背景:氟喹诺酮类药物是用于预防和治疗多种细菌感染的广谱抗生素。质粒介导的qnr基因在许多细菌物种中提供对氟喹诺酮的抗性,并且在临床环境中越来越多地遇到。在过去的十年里,已经发现并鉴定了几个qnr基因家族,但其真正的患病率和多样性仍不清楚.特别是,已经假设环境和宿主相关的细菌群落维持大量未知的qnr基因,这些基因可以被动员到病原体中。
结果:在这项研究中,我们使用计算方法来筛选新的qnr基因的基因组和宏基因组。与以前的研究相比,我们分析了一个几乎20倍大的数据集,该数据集包含近13TB的序列数据.总的来说,鉴定出362,843个潜在的qnr基因片段,从中重建了611个推定的qnr基因。这些基因序列包括所有先前描述的质粒介导的qnr基因家族。从宏基因组中重建了611个已鉴定的qnr基因中的52个,其中20个以前没有描述过。所有新的qnr基因都是从与水生环境相关的宏基因组组装的。选择了9个新基因进行验证,当在大肠杆菌中表达时,六个测试基因一致降低了对环丙沙星的敏感性。
结论:本研究的结果为环境微生物群落中qnr基因的普遍存在提供了额外的证据,扩大已知qnr基因变异的数量,并进一步阐明该类抗性基因的多样性。这项研究还加强了以下假设:环境细菌群落是先前未表征的qnr基因的来源。
BACKGROUND: Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are increasingly encountered in clinical settings. Over the last decade, several families of qnr genes have been discovered and characterized, but their true prevalence and diversity still remain unclear. In particular, environmental and host-associated bacterial communities have been hypothesized to maintain a large and unknown collection of qnr genes that could be mobilized into pathogens.
RESULTS: In this study we used computational methods to screen genomes and metagenomes for novel qnr genes. In contrast to previous studies, we analyzed an almost 20-fold larger dataset comprising almost 13 terabases of sequence data. In total, 362,843 potential qnr gene fragments were identified, from which 611 putative qnr genes were reconstructed. These gene sequences included all previously described plasmid-mediated qnr gene families. Fifty-two of the 611 identified qnr genes were reconstructed from metagenomes, and 20 of these were previously undescribed. All of the novel qnr genes were assembled from metagenomes associated with aquatic environments. Nine of the novel genes were selected for validation, and six of the tested genes conferred consistently decreased susceptibility to ciprofloxacin when expressed in Escherichia coli.
CONCLUSIONS: The results presented in this study provide additional evidence for the ubiquitous presence of qnr genes in environmental microbial communities, expand the number of known qnr gene variants and further elucidate the diversity of this class of resistance genes. This study also strengthens the hypothesis that environmental bacterial communities act as sources of previously uncharacterized qnr genes.