Farm-to-fork investigation of an outbreak of Shiga toxin-producing Escherichia coli O157

Microbial Genomics
Deborah WilsonRussell Gorton

Abstract

Fifteen cases of Shiga toxin-producing Escherichia coli (STEC) O157 infection were associated with the consumption of contaminated food from two related butchers' premises in the north-east of England. Ten cases were admitted to hospital and seven cases developed haemolytic uraemic syndrome. A case control study found a statistically significant association with the purchase of raw and/or ready-to-eat (RTE) food supplied by the implicated butchers' shops. Isolates of STEC O157 were detected in two raw lamb burgers taken from one of the butchers' premises. Subsequent environmental sampling identified STEC O157 in bovine faecal samples on the farm supplying cattle to the implicated butchers for slaughter. Whole genome sequencing (WGS) was performed on the Illumina HiSeq 2500 platform on all cultures isolated from humans, food and cattle during the investigation. Quality trimmed Illumina reads were mapped to the STEC O157 reference genome Sakai using bwa-mem, and single nucleotide polymorphisms (SNPs) were identified using gatk2. Analysis of the core genome SNP positions (>90 % consensus, minimum depth 10×, mapping quality (MQ)≥30) revealed that all isolates from humans, food and cattle differed by two SNPs. WGS analysis provided ...Continue Reading

References

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Citations

Dec 10, 2019·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Lyndsay BottichioLaura Gieraltowski
Jul 7, 2020·EFSA Journal·UNKNOWN EFSA Panel on Biological Hazards (EFSA BIOHAZ Panel)Lieve Herman
Nov 21, 2018·Emerging Infectious Diseases·Lisa ByrneClaire Jenkins
Jan 5, 2021·Foodborne Pathogens and Disease·Siobhán C McCarthyGeraldine Duffy
Jun 8, 2021·Epidemiology and Infection·Saira ButtUNKNOWN Outbreak Control Team
Aug 28, 2021·Animals : an Open Access Journal From MDPI·Leonela DíazMagaly Toro

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Datasets Mentioned

BETA
PRJNA248042
BA000007

Software Mentioned

bwa
gatk2
RaxML
mem

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