EcOH:In silicoserotyping ofE. colifrom short read data

Abstract

22"! 23"The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets 24"for serotyping that have traditionally been used to identify pathogenic lineages of E. coli. As 25"serotyping has several limitations, public health reference laboratories are increasingly 26"moving towards whole genome sequencing (WGS) for the rapid characterisation of bacterial 27"isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from 28"raw, short read sequence data, leveraging the known genetic basis for the biosynthesis of O- 29"and H-antigens. Our approach bypasses the need for de novo genome assembly by directly 30"screening WGS reads against a curated database of alleles linked to known E. coli O-groups 31"and H-types (the EcOH database) using the software package SRST2. We validated our 32"approach by comparing in silico results with those obtained via serological phenotyping of 33"197 enteropathogenic (EPEC) isolates. We also demonstrated the utility of our method to 34"characterise enterotoxigenic E. coli (ETEC) and the uropathogenic E. coli (UPEC) epidemic 35"clone ST131, and for in silico serotyping of foodborne outbreak-related isolates in the public 36"GenomeTrakr database.

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

“…Primers designed to detect clade-specific SNPs reported by Ben Zakour et al (2016) are presented in Supplemental Table S3. In silico serotyping was performed with SRST2 according to the investigator's instructions with the database provided (Ingle et al 2015). Here, serotype is defined by presence of known genes encoding serotype-determining enzymes.…”

Horsing Around: Escherichia coli ST1250 of Equine Origin Harboring Epidemic IncHI1/ST9 Plasmid with bla CTX-M-1 and an Operon for Short-Chain Fructooligosaccharide Metabolism

“…The draft genome assemblies from WGS and EnteroBase were analyzed for the presence of antibiotic resistance genes (ARGs), virulence genes, plasmid replicons, and serotypes. For this purpose, ABRicate (https://github.com/tseemann/abricate) was used with thresholds set to 90% identity and 95% query coverage against the databases ResFinder (43), VFDB (44), PlasmidFinder (45), and EcOH (46), respectively. Plasmid multilocus sequence typing (pMLST) was performed using pMLST by the Center for Genomic Epidemiology (45).…”

Phylogeography and Genetic Diversity of Francisella tularensis subsp. holarctica in France (1947–2018)

“…Annotation files were generated with Prokka v1.13.3 (Seemann, 2014) using the Franco-Iberian Fth FTNF002-00 genome (NC_009749) as a reference. Abricate v0.8.10 (Seemann, 2019) was used in order to detect genes associated with antibiotic resistance using ARG-ANNOT (Gupta et al, 2014), CARD (Jia et al, 2017), EcOH (Ingle et al, 2015), NCBI Bacterial Antimicrobial resistance Reference Gene Database (Accession: PRJNA313047) and ResFinder (Zankari et al, 2012) databases, with a minimum identity of 50%. CanSNPer v1.0.8 was used to assign the established canSNP nomenclature to the sequenced strains.…”