Microbiology Guide

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Table of Contents

General Information

Submit requests for culture identifying the type of specimen, the procedure(s) requested, and the collection time. Indicate the patient's special conditions (e.g., immunocompromised, transplant, cystic fibrosis, etc.), and any antimicrobial therapy. This information helps in the proper processing of the specimen and in the interpretation of the culture. Additional charges are incurred for identification and susceptibility testing.

Hours: Cultures are set up and Gram stain smears are read 24 hrs, 7 days a week. Preliminary results on stat gram stains from normally sterile sites and malarial smears are issued by the hospital-based Hematology sections.

Specimen Collection (by Anatomic Site)

GENERAL:

Most specimens submitted for culture should be kept at room temperature until brought by messenger to the laboratory, however, refrigerate urine and non-invasively collected respiratory specimens. Do not refrigerate blood cultures, swabs in charcoal transport medium, cerebrospinal, joint and other normally sterile body fluids, tissue, or specimens already inoculated to plates or broth. Such cultures should be brought to the main Clinical Laboratories for prompt handling. 

Label each specimen with patient's name, unit number, source, date, and time.
 
Microbiology Specimen Collection Guide for UCSF Operating Rooms
 

ABSCESS: see WOUND

AMNIOTIC FLUID:

Collection: Submit the fluid in a sterile, clear plastic black top tube.
 
Viruses: For CMV and HSV submit fluid specimen for testing by PCR. For rubella, consult the laboratory.
 

ASCITIC FLUID: see PERITONEAL FLUID

BLOOD:

Bacteria (routine): The yield of blood cultures in adults is volume-dependent and increases approximately 3% per mL of blood cultured; 20% of bacteremic adults have less than 1 colony-forming unit in 10 mL of blood. About 80% of patients who have positive blood cultures are positive on the first sampling, 90% are detected with two samplings, and nearly 99% with three samplings; optimal routine blood culture consists of 2 or 3 sets of aerobic and anaerobic bottles with 10 mL of blood in each bottle. Do not collect more than three blood cultures from a single patient within a 24 hr period.
 

Sites and Timing of Collection and Blood Volume Needed

  • It is best to not draw blood cultures within hours to days after administering antibiotics and if possible to avoid collecting the sample(s) from indwelling intravascular catheters or shunts, which are often externally contaminated, especially at 3-way stopcocks which are difficult to disinfect. To avoid dilution of the specimen by the infused fluids, draw specimens distal to existing intravenous lines. Samples for blood cultures should not be drawn from a vascular line unless: (1) collecting samples for the Differential Time To Positivity (DTTP) test or (2) it is specifically authorized to do so by the physician. Blood cultures should not be used to follow effectiveness of antiobiotic therapy.
Special bacterial culture: For Brucella spp. collect blood cultures. Notify Microbiology when this organism is suspect so that the cultures can be incubated for 14 days.
 
Fungi: Yeasts such as Candida spp. and Cryptococcus spp. will grow in routine blood cultures and do not require a separate fungal culture. To culture lipophilic Malassezia yeast and invasive molds including Histoplasma, Fusarium and Scedosporiumalso order Fungal Culture, Blood. Mycobacteria culture: Culture of blood for mycobacteria is unproductive except to detect Mycobacterium avium-intracellulare complex in patients who are HIV-positive. Order AFB Culture, Blood.
 
Mycobacteria culture: Routine culture of blood for mycobacteria is unproductive except to detect Mycobacterium avium-intracellulare complex in patients who are HIV-positive. Submit two Dark green (gel-free) sodium heparin tubes and indicate that the patient is immunocompromised when ordering the test.
 
Parasites including Malaria: Blood submitted in a lavender top tube is examined by Giemsa stain for bloodborne parasites: PlasmodiumTrypanosomaBabesia, visceral Leishmania and microfilaria spp. Review the patient's history for possible periodicity and an optimal time of sampling.
 
Viruses: PCR is more sensitive than viral culture for identification of viruses in blood samples, and is primarily indicated for immunocompromised patients to diagnose viremia. PCR detection from blood is most commonly done for CMV, EBV, BK, adenovirus, enterovirus, HSV and HHV6. Submit blood in a lavendar top EDTA tube for viral PCR testing.
 

BODY FLUID (e.g., Joint, Pericardial, Pleural; see also AMNIOTIC, CEREBROSPINAL, or  PERITONEAL FLUID):

Collection: Collect 15-20 mL of fluid in a sterile, clear plastic black top tube.
 

BONE MARROW:

Collection: Bone marrow specimens for culture can be collected independently or during a diagnostic bone marrow aspiration and biopsy procedure; schedule the latter in advance by calling Hematology.
 
Although bone marrow cultures may be helpful in identifying disseminated fungal and mycobacterial diseases, they are unlikely to assist in the identification of usual bacterial disease.
 
Submit the sample in a 1.5 mL Isolator yellow top tube, obtained from Hematology or Microbiology. 

 

BRONCHOALVEOLAR LAVAGE and LUNG BIOPSY:

Recommended Evaluation of Specimens From Immunocompromised Patients
Culture/Test AIDS Patients Other immunocompromised/
transplant patients
Bacteria (routine) Order routinely Order routinely

Aspergillus

Order if indicated Order if indicated

Fungal Culture with KOH

Order whenever histoplasmosis, coccidioidomycosis or other mycelial fungi are suspected; examine histology and culture biopsy specimen in parallel  Order if fungi other than yeasts and Aspergillus are suspected 

Mycobacteria

Order when M. tuberculosis, MAIC, or other mycobacteria are suspected  Order if suspected 

Legionella
(Culture + PCR)

Order if suspected (rare)  Order routinely

Viruses:

Respiratory Order if suspected Order if suspected

CMV

Not indicated Quantitative PCR on blood for monitoring or diagnosis. Histology on a biopsy specimen can be useful in assessing disease. CMV culture can be positive due to asymptomatic carriage.

Others, including HSV and VZV 

Order PCR when indicated Order PCR when indicated 

Parasites

Cytology for Pneumocystis carinii (by Anatomic Pathology)  Order if suspected

CATHETER TIP:

Collection: Catheter tip cultures are not performed. Catheter site cultures submitted on swabs are not predictive of catheter infection, but can be useful to determine the causative agent when localized site infection is apparent and a purulent specimen can be obtained. Urinary or peritoneal catheter tips are not appropriate for culture; send the urine or peritoneal fluid instead.
 
Bacteria (routine): Catheter tip cultures are no longer performed. Request Differential Time to Positivity of a peripheral vein blood culture and an intravenous line blood culture drawn within 15 minutes of each other. If organisms grow in the sample drawn through the line at least two hours earlier than from the peripheral blood, then the line is considered to be the source of infection.
 
Fungi: Notify the laboratory if Malassezia furfur infection is suspected on specimens from hyperalimentation patients.
 

CEREBROSPINAL FLUID:

Collection: Submit in sterile tube for bacterial culture (use the tube included in the LP kit or a sterile, clear plastic black top tube.
 
Bacteria (routine): Because of the relative fragility of many of the common etiologic organisms in meningitis, the fluid should be promptly delivered to the laboratory.
 
