肠道微生物中，益生菌弗雷格兰杆菌（Bacteroides fragilis）是数量最多和最致病的细菌之一，与儿童腹泻、炎症性肠病和结肠癌有关。它越来越耐碳青霉烯和甲硝唑等强效抗菌药物，因此是最耐药的厌氧菌之一。这些因素需要在全球范围内加强对B. fragilis及其群体结构的监测。我们通过开发一种多位点序列分型方案（MLST），提出了一种可能的解决方案。该方案基于七个核心基因片段：groL（hsp60）、rpoB、recA、dnaJ、rprX、prfA和fusA。这些基因片段具有高度的区分能力，同时与基于完整核心基因组的系统发育分析相符。该方案能够在菌株水平上区分出B. fragilis分离物。 它提供了一种分子分型的标准化方法，可应用于来自不同采样背景的分离物，例如患者分离物、环境样品和从食品和动物源获取的菌株。总共，我们对567个B. fragilis基因组进行了序列分型，并收集了它们的分离物数据。MLST方案清晰地将B. fragilis群体分为两个部分，取决于cfiA和cepA耐药基因的存在。然而，在分析的基因组中，没有发现与任何特定疾病或地理位置有关的特定亚群。我们希望通过这个MLST方案，在国际范围内提供一个强大的工具来研究和监测B. fragilis。 意义：我们首次提出了弗雷格兰杆菌的MLST方案，该菌是人体肠道微生物中数量最多的致病细菌之一。该方案可以在全球范围内标准化分类和监测B. fragilis，并将大部分当前的分离数据收集在一个地方。更统一的B. fragilis数据收集和分析方法可以提供重要洞见，了解该病原体的运作方式和作为物种如何发展。对B. fragilis的紧密监测特别重要，因为它越来越耐受强效抗菌药物，并与其他细菌进行水平基因转移。希望这种方法能指导新的发现，了解B. fragilis如何演变并与人类宿主相互作用。此外，该方案还可能适用于其他属的菌种。

Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.