摘要

碳青霉烯类耐药性是对我们治疗难治性细菌感染能力的快速增长的威胁。为了解碳青霉烯类抗药性如何在病原体之间动员和传播，研究潜在抗性机制的遗传背景非常重要。在这项研究中，六个临床碳青霉烯抗性分离株的五个不同物种 - 鲍曼不动杆菌，大肠杆菌，两个肺炎克雷伯菌，奇异变形杆菌和铜绿假单胞菌 - 的抗性组使用全基因组测序进行了表征。所有肠杆菌科分离株和鲍曼不动杆菌分离株都获得了大量抗菌素耐药基因（每种分离株7-18种不同基因），包括以下编码碳青霉烯酶：blaKPC-2，blaOXA-48，blaOXA-72，blaNDM-1， blaNDM-7和blaVIM-1。此外，还发现了一种新版本的blaSHV。鉴定了四种新的抗性质粒，并使用光学DNA作图验证了它们的完全组装序列。大多数抗性基因共定位于这些和其他质粒上，表明存在共选择的风险。相比之下，六个碳青霉烯酶基因中有五个存在于没有或几乎没有其他抗性基因的质粒上。预期的抵抗水平 - 基于获得性抗性决定因素 - 在大多数情况下与测量水平一致。然而，六种分离株中有四种与多种抗生素有关，存在几个重要差异。总之，我们的结果进一步阐明了碳青霉烯酶的多样性，它们的水平转移机制和可能的共选模式。该研究还强调了使用全基因组测序对具有复杂基因型的病原体的抗菌药物敏感性测试的难度。

Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species - Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa - were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7-18 different genes per isolate), including the following encoding carbapenemases: blaKPC-2, blaOXA-48, blaOXA-72, blaNDM-1, blaNDM-7 and blaVIM-1. In addition, a novel version of blaSHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance - based on acquired resistance determinants - was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.

https://www.ncbi.nlm.nih.gov/pubmed/30461373