Salmonella typing in New South Wales: current methods and application of improved epidemiological tools

Foodborne Illness Outbreak Investigation in a High-Profile Sports Club

A foodborne illness outbreak involving an elite sports team was investigated by a public health unit in Sydney, Australia. An epidemiological association was established between gastrointestinal illness and the consumption of food supplied by an external caterer, with a lamb meal most strongly associated with illness. Genetically identical Salmonella isolates were identified from clinical specimens, residual food items, and an environmental swab taken from the catering premises. The training schedule and other club operations were significantly affected by this outbreak. Increased susceptibility due to regular shared activities and the potential for significant impact upon performance indicates that sports clubs must ensure that food suppliers comply with the highest standards of hygiene. Collaboration with public health authorities assists in source identification and prevention of further transmission.

Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014

Background

Salmonella Typhimurium (STM) is an important cause of foodborne outbreaks worldwide. Subtyping of STM remains critical to outbreak investigation, yet current techniques (e.g. multilocus variable number tandem repeat analysis, MLVA) may provide insufficient discrimination. Whole genome sequencing (WGS) offers potentially greater discriminatory power to support infectious disease surveillance.

Methods

We performed WGS on 62 STM isolates of a single, endemic MLVA type associated with two epidemiologically independent, food-borne outbreaks along with sporadic cases in New South Wales, Australia, during 2014. Genomes of case and environmental isolates were sequenced using HiSeq (Illumina) and the genetic distance between them was assessed by single nucleotide polymorphism (SNP) analysis. SNP analysis was compared to the epidemiological context.

Results

The WGS analysis supported epidemiological evidence and genomes of within-outbreak isolates were nearly identical. Sporadic cases differed from outbreak cases by a small number of SNPs, although their close relationship to outbreak cases may represent an unidentified common food source that may warrant further public health follow up. Previously unrecognised mini-clusters were detected.

Conclusions

WGS of STM can discriminate foodborne community outbreaks within a single endemic MLVA clone. Our findings support the translation of WGS into public health laboratory surveillance of salmonellosis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0831-3) contains supplementary material, which is available to authorized users.

Salmonellosis outbreak traced to playground sand, Australia, 2007-2009

A community outbreak of gastroenteritis in Australia during 2007-2009 was caused by ingestion of playground sand contaminated with Salmonella enterica Paratyphi B, variant Java. The bacterium was also isolated from local wildlife. Findings support consideration of nonfood sources during salmonellosis outbreak investigations and indicate transmission through the animal-human interface.

Genotyping of Salmonella enterica serovar Typhi strains isolated from 1959 to 2006 in China and analysis of genetic diversity by genomic microarray

AIM

To determine the genotype of Salmonella enterica serovar Typhi (S. Typhi) strains in China and analyze their genetic diversity.

METHODS

We collected S. Typhi strains from 1959 to 2006 in five highly endemic Chinese provinces and chose 40 representative strains. Multilocus sequence typing was used to determine the genotypes or sequence types (ST) and microarray-based comparative genomic hybridization (M-CGH) to investigate the differences in gene content among these strains.

RESULTS

Forty representative S. Typhi strains belonged to 4 sequence types (ST1, ST2, ST890, and ST892). The predominant S. Typhi genotype (31/40) was ST2 and it had a diverse geographic distribution. We discovered two novel STs - ST890 and ST892. M-CGH showed that 69 genes in these two novel STs were divergent from S. Typhi Ty2, which belongs to ST1. In addition, 5 representative Typhi strains of ST2 isolated from Guizhou province showed differences in divergent genes.

CONCLUSION

We determined two novel sequence types, ST890 and ST892, and found that ST2 was the most prevalent genotype of S. Typhi in China. Genetic diversity was present even within a highly clonal bacterial population.