Test Catalog

Test Id : BTWGS

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Bacterial Typing, Whole Genome Sequencing, Varies

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Overview

Test Catalog

Useful For
Suggests clinical disorders or settings where the test may be helpful

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

 

May assist in identification of recurrent infection in an individual patient

Reflex Tests
Lists tests that may or may not be performed, at an additional charge, depending on the result and interpretation of the initial 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
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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 and report this finding at an additional charge.

 

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.

Method Name
A short description of the method used to perform the test

Whole Genome Sequencing

NY State Available
Indicates the status of NY State approval and if the test is orderable for NY State clients.

Yes

Reporting Name
Lists a shorter or abbreviated version of the Published Name for a test

Bacterial Typing, Whole Genome Seq

Aliases
Lists additional common names for a test, as an aid in searching

A baumannii

A. baumannii

Acinetobacter baumannii

aureus

Bacterial Typing

C difficile

C. difficile

Clostridioides difficile

Clostridium difficile

K pneumo

K pneumoniae

K. pneumoniae

Klebsiella pneumoniae

Klebsiella pneumoniae complex

L pneumophila

L. pneumophila

Legionella pneumophila

MRSA

MSSA

Next Gen Sequencing

S. aureus

Staph

Whole Genome Sequencing

WGS

E cloacae

E. cloacae

Enterobacter cloacae

C jejuni/coli

C. jejuni/coli

Campylobacter jejuni

C. jejuni

Campylobacter coli

C. coli

E faecalis

E. faecalis

Enterococcus faecalis

Enterococcus faecium

E faecium

E. faecium

NGS

E coli

E. coli

Escherichia coli

P aeruginosa

P. aeruginosa

Pseudomonas aeruginosa

S marcescens

S. marcescens

Serratia marcescens

S pyogenes

S. pyogenes

Streptococcus pyogenes

Typing

GAS

GBS

Group A Strep

Group B Strep

S agalactiae

S aureus

S epidermidis

S lugdunensis

S. agalactiae

S. epidermidis

S. lugdunensis

Staphylococcus aureus

Staphylococcus epidermidis

Staphylococcus lugdunensis

Streptococcus agalactiae

C acnes

C. acnes

Cutibacterium acnes

P acnes

P. acnes

Propionibacterium acnes

Clostridioides (Clostridium) difficile

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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 and report this finding at an additional charge.

 

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.

Specimen Type
Describes the specimen type validated for testing

Varies

Ordering Guidance

Acinetobacter baumannii, Campylobacter jejuni/coli, Clostridioides difficile (formerly Clostridium difficile), Cutibacterium (Propionibacterium) acnes, 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. For shipping information see Infectious Specimen Shipping Guidelines.

2. Place isolates in a large infectious container 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 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 subspecies rhinoscleromatis).

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

ORDER QUESTIONS AND ANSWERS

Question ID Description Answers
Q00M0047 Specimen Source (Required) and Organism Identification (Required)

Specimen Required
Defines the optimal specimen required to perform the test and the preferred volume to complete testing

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

Supplies:

-Anaerobe Transport Tube (T588)

-Infectious Container, Large (T146)

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 difficile or Cutibacterium [Propionibacterium] acnes).

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.

Special Instructions
Library of PDFs including pertinent information and forms related to the test

Forms

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

Reject Due To
Identifies specimen types and conditions that may cause the specimen to be rejected

Agar plate Reject

Specimen Stability Information
Provides a description of the temperatures required to transport a specimen to the performing laboratory, alternate acceptable temperatures are also included

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

Useful For
Suggests clinical disorders or settings where the test may be helpful

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

 

May assist in identification of recurrent infection in an individual patient

Testing Algorithm
Delineates situations when tests are added to the initial order. This includes reflex and additional tests.

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 and report this finding at an additional charge.

 

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.

Clinical Information
Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Bacterial strain typing may be useful for determining strain relatedness in the setting of possible nosocomial transmission or community outbreaks. Serial isolates obtained from the same patient may be typed to assess similarity. Typing may allow discrimination of 2 or more isolates of the same species, which can inform recognition of an outbreak, nosocomial transmission, or identify a potential source of infection in an individual patient.

 

Pulse-field gel electrophoresis (PFGE) has traditionally been used for strain typing but does not always discriminate between different bacterial strains (eg, 2 genetically dissimilar strains may have indistinguishable PFGE patterns). Whole genome sequencing offers a higher level of resolution of genetic relatedness of strains than PFGE does.

Reference Values
Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

Reported as isolates are "related," "possibly related," or "unrelated."

Interpretation
Provides information to assist in interpretation of the test results

The genomic sequence of individual isolates will be determined and compared to the genomic sequences of the other co-submitted isolates. The report will indicate the degree of relatedness between the isolates. A link to the interpretive report will be sent to the registered email address provided by the client.

