Deblais Loïc, Lorentz Benjamin, Scaria Joy, Nagaraja Kakambi V, Nisar Muhammad, Lauer Dale, Voss Shauna, Rajashekara Gireesh
Food Animal Health Research Program, Department of Veterinary Preventive Medicine, The Ohio State University, OARDC, Wooster, OH, United States.
Department of Plant Pathology, The Ohio State University, OARDC, Wooster, OH, United States.
Front Microbiol. 2018 Aug 10;9:1841. doi: 10.3389/fmicb.2018.01841. eCollection 2018.
is one of the leading causes of human foodborne gastroenteritis in the United States. In addition, contributes to morbidity and mortality in livestock. The control of is an increasing problematic issue in livestock production due to lack of effective control methods and the constant adaptation of to new management practices, which is often related to horizontal acquisition of virulence or antibiotic resistance genes. serotype Heidelberg is one of the most commonly isolated serotypes in all poultry production systems in North America. Emergence and persistence of multi-drug resistant Heidelberg isolates further impact the poultry production and public health. We hypothesized that distinct poultry production environments affect genomic content, and by consequence its survival and virulence abilities. This study compared the genomic composition of Heidelberg isolated from environmental samples (19 chicken and 12 turkey isolates) of different breeder farms (16 chicken and 8 turkey farms) in the Midwest, United States. Whole genome comparison of 31 genomes using RAST and SEED identified differences in specific sub-systems in isolates between the chicken- and turkey-associated farm environmental samples. Genes associated with the type IV secretion system ( = 12) and conjugative transfer ( = 3) were absent in turkey farm isolates compared to the chicken ones (-value < 0.01); Further, turkey farm isolates were enriched in prophage proteins ( = 53; -value < 0.01). Complementary studies using PHASTER showed that prophages were all phages and were more represented in turkey environmental isolates than the chicken isolates. This study corroborates that isolates from distinct farm environment show differences in Heidelberg genome content related to horizontal transfer between bacteria or through viral infections. Complementary microbiome studies of these samples would provide critical insights on sources of these variations. Overall, our findings enhance the understanding of genome plasticity and may aid in the development of future effective management practices to control .
在美国，它是导致人类食源性肠胃炎的主要原因之一。此外，它还会导致牲畜发病和死亡。由于缺乏有效的控制方法以及它不断适应新的管理措施，而这往往与毒力或抗生素抗性基因的水平获得有关，因此在牲畜生产中对它的控制成为一个日益棘手的问题。海德堡血清型是北美所有家禽生产系统中最常分离出的血清型之一。多重耐药性海德堡分离株的出现和持续存在进一步影响了家禽生产和公共卫生。我们假设不同的家禽生产环境会影响其基因组内容，进而影响其生存和毒力能力。本研究比较了从美国中西部不同种鸡场（16个鸡场和8个火鸡场）的环境样本（19株鸡源和12株火鸡源分离株）中分离出的海德堡的基因组组成。使用RAST和SEED对31个基因组进行全基因组比较，确定了鸡源和火鸡源农场环境样本分离株在特定子系统上的差异。与IV型分泌系统相关的基因（n = 12）和接合转移相关的基因（n = 3）在火鸡场分离株中比鸡场分离株中缺失（P值<0.01）；此外，火鸡场分离株中前噬菌体蛋白富集（n = 53；P值<0.01）。使用PHASTER进行的补充研究表明，前噬菌体均为噬菌体，并且在火鸡环境分离株中比鸡分离株中更常见。本研究证实，来自不同农场环境的分离株在海德堡基因组内容上存在差异，这与细菌之间的水平转移或通过病毒感染有关。对这些样本进行补充微生物组研究将为这些变异的来源提供关键见解。总体而言，我们的发现增进了对其基因组可塑性的理解，并可能有助于未来制定有效的控制管理措施。
