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SARS-CoV-2 Whole Genome Sequencing

Enviado por DobbiG1 el
Aliases

COVID, COVID-19, coronavirus

Test Name

SARS-CoV-2 Whole Genome Sequencing

Test Code

SC2GENO

Methodology

Whole genome sequencing

Overview/Supplementary

This assay identifies SARS-CoV-2 variants from positive clinical specimens using whole genome sequencing. For details on SARS-CoV-2 sample submission, please refer to the Next-Generation Sequencing COVID-19 Sample Submission website (https://www.health.state.mn.us/diseases/idlab/lisngs.html).

Patient-specific test reports are not generated for the SARS-CoV-2 sequencing assay. Minnesota-focused subsampling data can be found on the MDH Variants Dashboard under Case and Variant Data (https://www.health.state.mn.us/diseases/coronavirus/stats/case.html#NaN).

Turn Around Time

Not applicable

Specimen Requirements

Specimens in DMEM, EMEM, Sterile PBS, Sterile saline, UTM, or VTM: Bronchial wash, Bronchoalveolar lavage/BAL, Dual NP/OP swab, Nasal aspirate, Nasal swab, Nasal wash, Nasopharyngeal swab, Oropharyngeal swab, Sputum, or Tracheal aspirate 

Preferred volume: 3 mL 

Minimum volume: 200 µL

Special Considerations

None

Transport/Stability

Specimens stored refrigerated (2°C to 8°C) must be shipped on cold packs. Specimens stored frozen (≤0°C) must be shipped on dry ice (preferred) or cold packs.

Test Resource ID
958

Respiratory Syncytial Virus (RSV) Whole Genome Sequencing

Enviado por DobbiG1 el
Aliases

RSV

Test Name

Respiratory Syncytial Virus (RSV) Whole Genome Sequencing

Test Code

RSVSEQ

Methodology

Whole genome sequencing

Overview/Supplementary

This assay identifies RSV variants from positive clinical specimens using whole genome sequencing.

Patient-specific test reports are not generated for the RSV sequencing assay.

Turn Around Time

Not applicable

Specimen Requirements

Specimens in DMEM, EMEM, Sterile PBS, Sterile saline, UTM, or VTM: Bronchial wash, Bronchoalveolar lavage/BAL, Dual NP/OP swab, Nasal aspirate, Nasal swab, Nasal wash, Nasopharyngeal swab, Oropharyngeal swab, Sputum, or Tracheal aspirate 

Preferred volume: 3 mL 

Minimum volume: 200 µL

Special Considerations

None

Transport/Stability

Specimens stored refrigerated (2°C to 8°C) must be shipped on cold packs. 

Specimens stored frozen (≤0°C) must be shipped on dry ice (preferred) or must ship on cold packs.

Test Resource ID
959

Yersinia pestis PCR - Specimen

Enviado por StewaD1 el
Aliases

Bubonic plague, Plague, Pneumonic plague, Septicemic plague

Test Name
Yersinia pestis PCR - Specimen
Test Code

YPPCRSPEC

Methodology

Real-time PCR

Overview/Supplementary

This test identifies Yersinia pestis from clinical samples. MDH will determine if additional tests are required, including culture.

Turn Around Time

1-3 days

Specimen Requirements

Call IDL emergency response on-call phone 612-282-3723 for specimen submission requirements.

Special Considerations

Call IDL emergency response on-call phone 612-282-3723 before ordering this test.

This organism is reportable and submission of clinical materials is required by the MN Reportable Disease Rule 4605.7000 - 4605.7900 (https://www.health.state.mn.us/diseases/reportable/rule/index.html).

Transport/Stability

Store and ship at ambient (8°C to 25°C) or refrigeration (2°C to 8°C) temperature.

