Microbiology Laboratory Tests: Calicivirus to Cholera

Microbiology
Norovirus
Related Agents: Norwalk-like Virus, Norovirus
< Return to Table of Contents

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)
< Return to Table of Contents

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)
< Return to Table of Contents

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)
< Return to Table of Contents

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 – Identification)
< Return to Table of Contents

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)
< Return to Table of Contents

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)
< Return to Table of Contents

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)
< Return to Table of Contents

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: