Background Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in general been characterized as being a genetically diverse population. In the Nordic countries, poultry farmers depend on import of Swedish broiler breeders which are part of a breeding pyramid. During 2014 to 2016, an increased occurrence of colibacillosis on Nordic broiler chicken farms was reported. The aim of this study was to investigate the genetic diversity among E. coli isolates collected on poultry farms with colibacillosis issues, using whole genome sequencing.MethodsHundred and fourteen bacterial isolates from both broilers and broiler breeders were whole genome sequenced. The majority of isolates were collected from poultry with colibacillosis on Nordic farms. Subsequently, comparative genomic analyses were carried out. This included in silico typing (sero- and multi-locus sequence typing), identification of virulence and resistance genes and phylogenetic analyses based on single nucleotide polymorphisms.ResultsIn general, the characterized poultry isolates constituted a genetically diverse population. However, the phylogenetic analyses revealed a major clade of 47 closely related ST117 O78:H4 isolates. The isolates in this clade were collected from broiler chickens and breeders with colibacillosis in multiple Nordic countries. They clustered together with a human ST117 isolate and all carried virulence genes that previously have been associated with human uropathogenic E. coli.ConclusionsThe investigation revealed a lineage of ST117 O78:H4 isolates collected in different Nordic countries from diseased broilers and breeders. The data indicate that the closely related ST117 O78:H4 strains have been transferred vertically through the broiler breeding pyramid into distantly located farms across the Nordic countries.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3415-6) contains supplementary material, which is available to authorized users.

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Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli has been documented in humans as well as in food-producing birds, including chickens, and for unknown reasons the prevalence has increased significantly during the last decade. With E. coli as a major opportunistic pathogen in chickens and with a potential for zoonotic transfer to human beings, ESBL-producing E. coli represents a major risk both to poultry production and to human health. This review presents some of the current problems with ESBL-producing E. coli in relation to poultry production, with a focus on chickens. To illustrate issues in relation to screening and typing, two case studies are included where one collection of ESBL-producing E. coli isolates was obtained from asymptomatic carrier chickens while the other was obtained from lesions in chickens. Pulsed-field gel electrophoresis and multi-locus sequence typing revealed a highly heterogeneous population of ESBL-producing E. coli. All isolates harboured between one and three large plasmids (>100 kb). Among isolates associated with asymptomatic chickens, the ESBL types SHV and TEM dominated, while CTX-M-1 dominated in disease-associated isolates. The isolates from diseased birds were occasionally of sequence types often associated with human infections, such as ST131. With improved tools to trace and screen for ESBL-producing E. coli at farm level, strategies can be selected that aim to reduce or eliminate the presence of ESBL-producing E. coli in poultry and poultry products meant for human consumption.

APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.

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