Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore, Singapore.
Microbiol Spectr. 2024 Sep 3;12(9):e0053724. doi: 10.1128/spectrum.00537-24. Epub 2024 Jul 25.
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.
（转酮醇酶）基因是用于 的多位点序列分型（MLST）系统的七个基因片段之一。我们发现 tkt_134 等位基因源自同源基因（我们指定为 ），并非所有 都存在；所有含有与 tkt_134 等位基因匹配的已知菌株都含有与数据库中其他非 tkt_134 等位基因（即典型的 tkt 基因）序列同一性更高的基因序列。基于这些数据，自 2021 年 9 月起，tkt_134 等位基因已从 MLST 数据库中删除，所有包含 tkt_134 的序列类型也已被删除。
多位点序列分型（MLST）数据库是一种常见的资源，对于研究、医学和流行病学目的仍然很重要。即使在全基因组测序广泛应用的情况下也是如此。我们在 MLST 数据库中发现了一个 基因的污染等位基因，导致不稳定、模糊或错误的 MLST 分配。根据本文提出的结果，该等位基因已从公共数据库中删除。
