BugSeq Bioinformatics Inc, Vancouver, BC, Canada.
California Polytechnic State University, San Luis Obispo, CA, USA.
BMC Bioinformatics. 2024 Aug 27;25(1):280. doi: 10.1186/s12859-024-05913-4.
Commonly used approaches for genomic investigation of bacterial outbreaks, including SNP and gene-by-gene approaches, are limited by the requirement for background genomes and curated allele schemes, respectively. As a result, they only work on a select subset of known organisms, and fail on novel or less studied pathogens. We introduce refMLST, a gene-by-gene approach using the reference genome of a bacterium to form a scalable, reproducible and robust method to perform outbreak investigation.
When applied to multiple outbreak causing bacteria including 1263 Salmonella enterica, 331 Yersinia enterocolitica and 6526 Campylobacter jejuni genomes, refMLST enabled consistent clustering, improved resolution, and faster processing in comparison to commonly used tools like chewieSnake.
refMLST is a novel multilocus sequence typing approach that is applicable to any bacterial species with a public reference genome, does not require a curated scheme, and automatically accounts for genetic recombination.
refMLST is freely available for academic use at https://bugseq.com/academic .
常用于细菌爆发的基因组研究的方法，包括 SNP 和基因分型方法，分别受到背景基因组和经过整理的等位基因方案的限制。因此，它们仅适用于已知生物体的一个选择子集，并且在新型或研究较少的病原体上失败。我们介绍了 refMLST，这是一种基因分型方法，使用细菌的参考基因组来形成一种可扩展、可重复和强大的方法来进行爆发调查。
当应用于包括 1263 株沙门氏菌、331 株耶尔森氏菌和 6526 株空肠弯曲菌在内的多种爆发性细菌时，与 chewieSnake 等常用工具相比，refMLST 能够实现一致的聚类、提高分辨率和更快的处理速度。
refMLST 是一种新的多位点序列分型方法，适用于具有公共参考基因组的任何细菌物种，不需要经过整理的方案，并且自动考虑了遗传重组。
refMLST 可在 https://bugseq.com/academic 上免费供学术使用。
