscopic Bronchial Alveolar Lavage (miniBAL)” for additional collection instructions.
2. Order: For bacterial culture of endotracheal aspirate, transtracheal aspirate, or BAL, order CULTURE RESPIRATORY (INCLUDES GS), BACTI. For bacterial culture of bronchial brush specimens, order CULTURE BARTLETT BRUSH CATH. Note: Legionella culture is routinely done on Bartlett brush, bronchoalveolar lavage (BAL) and lung tissue specimens. If fungal or AFB culture is also desired, order CULTURE RESPIRATORY, FUNGAL, CULTURE RESPIRATORY, AFB or CULTURE RESPIRATORY, VIRAL if desired.
3. Transport on ice, is recommended. Add precisely 1 mL sterile saline to the tube containing the Bartlett brush in order to result in accurate quantization.

BODY FLUIDS (ABDOMINAL, AMNIOTIC, ASCITES, BILE, JOINT, PARACENTESIS, PERICARDIAL, PERITONEAL, PLEURAL SYNOVIAL, THORACENTESIS

1. Preparation of patient and collection:
   1. Disinfect overlying skin with chlorhexidine. For patients sensitive to chlorhexidine and neonates, use povidone iodine.
   2. Obtain specimen via percutaneous needle aspiration or surgical procedure.
   3. Aspirate fluids that collect in pericardial, pleural, peritoneal and synovial spaces with the utmost precaution to avoid introducing microorganisms and to avoid contamination of the specimen.
   4. Directly aspirate into a syringe (recommended). Preferably, the specimen (e.g., aspirate) should then be placed in an Anaerobic Transport Media vial (ATM) for transport to the laboratory. Samples submitted in ATM vials are used for both anaerobic and aerobic cultures. Collection steps: Disinfect the rubber septum with an alcohol wipe, wait 15-30 seconds and inject the fluid into the tube at a slow rate. Alternatively, if an ATM is not available, the syringe with the specimen may be submitted but the needle must be removed, discarded into sharps container and the syringe should be capped by screwing a sterile plastic cap into the luer lock on the end of the syringe. If the specimen cannot be aspirated into a syringe (e.g., tissue biopsy), unscrew the cap on an ATM vial, and place the specimen onto the surface of the medium using sterile instruments and technique. Do not push the tissue or specimen into the gel at the bottom of the tube. Immediately recap the ATM vial to minimize oxygen exposure. Do not use ATM vials that have expired (an expiration date is on the vial) or vials with blue coloration of the gel media indicating that the media is no longer anaerobic. Label the specimen appropriately.
   5. Inoculate body fluid specimens (in spontaneous bacterial peritonitis) at the bedside into blood culture bottles. Put 10 mL of fluid into aerobic and anaerobic blood culture bottles (20 mL total). Submit additional fluid in a sterile container, as much as possible, for Gram stain and additional lab processing (e.g., acid-fast bacilli [AFB], fungal cultures). Do not inject body fluids other than ascitic fluid, paracentesis fluid, peritoneal fluid, or peritoneal dialysate into blood culture bottles.
2. Order CULTURE BODY FLUID, BACTI, (anaerobic culture includes aerobic culture and a Gram stain). An anaerobic request should have a STAT sticker placed to flag it for prompt delivery and setup. Anaerobic cultures will not be done on swab specimens, nor are swabs needed as additional specimen for aerobic culture. Order CULTURE BODY FLUID, FUNGAL, CULTURE BODY FLUID, AFB or CULTURE BODY FLUID, VIRAL if desired. Order CULTURE FLUID IN BC BOTTLES and GRAM STAIN together.
3. Transport: To minimize the loss of anaerobic bacteria during transport, all tissue biopsy and sterile body fluids (except CSF and vitreous fluid) submitted for bacterial culture should be placed in Anaerobic Transport Medium immediately after collection. Maintain at room temperature. Specimens submitted in a capped syringe with the needle removed, or in a sterile container will be accepted, but are suboptimal. Transport properly labeled specimens immediately.

