High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach

Intraserovar lineages of S. Montevideo differ by thousands of SNPs, that are only slightly less than the number of SNPs observed between S. Montevideo and other distinct serovars. Much less variability was discovered within an individual S. Montevideo clade implicated in a recent foodborne outbreak as well as among individual NGS replicates. These findings were similar to previous reports documenting homopolymeric and deletion error rates with the Roche 454 GS Titanium technology. In no case, however, did variability associated with sequencing methods or sample preparations create inconsistencies with our current phylogenetic results or the subsequent molecular epidemiological evidence gleaned from these data.Implementation of a validated pipeline for NGS data acquisition and analysis provides highly reproducible results that are stable and predictable for molecular epidemiological applications. When draft genomes are collected at 15×-20× coverage and passed through a quality filter as part of a data analysis pipeline, including sub-passaged replicates defined by a few SNPs, they can be accurately placed in a phylogenetic context. This reproducibility applies to all levels within and between serovars of Salmonella suggesting that investigators using these methods can have confidence in their conclusions.Foodborne pathogens cause an estimated 9.4 million human illnesses in the U.S. each year, resulting in nearly 60,000 hospitalizations and over 1,300 deaths [1-4]. Salmonella enterica remains one of the most devastating of these foodborne pathogens with 11% of all food related deaths being attributed from exposure to this bacterium [4]. The genus Salmonella comprises two species, S. enterica and S. bongori, both of which have been found in the food supply. Six subspecies of S. enterica have been described (I-IIIa, IIIb, IV, and VI) that can be found in a variety of mammalian and non-mammalian hosts including humans, cattle, birds, turtles, and snakes. Most non-typhoid