Interface/Codes

LOINC: 33691-7

Test Resource ID
956

Yersinia pestis PCR - Isolate

Enviado por StewaD1 el
Aliases

Bubonic plague, Plague, Pneumonic plague, Septicemic plague

Test Name
Yersinia pestis PCR - Isolate
Test Code

YPPCRISO

Methodology

Real-time PCR

Overview/Supplementary

This test identifies Yersinia pestis from isolates. MDH will determine if additional tests are required, including culture.

Turn Around Time

1-3 days

Specimen Requirements

Isolates: Actively growing culture on media that support the growth of the bacterial isolate submitted.

Special Considerations

Call IDL emergency response on-call phone 612-282-3723 before ordering this test.

This organism is reportable and submission of clinical materials is required by the MN Reportable Disease Rule 4605.7000 - 4605.7900 (https://www.health.state.mn.us/diseases/reportable/rule/index.html)

Transport/Stability

Store and ship at ambient (8°C to 25°C) or refrigeration (2°C to 8°C) temperature.

Interface/Codes

LOINC: 33691-7

Test Resource ID
955

Yeast Identification - Isolate

Enviado por StewaD1 el
Aliases
Candida, Candida auris, Candidemia, Yeast
Test Name
Yeast Identification - Isolate
Test Code
YEASTID
Methodology
Biochemicals, Culture, Latex agglutination, MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry
Overview/Supplementary

This test identifies yeast species, including Candida auris, from submitted isolates.

Surveillance of candidemia as part of the Emerging Infections Program (EIP) includes submission of Candida isolates from blood culture from residents of the 7-county metro area.

Surveillance as part of the Antimicrobial Resistance Lab Networks (AR Lab Network) includes identification and antifungal susceptibility testing.

Turn Around Time
2-7 days
Specimen Requirements
Isolates: Actively growing culture on media that support the growth of the yeast isolate submitted.
Special Considerations

If submitting isolate for AR Lab Network, please fill out ARLAB Central Region Clinical Testing and Submission form https://www.health.state.mn.us/diseases/idlab/arln.html.

Candida auris and Candida from blood culture are rreportable and submission of clinical materials is required by the MN Reportable Disease Rule 4605.7000 - 4605.7900 (https://www.health.state.mn.us/diseases/reportable/rule/index.html).

Transport/Stability

Store and ship at ambient (8°C to 25°C) or refrigeration (2°C to 8°C) temperature.

Interface/Codes
LOINC: 15378-3
Test Resource ID
954

VISA/VRSA Identification Confirmation - Isolate

Enviado por StewaD1 el
Aliases

Vancomycin-intermediate Staphylococcus aureus, Vancomycin-resistant Staphylococcus aureus

Test Name
VISA/VRSA Identification Confirmation - Isolate
Test Code

VSAID

Methodology

Antimicrobial susceptibility testing (AST) by broth microdilution, MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry

Overview/Supplementary

This tests confirms vancomycin susceptibility in Staphylococcus aureus by broth microdilution.

Isolates with minimum inhibitory concentrations (MIC) ≥8 µg/mL will be referred to the Centers for Disease Control and Prevention (CDC) for additional characterization.

Turn Around Time

7 days

Specimen Requirements

Isolates: Actively growing culture on media that support the growth of the bacterial isolate submitted.

Isolates should be subcultured as few times as possible prior to testing to limit the potential for loss of resistance mechanisms during passage.

Special Considerations

Submit copy of antimicrobial susceptibility testing results from clinical lab along with the isolate.

This organism is reportable and submission of clinical materials is required by the MN Reportable Disease Rule 4605.7000 - 4605.7900 (https://www.health.state.mn.us/diseases/reportable/rule/index.html).

Transport/Stability

Store and ship at ambient (8°C to 25°C) or refrigeration (2°C to 8°C) temperature.