SKIN, SOFT TISSUE AND ABSCESS SPECIMENS (WOUND, ABSCESS, BURN WOUND, EXUDATE)

For closed lesions (e.g., abscess, superficial fluid collection), aspirated fluid or pus following sterile skin preparation is the specimen of choice. Swabs should not be used to sample abscesses. For open lesions (e.g., wound, burn), needle aspirate specimens or tissue biopsy specimens are preferred to superficial swab collected samples. In all cases, wound, burn or skin surfaces should be thoroughly decontaminated and if necessary, debrided prior to collection of microbiologic specimens. Failure to remove superficial contaminating/colonizing bacteria prior to specimen collection yields misleading results of culture and inappropriate therapy. Aspirates or biopsies should be obtained from the advancing margin or deep base of lesions. Culture of dry or crusted lesions or culture of superficial draining pus or exudates is not recommended.

1. Preparation and collection:
   1. Closed abscesses or fluid collections: Decontaminate the skin overlying the abscess with chlorhexidine (or povidone-iodine if patient is sensitive to chlorhexidine or patient is neonate) and aspirate the abscess contents with a syringe. Alternatively, after excision and draining, a portion of the abscess wall may be submitted for culture. Aspirates and liquid specimens should be injected into an Anaerobic Transport Media vial (ATM) for transport to the laboratory via the following steps: Disinfect the rubber septum with an alcohol wipe, wait 15-30 seconds and inject the fluid into the tube at a slow rate. Samples submitted in ATM vials are used for both anaerobic and aerobic cultures. Alternatively, if an ATM is not available, the syringe with the specimen may be submitted but the needle must be removed, and the syringe should be capped by screwing a sterile plastic cap into the leur lock on the end of the syringe. Tissue or solid specimens should also be transported in an ATM vial. First, unscrew the cap on an ATM vial and place the specimen onto the surface of the medium using sterile instruments and technique. Do not push the tissue or specimen into the gel at the bottom of the tube. Immediately recap the ATM vial. Do not use ATM vials that have expired (an expiration date is on the vial) or vials with blue coloration of the gel media indicating that the media is no longer anaerobic. Label the specimen appropriately.
   2. Open lesions and wounds: Prior to specimen collection, decontaminate the skin or wound surface by washing with surgical soap followed by 70 percent ethyl or isopropyl alcohol to remove as much of the superficial flora as possible. Rinse with sterile saline and dry with sterile gauze. For lesions with exudate, cleanse skin or lesion as above and remove exudate. Collect either needle aspirated fluid of deep wound, tissue biopsy / curettage or swab. For aspiration, injection of sterile saline into the area of sampling may aid in increasing aspirated material. Inject the specimen in an Anaerobic Transport Media vial (ATM) for transport to the laboratory via the following steps. Samples submitted in ATM vials are used for both anaerobic and aerobic cultures. Disinfect the rubber septum with an alcohol wipe, wait 15-30 seconds and inject the fluid into the tube at a slow rate. Alternatively, if an ATM is not available, the syringe with the specimen may be submitted but the needle must be removed, and the syringe should be capped by screwing a sterile plastic cap into the leur lock on the end of the syringe. For tissue biopsy, tissue should be obtained from either the deep base or margin. These should also be transported in an ATM vial whenever possible. First, unscrew the cap on an ATM vial and place the specimen onto the surface of the medium using sterile instruments and technique. Do not push the tissue or specimen into the gel at the bottom of the tube. Immediately recap the ATM vial. Do not use ATM vials that have expired (an expiration date is on the vial) or vials with blue coloration of the gel media indicating that the media is no longer anaerobic. For swab collection, firmly sample the base or margin of the lesion with a swab. Return the swab to the transport tube. Label the specimen.
   3. Burn wounds: Debride the area and disinfect the wound. As exudate appears, sample it firmly with a swab. Biopsy tissue is the specimen of choice; surface specimens usually represent colonization. Return the swab to the transport tube. Label the specimen.
   4. Pustules or vesicles: Select an intact pustule. Apply alcohol to the intact surface and allow it to dry. Unroof the pustule with a needle. Collect fluid and basal cells by rotating the swab vigorously in the pustule. If the lesion is older, the crust should be removed, and the moist base of the lesion sampled by swabbing with a pre-moistened (sterile saline) swab. For bacterial or fungal culture, return the swab to the tube. For viral culture, place the swab in M4 viral transport medium (refer to detailed viral culture collection instructions in section RR below).
2. Order CULTURE WOUND (INCLUDES GS) BACTI or CULTURE TISSUE (INCLUDES GS) BACTI. The appropriate culture (aerobic and anaerobic if indicated) is automatically ordered. Specify body site sampled. The exact body site is necessary to process the specimen using correct media and incubation for different pathogens encountered in different body sites. Include this information in the comment section of the order. Order CULTURE FUNGAL, AFB, or VIRAL as desired. Swab specimens are not acceptable for AFB or anaerobic cultures.
3. Transport swabs at room temperature and deliver to the lab without delay. Deliver tissue and syringe specimens to the lab immediately for optimum culture of anaerobic organisms.

