Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations

Shaoting Li; Shaokang Zhang; Leen Baert; Balamurugan Jagadeesan; Catherine Ngom-Bru; Taylor Griswold; Lee S Katz; Heather A Carleton; Xiangyu Deng

doi:10.1128/AEM.01985-19

Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations

Appl Environ Microbiol. 2019 Nov 27;85(24):e01985-19. doi: 10.1128/AEM.01985-19. Print 2019 Dec 15.

Authors

Shaoting Li¹, Shaokang Zhang¹, Leen Baert², Balamurugan Jagadeesan², Catherine Ngom-Bru², Taylor Griswold³, Lee S Katz^{1

3}, Heather A Carleton³, Xiangyu Deng⁴

Affiliations

¹ Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA.
² Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Vers-chez-les-Blanc, Lausanne, Switzerland.
³ Enteric Diseases Laboratory Branch, Centers for Diseases Control and Prevention, Atlanta, Georgia, USA.
⁴ Center for Food Safety, Department of Food Science and Technology, University of Georgia, Griffin, Georgia, USA xdeng@uga.edu.

Abstract

Single-nucleotide polymorphisms (SNPs) are widely used for whole-genome sequencing (WGS)-based subtyping of foodborne pathogens in outbreak and source tracking investigations. Mobile genetic elements (MGEs) are commonly present in bacterial genomes and may affect SNP subtyping results if their evolutionary history and dynamics differ from that of the bacterial chromosomes. Using Salmonella enterica as a model organism, we surveyed major categories of MGEs, including plasmids, phages, insertion sequences, integrons, and integrative and conjugative elements (ICEs), in 990 genomes representing 21 major serotypes of S. enterica We evaluated whether plasmids and chromosomal MGEs affect SNP subtyping with 9 outbreak clusters of different serotypes found in the United States in 2018. The median total length of chromosomal MGEs accounted for 2.5% of a typical S. enterica chromosome. Of the 990 analyzed S. enterica isolates, 68.9% contained at least one assembled plasmid sequence. The median total length of assembled plasmids in these isolates was 93,671 bp. Plasmids that carry high densities of SNPs were found to substantially affect both SNP phylogenies and SNP distances among closely related isolates if they were present in the reference genome for SNP subtyping. In comparison, chromosomal MGEs were found to have limited impact on SNP subtyping. We recommend the identification of plasmid sequences in the reference genome and the exclusion of plasmid-borne SNPs from SNP subtyping analysis.IMPORTANCE Despite increasingly routine use of WGS and SNP subtyping in outbreak and source tracking investigations, whether and how MGEs affect SNP subtyping has not been thoroughly investigated. Besides chromosomal MGEs, plasmids are frequently entangled in draft genome assemblies and yet to be assessed for their impact on SNP subtyping. This study provides evidence-based guidance on the treatment of MGEs in SNP analysis for Salmonella to infer phylogenetic relationship and SNP distance between isolates.

Keywords: SNP; Salmonella; WGS; mobile genetic elements; plasmid; subtyping; whole-genome sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosomes, Bacterial
Disease Outbreaks
Genome, Bacterial
Humans
Interspersed Repetitive Sequences / genetics*
Phylogeny
Plasmids / isolation & purification
Polymorphism, Single Nucleotide*
Salmonella enterica / classification*
Salmonella enterica / genetics*
Serogroup
Whole Genome Sequencing