Cryptococcus neoformans: For diagnosis of yeast and Cryptococcal meningitis, recommended tests are CSF bacterial culture (yeast, including Cryptococcus neoformans grow well on routine bacterial culture) and CSF and serum Cryptococcal Antigen.
 
Coccidioides immitis: Sensitivity of CSF Culture for Coccidiodes immitis is limited. Serum and/or CSF serology for Coccidioides (Coccidioides immitis Antibody, Immunodiffusion) are more sensitive than culture and are the recommended first-line diagnostic tests.
 
Mycobacteria: CSF will be processed for AFB culture only after consultation with the laboratory. Smears are positive in very few of culture-positive spinal fluids, and are only performed when the microbiology laboratory is notified that the index of suspicion is high. Greater than 2mL of CSF is required for culture. The yield of CSF AFB culture increases with greater specimen volume. Recommended volumes are at least 6ml for pediatrics and 15-20ml for adults. Mycobacterial culture of a clear acellular spinal fluid is unproductive and should not be ordered.
 
Parasites (Naegleria, Acanthamoeba, Trypanosoma, Toxoplasma): Consult the laboratory when diagnosis is suspected and deliver specimen to laboratory immediately. Culture is possible only if patient is not on antibiotic therapy. Rapid diagnosis may be possible by examination of Giemsa stain.
 
Viruses (identify the specific agent[s] sought):
 
Arbovirus: Contact laboratory for information about collection of specimens for diagnosis of mosquito-borne encephalitis. Requests are forwarded to the Viral and Rickettsial Disease Laboratory of the California Department of Health Services, and must be accompanied by a special referral form which includes the relevant clinical history.
 
Cytomegalovirus: PCR for CMV is indicated to diagnose the cause of polyradiculopathy or encephalitis when CSF neutrophilic leukocytosis is unexplained by bacterial infection.
 
Enterovirus: Enterovirus PCR is performed on CSF. 
 
Herpes simplex: HSV DNA by PCR is performed on CSF.
 
Varicella-Zoster: VZV virus occasionally causes encephalitis in normal persons, usually in association with skin lesions, and in HIV-infected patients. PCR and serology of CSF for VZV is suggested for patients with possible CNS disease.
 

CERVIX/ENDOCERVIX: see VAGINA/CERVIX

COLONIC and OTHER INTESTINAL (e.g., Duodenal) ASPIRATES and BIOPSIES (see also GASTRIC ASPIRATE):

Collection: Submit aspirate or biopsy specimens in a plastic cup with a tight fitting lid. Keep the tissue moist, but do not put it into transport medium.
 

Parasites: For GiardiaStrongyloides, and other intestinal parasites, deliver specimen to laboratory within 30 minutes of collection on Monday-Friday. For Giardia, stool antigen detection by EIA is more sensitive and specific than microscopic examination. Proctoscopic exam for E. histolytica is seldom performed. A series of at least 3 routine stool examinations for parasites should be performed on each patient before sigmoidoscopy examination is done. Aspirate or scrapings from suspicious colonic lesions can be submitted in SAF fixative with 1 part sample to 3 parts of SAF. Consult the laboratory prior to collecting the specimen. Lesion biopsy specimens should be examined by routine histopathology. Serology for E. histolytica is quite useful, particularly in diagnosing amebic liver abscess.

Viral culture: For CMV and Herpes simplex, place biopsies in UTM (flocked swab).
 

CONJUNCTIVAE: see EYE

DIALYSIS FLUID: see PERITONEAL FLUID

DRAINAGE: see WOUND

EYE:

Collection: Conjunctival scrapings are obtained and collected with a swab and placed in transport tube appropriate to the test requested: transport medium for bacterial culture, viral holding medium for viruses, and UTM medium for Chlamydia (obtain from Microbiology).
 
Bacteria (routine): If submitting cultures from both eyes, be sure to note which sample is from the right or left eye.
 
Chlamydia trachomatis: Conjunctival scrapings are required to diagnose chlamydial conjunctivitis.
 
Parasites: Submit corneal scrapings on non-nutrient agar plate for Acanthamoeba culture.  For Loa Loa, send specimen to Anatomic Pathology. 
 
Viruses: Submit flocked swab in UTM.
 

GASTRIC ASPIRATES and BIOPSIES:

Collection: Gastric aspirate specimens should rapidly be brought to the laboratory immediately after collection, and only between the hours of, 06:30 and 19:00, for neutralization of the antibacterial acid content.
 
Bacteria (routine): Gastric samples will be cultured for Helicobacter pylori when specified. The culture of gastric contents may perhaps be useful to diagnose neonatal sepsis; the routine laboratory examination of these specimens includes a search for group B streptococci and Listeria monocytogenes, as well as less common pathogens. Blood and amniotic fluid cultures are more sensitive and more specific for diagnosing group B streptococcal infection than culture of gastric aspirate.
 
Mycobacteria: Culture of gastric contents is usually less productive than sputum or other respiratory cultures. First morning gastric aspirates are most useful for diagnosing tuberculosis when the patient is unable to produce sputum.
 

JOINT FLUID: see BODY FLUID

NASOPHARYNGEAL SPECIMENS:

Flocked swab in Universal Transport medium is the primary method for nasopharyngeal specimen collection for respiratory virus testing and Bordetella pertussis PCR.
 

NASOPHARYNGEAL SWAB (FLOCKED SWAB):

 
Collection: Use flocked swab/Universal Transport Medium for collection. Insert swab into the nostril, gently rotating the swab inward until resistance is met at the level of the turbinates. Rotate the swab a few times against the nasopharyngeal wall (approximately 10 sec) and then withdraw swab.  Insert swab into container with Universal Transport Medium. Break end of swab so top of vial can be screwed on securely. Appropriately label specimen and send to the laboratory.
 
Respiratory viruses: Nasopharyngeal flocked swabs in universal transport medium are the preferred specimen type for respiratory virus testing.
 
 
Image of the UCSF respiratory virus testing algorithm
 

NASAL ASPIRATE or WASH:

 
Collection: Specimens for virus PCR or Bordetella pertussis PCR should be collected within 5 to 7 days after onset of illness and preferably in the first 4 days. Specimens collected after 7 days rarely yield a pathogen. 
 

Nasal Aspirate:

  1. Adult and Older Child: Position patient comfortably in sitting position, neck slightly hyper-extended
  2. Infant and Younger Child: Sit child on parent’s lap facing forward, with the child’s back against the parent’s chest. The parent should wrap one arm around the child in a manner that will restrain the child’s body and arms.
  3. Neonates: Swaddle tightly for comfort
  4. For adults, children, and infants, proceed as follows:
    1. Attach one end of the suction catheter to the mucus trap (both available from Materials Services)
    2. Attach other end to wall suction. DO NOT employ mouth suction.
    3. Turn on suction and adjust vacuum pressure to 40-60 mmHg. Use thumb control to apply suction when withdrawing the catheter from the nasopharynx.
    4. With patient’s head slightly hyper-extended, instill 1 to 2 ml of sterile saline into the patient’s nostril. 
    5. Gently thread the tube through the external nostril, into the nasopharnyx. NOTE: depth of insertion necessary to reach posterior pharynx is equivalent to distance between external nostril and external opening of the ear.
    6. Apply suction and using a rotating movement, aspirate material as the tube is withdrawn, at a pressure of 40-60 mmHg. NOTE: catheter should remain in nasopharynx no longer than 10 seconds.
    7. If needed, draw material into the specimen trap using sterile saline. Hold specimen trap upright to prevent secretions from going into the suction tubing.
    8. Repeat procedure until adequate sample (2ml) is obtained.
    9. Offer the patient tissues as appropriate.
    10. Disconnect and turn off suction device. Tie off the tubing, or seal mucus trap with cap found on bottom of the trap.

