美国得克萨斯州潘汉德尔地区牛临床沙门氏菌分离物中抗菌药耐药性基因的基因组分析

Max Chung, Ethan Dudley, Hatem Kittana, Alexis C. Thompson, Matthew Scott, Keri Norman, Robert Valeris-Chacin
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引用次数: 0

摘要

与牛宿主相适应的沙门氏菌血清型中抗菌药耐药性(AMR)的上升日益引起牛肉和乳制品行业的关注。现有文献主要关注屠宰后的 AMR。相比之下,人们对收获前牛体内沙门氏菌 AMR 的了解还很有限,尤其是在美国牛肉和乳制品出口量排名前五的得克萨斯州;得克萨斯州牛的健康状况对美国牛肉和乳制品行业的健康状况有着全国性的影响。本研究利用长线程全基因组测序和生物信息学方法分析了得克萨斯州潘汉德尔地区 98 个肉牛和奶牛分离物中的抗菌药耐药性基因 (ARGs)。利用费雪精确检验和考虑种群结构的弹性网模型来推断基因组 ARG 图谱与抗菌药表型图谱和元数据之间的关联。还进行了基因图谱绘制,以评估移动遗传因子在携带 ARGs 方面的作用。研究发现,不同养牛场类型和沙门氏菌血清型之间的抗菌药耐药性基因存在统计学差异。与奶牛饲养相比,牛肉饲养在统计学上与更多的 ARGs 相关。海德堡沙门氏菌与最多的 ARGs 相关,其次是都柏林沙门氏菌分离物。此外,特定类别的 ARGs 只存在于移动遗传因子中。
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Genomic Profiling of Antimicrobial Resistance Genes in Clinical Salmonella Isolates from Cattle in the Texas Panhandle, USA
Rising antimicrobial resistance (AMR) in Salmonella serotypes host-adapted to cattle is of increasing concern to the beef and dairy industry. The bulk of the existing literature focuses on AMR post-slaughter. In comparison, the understanding of AMR in Salmonella among pre-harvest cattle is still limited, particularly in Texas, which ranks top five in beef and dairy exports in the United States; inherently, the health of Texas cattle has nationwide implications for the health of the United States beef and dairy industry. In this study, long-read whole genome sequencing and bioinformatic methods were utilized to analyze antimicrobial resistance genes (ARGs) in 98 isolates from beef and dairy cattle in the Texas Panhandle. Fisher exact tests and elastic net models accounting for population structure were used to infer associations between genomic ARG profiles and antimicrobial phenotypic profiles and metadata. Gene mapping was also performed to assess the role of mobile genetic elements in harboring ARGs. Antimicrobial resistance genes were found to be statistically different between the type of cattle operation and Salmonella serotypes. Beef operations were statistically significantly associated with more ARGs compared to dairy operations. Salmonella Heidelberg, followed by Salmonella Dublin isolates, were associated with the most ARGs. Additionally, specific classes of ARGs were only present within mobile genetic elements.
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