CERVICAL, VAGINAL AND URETHRAL CULTURES

Genital cultures may be used for detection of Group B Streptococcus for perinatal screening purposes or for culture based detection of N. gonorrhoeae (GC). However, deoxyribonucleic acid (DNA) – based testing of urine or genital samples (e.g., PCR or transcription mediated amplification, Gen-Probe Aptima™) is preferable to genital culture for detection of GC and Chlamydia because of improved sensitivity, faster turnaround time, and greater stability of samples during transit. Culture for detection of GC may be performed when necessary for legal documentation (e.g., suspected sexual abuse in pediatric patients, forensic specimens) or for specimens that are very bloody. In such cases, it is advisable to submit separate specimens for DNA-based method in addition to culture as additional positive cases may be detected. Vaginal bacterial culture is not indicated for diagnosis of bacterial vaginosis and trichomonas or other suspected infection in post-pubertal females. However, vaginal bacterial culture may be helpful in prepubescent girls with vaginal discharge. Fungal culture may be indicated for vaginal yeast infection. Bedside or point-of-care performance of pH testing of vaginal secretions, Potassium hydroxide (KOH) preparation, vaginal wet mount and “whiff” test in combination with clinical exam (e.g., application of Amsel criteria) is the recommended method for routine diagnosis of bacterial vaginosis. Pediatric Vaginitis culture is available for pre-pubescent females with symptomatic vaginitis. This is a targeted culture for predominant Group A Strep (Streptococcus pyogenes), Haemophilus influenza and Shigella spp. Neisseria gonorrhoeae is not detected by this test. For Trichomonas detection, point-of-care wet mount or Giemsa stained preparation performed at the Microbiology Laboratory are necessary. For collection guidelines for DNA-based testing (Gen-Probe Aptima GC/CT), call the UC Davis Medical Center Molecular Laboratory at 731-3813.

1. Preparation and collection for culture:
   1. Cervix (endocervix): Wipe the cervix clean of vaginal secretion and mucus. Use a speculum without lubricant; it may be toxic to certain bacteria. Under direct visualization, gently compress the cervix with the blades of speculum, and use a rotary motion with a swab. Obtain exudate from endocervical glands. Alternatively, insert the swab into the cervical os and gently rotate, allow it to remain in place for a few seconds, and remove it. Return the swab to the base.
   2. Urethra: Collect specimen one hour or more after urinating. Wipe urethral meatus clean with sterile gauze or swab. If discharge cannot be obtained by "milking" the urethra, insert swab 1-2 cm into the urethra and rotate briefly. Remove swab and return to the base.
   3. Vaginal: Routine culture for vaginal specimen is not recommended. Vaginal specimens are less sensitive than endocervical specimens and should only be used when endocervical specimens cannot be obtained. Use a speculum without lubricant. Swab mucosa high in the vaginal canal under direct visualization. For detection of Group B streptococci in pregnant women, public health guidelines suggest obtaining one or two swabs of the vaginal introitus and the anorectum for optimal recovery. Cervical swabs are not acceptable.
2. Order CULTURE GC ONLY or GROUP B STREPTOCOCCUS SCREEN BY PCR (for recto-vaginal source) or CULTURE PEDIATRIC VAGINITIS (for pre-pubescent, symptomatic females). Order GRAM STAIN if desired. Gram stain is helpful in diagnosing GC in males but is not recommended for females. Other organisms in the vaginal or cervical flora may have morphology similar to gonococci.
3. Transport: Return the swab to the base of the tube, label and send to the lab immediately at room temperature (do not refrigerate). Specimen must be received within 12 hours of collection to allow recovery of Neisseria gonorrhoeae. Viability of this organism rapidly diminishes over time. DNA probe specimens are stable even after prolonged transit times (see below).

