Microbiology Laboratory Tests: Calicivirus to Cholera

Microbiology
Norovirus
Related Agents: Norwalk-like Virus, Norovirus
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Microbiology - Calicivirus
Test Includes: Real-Time PCR for Norovirus 

Reporting

Results Available: 1-3 days Contact #s: 512-458-7735

Reference

Method: Real-Time PCR  
Turnaround Time:  1-3 days Reference Range:  Negative
Limitations: May not detect nucleic acid material in all cases Interpretation: A negative result does not indicate that the patient is not infected. The laboratory test may not be able to detect very low levels of virus.

Specimen Requirements

Specimen Collection: Feces Sample Type: Feces
Volume/Amount Required: At least 200 µL Preferred Specimen:  Feces
Collection/Preservation: Collect fresh, no preservatives Storage Instructions: store cold,  4° C, do not freeze
Causes for Rejection: Improper specimen, bloody stool Sample Container: Stool specimen must be in sterile container without preservatives.
Sample Test Kit: Availability: Test is performed 1-2 times per week
Diagnostic Information:  Detection of viral RNA by real-time PCR. Absence of viral RNA does not necessarily indicate lack of infection. Testing performed on outbreak specimens.

Specimen Submission

Required Request Form: G-2B  Specimen Handling: Keep cold,  4° C, do not freeze
Transport Temperature:  2-8° C (refrigerated) Shipping Requirements: Ship on wet ice

Billing

CPT Code: 87798 Fees:


Microbiology
California Encephalitis (Serological)
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Microbiology - California Encephalitis (Serological)
Test Includes: Enzyme assay for IgM and IgG antibody to California Virus

Reporting

Results Available: 2-3 days Contact #s: 512-458-7514

Reference

Method: EIA  
Turnaround Time: 2-3 Days Reference Range: Nonreactive
Limitations: May not detect a recent infection, or infection in a person with a severely compromised immune system. May be cross reactivity with other arthropod borne viruses. Interpretation: Nonreactive indicates that the patient does not have detectable antibody to the infectious agent. Reactive indicates that the patient has detectable antibody to the infectious agent, and depending on the clinical picture, may have a current or past infection.

Specimen Requirements

Specimen Collection: Venipuncture, spinal tap Sample Type: Serum, CSF
Volume/Amount Required: 10 mL whole blood, 3-4 mL CSF Preferred Specimen:  Paired Sera
Collection/Preservation: red or tiger top tube Storage Instructions: Ambient (Room) temperature
Causes for Rejection: Discrepancy between name on tube and name on form, insufficient quantity of serum for testing Sample Container: red top or tiger top tube
Sample Test Kit: Availability: Test performed on request
Diagnostic Information:  Generally seen in children less than five years of age in late summer.

Specimen Submission

Required Request Form: G-2A Specimen Handling: Use Universal Precautions
Transport Temperature: Ambient temperature for specimens on the blood clot, separated serum at 2-8° C (refrigerated) or -20° C (frozen). CSF must be shipped frozen. Shipping Requirements: Triple contain, separated serum may be shipped on cold packs (2-8° C), or frozen (-20° C) and mailed on dry ice.

Billing

CPT Code: 86651 Fees:


Microbiology
Campylobacter Culture (Isolation)
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Microbiology - Campylobacter Culture (Isolation)
Test Includes: Conventional biochemicals

Reporting

Results Available: 4-10 days Contact #s: (512) 458-7582

Reference

Method: Conventional biochemicals  
Turnaround Time:  4-10 days Reference Range:  No Campylobacter species isolated
Limitations: Specimens should be collected before antibiotic therapy is initiated. Interpretation: Absence of Campylobacter species indicates that no viable organisms were present in the specimen submitted.