Nasal washing:

  1. Adult and Older Child: Position patient comfortably in sitting position, neck slightly hyper-extended
    1. Prior to the procedure, have the patient blow their nose.
    2. Using a sterile syringe, introduce 3 ml of sterile saline into one nostril
    3. If possible, have the patient retain the saline for a few seconds.
    4. Place specimen container directly under the nose with slight pressure on the upper lip. 
    5. Tilt the head forward and allow the fluid to flow into the specimen container. 
    6. Repeat procedure on other nostril, collecting fluid into the same container.
    7. Offer the patient tissues.
  2. Infant and Younger Child: Sit child on parent’s lap facing forward, with the child’s back against the parent’s chest. The parent should wrap one arm around the child in a manner that will restrain the child’s body and arms.
    1. Fill bulb syringe with 1-3 ml of sterile saline, depending on size of the patient, and instill saline into one nostril, while the head is tilted back.
    2. Release the pressure on the bulb to aspirate the specimen back into the bulb. 
    3. Transfer the specimen into specimen container. 
    4. Repeat procedure on other nostril, transferring second specimen into the same specimen container.
    5. Offer tissues as appropriate.

PERICARDIAL FLUID: see BODY FLUID

PERITONEAL FLUID (including Abdominal, Ascitic and Dialysis Fluid):

Bacteria (routine): First inoculate 10ml into each of aerobic and anaerobic blood culture bottles at the patient's bedside for optimal growth and recovery of organisms. Divide the fluid equally among the bottles if < 20 mL is obtained. Additional fluid may be submitted in a sterile tube, which allows for gram stain to be performed and faster identification of bacteria present at high concentrations. Includes cultures to isolate aerobic and anaerobic bacteria, and Candida.
 
Other organisms: Submit fluid in a sterile tube. Order "Other Fungal Culture with KOH Stain" if histoplasmosis is being considered, and/or mycobacterial culture if peritoneal tuberculosis is a diagnostic consideration.
 

PLEURAL FLUID: see BODY FLUID

PUS (see also WOUND):

Collection: Submit in a sterile, clear plastic black top tube. A tissue specimen is preferred to a specimen of pus, but pus is a better sample than swabs submitted in transport medium.
 

RECTAL:

Neisseria gonorrhoeae and  Chlamydia trachomatis:
 
Nucleic acid detection is a sensitive method for diagnosis of CT / NG infections and is the recommended method for most patients.
 
CT/NG DNA Specimen Collection Instructions
 
Chlamydia trachomatis culture is generally indicated to assess clinical treatment failure, where DNA may persist post-treatment. Culture requires transport of tissue or swab in special UTM media, available from the Microbiology Laboratory.
 
Neisseria gonorrhoeae culture is generally indicated to assess clinical treatment failure, and to provide an isolate for susceptibility testing. Culture requires a swab in Amies transport medium with charcoal.
 

SPUTUM and TRACHEAL ASPIRATE:

Collection: Specimens are collected by direct expectoration into a clean, plastic cup capped with a lid which does not leak (a clean, non-sterile container is satisfactory). Sputum induction, if needed, must be arranged with Respiratory Therapy, usually the day prior to collection. Luken traps may be submitted. If possible, the patient should rinse out gross oral contamination from the mouth with freshly obtained water before attempting to expectorate a sputum sample.
 
Bacteria (routine): Gram-stained is performed upon arrival in the laboratory. Samples demonstrating a large number of squamous cells as evidence of pharyngeal contamination will not be processed further and the submitting location will be asked to submit a new, properly collected specimen.
 
Fungi: Order culture for Aspergillus if suspected. Candida spp. often contaminate the respiratory tract and are only evaluated from lung transplant patients and from other patients in whom they are found to be numerous and in pure culture. When systemic infection with Histoplasma, Coccidioides, Blastomyces, or the agents of mucormycosis is suspected, order "Fungal Culture". Specimens collected by more invasive procedures, such as bronchial lavage, have a better yield in detecting these organisms. Indicate the suspected agents in the Alert/Instructions field when ordering the test in Apex. KOH is routinely included as part of Fungal culture. 
 
Mycobacteria: Collect 3 separate sputum samples in 8-12 hour intervals, including at least one early morning sample. Sputum samples collected <8 hours apart are pooled & tested as a single specimen.
 
Parasites: Refer samples for Pneumocystis carinii to Cytology. For other parasites, specify the organism sought when ordering the test.
 
Viruses: SPUTUM is not an appropriate specimen.
 
Herpes simplex: Because HSV is frequently excreted asymptomatically, sputum is a poor specimen for the diagnosis of HSV pneumonitis. See Bronchoalveolar lavage above.
  
Respiratory viruses: For tracheal aspirates, Respiratory Virus Panel PCR may be ordered.
 

SKIN (see also WOUND):

Collection: Tissue obtained by biopsy is often the best specimen for the diagnosis of skin infections, but aspirated or drained pus, vesicular fluid, or skin scrapings may be useful for the diagnosis of some infections.
 
Bacteria (routine): For erysipelas, impetigo, and cellulitis swabs taken from superficially crusted and weeping lesions, when present, should be submitted in transport medium. Needle aspiration of the center or the margin of the area involved is of limited utility in these infections. For paronychia, whitlow, folliculitis, and carbuncles, submit the aspirated pus or - less desirable - submit the purulent drainage on a swab in transport medium.
 
Fungi: For ulcerated and/or nodular fungal skin infections (sporotrichosis, blastomycosis, or infections due to Cryptococcus spp.), submit a skin biopsy from the margin of the lesion in parallel with a specimen submitted to Dermatopathology for histologic examination. Order “Fungal Culture with KOH Stain”. For superficial mycoses (e.g., Candida, Epidermophyton, Trichophyton, or Microsporum spp.) submit skin scrapings, hair, or nails in a clean tube and order  “Fungal Culture, Dermatophytes with KOH Fungal Stain”  Alternatively, specimens collected in the dermatology clinic may be inoculated directly onto mycobiotic agar and submitted to the lab for culture only, ordering “Fungal Culture, Dermatophytes (Dermatology Clinic).”
 
Mycobacteria and Nocardia spp.: For ulcerated and/or nodular skin lesions due to acid-fast organisms (e.g., Mycobacterium marinum, Nocardia asteroides) submit a skin biopsy for mycobacterial culture in parallel with a specimen submitted to Dermatopathology for histologic examination.
 
