2015
DOI: 10.1128/jcm.03235-14
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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 … Show more

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Cited by 83 publications
(99 citation statements)
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“…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).…”
Section: Discussionmentioning
confidence: 90%
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“…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).…”
Section: Discussionmentioning
confidence: 90%
“…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.…”
Section: Methodsmentioning
confidence: 99%
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“…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.…”
Section: Resultsmentioning
confidence: 99%
“…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.…”
mentioning
confidence: 99%