RefMLST: Reference-based Multilocus Sequence Typing Enables Universal Bacterial Typing

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2024 Aug 27

PMID 39192191

Authors

Mondher Khdhiri

Ella Thomas

Chanel de Smet

Priyanka Chandar

Induja Chandrakumar

Jean M Davidson

Paul Anderson

Samuel D Chorlton

Affiliations

Soon will be listed here.

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

Availability And Implementation: refMLST is freely available for academic use at https://bugseq.com/academic .

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