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Background  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. 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.    Methods  From 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.    Results  The 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.    Conclusion  Hybrid 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.    Electronic supplementary material  The online version of this article (10.1186/s12879-018-3449-2) contains supplementary material, which is available to authorized users.

bmc infectious diseases

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