An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants

• DOI: 10.1128/aem.02248-20
• Publication Date: 2020-10-20T13:43:50Z
• Authors: Swarnali Louha; Richard J. Meiner...; Zaid Abdo; Mark E. Berrang; Travis C. Glenn
• Keywords: 0301 basic medicine; 03 medical and health sciences; Whole Genome Sequencing; Environmental Microbiology; Animals; Genetic Variation; Listeria monocytogenes; Abattoirs; Poultry; Multilocus Sequence Typing

We have developed an open-source tool ( https://github.com/swarnalilouha/Haplo-ST ) that provides allele-based subtyping of L. monocytogenes isolates at the whole-genome level. Along with allelic profiles, this tool also generates allele sequences and identifies paralogs, which is useful for phylogenetic tree reconstruction and deciphering relationships between closely related isolates. More broadly, Haplo-ST is flexible and can be adapted to characterize the genome of any haploid organism simply by installing an organism-specific gene database. Haplo-ST also allows for scalable subtyping of isolates; fewer reference genes can be used for low-resolution typing, whereas higher resolution can be achieved by increasing the number of genes used in the analysis. Our tool enabled clustering of L. monocytogenes isolates into lineages and detection of potential loci for adaptation and persistence in food processing environments. Findings from these analyses highlight the effectiveness of Haplo-ST in subtyping and evaluating relationships among isolates in studies of bacterial population genetics.