STOOL (FECES) AND RECTAL SWABS FOR THE DETECTION OF STOOL PATHOGENS

Infectious gastroenteritis is associated with a wide range of etiologic agents. Identification of these pathogens using conventional methods involves a complex workflow requiring multiple tests, long turnaround times, and reduced sensitivity. Multiplex molecular testing offers a rapid, streamlined approach, helping clinicians make timely and targeted therapeutic decisions. In most cases, testing should be limited to initial diagnosis and not as “test of cure” without specific recommendation from an Infectious Disease specialist or the Public Health Department. Rectal swabs are insensitive for detection of cause of invasive bacterial infection and their use should be limited to infants. Infant rectal swabs are acceptable for routine stool culture.  In most cases, stool should be loose, conforming to the shape of the container and may be bloody. Bacterial causes of gastroenteritis are more often accompanied by fever than viral causes and often have historical features compatible with exposure. Routine stool culture of infant rectal swabs includes immunoassay for Shiga Toxin (1 and 2) and culture for Campylobacter spp., Shigella spp., Salmonella spp., E.coli 0157:H7, Aeromonas, and Pleisiomonas spp. Culture/media for Yersinia spp. and Vibrio spp. are not routinely performed and must be requested when clinical suspicion and / or history suggests risk for these organisms. Stool culture is added on reflexively as appropriate.  Patients tested for C. difficile disease should have symptoms compatible with C. difficile infection (≥3 loose or liquid bowel movements per 24 hours +/- abdominal pain) not attributable to another cause (e.g., laxative/enema overdose). Asymptomatic and / or colonized patients may still test positive for C. difficile toxin and should not be tested. Formed stool specimens should not be tested and “test of cure” testing or screening of asymptomatic patients is also not recommended. In general, C. difficile does not cause symptomatic disease in patients less than 2 years of age and testing should not be performed for patients in this age group. Samples from patients’ ≤1 year old will be rejected without prior approval. If testing is performed, results will be reported with the following comment: “The clinical significance of a positive result for C. difficile toxin in patients less than 2 years of age is uncertain and commonly represents colonization. Clinical correlation is recommended.”

1. Specimen collection method and volume:
   1. Collect sample prior to the administration of antibiotics.
   2. For PCR testing: fresh stool should be placed in “Cary Blair” enteric transport medium. Add stool (approximately 10gm) to the red fill line on the transport vial label. The liquid medium should be red prior to addition of the sample; if the indicator is yellow, the product should not be used. Check the expiration date. Mix the stool thoroughly into the medium.
   3. Rectal swabs are discouraged as a means to diagnose invasive bacterial infection but may be used for pediatric patients when feces are not readily obtainable. Insert the swab beyond the anal sphincter, carefully rotate then withdraw swab. The swab must show feces. Return the swab to the base.
   4. For C. difficile toxin A and B EIA, collect 10-20 mL fresh, loose or liquid stool in a clean container and transport, on ice. If not submitted on ice, it will be rejected. Formed stool or stool not conforming to the shape of the container will also be rejected.
   5. For C. difficile surveillance testing, collect a rectal fecal specimen using an appropriate swab for this test.
2. Recommended number:
   1. One stool specimen per day. Duplicate specimens within a 24-hour period will be rejected.
   2. No more than two specimens/GI episode.
   3. Feces collected from in-house patients more than 3 days after admission will not be cultured. This utilization restriction has been widely implemented in hospitals because of the low yield of bacterial pathogens from patients whose diarrhea began after admission.
3. Order:
   1. Order GI (GASTROINTESTINAL) PANEL. Rectal swabs collected on pediatric patients will be revised accordingly and routine stool culture will be performed.  
   2. If other organisms are suspected, (e.g., Yersinia enterocolitica, Vibrio spp., Aeromonas spp.), note specific organism(s) in order comments. Additional culture techniques must be employed to recover these other agents. If blood has been observed in the stool, please note this in the order comments.
   3. For C. difficile toxin A and B EIA, order C DIFFICILE DIAGNOSTIC TEST.
   4. For C. difficile surveillance, order C DIFFICILE SURVEILLANCE TEST
4. Transport:
   1. Submit specimens in Cary Blair enteric transport medium at room temperature. Samples in this medium are stable for 72 hours.
   2. Submit rectal swabs at room temperature. Swabs over 24 hours old are unacceptable.
   3. Submit fresh stool on ice.