Parasites: For Leishmania spp., smears of aspirates or touch preparations are stained with Giemsa and examined microscopically. Wet mounts from skin snips from the buttock, calf, or area over the scapula can be examined to diagnose filarial (onchocercal) infection; this test is not useful for the diagnosis of cutaneous larval migrans. Tissues should be submitted to Dermatopathology for histologic examination for parasites.
 
Viruses:
Herpes simplex: To obtain a sample for culture, unroof the vesicle and collect the fluid contents and basal cell layer with a flocked swab. Place swab in Universal Transport Medium (UTM). Dried crusts from older lesions are unsuitable. Swabs with wooden shafts may contain compounds which are toxic to the virus. To obtain a sample suitable for direct examination with fluorescent antibody, scrape the base of an opened vesicle with a sterile scalpel blade and transfer the cells obtained onto two clean glass slides, making two spots on each slide, each approximately 1.5 cm. in diameter (the size of a dime). Let the slides air-dry and submit them for staining. See also Varicella-zoster below.  
 
Varicella-zoster: Direct antigen testing is the most effective means of detection. To obtain a sample suitable for direct examination with fluorescent antibody, scrape the base of an opened vesicle with a sterile scalpel blade and transfer the cells obtained onto two clean glass slides, making two spots on each slide, each approximately 1.5 cm. in diameter (the size of a dime). Let the slides air-dry and submit them for staining.
 

STOOL:

Collection: Collect a fresh specimen in a clean, plastic cup with lid that does not leak (a non-sterile container is satisfactory). Deliver in <1 hr to the laboratory. Outpatients should obtain instructions and containers from the laboratory or from the outpatient phlebotomy stations. For samples requiring a preservative, the method of preservation is described below with the test description. 
 
Bacteria (routine): Fresh stool must be received in the Microbiology Laboratory within 3 hours of collection. Recovery of Shigella is probably improved if the specimen is brought to the Laboratory within 15 minutes of collection. Vials containing Cary-Blair transport medium are available for bacterial culture of stool specimens which cannot be delivered to the laboratory within 3 hrs of passage. Fill these containers only up to the red line. Stool specimens give better recovery rates for enteric pathogens than do rectal swabs. Two specimens collected 24-48 hrs apart are sufficient for the detection of the great majority of cases; a greater number of specimens require consultation with the laboratory. Swabs should be submitted in Cary-Blair preservative.
 
Nosocomial acquisition of stool pathogens is extremely uncommon. If bacterial enteritis is suspected, stool cultures should be requested upon admission to the hospital; they will not be accepted routinely on patients who have been hospitalized for >3 days. Contact the laboratory for exceptions.
 
Specimens are routinely cultured for Salmonella, ShigellaCampylobacter spp. and E. coli O157, and tested for Shiga toxin. Aeromonas, Edwardsiella, and Plesiomonas can also be recovered from a routine stool culture. If Yersinia or vibrios (Vibrio cholerae or V. parahaemolyticus) are suspected, order culture for these agents separately.
 
Clostridium difficile toxin: Submit fresh stool. Asymptomatic carriage is common, so only symptomatic patients should be tested. Submit stools from patients with diarrhea ONLY (>= 3 unformed stools in <= 24 hours, stool must conform to shape of container). A rectal swab can be collected from patients with ileus - indicate "ileus" in the comment field when ordering the test. Repeat tests within 1 week are not allowed without approval by the microbiology laboratory. Testing on patients under 1 year of age requires approval from the Pediatric Infectious Disease service.
 
Fecal WBCs: Select a sample of diarrheal stool with an applicator stick, including the bloody or mucous discharge if present. Because WBCs lyse in old specimens, the specimen should be brought to the laboratory within 3 hours of collection. This test lacks sensitivity and specificity to diagnose cause of hospital-acquired diarrhea and is only done on outpatients and in patients <72 hrs post admission.
 
Fat Globules, Qualitative Smear for: Submit unpreserved stool. This test is only useful in patients over 6 months of age.
 
Fungi: Test not offered.
 
Mycobacteria: Test not offered.
 
Parasites ("O & P"): Collect 3 samples (no more than one per 24-48 hours) to improve the chance of a positive result. Fresh stool must be received in the Microbiology Laboratory within 1 hour of collection. Alternatively, submit stool in SAF (Sodium Acetate-Acetic Acid-Formalin) fixative vials. Follow the instructions which accompany the vials. Fill to the red line only. Patients should not have received antimicrobial therapy or barium contrast medium for at least 7 days prior to sample collection. 
 
Cryptosporidium: Routine ova and parasite examination includes a screening test for Cryptosporidium. If the routine O & P examination is negative for Cryptosporidium and infection is still suspected, order a Coccidia Exam, which will detect low numbers of the organism.
 
Giardia lamblia: Submit fresh stool or stool in SAF fixative. The antigen test is preferred to Ova and Parasite Examination if Giardia is the only intestinal parasite in the differential diagnosis. Nosocomial acquisition of parasites is even more uncommon than nosocomial shigellosis. If parasitic enteritis is suspected, O & P examinations should be requested upon admission to the hospital; these will not be accepted routinely on patients who have been hospitalized for >3 days. Contact the laboratory for exceptions.
 
Microsporidium: Order separately from routine Ova and Parasite exam.
 
Pinworm: Collect 3 swube paddles from 3 consecutive mornings. Collect each specimen BEFORE defecation or bathing. Collection paddles are available from outpatient phlebotomy stations or from the laboratory. If these paddles are unavailable, transparent, clear Scotch tape (not Magic Mending tape) can be used for collection and applied sticky side down to a clean glass microscope slide.
 
Viruses: The agents of viral gastroenteritis are generally not cultivable, including Adenovirus 40 and 41, Norwalk agent and Rotavirus.
 
Enterovirus: PCR for enteroviruses is used only to aid in defining the cause of aseptic meningitis and/or neonatal viral sepsis. Submit fresh, unpreserved stool in a sterile container. 
 
Rotavirus antigen: A test for Rotavirus antigen assay by EIA is available to diagnose diarrheal disease in pediatric patients. Submit fresh stool in a plastic cup. Repeat testing may be performed every 7 days.
 

THROAT:

Bacteria (routine): Submit dacron swab in paper wrapper. Unless a search for a specific organism or diagnosis is requested (e.g., diphtheria, gonorrhoea, thrush), throat cultures are routinely processed only to exclude the possibility of group A streptococcal pharyngitis.
 
Neisseria gonorrhoeae and  Chlamydia trachomatis:
 
Nucleic acid detection is a sensitive method for diagnosis of CT / NG infections and is the recommended method for most patients.
 
CT/NG DNA Specimen Collection Instructions
 
Chlamydia trachomatis culture is generally indicated to assess clinical treatment failure, where DNA may persist post-treatment. Culture requires transport of tissue or swab in special UTM media, available from the Microbiology Laboratory.
 
Neisseria gonorrhoeae culture is generally indicated to assess clinical treatment failure, and to provide an isolate for susceptibility testing. Culture requires a swab in Amies transport medium with charcoal.
 
Fungi: see Bacteria (routine) - specify a diagnosis of possible thrush.
 
Viruses: Refer to NASOPHARYNGEAL SPECIMENS for appropriate collection of specimens for respiratory viruses.
 

