Details:

Alternative Title:
Front Microbiol
Personal Author:
Lindsey, Rebecca L. ; Pouseele, Hannes ; Chen, Jessica C. ; Strockbine, Nancy A. ; Carleton, Heather A.
Lindsey, Rebecca L. ; Pouseele, Hannes ; Chen, Jessica C. ; Strockbine, Nancy A. ; Carleton, Heather A. Less -
Description:
Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen capable of causing severe disease in humans. Rapid and accurate identification and characterization techniques are essential during outbreak investigations. Current methods for characterization of STEC are expensive and time-consuming. With the advent of rapid and cheap whole genome sequencing (WGS) benchtop sequencers, the potential exists to replace traditional workflows with WGS. The aim of this study was to validate tools to do reference identification and characterization from WGS for STEC in a single workflow within an easy to use commercially available software platform. Publically available serotype, virulence, and antimicrobial resistance databases were downloaded from the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org) and integrated into a genotyping plug-in with in silico PCR tools to confirm some of the virulence genes detected from WGS data. Additionally, down sampling experiments on the WGS sequence data were performed to determine a threshold for sequence coverage needed to accurately predict serotype and virulence genes using the established workflow. The serotype database was tested on a total of 228 genomes and correctly predicted from WGS for 96.1% of O serogroups and 96.5% of H serogroups identified by conventional testing techniques. A total of 59 genomes were evaluated to determine the threshold of coverage to detect the different WGS targets, 40 were evaluated for serotype and virulence gene detection and 19 for the stx gene subtypes. For serotype, 95% of the O and 100% of the H serogroups were detected at > 40x and ≥ 30x coverage, respectively. For virulence targets and stx gene subtypes, nearly all genes were detected at > 40x, though some targets were 100% detectable from genomes with coverage ≥20x. The resistance detection tool was 97% concordant with phenotypic testing results. With isolates sequenced to > 40x coverage, the different databases accurately predicted serotype, virulence, and resistance from WGS data, providing a fast and cheaper alternative to conventional typing techniques.
Subjects:
[+]
Escherichia Coli Escherichia Coli Serotypes Microbiology Next Generation Sequencing STEC Stx Subtyping Whole Genome Sequence
Source:
Front Microbiol. 2016; 7.
Pubmed ID:
27242777
Pubmed Central ID:
PMC4876609
Document Type:
Journal Article
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:40e347e0f568e830a6494269111ee786d185cda27b95685aaf44d3dfe6392f08
Download URL:
https://stacks.cdc.gov/view/cdc/39818/cdc_39818_DS1.pdf
File Type:

Supporting Files

• 	fmicb-07-00766.nxml	bin
  	license.txt	txt
  	Table1.xlsx	xlsx

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