STOOL, GI AND MISCELLANEOUS SPECIMENS FOR PARASITOLOGY

Feces/Stool is the most common specimen submitted for diagnosis of intestinal parasitic infection but examination of other sources (e.g., duodenal aspirate, bile, urine, respiratory secretion) may be indicated in specific cases. Note: Infection by most gastrointestinal parasites (e.g., Helminths) is rare or uncommon in the United States without specific risk factors for exposure or severe disease. The majority of parasitic infections in persons without specific risk factors for exposure are limited to Giardia lamblia, Cryptosporidium spp. and occasionally Entamoeba histolytica. These are best detected by PCR and do not require traditional manual microscopic Ova and Parasite (O&P) examination. Conversely, specific detection methods such as EIA, PCR, DFA are not available for Helminths or other less common parasites and traditional O&P is still necessary to detect these agents. Because of the rarity of parasites requiring traditional O&P, specification of risk factor and indication for testing is necessary when these are requested. For detection of Cyclospora or Cystoisospora spp. (e.g., HIV patients), modified Acid Fast Stained preparation should be performed.  Cyclospora cayetanensis can be detected by PCR.

1. Fecal specimen collection:
   1. Collect fecal specimens prior to the administration of antibiotics or antidiarrheal agents. Avoid the use of mineral oil, bismuth and barium prior to fecal collection, since these substances interfere with the detection or identification of intestinal parasites. Wait at least one week if any of these have been used.
   2. Collect the fecal specimen in a clean, wide-mouthed container or on a newspaper.
   3. For Cryptosporidium spp., Giardia lamblia, Cyclospora cayetanensis, and Entamoeba histolytica, submit stool in a Cary-Blair enteric transport medium. For O&P, modified AFB, and Microsporidia stains, preserved specimens submitted in 2 vial transport system are required. Transfer portion of stool specimen to commercial transport system (e.g., Cary-Blair or Para-pak) and transport to the laboratory. Add feces to the fill line and thoroughly mix the sample into the preservatives. Cap specimens tightly. Unpreserved specimens are not acceptable for these tests.
   4. Avoid contamination with urine or water from the toilet.
   5. Only one specimen per 24 hour period will be processed.
   6. Feces collected from inpatients greater than 3 days after admission will not be examined (except when a series of specimens is in progress).
   7. Rectal swabs are not satisfactory for parasite examination and will be rejected.
2. Recommendations for specific parasites and miscellaneous specimen types:
   1. Acanthamoeba--Corneal scrapings, vitreous fluid, ocular, contact lens, contact lens fluid; obtain non-nutrient agar plate from microbiology lab prior to specimen collection. Call the lab at (916) 731-3832 for instructions.
   2. Amebiasis--For diagnosis of intestinal Entamoeba histolytica infection, submit stool preserved in enteric transport medium (e.g. Cary-Blair) for PCR testing. For suspected extra-intestinal amebiasis (e.g., liver abscess), serology is the preferred test method
   3. Cryptosporidium spp., Cyclospora cayetanensis, Giardia lamblia, --submit stool in enteric transport medium (e.g. Cary-Blair) for PCR testing
   4. Cystoisospora spp. --Special stain is required. Submit preserved stool specimen and request modified AFB stain.
   5. Microsporidia--Special stains are required for detection of these organisms (e.g., Enterocytozoon bieneusi, Encephalitozoon spp.). Submit preserved fecal specimen and request Microsporidia stain. In suspected cases of extra intestinal microsporidial infection, contact laboratory prior to submitting other specimens (e.g., respiratory secretions).
   6. Duodenal aspirate--Occasionally used to aid in diagnosis of infection due to Giardia lamblia, Clonorchis, Strongyloides spp., Cryptosporidium spp., and Cystoisospora. Transfer specimen to clean, tight closing container and transport immediately to lab at room temperature.
   7. Helminths--Collection of 2- 3 stool specimens over a 10-day period is recommended. Presence and indication of risk factor for Helminthic infection is required (e.g., history of emigration or travel to endemic region or immunocompromised state).
   8. Pinworm--Peri-anal “tape” preparation collected on arising in the morning is the preferred specimen for diagnosis. Feces are not appropriate. Collect specimen before bathing or going to the bathroom. Apply clear cellophane tape, sticky side toward the body, to the uncleansed perianal area. Remove the tape and then apply it, sticky side down, to a clean microscope slide. Label the slide. A minimum of 4-6 consecutive collections are necessary to rule out infection. "Pinworm paddles" may be available in pediatric outpatient clinics.
   9. Sigmoidoscopic material-- Rarely indicated. Contact laboratory, ID or GI Specialist. Strongyloidiasis--For chronic, asymptomatic Strongyloidiasis, single stool O&P is insensitive. Serology and examination of multiple specimens with concentration may aid in diagnosis. Consult laboratory. For suspected hyper infection syndrome, O&P examination of feces and / or other specimen types (e.g., respiratory) usually is sufficient.
   10. Trichomonas--Make a thin smear of the fluid or exudate on a microscope slide, air dry, and submit this to the laboratory for staining. Urine may be submitted for examination for Trichomonas vaginalis. Submit the first AM urine or urine passed after prostatic massage.
   11. Urine--Appropriate for examination for Schistosoma ova. Submit all urine passed between noon and 3 PM. A 24-hour collection without preservative is also acceptable.
   12. Worm/Arthropod identification--Suspected human parasites may be submitted for examination and attempted identification. Submit worm in a sterile container with saline at room temperature. Submit arthropod in a sterile container with a water moist cotton ball at room temperature. DO NOT submit formalin.
3. Order GI (GASTROINTESTINAL) PANEL to rule out parasitic cause of diarrhea or abdominal symptoms in routine patients. For patients at increased risk for helminthic infection or severe infection, (e.g., immunocompromised, persistent symptoms with history of travel, history of residence in parasite endemic region), order HELMINTH OVA and LARVA TEST. Specification of risk factor is required. Order PARASITE STAIN, MOD. ACID FAST. Microsporidia stain require a send-out order when indicated and desired.
4. Transport: Unless otherwise noted, submit preserved fecal specimens in two vial transport systems. Transport to laboratory at room temperature.

