Abstract：
Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for treatment decisions and support antimicrobial stewardship. Diagnostic sequencing can provide information about antimicrobial resistance genes in M. haemolytica more rapidly than conventional diagnostics. Realizing the full potential of diagnostic sequencing requires a comprehensive understanding of the genetic markers of antimicrobial resistance. We identified genetic markers of resistance in M. haemolytica to macrolide class antibiotics commonly used for control of BRD. Genome sequences were determined for 99 M. haemolytica isolates with six different susceptibility phenotypes collected over 2 years from a feedlot in Saskatchewan, Canada. Known macrolide resistance genes estT, msr(E), and mph(E) were identified in most resistant isolates within predicted integrative and conjugative elements (ICEs). ICE sequences lacking antibiotic resistance genes were detected in 10 of 47 susceptible isolates. No resistance-associated polymorphisms were detected in ribosomal RNA genes, although previously unreported mutations in the L22 and L23 ribosomal proteins were identified in 12 and 27 resistant isolates, respectively. Pangenome analysis led to the identification of 79 genes associated with resistance to gamithromycin, of which 95% (75 of 79) had no functional annotation. Most of the observed phenotypic resistance was explained by previously identified antibiotic resistance genes, although resistance to the macrolides gamithromycin and tulathromycin was not explained in 39 of 47 isolates, demonstrating the need for continued surveillance for novel determinants of macrolide resistance.IMPORTANCEBovine respiratory disease is the costliest disease of beef cattle in North America and the most common reason for injectable antibiotic use in beef cattle. Metagenomic sequencing offers the potential to make economically significant reductions in turnaround time for diagnostic information for evidence-based selection of antibiotics for use in the feedlot. The success of diagnostic sequencing depends on a comprehensive catalog of antimicrobial resistance genes and other genome features associated with reduced susceptibility. We analyzed the genome sequences of isolates of Mannheimia haemolytica, a major bovine respiratory disease pathogen, and identified both previously known and novel genes associated with reduced susceptibility to macrolide class antimicrobials. These findings reinforce the need for ongoing surveillance for markers of antimicrobial resistance to support improved diagnostics and antimicrobial stewardship.
摘要：
溶血曼海姆菌是牛呼吸道疾病（BRD）的主要贡献者，这给牛肉行业造成了巨大的经济损失，迫切需要快速准确的诊断测试，为治疗决策提供证据并支持抗菌药物管理。诊断测序可以比常规诊断更快地提供关于溶血分枝杆菌中的抗微生物抗性基因的信息。要实现诊断测序的全部潜力，需要全面了解抗菌素耐药性的遗传标记。我们确定了溶血分枝杆菌对通常用于控制BRD的大环内酯类抗生素的抗性的遗传标记。在2年内从萨斯喀彻温省的一个饲养场收集的具有六种不同敏感性表型的99株溶血分枝杆菌分离株的基因组序列。加拿大。已知的大环内酯抗性基因estT，msr(E),在预测的整合和共轭元件（ICE）中，在大多数抗性分离株中鉴定出mph（E）。在47个易感分离株中的10个中检测到缺乏抗生素抗性基因的ICE序列。在核糖体RNA基因中未检测到抗性相关的多态性，尽管在12个和27个耐药分离株中发现了L22和L23核糖体蛋白的先前未报道的突变，分别。Pangenome分析鉴定了79个与加米霉素抗性相关的基因，其中95%(79个中的75个)没有功能注释。大多数观察到的表型抗性是由先前鉴定的抗生素抗性基因解释的。尽管在47个分离株中的39个中没有解释对大环内酯类加米霉素和妥拉霉素的耐药性，证明有必要继续监测大环内酯耐药的新决定因素。IMPORTANCEBovine呼吸道疾病是北美肉牛最昂贵的疾病，也是肉牛使用可注射抗生素的最常见原因。宏基因组测序提供了在经济上显着减少诊断信息的周转时间的潜力，用于基于证据的选择用于饲养场的抗生素。诊断测序的成功取决于抗微生物耐药性基因的综合目录和与降低的易感性相关的其他基因组特征。我们分析了溶血曼海姆菌分离株的基因组序列，一种主要的牛呼吸道疾病病原体，并鉴定了与大环内酯类抗微生物剂敏感性降低相关的先前已知和新基因。这些发现加强了对抗菌素耐药性标志物进行持续监测的必要性，以支持改进的诊断和抗菌素管理。
