Cummins Max L, Li Dmitriy, Ahmad Aeman, Bushell Rhys, Noormohammadi Amir H, Wijesurendra Dinidu S, Stent Andrew, Marenda Marc S, Djordjevic Steven P
Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW 2007, Australia.
The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, NSW 2007, Australia.
Microorganisms. 2023 Jun 6;11(6):1513. doi: 10.3390/microorganisms11061513.
Bacterial chondronecrosis with osteomyelitis (BCO) impacts animal welfare and productivity in the poultry industry worldwide, yet it has an understudied pathogenesis. While Avian Pathogenic (APEC) are known to be one of the main causes, there is a lack of whole genome sequence data, with only a few BCO-associated APEC (APEC) genomes available in public databases. In this study, we conducted an analysis of 205 APEC genome sequences to generate new baseline phylogenomic knowledge regarding the diversity of sequence types and the presence of virulence associated genes (VAGs). Our findings revealed the following: (i) APEC are phylogenetically and genotypically similar to APEC that cause colibacillosis (APEC), with globally disseminated APEC sequence types ST117, ST57, ST69, and ST95 being predominate; (ii) APEC are frequent carriers of ColV-like plasmids that carry a similar set of VAGs as those found in APEC. Additionally, we performed genomic comparisons, including a genome-wide association study, with a complementary collection of geotemporally-matched genomes of APEC from multiple cases of colibacillosis (APEC). Our genome-wide association study found no evidence of novel virulence loci unique to APEC. Overall, our data indicate that APEC and APEC are not distinct subpopulations of APEC. Our publication of these genomes substantially increases the available collection of APEC genomes and provides insights for the management and treatment strategies of lameness in poultry.
细菌性软骨坏死伴骨髓炎（BCO）影响着全球家禽业的动物福利和生产力，但其发病机制尚未得到充分研究。虽然已知禽致病性大肠杆菌（APEC）是主要病因之一，但缺乏全基因组序列数据，公共数据库中仅有少数与BCO相关的APEC基因组。在本研究中，我们对205个APEC基因组序列进行了分析，以生成关于序列类型多样性和毒力相关基因（VAGs）存在情况的新的系统发育基因组学基线知识。我们的研究结果如下：（i）APEC在系统发育和基因型上与引起大肠杆菌病的APEC相似，全球传播的APEC序列类型ST117、ST57、ST69和ST95占主导地位；（ii）APEC是ColV样质粒的常见携带者，这些质粒携带的VAGs与在引起大肠杆菌病的APEC中发现的相似。此外，我们进行了基因组比较，包括全基因组关联研究，与来自多例大肠杆菌病（APEC）的地理时间匹配的APEC基因组的补充集合进行比较。我们的全基因组关联研究没有发现APEC特有的新毒力位点的证据。总体而言，我们的数据表明APEC和引起大肠杆菌病的APEC不是APEC的不同亚群。我们公布这些基因组大大增加了可用的APEC基因组集合，并为家禽跛行的管理和治疗策略提供了见解。
