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Test Code MISC2MAYOBTWGS Bacterial Typing by Whole Genome Sequencing, Varies

Biohazard Infectious

Secondary ID

65162

Useful For

Aiding in the investigation of a potential outbreak by a single bacterial species

 

May assist in identification of recurrent infection in an individual patient

Method Name

Whole Genome Sequencing

Reporting Name

Bacterial Typing, Whole Genome Seq

Specimen Type

Varies


Advisory Information


Acinetobacter baumannii, Campylobacter jejuni/coli, Clostridioides (Clostridium) difficile, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Streptococcus agalactiae, and Streptococcus pyogenes are tested by this method.



Additional Testing Requirements


If uncertain of organism identification, concomitantly order IDENT / Organism Referred for Identification, Aerobic Bacteria or ANIDE / Organism Referred for Identification, Anaerobic Bacteria.



Shipping Instructions


1. See Infectious Specimen Shipping Guidelines in Special Instructions for shipping information.

2. Place isolates in a large infectious container (T146) and label as an etiologic agent/infectious substance.

3. Place all isolates (all patients and/or sites to be compared) submitted for whole genome sequencing (WGS) together in 1 large bag, and send in the same shipping container. This is necessary for comparison of isolates by this method.



Necessary Information


1. Organism identification and specimen source are required.

2. Acinetobacter baumannii: Isolate must be A baumannii. Identifications of A baumannii complex and A baumannii/calcoaceticus complex are not acceptable.

3. Enterobacter cloacae: Isolate must be a member of the E cloacae complex (ie, Enterobacter asburiae, Enterobacter bugandensis, E cloacae, E cloacae subspecies cloacae, E cloacae subspecies dissolvens, Enterobacter hormaechei subspecies hormaechei, Enterobacter kobei, Enterobacter ludwigii, Enterobacter xiangfangensis).

4. Klebsiella pneumoniae: Isolate must be a member of the K pneumoniae complex (ie, K pneumoniae, K pneumoniae subspecies pneumoniae, K pneumoniae subspecies ozaenae, or K pneumoniae subpecies rhinoscleromatis).

5. An email address registered on the Mayo Clinic Laboratories website is required for report delivery.



Specimen Required


Aerobic Bacteria

Supplies: Infectious Container, Large (T146)

Container/Tube: Agar slant

Specimen Volume: Isolates on separate agar slants in pure culture

Collection Instructions:

1. Isolate the bacteria (must be Acinetobacter baumannii, Campylobacter jejuni/coli, Enterobacter cloacae, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Klebsiella pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Serratia marcescens, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus lugdunensis, Streptococcus agalactiae, or Streptococcus pyogenes).

2. Bacterial isolate must be in pure culture, actively growing. Do not submit mixed cultures.

3. Each isolate must be submitted under a separate order.

 

Anaerobic Bacteria: Clostridioides (Clostridium) difficile

Supplies:

-Anaerobic Transport Tube (T588)

-Infectious Container, Large (T146)

Specimen Type: Pure culture of C difficile

Container/Tube:

Preferred: Anaerobic transport tube

Acceptable: Thioglycollate broth or any other suitable anaerobic transport system

Specimen Volume: Isolates in separate transport tubes in pure culture

Collection Instructions:

1. Isolate the bacteria (must be Clostridioides (Clostridium) difficile).

2. Do not submit growth directly from a CHROMagar plate; subculture to anaerobic media to obtain pure isolate, and confirm identification prior to submission.

3. Bacterial isolate must be in pure culture, actively growing. Do not submit mixed cultures.

4. Each isolate must be submitted under a separate order.


Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Reject Due To

Agar plate Reject

Reference Values

Reported as isolates are "related", "possibly related", or "unrelated" by whole genome sequencing.

Day(s) and Time(s) Performed

Varies; Batch tested 1 time per week

Performing Laboratory

Mayo Clinic Laboratories in Rochester

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

0010U-Bacterial Typing, Whole Genome Seq

87900-Bioinformatics Reanalysis (if appropriate)

87077-Ident by MALDI-TOF mass spec (if appropriate)

87153-Aerobe ident by sequencing (if appropriate)

87077-Additional identification procedure (if appropriate)

87076-Id MALDI-TOF mass spec anaerobe (if appropriate)

87076-Anaerobe Ident (if appropriate)

87153-Anaerobe ident by sequencing (if appropriate)

LOINC Code Information

Test ID Test Order Name Order LOINC Value
BTWGS Bacterial Typing, Whole Genome Seq 90246-0

 

Result ID Test Result Name Result LOINC Value
BTWGS Bacterial Typing, Whole Genome Seq 90246-0

Reflex Tests

Test ID Reporting Name Available Separately Always Performed
BIORE Bioinformatics Reanalysis No, (Bill Only) No
RMALD Ident by MALDI-TOF mass spec No, (Bill Only) No
ISAE Aerobe Ident by Sequencing No, (Bill Only) No
REFID Additional Identification Procedure No, (Bill Only) No
RMALA Id MALDI-TOF Mass Spec Anaerobe No, (Bill Only) No
ANAID Anaerobe Ident No, (Bill Only) No
ISAN Anaerobe Ident by Sequencing No, (Bill Only) No

Testing Algorithm

Organism identification is required. All bacteria submitted will be tested. Organism identifications that are incorrect or incomplete may result in no results at final analysis. Laboratory may perform matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) or other testing as listed in Reflex Tests to confirm identification, report this finding, and charge accordingly.

 

When reanalysis of previously submitted isolates for comparison to new isolates is requested, bioinformatics reanalysis will be added by Mayo Clinic Laboratories. Original patient submission information (names and order numbers) must be provided.

Forms

If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.