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Whole genome and core genome multilocus sequence typing and single nucleotide polymorphism analyses of Listeria monocytogenes isolates associated with an outbreak linked to cheese, United States, 2013

Lookup NU author(s): Robert Stones

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).


Abstract

© 2017 American Society for Microbiology. Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS 3 months later revealed that the equipment purchased by company B from company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses results were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a nonimplicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, the minimum spanning tree from the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering analysis generated by phylogenetically meaningful algorithms on a sufficient number of isolates, and the SNP/allele threshold alone does not provide sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b and had an identical inlA sequence which did not have premature stop codons.


Publication metadata

Author(s): Chen Y, Luo Y, Carleton H, Timme R, Melka D, Muruvanda T, Wang C, Kastanis G, Katz LS, Turner L, Fritzinger A, Moore T, Stones R, Blankenship J, Salter M, Parish M, Hammack TS, Evans PS, Tarr CL, Allard MW, Strain EA, Brown EW

Publication type: Article

Publication status: Published

Journal: Applied and Environmental Microbiology

Year: 2017

Volume: 83

Issue: 15

Print publication date: 01/08/2017

Online publication date: 26/05/2014

Acceptance date: 17/05/2014

Date deposited: 11/08/2017

ISSN (print): 0099-2240

ISSN (electronic): 1098-5336

Publisher: American Society for Microbiology

URL: https://doi.org/10.1128/AEM.00633-17

DOI: 10.1128/AEM.00633-17


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