Cautions
Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Genomic relatedness does not prove that tested bacterial isolates are epidemiologically related. Establishment of an epidemiologic relationship requires correlation with clinical and epidemiological information. An epidemiological link may be ascribed if a common contact can be established between patients with bacterial strains demonstrating a high degree of genetic relatedness. Similar to other types of stain typing (eg, pulse-field gel electrophoresis), sequence-based strain typing is most powerful in demonstrating genetic dissimilarity, decreasing the likelihood that the strains share a similar source.

Clinical Reference
Recommendations for in-depth reading of a clinical nature

1. Cunningham SA, Chia N, Jeraldo PR, et al. Comparison of whole-genome sequencing methods for analysis of three methicillin-resistant Staphylococcus aureus outbreaks. J Clin Microbiol. 2017;55(6):1946-1953. doi;10.1128/JCM.00029-17

2. Park KH, Greenwood-Quaintance KE, Uhl JR, et al. Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing. PLoS ONE. 2017;12(6):e0179003. doi:10.1371/journal.pone.0179003

3. Madigan T, Cunningham SA, Patel R, et al. Whole-genome sequencing for methicillin-resistant Staphylococcus aureus (MRSA) outbreak investigation in a neonatal intensive care unit. Infect Control Hosp Epidemiol. 2018; 39(12):1412-1418. doi:10.1017/ice.2018.239

4. Trees E, Fei Fan Ng T, MacCannell D, et al. Molecular epidemiology. In: Carroll K, Pfaller M, eds. Manual of Clinical Microbiology. 12th ed. ASM Press; 2019:167-196

Method Description
Describes how the test is performed and provides a method-specific reference

Following whole genome sequencing of each submitted isolate on a MiSeq, sequences will be compared by core genome multilocus sequence typing analysis using SeqSphere+ Software (Ridom GmbH. Allelic profiles will be used to generate a phylogenetic tree showing isolate relatedness.(Leopold SR, Goering RV, Witten A, et al: Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes. J Clin Microbiol. 2014;52[7]:2365-2370)

PDF Report
Indicates whether the report includes an additional document with charts, images or other enriched information

No

Day(s) Performed
Outlines the days the test is performed. This field reflects the day that the sample must be in the testing laboratory to begin the testing process and includes any specimen preparation and processing time before the test is performed. Some tests are listed as continuously performed, which means that assays are performed multiple times during the day.

Once per week

Report Available
The interval of time (receipt of sample at Mayo Clinic Laboratories to results available) taking into account standard setup days and weekends. The first day is the time that it typically takes for a result to be available. The last day is the time it might take, accounting for any necessary repeated testing.

30 to 40 days

Specimen Retention Time
Outlines the length of time after testing that a specimen is kept in the laboratory before it is discarded

1 month

Performing Laboratory Location
Indicates the location of the laboratory that performs the test

Rochester

Fees
Several factors determine the fee charged to perform a test. Contact your U.S. or International Regional Manager for information about establishing a fee schedule or to learn more about resources to optimize test selection.

  • Authorized users can sign in to Test Prices for detailed fee information.
  • Clients without access to Test Prices can contact Customer Service 24 hours a day, seven days a week.
  • Prospective clients should contact their account representative. For assistance, contact Customer Service.

Test Classification
Provides information regarding the medical device classification for laboratory test kits and reagents. Tests may be classified as cleared or approved by the US Food and Drug Administration (FDA) and used per manufacturer instructions, or as products that do not undergo full FDA review and approval, and are then labeled as an Analyte Specific Reagent (ASR) product.

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

CPT Code Information
Provides guidance in determining the appropriate Current Procedural Terminology (CPT) code(s) information for each test or profile. The listed CPT codes reflect Mayo Clinic Laboratories interpretation of CPT coding requirements. It is the responsibility of each laboratory to determine correct CPT codes to use for billing.

CPT codes are provided by the performing laboratory.

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® Information
Provides guidance in determining the Logical Observation Identifiers Names and Codes (LOINC) values for the order and results codes of this test. LOINC values are provided by the performing laboratory.

Test Id Test Order Name Order LOINC Value
BTWGS Bacterial Typing, Whole Genome Seq 90246-0
Result Id Test Result Name Result LOINC Value
Applies only to results expressed in units of measure originally reported by the performing laboratory. These values do not apply to results that are converted to other units of measure.
BTWGS Bacterial Typing, Whole Genome Seq 90246-0

Test Setup Resources

Setup Files
Test setup information contains test file definition details to support order and result interfacing between Mayo Clinic Laboratories and your Laboratory Information System.

Excel | Pdf

Sample Reports
Normal and Abnormal sample reports are provided as references for report appearance.

Normal Reports | Abnormal Reports

SI Sample Reports
International System (SI) of Unit reports are provided for a limited number of tests. These reports are intended for international account use and are only available through MayoLINK accounts that have been defined to receive them.

SI Normal Reports | SI Abnormal Reports