Ronco Troels, Stegger Marc, Olsen Rikke Heidemann, Sekse Camilla, Nordstoga Anne Bang, Pohjanvirta Tarja, Lilje Berit, Lyhs Ulrike, Andersen Paal Skytt, Pedersen Karl
National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870, Frederiksberg C, Denmark.
Statens Serum Institut, Department of Microbiology and Infection Control, Artillerivej 5, 2300, Copenhagen S, Denmark.
BMC Genomics. 2017 Jan 3;18(1):13. doi: 10.1186/s12864-016-3415-6.
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.
Hundred 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.
In 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.
The 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.
大肠杆菌感染即大肠杆菌病，在动物福利降低和生产经济性方面给全球家禽养殖户带来了巨大挑战。大肠杆菌病由禽致病性大肠杆菌（APEC）引起。APEC菌株是肠道外致病性大肠杆菌，总体上被认为是一个基因多样化的群体。在北欧国家，家禽养殖户依赖进口瑞典肉种鸡，这些种鸡是育种金字塔的一部分。2014年至2016年期间，据报道北欧肉鸡养殖场大肠杆菌病的发病率有所上升。本研究的目的是使用全基因组测序来调查在有大肠杆菌病问题的家禽养殖场收集的大肠杆菌分离株之间的遗传多样性。
对来自肉鸡和肉种鸡的114株细菌分离株进行全基因组测序。大多数分离株是从北欧农场患有大肠杆菌病的家禽中收集的。随后，进行了比较基因组分析。这包括计算机分型（血清型和多位点序列分型）、毒力和抗性基因的鉴定以及基于单核苷酸多态性的系统发育分析。
总体而言，所鉴定的家禽分离株构成了一个基因多样化的群体。然而，系统发育分析揭示了一个由47株密切相关的ST117 O78:H4分离株组成的主要分支。该分支中的分离株是从多个北欧国家患有大肠杆菌病的肉鸡和种鸡中收集的。它们与一株人类ST117分离株聚集在一起，并且都携带先前与人类尿路致病性大肠杆菌相关的毒力基因。
调查揭示了在不同北欧国家从患病肉鸡和种鸡中收集到的ST117 O78:H4分离株谱系。数据表明，密切相关的ST117 O78:H4菌株已通过肉鸡育种金字塔垂直传播到北欧各国相距遥远的农场。
