Delineating Community Outbreaks of Salmonella enterica Serovar Typhimurium by Use of Whole-Genome Sequencing: Insights into Genomic Variability within an Outbreak

Abstract

c Whole-genome next-generation sequencing (NGS) was used to retrospectively examine 57 isolates from five epidemiologically confirmed community outbreaks (numbered 1 to 5) caused by Salmonella enterica serovar Typhimurium phage type DT170. Most of the human and environmental isolates confirmed epidemiologically to be involved in the outbreaks were either genomically identical or differed by one or two single nucleotide polymorphisms (SNPs), with the exception of those in outbreak 1. The isolates from outbreak 1 differed by up to 12 SNPs, which suggests that the food source of the outbreak was contaminated with more than one strain while each of the other four outbreaks was caused by a single strain. In addition, NGS analysis ruled in isolates that were initially not considered to be linked with the outbreak, which increased the total outbreak size by 107%. The mutation process was modeled by using known mutation rates to derive a cutoff value for the number of SNP difference to determine whether or not a case was part of an outbreak. For an outbreak with less than 1 month of ex vivo/in vivo evolution time, the maximum number of SNP differences between isolates is two or four using the lowest or highest mutation rate, respectively. NGS of S. Typhimurium significantly increases the resolution of investigations of community outbreaks. It can also inform a more targeted public health response by providing important supplementary evidence that cases of disease are or are not associated with food-borne outbreaks of S. Typhimurium. Salmonella enterica serovar Typhimurium is the most common serovar isolated from humans and animals in Australia. Traditionally, surveillance and outbreak investigations of S. Typhimurium rely upon phage typing, which is based on the susceptibility of isolates to a set of bacteriophages. Phage type DT170 has been increasing steadily over the last decade in Australia and became the most frequent phage type in 2004. Therefore, phage typing has limited resolution for outbreak detection. More recently, multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) has been adopted in public health reference laboratories across Australia for epidemiological typing because of its relatively high discriminatory power and ability to be harmonized (1). MLVA has also been used as a standardized method for outbreak detection in Europe (2, 3).In New South Wales (NSW), Australia, all Salmonella isolates from public and private pathology providers are routinely referred to the NSW Enteric Reference Laboratory, Institute for Clinical Pathology and Medical Research (ICPMR), Westmead Hospital, for serotyping and MLVA typing using five VNTR loci (MLVA-5) (1). Prospective MLVA typing of S. Typhimurium has been useful for identifying outbreak clusters (1). In our current practice, recovery of five or more geographically clustered isolates of the same MLVA profile from patients with diarrhea within a 4-week period (cases in the same household are counted as one episode) signals that an outbreak has occurred and...

Defining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing

“…The S. Typhimurium core genome contained 956 (33.45%) more genes than the Salmonella core genome, which contains only 2,882 genes as defined previously (16). We showed that the use of the STCG or the STCG plus core IGRs increases the resolution of the genome sequencing for epidemiological typing using published and epidemiologically investigated outbreaks (14,15,25,26).…”

“…To evaluate the performance of the S. Typhimurium core genome (STCG with and without core IGRs) typing, 21 strains from SARA sequenced in this study and 94 isolates from 13 different outbreaks were used (see Table S2 in the supplemental material) (14,15,25,26). The selection of outbreaks was either based on representative phage type or ST, including DT135, DT135a, U292, DT3, DT104, DT12, DT120, and ST313.…”

“…NGS has major advantages over other pathogen-typing methods, as it promises a standardized universal solution for high-resolution typing. We recently demonstrated the utility and resolution of NGS for outbreak investigation of S. Typhimurium by sequencing 57 isolates from five distinct and epidemiologically confirmed point-source S. Typhimurium DT170 outbreaks in Australia (15). Our study utilized all single nucleotide polymorphisms (SNPs) identified from the genomes of the outbreak isolates.…”

Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage

“…Patient 1 and patient 3 isolates had the same profile but differed by 8 SNPs, while patient 6 and patient 10 isolates had the same profile but differed by 19 SNPs. We previously also observed that isolates with identical MLVA types had one or more SNP difference (6). The genome data offered a much higher resolution than the MLVA data and demonstrated that MLVA lacks the power to reveal the true relationships of the isolates from carriers.…”

“…In the state of New South Wales (NSW), the notification rate has been around 50 cases per 100,000 population (5). Sequencing of S. Typhimurium genomes or analyses of tandem repeats within the genome have increasingly been employed for tracking community outbreaks and transmission chains (6,7). However, the magnitude of genomic variation in isolates associated with carriage remains unknown.…”