Multilocus Sequence Typing Database for Contains a Spurious Allele of the Transketolase Gene

Overview

Journal Microbiol Spectr

Specialty Microbiology

Date 2024 Jul 25

PMID 39052441

Authors

Swaine L Chen

Suma Tiruvayipati

Wen Ying Tang

Timothy M S Barkham

Affiliations

Soon will be listed here.

Abstract

The (transketolase) gene is one of the seven gene fragments used in the multilocus sequence typing (MLST) system for . We discovered that the tkt_134 allele is derived from a homologous gene (which we designate ) that is not present in all ; all known strains that contain a match to the tkt_134 allele also contain a gene sequence that is much closer in sequence identity to the other non-tkt_134 alleles (i.e., the canonical tkt gene) in the database. Based on these data, the tkt_134 allele has been removed from the MLST database as of September 2021, and all sequence types containing tkt_134 have also been removed.IMPORTANCEMultilocus sequence typing (MLST) databases are a common good and remain important for research, medical, and epidemiological purposes. This remains true even in the context of widespread whole-genome sequencing. We discovered a contaminating allele of the gene in the MLST database that led to unstable, ambiguous, or erroneous MLST assignment. The allele has since been removed from the public database based on the results presented in this manuscript.

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