Specimen Requirements

Specimen Collection: Fresh stool in leakproof container. Sample Type: Feces; Rectal swab.
Volume/Amount Required: > 10 mL for liquid stools; > 20 g solid or semi-solid stool. Preferred Specimen:  Feces; Rectal Swab in Cary-Blair transport media; <24 hrs
Collection/Preservation: collect fresh stool and store in container that will not leak between 2-8° C. Storage Instructions: Keep stool between 2-8° C.
Causes for Rejection: Insufficient amount of sample; specimen> 24 hours old and not in transport media. Specimen received at temperatures> 8° C Sample Container: Clean, dry leakproof container; Cary-Blair transport media tube.
Sample Test Kit: Availability: Tested Monday – Friday
Diagnostic Information:  See Bacterial Culture, Stool (Isolation)

Specimen Submission

Required Request Form: G-2B Specimen Handling: Body fluids handled taking universal precautions.
Transport Temperature:  2-8° C  Shipping Requirements: Triple contained in accordance with federal shipping regulations for diagnostic specimens.

Billing

CPT Code: 87046 Fees:


Microbiology
Campylobacter (Culture – Identification)
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Microbiology - Campylobacter (Culture – Identification)
Test Includes: Conventional biochemicals

Reporting

Results Available: 4-10 days Contact #s: (512) 458-7582

Reference

Method: Conventional biochemicals  
Turnaround Time:  4-10 days Reference Range:  Genus and species reported
Limitations: Time between collection of sample and receipt in this laboratory; atmospheric conditions that the sample is kept at prior to shipping. Interpretation: Campylobacter species is considered an enteric pathogen and usually significant when isolated.

Specimen Requirements

Specimen Collection: See Aerobic Bacterial Culture (Isolation) Sample Type: Pure culture.
Volume/Amount Required: One slant, one broth, one plate, or one deep Preferred Specimen:  Pure culture
Collection/Preservation: Collect sample in appropriate manner and keep in microaerophilic conditions. Storage Instructions: Microaerophilic conditions.
Causes for Rejection: No identifying marks on the sample and/or paperwork. Sample Container: Agar slant in tube or plating media in microaerophilic atmosphere.
Sample Test Kit: Availability: Tested Monday – Friday.
Diagnostic Information:  See Aerobic Bacterial Culture (Isolation)

Specimen Submission

Required Request Form: G-2B Specimen Handling: Infectious agent, enteric pathogen biosafety level 2.
Transport Temperature:  Ambient temperature Shipping Requirements: Triple contained in accordance with federal shipping regulations for infectious agents.

Billing

CPT Code: 87046 Fees:


Microbiology
Candidiasis (Culture – Isolation)
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Microbiology - Candidiasis (Culture – Isolation)
Test Includes: Isolation of fungus and morphological and/or biochemical testing for identification to species

Reporting

Results Available: 21-28 days Contact #s: 512-458-7455 for prior approval
Technical questions:  512-458-7586

Reference

Method: Germ tube; biochemical testing  
Turnaround Time:  21-28 days Reference Range:  Negative
Limitations: Delay in transport of specimen could compromise isolation of organism. Interpretation:

Specimen Requirements

Specimen Collection: Sample Type: Clinical Specimen
Volume/Amount Required: 3 mL to 15 mL Preferred Specimen:  Sputum; Exudate; Scrapings; Tissue; Blood
Collection/Preservation: No preservative Storage Instructions: Transport specimen as soon as possible.  If transport is delayed over one hour, refrigerate specimen, unless blood.
Causes for Rejection: Specimens received frozen, in formalin, or in culture medium will be rejected.  Swabs are discouraged unless the only specimen available; submit swabs in 5 mL sterile saline.  Blood specimens less than 5 mL are not acceptable.  Refrigerated blood specimens will be rejected. Sample Container: Triple-contained.  Sterile, leak-proof, 50 mL conical tube preferred for primary container.  Add up to 10 mL of sterile saline to tissue if needed to maintain moisture during transport.  If blood, prefer yellow-top with ACD; may also contain SPS.  Green-top is acceptable with lithium or heparin.
Sample Test Kit: Availability: Testing available upon approval by Dr. Penfield.
Diagnostic Information:  Approval for this testing must be obtained prior to shipping by telephoning Dr. Susan Penfield at 512-458-7455.