ACID FAST BACILLI (AFB) SPECIMENS

Acid Fast Bacilli refers to Mycobacterium spp. including M. tuberculosis, M. avium – intracellular complex and others. Stains and cultures for detection of these organisms require special methods and prolonged incubation. Most are performed at the Sacramento County Public Health Laboratory or other outside laboratory.

1. Preparation of patient and collection:
   1. Sputum - Collect only material brought up from the lungs after a productive cough. Do not collect sputum immediately after a mouth wash. A series of three specimens, each submitted promptly to the lab after collection, is recommended. A minimum of 5 mL is required. These specimens must be collected at least 8 hours apart with one being an early morning specimen. For patients who have difficulty in producing sputum, specimens collected by inhalation of hypertonic saline induction may be used. Submit the specimen in a sterile, labeled container. Close lid tightly.
   2. Urine - There are limited indications for urine AFB culture. Consult ID. First morning midstream specimens are recommended. Instruct patient to wash and rinse the genital area well as described above for urine culture prior to collection of specimen. Submit at least 50 mL in sterile labeled cup (urine transport tube volume is inadequate for AFB culture).
   3. Other specimens -Submit spinal fluids in sterile lumbar collection tubes, other fluids in sterile containers. Pieces of tissue must be kept moist with a small amount of sterile saline. Submit as much CSF, other body fluid or tissue as possible.
   4. Blood - Submit 7 mL heparinized blood (green top Vacutainerä).
   5. Label the specimen according to Administrative Policy 18004 Specimen Labeling for Laboratory Processing and 2702 Patient Identification for the Hospitalized Patient.

2. Order "CULTURE (i.e. respiratory, tissue, body fluid etc.) AFB." Note culture detection of Mycobacterium marinum requires special incubation. If this is suspected, i.e., cutaneous infections on extremities, note this on the requisition.
3. Transport: Specimens should be delivered promptly to the lab on ice (exception: blood specimen should be kept and transported at ambient temperature).). Specimens are processed at the Sacramento County Public Health Laboratory. They are picked up from the Microbiology Lab at 0800, Monday through Friday, excluding County holidays. To assure specimens are processed on the day of collection, samples from hospitalized patients should be received at the hospital central laboratory no later than 0600.