TISSUE (see also WOUND): 

Submit in an anaerobe transport vial (available in the operating rooms and Microbiology), or in a sterile container if too large to fit in an anaerobic transport vial. Do not place the tissue in Amies transport medium with charcoal
 

TRACHEAL ASPIRATE: see SPUTUM

URETHRA:

Collection: Wipe the urethra clean and preferably collect specimen >1 hr after urination
 
Bacteria: "Milk" the urethra and collect the discharge. If no discharge is present, insert a swab 2-4 cm into the urethra and rotate for 15-30 seconds. Place the collection swab in Amies charcoal-containing transport medium and submit it to the laboratory within 6 hours of collection.
 
Neisseria gonorrhoeaeChlamydia trachomatis and Trichomonas vaginalis:
 
Nucleic acid detection is a sensitive method for diagnosis of CT / NG and Trhichomonas vaginalis infections and is the recommended method for most patients.
 
CT/NG RNA and Trichomonas vaginalis Specimen Collection Instructions
 
Chlamydia trachomatis culture is generally indicated to assess clinical treatment failure, where DNA may persist post-treatment. Culture requires transport of tissue or swab in special UTM media, available from the Microbiology Laboratory.
 
Neisseria gonorrhoeae culture is generally indicated to assess clinical treatment failure, and to provide an isolate for susceptibility testing. Culture requires a swab in Amies transport medium with charcoal.
 

URINE:

Collection: The culture should be refrigerated promptly and should not sit at the patient's bedside at room temperature. 
  1. Clean-voided urine for culture is collected in a clean, dry plastic cup with a non-leaking lid (non-sterile containers are OK):
    1. Females:
      1. Instruct patient to:
        1. Wash hands with soap and water
        2. Holding the labia apart, wash the entire area with the sterile cleansing towelette provided; wiping from front to back.
        3. Continue spreading the labia and start to urinate directly into the toilet.
        4. During midstream, position the container, and then begin urinating into the container. Do not touch the container to the genital area
        5. It is not necessary to fill the cup, half full is enough.
        6. Instruct patient to return sample to a specified location.
      2. Males:
        1. Instruct patient to:
          1. Wash hands with soap and water
          2. Pull back foreskin if present
          3. Completely wash the glans penis (“head” of penis) using a sterile cleansing towelette provided.
          4. Start to urinate directly into the toilet
          5. During mid-steam, position the container, then begin urinating into the container. Do not touch the container to the genital area
          6. It is not necessary to fill the cup, half full is enough.
          7. Return sample to a specified location.
    2. Indwelling catheter urine is collected by aspirating the urine through the catheter port using a sterile vacutainer tube with a red stopper ("plain, sterile"). Alternatively, the urine can be collected using a needle and syringe, and transferred to a red stopper vacutainer tube (pop the top of the vacutainer tube; there is no need to go through the rubber diaphragm with a needle). Do not send urine obtained from the long drainage tube or a collection bag.
    3. The first collection immediately after insertion of a catheter is considered a "straight cath urine." Straight catheter urine is collected using catheter collection kits. Urine is placed in screw-capped cup.
    4. Foley catheter tip cultures are unsuitable for the diagnosis of urinary infection and are not accepted for processing. 
Bacteria (routine): Quantitative culture is performed on all urine specimens. Gram stains are performed only on request. A single culture is adequate in a clinical situation requiring rapid institution of therapy. There is no need for repeat specimens to be submitted at daily or other frequent intervals. 
Reports of genital flora mixed with other organisms in amounts >1000 colony-forming units (CFU)/mL will be accompanied by a notation such as "Mixed flora present. Suggest recollection if clinically indicated". Mixed flora are not routinely identified unless the specimen was properly collected from a catheter or nephrostomy tube. If a culture yields one organism, the organism will be identified. If two or more organisms are present they will be identified according to an algorithm that takes into account the clinical setting and total bacterial count in the urine. Susceptibility tests are routinely performed only if >10,000 CFU/mL are found in midstream urine or if >1000 CFU/mL are present in specimens obtained by catheter, ureterostomy, or nephrostomy drainage. A physician desiring a different procedure on a specimen should contact the laboratory.
 
Screening Culture: A screening culture may be requested by clicking the "Omit ID" and "Omit Susceptibility" buttons in the Alerts/Instructions field when ordering a urine culture in Apex. This is a less expensive quantitative culture for which species identification and susceptibility testing will only be performed (at an additional charge) if specifically requested after results are reported. Plates from positive urine screening cultures are saved for 7 days. This test is particularly appropriate for screening of children, pregnant women, young women with first UTIs, and patients on Foley catheter drainage.
 
Fungi: Order a bacterial culture when urinary tract infection due to yeast is suspected. Consult with the laboratory prior to submission of urine when infection with other fungal agents are suspected.
 
Mycobacteria: The best urinary specimen is the first morning void, which is approximately an 8-hour specimen held under conditions usually free of other bacteria. Twenty-four hour urine cultures are not performed because overgrowth with contaminants is a frequent cause of unsuccessful acid-fast culture. Specimens should be collected by a "clean-voided" technique (see above). Because tuberculosis of the urinary tract is extremely uncommon in our patient population, urine cultures for mycobacteria require consultation with the laboratory. Cultures are generally restricted to patients with positive PPDs who are found to have unexplained pyuria with negative routine bacterial cultures. Urine cultures should not be used to detect cases of pulmonary tuberculosis. AFB stain is not routinely performed on urine because urine is rarely positive, and nonpathogenic mycobacteria which are morphologically similar to M. tuberculosis are frequently present in the genitourinary tract.
 
Parasites: Urine collected and pooled between 1000 and 1400 hrs can be examined for Schistosoma haematobium and (rarely) microfilariae.
 
Viruses:
 
CMV: Urine culture for CMV is only appropriate for newborns up to 3 weeks to attempt to document congenital infection as opposed to infection acquired during delivery which becomes urine positive after 3-4 weeks postpartum. Urine from patients >3 weeks of age requires approval by Infectious Diseases Service or the Section Chief.
 
Adenovirus, BK virus (papovavirus), mumps, measles, rubella: Requests for measles and rubella require consultation with SF Department of Public Health. Order the BK virus DNA Quantitative PCR test for BK virus, which is more sensitive than culture.
 

VAGINA/CERVIX:

Collection: Use a speculum without lubricant (the lubricant can be toxic to the cells and microorganisms of interest). Wipe the cervix clean of vaginal secretions and mucus.
 
Bacteria: Collect the endocervical exudate on a dacron swab with a rotating motion. Place the swab in Amies charcoal-containing transport medium and submit it to the laboratory within 6 hrs of collection.
 
If culture for potential pathogens other than Neisseria gonorrhoeae is indicated, order Bacterial Culture and Gram Stain, Genital and when possible indicate what potential pathogens are of concern. Potential pathogens include beta-hemolytic streptococci, Staphlococcus aureus, large numbers of yeasts and gram-negative rods, and Haemophilus species, etc.
 
Vaginal-rectal cultures of pregnant women for group B streptococci should be ordered as Streptococcus Group B Culture.
 