Specimen Submission

Required Request Form: G-2B Specimen Handling:
Transport Temperature:  Ambient acceptable but 2-8º C preferred for non-sterile specimens. Shipping Requirements: Triple-contained and packaged to meet requirements of DOT, USPS, PHS, and IATA for shipping of clinical specimens.

Billing

CPT Code: 87106 Fees:


Microbiology
Candidiasis (Culture – Identification)
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Microbiology - Candidiasis (Culture – Identification)
Test Includes: Morphological and/or biochemical identification to species level.

Reporting

Results Available: 7-10 days Contact #s: 512-458-7586.

Reference

Method: Morphological and/or biochemical testing.  
Turnaround Time:  7-10 days Reference Range:  By report
Limitations: Interpretation:

Specimen Requirements

Specimen Collection: Sample Type:
Volume/Amount Required: Preferred Specimen:  Pure Culture
Collection/Preservation: No preservative. Storage Instructions:
Causes for Rejection: Culture infested with mites. Sample Container: Triple-contained.
Sample Test Kit: Availability: Tested 5 days/week: Monday - Friday
Diagnostic Information:  Fungal isolates (pure culture) submitted to this Laboratory for definitive identification.  Drug susceptibility testing on these organisms not available at TDSHS laboratory.

Specimen Submission

Required Request Form: G-2B Specimen Handling:
Transport Temperature:  Room temperature Shipping Requirements: Triple-contained and packaged to meet rigorous performance tests as outlined in the DOT, USPS, PHS, and IATA regulations for shipping of infectious substances.

Billing

CPT Code: 87106 Fees:


Microbiology
Chagas’ Disease (Serological – Forwarded by TDSHS to CDC for testing)
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Microbiology - Chagas’ Disease (Serological – Forwarded by TDSHS to CDC for testing)
Test Includes:

Reporting

Results Available: Contact #s:

Reference

Method:  
Turnaround Time:  3 weeks Reference Range:  Nonreactive
Limitations: May not detect a recent infection, or infection in a person with a severely compromised immune system. Interpretation:

Specimen Requirements

Specimen Collection: Venipuncture Sample Type:
Volume/Amount Required: 10 mL whole blood Preferred Specimen:  Single Serum; Paired Sera
Collection/Preservation: Red top or tiger top tube Storage Instructions: Do not freeze or refrigerate whole blood. Separated serum may be held at 2-8° C
Causes for Rejection: Discrepancy between name on tube and name on form, insufficient quantity of serum for testing Sample Container: Red top or tiger top tube
Sample Test Kit: Availability:
Diagnostic Information:  Prior notification is requested (512) 458-7760. A detailed patient history is required. Serum specimens are forwarded to the CDC. A four-fold rise in titer between acute and convalescent specimens is considered evidence of recent infection.

Specimen Submission

Required Request Form: G-2A Specimen Handling: Use Universal Precautions
Transport Temperature:  Ambient temperature for specimens on the blood clot, separated serum at 2-8° C (refrigerated) or -20° C (frozen). Shipping Requirements: Triple contain, separated serum may be shipped on cold packs (2-8° C), or frozen (-20° C) and mailed on dry ice.

Billing

CPT Code: 86753 Fees:


Microbiology
Chancroid (Culture – Identification)
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Microbiology - Chancroid (Culture – Identification)
Test Includes: Conventional Biochemical Studies

Reporting

Results Available: 3-21 days Contact #s: (512) 458-7582

Reference

Method: Conventional biochemical studies
Turnaround Time: 21 days Reference Range:  No bacteria isolated.
Limitations: Careful selection and disinfection of specimen collection sites is imperative in obtaining a suitable specimen for isolation of Haemophilus species. Interpretation: Isolation of H. ducreyi is considered clinically significant.