MYCOLOGY (FUNGAL CULTURE) SPECIMENS

1. Preparation of patient and collection:
   1. Skin scrapings - Clean site with 70 percent alcohol on sterile gauze to minimize surface contaminants. Using a sterile, fresh scalpel blade, collect superficial scrapings, from the active periphery of the lesion. Submit scrapings in a closed, sterile container.
   2. Nails - Clean nail and surrounding skin with 70 percent alcohol on sterile gauze pad, not cotton ball. Collect nail clippings and or shavings and material from under the nail plate. Scraping should be deep enough to assure acquiring recently invaded tissue. Submit nail clippings and scrapings in a closed, sterile container.
   3. Hair - Use forceps to pluck 10-12 involved hairs from the edges of the involved patches. Select hairs that fluoresce under a Wood’s lamp if available. Submit hair, including shaft, in a closed, sterile container.
   4. Ocular – Appropriate for sterilely collected specimens only. Submit tissue biopsy or a minimum of 0.5 mL intraocular fluid for fungal culture.
   5. Other specimens - Collect and submit specimens as described for specific type. Specimens associated with the systemic and deep-seated mycoses are obtained from a wide variety of sources. They should be obtained, whenever possible, under aseptic conditions and in sufficient quantity for both microscopic and cultural examinations. Indicate specific organism suspected, if possible.
2. Order CULTURE (specimen type), FUNGAL culture (mycology); order KOH PREPARATION if direct examination is desired.
3. Transport properly labeled specimens promptly to the laboratory at room temperature.

CRYPTOCOCCAL ANTIGEN TESTING

Cryptococcal infection typically involves the lungs, blood or central nervous system. Detection of Cryptococcal antigen is the preferred, most rapid test method and may be performed on serum or cerebrospinal fluid (CSF). Cryptococcus spp. may also be detected in routine blood, bacterial and fungal cultures but these methods may result in diagnostic delay.

1. Cryptococcal antigen testing may be done on CSF and serum.
2. Specimen Collection and Transport: Collect CSF in sterile containers. Submit blood in a serum separator tube for serum testing. Transport specimens to the laboratory promptly on ice.
3. Order CRYPTOCOCCAL ANTIGEN.

VIROLOGY TESTING AND CULTURES

Virological testing is available for detection of routine causes of vesicular skin lesions (e.g., HSV I, HSV II, VZV), Cytomegalovirus, common causes of respiratory viral infection (e.g., Influenza A and B, RSV, Parainfluenza 1, 2, and 3, Adenovirus, and human Metapneumovirus), cultivable Picornaviruses (e.g., Enteroviruses) Not all picornaviruses are cultivable in routine viral cell culture. Rotavirus,, Norovirus, West Nile Virus, other Herpes viruses, HIV, Hepatitis viruses and a number of other clinically relevant viruses are not detectable by viral culture.

