In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages

Abstract

The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival of E. coli within mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read WGS data. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known and novel E. coli O-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparing in silico results for 197 enteropathogenic E. coli isolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500 E. coli genomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci between E. coli chromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting that E. coli ‘strain space’ may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

“…The superiority of sequence typing over serotyping is illustrated by the ST131 UPEC pandemic strain, in which most isolates are serotype O25b:H4, but some are serotype O16:H5 (Nicolas-Chanoine et al, 2014). Importantly, E. coli serotypes can be reliably predicted from whole genome sequences (Ingle et al, 2016b). Indeed, in-silico serotyping offers a number of advantages over traditional serotyping, including the non-reliance on typing sera that may vary in quality, and the ability to type strains that do not express the O- or H-antigens in vitro or that autoagglutinate (Ingle et al, 2016b).…”

“…Importantly, E. coli serotypes can be reliably predicted from whole genome sequences (Ingle et al, 2016b). Indeed, in-silico serotyping offers a number of advantages over traditional serotyping, including the non-reliance on typing sera that may vary in quality, and the ability to type strains that do not express the O- or H-antigens in vitro or that autoagglutinate (Ingle et al, 2016b). For these reasons, in-silico serotyping is likely to replace traditional serotyping in future.…”

Pan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar

“…It has also recently been shown that antimicrobial resistance (Tyson et al, 2015; McDermott et al, 2016; Zhao et al, 2016), serovar (Levine et al, 2016; Yoshida et al, 2016b), and the results of other traditional sub-typing schemes such as multi-locus sequence typing (Sheppard et al, 2012) can be accurately predicted in silico through the analysis of bacterial genome sequences. However, identifying bacterial isolates that are most likely to cause disease in humans, based on the genome sequence alone, is a more complex task.…”

Enterohaemorrhagic and other Shiga toxin-producingEscherichia coli(STEC): Where are we now regarding diagnostics and control strategies?

“…Both use antisera in simple agglutination assays. To date, over 180 E. coli O‐serogroups and over 50 H‐serotypes have been identified (Ingle et al., ) and there are more than 100 serotypes of STEC associated with human disease (Ferdous et al., ). Surveillance of STEC infections is often undertaken using serotyping (full or partial) only or using methods which only recover and identify O157:H7 strains.…”