Specimen Requirements

Specimen Collection: scrapings from genital lesions Sample Type: genital lesion, aspirates from buboes, urethral swabs
Volume/Amount Required: small amount of scrapings Preferred Specimen:  genital lesions
Collection/Preservation: Material should be collected from the exposed base or margin of the lesion. Needle aspirates of pus from buboes should not replace lesional smears and cultures. Recovery of nonchancroid isolates from the urogenital tract can be accomplished by collecting urethral swab with a flexible shaft mini-tipped swab. Storage Instructions: 2-8° C
Causes for Rejection: Expired transport medium. Sample Container: Sterile screw-cap tube or modified stuart’s transport.
Sample Test Kit: Availability: Monday-Friday
Diagnostic Information:  Prior notification requested. (512) 458-7582 – Clinical Bacteriology

Specimen Submission

Required Request Form: G-2B Specimen Handling: Body fluids handled with universal precautions.
Transport Temperature:  2-8° C Shipping Requirements: Triple contained in accordance with federal shipping regulations for diagnostic specimens.

Billing

CPT Code: 87070 Fees:


 
Microbiology
Chlamydia (Genetic Probe)
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Microbiology - Chlamydia (Genetic Probe)
Test Includes: GEN-PROBE APTIMA COMBO 2® Assay

Reporting

Results Available: 2-3 days   Contact #s: (512) 776-7657

Reference

Method: GEN-PROBE APTIMA COMBO 2® Assay  
Turnaround Time:  2-3 days   Reference Range:  Negative for Chlamydia trachomatis
Limitations: Results dependent on adequacy of sampling. Refer to package insert of the appropriate GEN-PROBE specimen collection kit. The APTIMA COMBO 2® Assay is not intended for the evaluation of suspected sexual abuse or for other medico-legal indications Interpretation: Negative results indicate that the patient does not have detectable amounts of C. trachomatis rRNA.

Specimen Requirements

Specimen Collection: Only specimens collected in APTIMA ®collection kits can be processed for testing. There are three kits we use for our testing;
APTIMA® Urine Specimen Collection Kit for Male and Female Urine Specimens
APTIMA® Unisex Swab Specimen Collection Kit for Endocervical and Male Urethral Swab Specimens
APTIMA® Vaginal Swab Specimens kit		 Sample Type: Female urine, vaginal and endocervical swab. Male urine and urethral swab.
Volume/Amount Required: Refer to package insert of APTIMA® Specimen Collection Kit for detailed directions. Preferred Specimen:  Urine (Male or Female);
Female Endocervical Swab;
Female Vaginal Swab;
Male Urethral Swab
Collection/Preservation: Only swabs contained in the GEN-PROBE® APTIMA®specimen collection kit can be used to collect patient specimens. Storage Instructions: Store at ambient temperature.
Causes for Rejection: Wrong name on collection tube, two swabs in tube, no swab on tube, a cleaning swab or a swab not supplied by GEN-PROBE. Urine must fall between the two black indicator lines on the tube label. Sample Container: APTIMA® Urine Specimen Collection Kit for Male and Female Urine Specimen,swabs
APTIMA® Unisex Swab Specimen Collection Kit for Endocervical and Male Urethral Swab Specimens and APTIMA® Vaginal Swab Specimens
Sample Test Kit: GEN-PROBE APTIMA 2 COMBO ASSAY Availability: Tested Monday – Friday.
Diagnostic Information:  GEN-PROBE APTIMA COMBO 2® Assay is available only to those in STD and Family Planning Programs and to adolescent THSteps (EPSDT) patients for whom collectors are provided. Specimen requirements: Female urine, vaginal swab, or endocervical swab and male urine and urethral swabs using the appropriate GEN-PROBE® APTIMA®Specimen Collection Kit. Only swabs contained in the GEN-PROBE® APTIMA® specimen collection kit can be used to collect patient specimens.

