publication . Other literature type . Article . 2014

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

Flemming Scheutz; Eva Møller Nielsen; Frank Møller Aarestrup; Katrine Grimstrup Joensen; Rolf Sommer Kaas; Ole Lund; Henrik Hasman;
Open Access
  • Published: 26 Feb 2014
  • Publisher: American Society for Microbiology
  • Country: Denmark
Abstract
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all i...
Subjects
free text keywords: Microbiology (medical), Epidemiology, DENMARK, ESCHERICHIA, ESCHERICHIA COLI, FOOD SAFETY, GENETIC TECHNIQUES, TOXINS, VERO CYTOTOXINS, Hygiene and toxicology, Microbiological aspects, Biology, Virology, Intimin, Computational biology, Multilocus sequence typing, Virulence, Verocytotoxin, chemistry.chemical_compound, chemistry, Whole genome sequencing, Outbreak, VTEC, Typing
Abstract
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. The aim of this study was to perform a real-time evaluation of WGS for routine typing and surveillance of verocytotoxin-producing Escherichia coli (VTEC). In Denmark, the Statens Serum Institut (SSI) routinely receives all suspected VTEC isolates. During a 7-week period in the fall of 2012, all i...
Subjects
free text keywords: Microbiology (medical), Epidemiology, DENMARK, ESCHERICHIA, ESCHERICHIA COLI, FOOD SAFETY, GENETIC TECHNIQUES, TOXINS, VERO CYTOTOXINS, Hygiene and toxicology, Microbiological aspects, Biology, Virology, Intimin, Computational biology, Multilocus sequence typing, Virulence, Verocytotoxin, chemistry.chemical_compound, chemistry, Whole genome sequencing, Outbreak, VTEC, Typing
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