High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples

Bjørn-Arne Lindstedt,Davide Porcellato,Lin T. Brandal,Misti D. Finton

doi:10.1186/s12879-018-3449-2

Abstract

BackgroundClassification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof. For E. coli isolated from faecal samples, the presence of specific genes associated with different intestinal pathogenic pathovars will determine their classification and further course of action. However, the E. coli genome is not a static entity, and hybrid strains are emerging that cross the pathovar definitions. Hybrid strains may show gene contents previously associated with several distinct pathovars making the correct diagnostic classification difficult. We extended the analysis of routinely submitted faecal isolates to include known virulence associated genes that are usually not examined in faecal isolates to detect the frequency of possible hybrid strains.MethodsFrom September 2012 to February 2013, 168 faecal isolates of E. coli routinely submitted to the Norwegian Institute of Public Health (NIPH) from clinical microbiological laboratories throughout Norway were analysed for 33 VAGs using multiplex-PCR, including factors associated with extraintestinal pathogenic E. coli (ExPEC) strains. The strains were further typed by Multiple Locus Variable-Number Tandem-Repeat Analysis (MLVA), and the phylogenetic grouping was determined. One isolate from the study was selected for whole genome sequencing (WGS) with a combination of Oxford Nanopore’s MinION and Illumina’s MiSeq.ResultsThe analysis showed a surprisingly high number of strains carrying ExPEC associated VAGs and strains carrying a combination of both intestinal pathogenic E. coli (IPEC) and ExPEC VAGs. In particular, 93.5% (101/108) of isolates classified as belonging to an IPEC pathovar additionally carried ExPEC VAGs. WGS analysis of a selected hybrid strain revealed that it could, with present classification criteria, be classified as belonging to all of the Enteropathogenic Escherichia coli (EPEC), Uropathogenic Escherichia coli (UPEC), Neonatal meningitis Escherichia coli (NMEC) and Avian pathogenic Escherichia coli (APEC) pathovars.ConclusionHybrid ExPEC/IPEC E. coli strains were found at a very high frequency in faecal samples and were in fact the predominant species present. A sequenced hybrid isolate was confirmed to be a cross-pathovar strain possessing recognised hallmarks of several pathovars, and a genome heavily influenced by horizontal gene transfer.

Highlights

Classification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof
The fully sequenced FHI_NMBU_03 phylogroup B2 strain from this study shows hallmarks of extraintestinal pathogenic E. coli (ExPEC) pathovars uropathogenic E. coli (UPEC), avian pathogenic E. coli (APEC), neonatal meningitis-associated E. coli (NMEC) and the intestinal pathogenic E. coli (IPEC) pathovar Atypical enteropathogenic Escherichia coli (aEPEC) with some VAGs related to Enterotoxigenic Escherichia coli (ETEC) (K88, 987P- and colonization factor antigen I fimbriae (CFA/I)- fimbrial genes), it constitutes a truly pathovar-hybrid strain (Additional file 3)
We report that a high frequency (> 93%) of routinely submitted faecal E. coli strains from Norwegian hospitals, previously characterized as IPEC, harbour ExPEC virulence factors

Summary

Introduction

Classification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof. For E. coli isolated from faecal samples, the presence of specific genes associated with different intestinal pathogenic pathovars will determine their classification and further course of action. ExPEC frequently cause urinary tract infection (UTI), septicaemia, meningitis, as well as causing soft tissue damage [2, 3]. ExPEC includes, among others, the pathovars uropathogenic E. coli (UPEC) associated with urinary tract infection in human and animals, neonatal meningitis-associated E. coli (NMEC), septicaemic E. coli (SePEC) causing systemic infection in human and animals, avian pathogenic E. coli (APEC) that cause avian colibacillosis, and a potentially emerging ExPEC lineage named endometrial pathogenic E. coli (EnPEC) [4, 5]

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