Bacterial vaginosis/vaginitis: Order Vaginal Smear for Bacterial Vaginosis/Yeast and submit thin smears of vaginal discharge on 2 slides, or collect swab in Amies transport medium with charcoal. Microscopic examination of a Gram-stained smear of vaginal secretions can disclose both "clue" cells, consistent with a diagnosis of bacterial vaginosis, and yeasts.
 
Neisseria gonorrhoeae, Chlamydia trachomatis and Trichomonas vaginalis:
 
Nucleic acid detection is a sensitive method for diagnosis of CT / NG and Trichomonas vaginalis infections and is the recommended method for most patients.
 
CT/NG RNA and Trichomonas vaginalis Specimen Collection Instructions
 
Chlamydia trachomatis culture is generally indicated to assess clinical treatment failure, where DNA may persist post-treatment. Culture requires transport of tissue or swab in special UTM media, available from the Microbiology Laboratory.
 
Neisseria gonorrhoeae culture is generally indicated to assess clinical treatment failure, and to provide an isolate for susceptibility testing. Culture requires a swab in Amies transport medium with charcoal.
 
Herpes simplex: To obtain a sample for culture, gently clean the surface of an intact genital vesicle with saline. Unroof the vesicle and collect the fluid contents and basal cell layer with a flocked swab. Place a swab in Universal Transport Medium (UTM). Swabs with wooden shafts may contain compounds which are toxic to the virus. To obtain a sample suitable for direct examination with fluorescent antibody, scrape the base of an open vesicle with a sterile scalpel blade and transfer the cells obtained onto two clean glass slides, making two spots on each slide, each approximately 1.5 cm. in diameter (the size of a dime). Let the slides air-dry and submit them for staining. 
 
Group B streptococcus: For optimal sensitivity, obtain selective broth medium from Microbiology. Swab the lower vagina and rectum, and submit the swabs to the laboratory in the medium. Alternatively, submit the swabs in Amies charcoal-containing transport medium.
 
Trichomonas vaginalis: Submit APTIMA vaginal or cervical swab, see CT/NG DNA Specimen Collection Instructions.
 
Yeast: see Bacterial vaginosis above. Vaginal Smear for Bacterial Vaginosis/Yeast will readily detect clinically active vaginal yeast infection. Culture is generally unnecessary unless isolation of the organism is required for susceptibility testing in cases of treatment failure.
 

WOUND (including Abscess and Drainage; see also SKIN and TISSUE):

Collection: A tissue specimen is preferred to a specimen of pus, but pus is superior to swabs submitted in transport medium. 
Submit tissue in an anaerobe transport vial (available in the operating rooms and Microbiology), or in a sterile container if too large to fit in an anaerobic transport vial. Do not place the tissue in Amies transport medium with charcoal. Submit fluid in a sterile, clear plastic black top tube. When neither tissue nor sufficient pus or fluid is available, send at least two dacron swabs in Amies charcoal transport medium.
 
Bacteria (routine): Includes procedures to isolate aerobic and anaerobic bacteria. Anaerobic cultures can only be performed from swabs if the swabs are submitted in Amies transport medium with charcoal. Anaerobic cultures are not done on specimens such as swabs from boils, cath tip swab, cellulitis, decubiti, pustule/pus, skin, sutures, ulcers (and not from OR), and peritoneal shunt tips.
 
Fungi:
 
Candida and Aspergillus: Cultures for these pathogens should be specifically requested when their presence in abscesses and superficial wounds is suspected. Tissues and fluids from normally sterile sites are automatically examined for both yeast and Aspergillus.
 
Other species: When other, mycelia-forming fungi are suspected, the optimal sample is a biopsy of the involved tissue. Cultures are held for 30 days. Swabs are unacceptable specimens for culture of mycelia-forming organisms, particularly organisms such as those causing mucormycosis, because they frequently fail to yield the pathogen seen in and grown from biopsies.
 
Mycobacteria: Wound cultures for mycobacteria are infrequently indicated and are not performed from swab specimens. If Nocardia spp. are suspected, order AFB culture, and indicate "Look for Nocardia".
 
Parasites: see Skin
 
Viruses: Request testing for the specific viruses of clinical interest. Tissue from infected areas should be collected aseptically and transported to the laboratory in Universal Transport Medium (UTM). 
 
Cytomegalovirus: Tissues can be cultured for CMV but the distinction between shedding of CMV (carriage) and active disease is difficult to make.
 

Reporting and Normal Flora

All organisms present in normally sterile materials are reported whether or not they are likely to be contaminants. Species known to be frequently pathogenic may be reported from normally nonsterile areas; however, when present in scant numbers, they are not necessarily clinically significant. The normal flora are listed in the following table

 

ORGANISMS CONSISTENT WITH NORMAL FLORA

Gastrointestinal and Rectal Cultures

  • various gram-negative bacteria other than Salmonella, Shigella, Campylobacter, Aeromonas, Yersinia, Edwardsiella and Vibrio species 
  • non-dextrose-fermenting gram-negative rods enterococci 
  • enterococci
  • Staphylococcus epidermidis
  • alpha-hemolytic and nonhemolytic streptococci 
  • diphtheroids 
  • Staphylococcus aureus in small numbers 
  • yeast in small numbers 
  • anaerobes in large numbers 

Genital Cultures

  • Any amount of the following:
  1. Corynebacterium species 
  2. Lactobacillus species 
  3. alpha-hemolytic and nonhemolytic streptococci 
  4. nonpathogenic Neisseria species 
  • The following when mixed and not predominant:
  1. Enterococci 
  2. Enterobacteriaceae and other gram-negative rods 
  3. Staphylococcus epidermidis
  4. Staphylococcus aureus
  5. Gardnerella vaginalis
  6. Candida species and other yeasts 
  7. Anaerobes (too many species to list) 

Oronasal (oral, nasal, and pharyngeal) Cultures

  • Any amount of the following:
  1. Corynebacterium species
  2. nonpathogenic Neisseria species 
  3. alpha-hemolytic and non-hemolytic streptococci 
  4. Staphylococcus epidermidis
  5. anaerobes (too many species to list; varying amounts of Prevotella species, anaerobic cocci, Fusobacterium species, etc.) 
  • Lesser amounts of the following when accompanied by the above:
  1. yeasts 
  2. Haemophilus species 
  3. pneumococci 
  4. Staphylococcus aureus
  5. gram-negative rods 
  6. Neisseria meningitidis

Skin Cultures

  • Staphylococcus epidermidis
  • Staphylococcus aureus (in small numbers) 
  • micrococcus species 
  • nonpathogenic Neisseria
  • alpha-hemolytic and nonhemolytic streptococci 
  • Propionibacterium species 
  • small numbers of other organisms (e.g., Candida or Acinetobacter species) 

 


Susceptibility Testing

Susceptibility testing is performed by the microtiter broth dilution technique, and   in special situations by the disk diffusion [Bauer-Kirby] method. Susceptibility testing and reporting formats provide both numerical and interpretive reports of the minimum inhibitory concentration (MIC) of each drug tested. The MIC, the lowest concentration of a drug that inhibits the growth of the organism in vitro, is reported in mg/L (µg/mL).