Specimen Submission

Required Request Form: G-2B, G-THSTEPS for THSteps Medicaid  Specimen Handling: body fluid handled with universal precautions
Transport Temperature:  Ambient temperature (2°-30°C) Shipping Requirements: In accordance with federal shipping regulations for diagnostic specimens, noninfectious.

Billing

CPT Code: 87491 Fees:


Microbiology
Cholera (Culture – Isolation)
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Microbiology - Cholera (Culture – Isolation)
Test Includes: Conventional biochemicals, serological typing for V. cholerae 01 and 0139.

Reporting

Results Available: 4-7 days. Contact #s: (512) 458-7582

Reference

Method: Conventional biochemicals, serological typing for V. cholerae 01 and 0139.
Turnaround Time:  4-7 days   Reference Range:  No Vibrio species isolated 
Limitations: Specimen must be collected before antibiotic therapy has been initiated. Organisms must be viable for culture testing. Interpretation: No Vibrio species isolated indicates that there were no viable Vibrio organisms in the specimen

Specimen Requirements

Specimen Collection: Fresh stool or rectal swab. Sample Type: Feces; Rectal swab.
Volume/Amount Required: > 10 mL for liquid stools; > 20 g solid or semi-solid stools. Preferred Specimen:  Feces < 24 hours old; Feces or rectal Swab in Cary-Blair medium.
Collection/Preservation: Collect fresh stool in clean, dry leak-proof container. Transfer indicated amount to the Cary-Blair transport as indicated by instructions on or with the transport tube. Storage Instructions: Store between 2-8° C.
Causes for Rejection: Insufficient amount of stool to test, unpreserved stool > 24 hours; incorrect preservative for bacterial examination. Sample Container: Clean, dry leakproof container or Cary-Blair transport tube.
Sample Test Kit: Availability: Tested Monday – Friday.
Diagnostic Information:  Stool should be collected prior to antibiotic therapy.  See Vibrio parahaemolyticus and other Vibrio species (Culture – Identification) Serological typing performed on all V. cholerae isolated for detection of O1 and O139 strains.  See Cholera Culture – (Typing) Toxin testing forwarded to CDC.  See Cholera Culture (Toxin Testing). 
Organisms identified as Vibrio cholerae will be serologically typed for serotype 01 and 0139.

Specimen Submission

Required Request Form: G-2B Specimen Handling: Body fluids handled with universal precautions.
Transport Temperature:  2-8° C  Shipping Requirements: Triple contained in accordance with federal shipping regulations for diagnostic specimens.

Billing

CPT Code: 87046 Fees:


Microbiology
Cholera (Culture – Identification)
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Microbiology - Cholera (Culture – Identification)
Test Includes: Conventional biochemicals and serology.

Reporting

Results Available: 7 days Contact #s: (512) 458-7582

Reference

Method: Conventional biochemicals and serology
Turnaround Time:  7 days Reference Range:  By report
Limitations: Vibrio species do not survive when exposed to refrigeration unless in clinical specimens. Isolates on agar slants or in transport media will not survive refrigeration. Interpretation: Biochemical tests and serology confirm Vibrio cholerae. The isolation of a pathogenic Vibrio species from a clinical specimen should be considered a significant finding.

Specimen Requirements

Specimen Collection: Pure culture 24 hours growth on appropriate media. Sample Type: Pure culture.
Volume/Amount Required: One specimen per patient. Preferred Specimen:  Pure Culture on agar slant.
Collection/Preservation: Pure culture, 24 hour growth, held at ambient temperature after incubation. Storage Instructions: Keep culture at ambient temperature. DO NOT refrigerate.
Causes for Rejection: No identifying marks on sample and/or paperwork. Viability lost due to refrigeration of isolate. Sample Container: Dependent upon method of transport.
Sample Test Kit: Availability: Tested Monday – Friday.
Diagnostic Information:  Stool should be collected prior to antibiotic therapy.  See Vibrio parahaemolyticus and other Vibrio species (Culture – Identification). 

