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. 2019 Jul 12;10:1591.
doi: 10.3389/fmicb.2019.01591. eCollection 2019.

Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

Free PMC article

Assessment and Comparison of Molecular Subtyping and Characterization Methods for Salmonella

Silin Tang et al. Front Microbiol. .
Free PMC article


The food industry is facing a major transition regarding methods for confirmation, characterization, and subtyping of Salmonella. Whole-genome sequencing (WGS) is rapidly becoming both the method of choice and the gold standard for Salmonella subtyping; however, routine use of WGS by the food industry is often not feasible due to cost constraints or the need for rapid results. To facilitate selection of subtyping methods by the food industry, we present: (i) a comparison between classical serotyping and selected widely used molecular-based subtyping methods including pulsed-field gel electrophoresis, multilocus sequence typing, and WGS (including WGS-based serovar prediction) and (ii) a scoring system to evaluate and compare Salmonella subtyping assays. This literature-based assessment supports the superior discriminatory power of WGS for source tracking and root cause elimination in food safety incident; however, circumstances in which use of other subtyping methods may be warranted were also identified. This review provides practical guidance for the food industry and presents a starting point for further comparative evaluation of Salmonella characterization and subtyping methods.

Keywords: MLST; PFGE; Salmonella; WGS; food industry; serotyping; subtyping.


Timeline of the development of selected molecular subtyping and characterization methods for Salmonella (Salmonella Subcommittee of the Nomenclature Committee of the International Society for, Microbiology, 1934; Gilson et al., 1990; Threlfall and Frost, 1990; Hulton et al., 1991; Martin et al., 1992; Lindstedt et al., 2003, 2013; Healy et al., 2005; Grimont and Weill, 2007; Zou et al., 2010; Wattiau et al., 2011; PulseNet, 2014; CDC, 2016a, 2019; Nadon et al., 2017).

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