Varying batteries of drugs are employed. The tables on the following pages give the drugs reported for specific organism types. The system is continuously adjusted in response to new information and current needs. Susceptibility testing for other drugs  is not performed  without consultation by Infectious Diseases Service or  Infectious Diseases Pharmacy.

Susceptibility tests will routinely be set up on any organism judged potentially significant by the laboratory, if the test has not been performed on the same organism within 7 days (4 days for Nafcillin-resistant Staphylococcus aureus, Pseudomonas aeruginosa, Citrobacter, Enterobacter, and Serratia spp.). The plates from significant cultures are held in the lab for 7 days after the final report isissued. Thus it is possible to obtain susceptibilities after the report is received. 

 

Conditional Reporting of Antimicrobial Susceptibility 

In conjunction with the Pharmacy and Therapeutics Committee and the Infectious Disease Service, the Microbiology section of the Clinical Laboratories has developed a heirarchical scheme of reporting antimicrobial susceptibility test results. The intent of conditional reporting is to reduce the use of the more costly or toxic antimicrobials in instances where they are not needed, and thus decrease the enormous costs of antimicrobial usage at UCSF. 

Susceptibility results will be reported for a panel of primary drugs consisting of standard, less expensive (often generic), and less toxic agents. If organisms are resistant to these primary drugs, additional results will be reported for more expensive, potentially more toxic drugs of second choice. This procedure follows the general principles set forth by the Clinical and Laboratory Standards Institute, and has been recommended by the UCSF Antibiotic Advisory Subcommittee of the Pharmacy and Therapeutics Committee.

Drug panels have been devised for staphylococci, streptococci, enterococci , enterobacteriaceae, Pseudomonas aeruginosa, and other organisms, and take into account whether the isolates are from urine or from other sites. Primary drugs are always reported; secondary drugs are reported only if resistance is found to the specific primary drug. These panels and the conditionally reported secondary drugs are described below:  

Staphylococcus (except S. saprophyticus)

Primary drugs Secondary drugs
Clindamycin (supressed on urine and CSF; suppressed on S. epidermidis group if erythromycin-R and Clindamycin-S or -I)  
Erythromycin (supressed on urine and CSF)  
Nafcillin, if resistant report:
For nafcillin susceptible isolates, nafcillin or cefazolin is the treatment of choice.
Vancomycin
Penicillin (If not reported but being considered for therapy, contact Microbiology.)  
Tetracycline (suppressed on CSF and blood)  
Trimethoprim-sulfamethoxazole (suppressed on blood)  

 

 

Staphylococcus saprophyticus

Not routinely tested. Note added: Urinary tract infections with this organism respond to antimicrobial agents such as nitrofurantoin, TMP SMZ, or a fluoroquinolone at concentrations achieved in urine in patients with normal renal function. Contact laboratory for susceptibility testing in cases of treatment failure or allergy.

 

 

Enterococcus

Primary drugs Secondary drugs
Ampicillin  
Ciprofloxacin (urine only)  
Gentamicin, high level (suppressed on urine)  
Nitrofurantoin (urine only)  
Tetracycline (urine only)  
Vancomycin, if resistant report: Tetracycline (non-sterile sites only)
Daptomycin, (reported on VRE from sterile sites, except CSF)
Linezolid (reported on VRE from sterile sites, including CSF)

 

Group A, C and G Streptococcus

Primary drugs
Clindamycin
Erythromycin
Penicillin

 

Group B Streptococcus (done on OB patients if penicillin allergic)

Primary drugs
Clindamycin

 

Group B Streptococcus (sterile sites)

Not routinely tested. Note added: (This species is universally susceptible to penicillin. Susceptibility testing is only indicated for allergic patients.)

 

 

Viridans Streptococcus

Primary drugs
Cefotaxime
Ceftriaxone
Clindamycin (suppressed on CSF)
Erythromycin (suppressed on CSF)
Levofloxacin (suppressed on CSF)
Penicillin 
Vancomycin

 

Streptococcus pneumoniae

 
Sites other than blood and CSF) and isolate from nonsterile site with reduced susceptibility to penicillin:
Primary drugs Secondary drugs
Cefotaxime  
Ceftriaxone, if intermediate or resistant report: Meropenem
Clindamycin  
Erythromycin  
Levofloxacin  
Penicillin  
Tetracyline   
Trimethoprim-sulfamethoxazole  
Vancomycin   
Blood or CSF:
Primary drugs Secondary drugs
Cefotaxime  
Ceftriaxone, if intermediate or resistant report: Meropenem
Penicillin   
Vancomycin  

 

Corynebacteria

Susceptibilities are done on request.

 

Neisseria meningitidis

Susceptibilities are done on isolates from sterile sites.
The following drugs are reported for prophylaxis of meningococcal case contacts and not for therapy of patients with invasive meningococcal disease:

 

Primary drugs
Azithromycin
Ciprofloxacin
Minocycline 
Rifampin

 

Haemophilus influenzae

Susceptibilities are done on request.

 

Salmonella

 

Criteria for performing susceptibilities on isolates from stool:

  • infant <6 months
  • Salmonella typhi, S. paratyphi A, S. choleraesuis

Primary drugs

Secondary drugs

Ampicillin (suppressed on CSF), if intermediate or resistant report:

Ampicillin-sulbactam (suppressed on CSF)

Ceftriaxone (suppressed on stool, except if Salmonella typhi, S. paratyphi A, S. choleraesuis

 

Trimethoprim-sulfamethoxazole

 

Ciprofloxacin(suppressed on CSF)

 

Levofloxacin (suppressed on CSF)

 

 

Shigella/Plesiomonas/Edwardsiella tarda                                                                                                                                       

Primary drugs

Secondary drugs

Ampicillin (suppressed on CSF), if intermediate or resistant report:

Ampicillin-sulbactam (suppressed on CSF)

Ceftriaxone (suppressed on stool)

 

Ciprofloxacin (suppressed on CSF)

 

Levofloxacin (suppressed on CSF)

 

Trimethoprim-sulfamethoxazole

 

 

Aeromonas                                                                                                

Primary drugs

Ceftriaxone (suppressed on stool)

Ciprofloxacin(suppressed on CSF)

Levofloxacin(suppressed on CSF)

Trimethoprim-sulfamethoxazole

 

Vibrio cholerae                                                                                                                                                                         

Primary drugs

Ampicillin

Trimethoprim-sulfamethoxazole

Tetracycline

 

Vibrio spp., not V. cholerae                                                                              

Primary drugs

Secondary drugs

Ampicillin (suppressed on CSF), if intermediate or resistant report:

Ampicillin-sulbactam (suppressed on CSF)

Ceftazidime (suppressed on stool)

 

Ciprofloxacin(suppressed on CSF)

 

Levofloxacin(suppressed on CSF)

 

Trimethoprim-sulfamethoxazole

 

Tetracycline

 

 

Campylobacter

Drug is reported only if resistant                                          

Primary drugs

Ciprofloxacin

Erythromycin

 

 

Enterobacteriaceae, other than Salmonella, Shigella, Plesiomonas and Edwardsiella tarda