Specimen Submission

Required Request Form: G-2B Specimen Handling: Infectious agents, Biosafety level 2.
Transport Temperature:  Ambient temperature Shipping Requirements: Triple contained in accordance with federal shipping regulations for infectious agents.

Billing

CPT Code: 87077 Fees:


Microbiology
Cholera (Culture – Typing)
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Microbiology - Cholera (Culture – Typing)
Test Includes: Serological typing of O1 and O139

Reporting

Results Available: 7 days Contact #s: (512) 458-7582

Reference

Method: Serological typing of O1 and O139, otherwise sent to CDC for typing.
Turnaround Time:  7 days Reference Range:  By report  
Limitations: Serological typing does not establish the toxigenicity of the organism. Interpretation: Agglutination of O1 or O139 indicates serotype of organism.

Specimen Requirements

Specimen Collection: Dependent upon source of sample. Sample Type: Pure culture
Volume/Amount Required: one specimen per patient. Preferred Specimen:  Pure culture.
Collection/Preservation: Collect in appropriate manner and keep at ambient temperature. DO NOT refrigerate. Storage Instructions: DO NOT refrigerate – keep at ambient temperature.
Causes for Rejection: no identifying marks on sample and/or paperwork, broken transport tube. Sample Container: Agar slant in transport tube, or agar plate in transport box.
Sample Test Kit: Availability: Tested Monday – Friday.
Diagnostic Information:  Serological typing performed for detection of O1 and O139 strains. Additional typing requests forwarded by TDH to CDC with prior approval. Molecular typing performed at TDSHS upon request see Molecular typing (PFGE).

Specimen Submission

Required Request Form: G-2B Specimen Handling: Infectious agents, biosafety level 2
Transport Temperature:  Ambient temperature   Shipping Requirements: Triple contained in accordance with federal shipping regulations for infectious agents.

Billing

CPT Code: 87147 Fees:


Microbiology
Cholera (Culture - Toxin Testing)
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Microbiology - Cholera (Culture - Toxin Testing)
Test Includes: Test not performed at TDSHS. Submitted to the CDC for testing.

Reporting

Results Available: Contact #s:

Reference

Method:  
Turnaround Time:  Determined by CDC report Reference Range:  By report  
Limitations: Interpretation:

Specimen Requirements

Specimen Collection: Sample Type: Pure culture
Volume/Amount Required: one specimen per patient Preferred Specimen:  Pure culture
Collection/Preservation: Store at ambient temperature Storage Instructions: ambient temperature
Causes for Rejection: Insufficient clinical information submitted. Sample Container:
Sample Test Kit: Availability: Cultures are shipped to the CDC Monday-Thursday. Special request supported by clinical information
Diagnostic Information:  Forwarded by TDSHS to CDC for testing. 

Specimen Submission

Required Request Form: G-2B Specimen Handling: Infectious agent, Biosafety level 2.
Transport Temperature:  Ambient  temperature Shipping Requirements: Triple contained in accordance with federal shipping regulations for infectious agents.

Billing

CPT Code: Fees:


Microbiology
Cholera (Serological – Vibriocidal Antibody)
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Microbiology - Cholera (Serological – Vibriocidal Antibody)
Test Includes:

Reporting

Results Available: Contact #s:

Reference

Method:  
Turnaround Time: Reference Range:
Limitations: Interpretation:

Specimen Requirements

Specimen Collection: Sample Type:
Volume/Amount Required: Preferred Specimen:  Culture; Feces; Rectal Swab  
Collection/Preservation: Storage Instructions:
Causes for Rejection: Sample Container:
Sample Test Kit: Availability:
Diagnostic Information:  Immunization and cross-reactions with Brucella, Yersinia, and Citrobacter must be considered.

Specimen Submission

Required Request Form: G-2B Specimen Handling:
Transport Temperature: Shipping Requirements:

Billing

CPT Code: 87158 Fees:


Last updated May 14, 2018