1. Virus isolation (culture) and immunofluorescence: Specimens for virus isolation should be collected as soon as possible after the onset of symptoms. Acceptable collection container information is available in the Lab Test Directory, refer to specimen test for collection information. Viral isolation specimens should be sent to the Microbiology lab on ice, as soon as possible after collection.
   1. Specimen collection - NOTE: Use wire- or plastic-shafted swabs for collecting specimens for viral culture. Do not use wooden-shafted swabs.
      • Autopsy and biopsy specimens: Collect tissues from probable sites of pathology using a separate sterile instrument for each sample. Samples should be about 1-2 cm cubes. Place each specimen in a separate container; add a small amount of sterile saline.
        1. In cases of central nervous system disease, submit samples of brain (temporal lobe cortex, mid-brain, medulla) and spinal cord. A 2-3" segment of descending colon, tied off with contents, should be included for the recovery of enteroviruses.
        2. For influenza and other respiratory diseases, include samples of lung tissue, bronchus and trachea. Heart muscle, liver and kidney are less common sources of virus but may be included if involvement is suspected.
      • Conjunctival scrapings: Carefully scrape the conjunctiva with an ophthalmologic spatula or a swab. For virus culture, place the scrapings or break off the swab into viral transport media. For direct immunofluorescence, prepare a smear of the scrapings in one dime-sized area on a clean microscope slide; air dry. Prepare a separate slide for each agent to be tested.
      • Nasopharyngeal/throat swabs and nasopharyngeal/throat washing: Swab the throat and/or nasopharynx using the appropriate swab type (nasopharyngeal swabs are best collected using dacron-tipped wire swabs). Break the swab off into viral collection media. For throat washing, have the patient gargle 5-10 mL of sterile non-bacteriostatic normal saline on the back of his/her throat and expel the contents into a sterile cup. Close lid tightly, label completely and send to Microbiology Lab immediately on ice. Nasopharyngeal swabs for the detection of respiratory viruses are performed by the Molecular Lab.
      • Urine: For cytomegalovirus (CMV) collect 10-20 mL (volumes as low as 2 mL are acceptable) and deliver immediately to the Microbiology Lab on wet ice. Do not freeze. Do not submit in a urine culture transport tube.
      • Vesicular lesion material:
        1. Obtain cellular scrapings from the base of vesicles with a fresh sterile scalpel, swab or applicator stick. Rupture a young vesicle, absorb vesicular fluid with a swab and scrape the base of lesion. Do not draw blood. If pus is present, clean lesion and discard swab prior to taking the specimen.
        2. For virus culture, place the scrapings or break the swab off into a viral culture collection media.
        3. For direct immunofluorescence, prepare two smears of the lesions with a dime-sized area on each of two clean microscope slides; air dry.
      • Nasal washing (for respiratory viruses): Wash the posterior nasopharynx using 5 mL sterile 0.9 percent saline and a rubber bulb. Place 1 mL of nasal washing in viral culture collection media and the remainder of the washing in a sterile the tube for direct detection of RSV or FLU A/B by immunofluorescence. Submit on ice; deliver immediately to the lab.
      • Blood (buff coat): Collect 3-7 mL blood in an EDTA (purple top) tube. Transport specimen at room temperature immediately to the lab.
      • Rectal swab: Scrape rectal mucosa with a Dacron swab and break off swab into viral culture media.
   2. Order
      • For non-respiratory specimens requiring routine virus isolation (culture) - Order CULTURE (SPECIMEN TYPE) VIRAL. Include source of specimen, date of onset and clinical history.
      • For most respiratory specimens (e.g., throat swab, wash, aspirate, BAL), order RESPIRATORY VIRUS DFA and CULTURE, or CULTURE RESPIRATORY, VIRAL.
      • For skin or ocular lesions for which rapid immunofluorescent detection of HSV / VZV is desired -- Order HSV or VZV IMMUNOFLUORESCENCE.
      • Whenever possible, specify virus (e.g., RSV, HSV, etc.) clinically suspected) and include source of specimen on order.
   3. Transport
      • Virus isolation - all specimens except blood should be transported on ice immediately to the lab. EDTA blood should be transported at room temperature.
      • Immunofluorescence - transport primary specimen as above and transport slides promptly to the lab in a clean cardboard slide holder or specimen cup.
   4. Virus detection (fecal specimens ONLY):
      • Collection: Collect fecal specimens during the acute phase of illness, preferably within the first 3 to 5 days. For pediatric patients in diapers, liquid stool may be collected by lining a clean diaper with plastic wrap or a disposable diaper can be put on inside out. Alternatively, pediatric urine bag can be placed over the anal area to collect watery stool. Submit stool in an enteric transport medium (e.g. Cary-Blair).
      • Order GI (GASTROINTESTINAL) PANEL. The following viruses can be detected: Adenovirus F 40/41, Astrovirus, Norovirus GI/GII, Rotavirus A, Sapovirus.
      • Transport: Submit preserved stool in enteric transport medium at room temperature to the lab.

ROUTINE SUSCEPTIBILITY TESTING

In general, quantitative microdilution is used to yield MICs, (minimum inhibitory concentration) and requires 18 - 24 hours of incubation once the isolate is obtained in pure culture. The procedure is initiated in the Microbiology Laboratory on appropriate organisms and sources. The following organisms are routinely tested: E.coli and other Enterobacteriaceae, Pseudomonas areuginosa, Acinetobacter spp. and other miscellaneous Gram-negative bacilli, Staphylococcus aureus, Enterococcus spp., and Streptococcus pneumonia. Haemophilus influenzae is tested for beta-lactamase production only. Consult the UC Davis Medical Center Antibiogram for the current list of antimicrobics.

REFERENCES

Clinical Policy 9010: Urethral Catheter Insertion, Maintenance, and Removal Policy

Clinical Policy 13015: Drawing Blood Cultures

Standardized Procedure #4: Obtaining Urine Culture Specimen from a Catheterized Patien