Primary drugs Secondary drugs
Ampicillin-sulbactam (suppressed on CSF and Enterobacter spp.) Ampicillin-sulbactam (suppressed on CSF and Enterobacter spp.)
Cefazolin(suppressed on CSF)  
Cefepime (Enterobacter spp. only)  
Ceftriaxone, (suppressed on Enterobacter spp.), if intermediate or resistant report: Cefepime and Ertapenem
If Ertapenem-I or R, Meropenem is reported
Ciprofloxacin(suppressed on CSF)  
Ertapenem (Suppressed on CSF; Enterobacter spp. only), if intermediate or resistant report: Meropenem
Gentamicin  
Levofloxacin(suppressed on CSF)  
Nitrofurantoin (urine only)  
Piperacillin-tazobactam (suppressed on CSF and Enterobacter spp. from all sites except urine)  
Tobramycin  
Trimethoprim-sulfamethoxazole  

 

Pseudomonas aeruginosa

Primary drugs Secondary drugs
Aztreonam (suppressed if ceftazidime I or R)  
Ceftazidime, if intermediate or resistant report: Cefepime & Meropenem
Ciprofloxacin(suppressed on CSF)  
Levofloxacin(suppressed on CSF)  
Piperacillin-tazobactam (suppressed on CSF)  
Tobramycin, if resistant report: Amikacin

 

Stenotrophomonas maltophilia

Isolation of this organism from non-sterile sites may represent colonization. For drug susceptibility, contact microbiology lab. For empiric therapy recommendations, contact ID pharmacy. Susceptibilities are routinely performed on normally sterile sites and from cystic fibrosis patients:

 

Primary drugs
Ceftazidime
Minocycline
Trimethoprim-sulfamethoxazole

 

Acinetobacter spp.

Primary drugs Secondary drugs
Ampicillin-sulbactam (suppressed on CSF)  
Ceftriaxone, if intermediate or resistant report: Cefepime & Meropenem
Ciprofloxacin(suppressed on CSF)  
Gentamicin  
Levofloxacin(suppressed on CSF)  
Piperacillin-tazobactam (suppressed on CSF)  
Tobramycin  
Trimethoprim-sulfamethoxazole  

 

Glucose nonfermenters, not S. maltophilia, Acinetobacter spp., and B. cepacia

Primary drugs Secondary drugs
Aztreonam (suppressed if ceftazidime I or R)  
Ceftazidime, if intermediate or resistant report: Cefepime & Meropenem
Ciprofloxacin(suppressed on CSF)  
Gentamicin  
Levofloxacin (suppressed on CSF)  
Piperacillin-tazobactam (suppressed on CSF)  
Tobramycin  
Trimethoprim-sulfamethoxazole  

 

Burkholderia cepacia

Primary drugs
Ceftazidime
Meropenem
Minocycline
Trimethoprim-sulfamethoxazole

 

Campylobacter

Drug is reported only if resistant

 

 

Nocardia

Primary drugs
Amikacin
Cefotaxime
Ceftriaxone
Ciprofloxacin 
Imipenem
Minocycline
Trimethoprim-sulfamethoxazole  

 

Rapid growing mycobacteria

Primary drugs
Amikacin
Cefoxitin 
Ciprofloxacin 
Clarithromycin
Doxycycline
Tobramycin (only reported if M. chelonae) 
Trimethoprim-sulfamethoxazole

 

If a suitable primary or secondary drug is unavailable, testing against appropriate additional antimicrobial agents can be undertaken on request. Consult the laboratory.

Criteria for Susceptibility

Susceptibility results are interpreted using CLSI guidelines based on MIC values or Kirby-Bauer zone sizes. The interpretations of the susceptibility test results are definedas follows: 

S- Susceptible: The organism is inhibited by the antimicrobial at a concentration readily achieved in blood and urine with the usual dosing. 

I- Intermediate (or indeterminate): Higher doses of the antimicrobial than usual may be required to achieve an inhibitory serum concentration. An interpretation of I for anti-pseudomonal penicillins suggests only that the drug should not be used as a single agent, but should be employed in combination with an aminoglycoside. 

R- Resistant: The organism is not inhibited by the antimicrobial, even at concentrations achievable in serum or in urine using high doses. 

Antimicrobial Susceptibility Patterns

Current information regarding the cumulative percentage of commonly isolated bacterial species which are susceptible to a given level of antimicrobial and the number of strains in the UCSF data base can be found at http://clinicalpharmacy.ucsf.edu/idmp/antibiogram_home.htm. The data include isolates from both community-acquired and nosocomial infections which have met the laboratory criteria for potential clinical importance (e.g., urine >=100,000/mL, isolates from normally sterile sites such as blood, predominant organisms from a wound, etc.). However, not all the bacteria unequivocally represent clinically significant infections (e.g., S. epidermidis).

Appropriate Specimens for Identifying Most Common Viral Etiologies

Syndromes and Probable
Viral Agents

Nasopharynx*

Throat

Stool

CSF

Urine

Other

Respiratory syndrome
   Influenza A,B virus

+++(PCR)

         
   Parainfluenza

++(PCR)

         
   Respiratory syncytial virus

++++(PCR)

         
   Adenovirus

++(PCR)

         
   Rhinovirus

+++(PCR)

         
   Metapneumovirus

++(PCR)

         
   Corona (incl. SARS)

++(PCR)

         
Dermatologic and mucous membrane disease
Vesicular
   Herpes simplex          

vesicle (C, FA) +++

   Varicella zoster          

vesicle (FA) ++++

   Enterovirus (hand, foot mouth syndrome)  

 

 

   

vesicle (PCR) ++

Exanthematous
   Enterovirus  

 

 

   

plasma (PCR) +++

   Measles

+++(C,PCR)

     

++(C,PCR)

blood (S) +++ 

   Rubella

+++(PCR)

 

   

+++(PCR)

blood +++ 

Meningoencephalitis
   Arbovirus (eg. West Nile)      

+++(PCR)

 

blood (S) +++

   Enterovirus  

 

 

+++(PCR)

   
   Herpes simplex      

+++(PCR)

   
   VZV      

++(PCR, S)

   
Gastrointestinal
   Rotavirus    

++(Ag, PCR)

     
   Noroviruses    

++(PCR,Ag)

   

blood (S)

Congenital and perinatal
   Cytomegalovirus        

++++(C)

 
   Enterovirus  

 

 

   

blood (PCR) +++

   Herpes simplex virus  

++(C)

 

++(PCR)

 

vesicle (FA,C) ++++

CMV infection
   Cytomegalovirus (CMV)        

++++(C)

blood (PCR) +++
tissue (H) ++

Hepatitis (A-E)

blood (S,PCR) ++++

Hepatitis B and C

blood (S,PCR) +++

AIDS
   HIV          

blood (S) ++++
(PCR) ++++ 

Myocarditis, pericarditis and pleurodynia
   Coxsackie B  

 

 

   

pericardial fluid (PCR)+

 

Ag = antigen detection
bDNA = branched DNA
C = culture
FA = fluorescent antibody
H = histology
PCR = polymerase chain reaction
S = serology
++++ = likelihood of positivity