refMLST: reference-based multilocus sequence typing enables universal bacterial typing.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Traditional genomic outbreak investigation methods like SNP and gene-by-gene typing have limitations.
• These methods require background genomes or curated allele schemes, restricting their use to known organisms.
• Novel or less-studied pathogens are often not amenable to these existing approaches.

Purpose of the Study:

• To introduce refMLST, a novel gene-by-gene approach for bacterial outbreak investigation.
• To provide a scalable, reproducible, and robust method for genomic epidemiology.
• To overcome limitations of existing methods for novel and less-studied pathogens.

Main Methods:

• Developed refMLST, a gene-by-gene approach utilizing a bacterium's reference genome.
• Applied refMLST to large datasets of Salmonella enterica, Yersinia enterocolitica, and Campylobacter jejuni genomes.
• Compared refMLST performance against established tools such as chewieSnake.

Main Results:

• refMLST demonstrated consistent clustering across diverse bacterial species.
• The method provided improved resolution for outbreak analysis.
• refMLST achieved faster processing times compared to existing tools.
• Consistent clustering, improved resolution, and faster processing were observed for Salmonella enterica, Yersinia enterocolitica, and Campylobacter jejuni.

Conclusions:

• refMLST is a novel multilocus sequence typing approach.
• Applicable to any bacterial species with a public reference genome.
• Does not require a curated scheme and automatically accounts for genetic recombination.
• Offers a versatile and efficient solution for bacterial outbreak investigation.