Interface/Codes

LOINC: 50545-3

Test Resource ID
953

Virus Isolation and Identification - Specimen

Enviado por StewaD1 el
Aliases

Viral culture

Test Name
Virus Isolation and Identification - Specimen
Test Code

VICULTS

Methodology

Culture, Direct fluorescent antibody (DFA)

Overview/Supplementary

This test isolates and identifies viruses from clinical specimens. Viral culture can detect several viruses (e.g. parainfluenza, RSV, adenovirus).

Turn Around Time

Up to 6 weeks

Specimen Requirements

Specimens submitted in DMEM, EMEM, Liquid Amies, Liquid Stuart, Modified liquid Amies, Sterile PBX, Sterile saline, UTM, or VTM: 
Bronchial wash, Bronchoalveolar lavage/BAL, Genital swab, Lower respiratory tract, Nasopharyngeal swab, Nasopharyngeal aspirate, Non-vesicular lesion swab, Ocular swab, Rectal swab, Stool, Throat swab, Tissue aspirate, Tissue biopsy, or Vesicular lesion swab 

Specimen submitted in sterile containers: Cerebrospinal fluid/CSF, Pericardial fluid, Pleural fluid, or Urine

Preferred volume: 1 mL 
Minimum volume: 200 µL

Special Considerations

None

Transport/Stability

Store and ship at refrigeration (2°C to 8°C) temperature. Alternatively, ship frozen (≤0°C). Lab must receive within 5-10 days of collection.

Interface/Codes
Test Resource ID
952

Virus Isolation and Identification - Isolate

Enviado por StewaD1 el
Aliases

Viral culture

Test Name
Virus Isolation and Identification - Isolate
Test Code

VICULTI

Methodology

Culture, Direct fluorescent antibody (DFA)

Overview/Supplementary

This test isolates and identifies viruses from cell sheets. Viral culture can detect several viruses (e.g. parainfluenza, RSV, adenovirus).

Turn Around Time

Up to 6 weeks

Specimen Requirements

Isolates: Supernatant from cell sheet. 

Preferred volume: 1 mL  
Minimum volume: 200 µl

Special Considerations

None

Transport/Stability

Store and ship at refrigeration (2°C to 8°C) temperature.

Interface/Codes
Test Resource ID
951

Viral Diarrheal PCR Panel

Enviado por StewaD1 el
Aliases

Adenovirus, Astrovirus, Rotavirus, Sapovirus, VDP

Test Name
Viral Diarrheal PCR Panel
Test Code

VDPPCR

Methodology

Real-time multiplex PCR

Overview/Supplementary

This test detects enteric viruses, such as adenovirus, astrovirus, rotavirus, and sapovirus clinical specimens.

Turn Around Time

Not Applicable

Specimen Requirements

Specimens: Stool in enteric transport media (Cary Blair) or unpreserved stool.

Special Considerations

Submitters will not receive results.

Contact Infectious Disease Epidemiology Prevention and Control (IDEPC) at 651-201-5414 or 877-676-5414 before requesting this test.

Transport/Stability

Store at ambient (8°C to 25°C) temperature. Ship at ambient (8°C to 25°C) or refrigeration (2°C to 8°C) temperature.

Interface/Codes
Test Resource ID
950

Vibrio Identification - Isolate

Enviado por StewaD1 el
Aliases

Cholera

Test Name
Vibrio Identification - Isolate
Test Code

VIBRIOID

Methodology

Biochemicals, Culture, MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry, Whole genome sequencing

Overview/Supplementary

This test identifies the Vibrio spp. in the submitted isolate.

Turn Around Time

3-5 days

Specimen Requirements

Isolates: Actively growing culture on media that support the growth of the bacterial isolate submitted.

Special Considerations

This organism is reportable and submission of clinical materials is required by the MN Reportable Disease Rule 4605.7000 - 4605.7900 (https://www.health.state.mn.us/diseases/reportable/rule/index.html).

Transport/Stability

Store at ambient (8°C to 25°C) temperature. Ship at ambient (8°C to 25°C) or refrigeration (2°C to 8°C) temperature.

Interface/Codes
Test Resource ID
949