Boulund Fredrik, Berglund Fanny, Flach Carl-Fredrik, Bengtsson-Palme Johan, Marathe Nachiket P, Larsson D G Joakim, Kristiansson Erik
Department of Mathematical sciences, Chalmers university of Technology and University of Gothenburg, Gothenburg, Sweden.
Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden.
BMC Genomics. 2017 Sep 2;18(1):682. doi: 10.1186/s12864-017-4064-0.
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.
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.
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.
氟喹诺酮类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基因可使许多细菌种类对氟喹诺酮产生耐药性，并且在临床环境中越来越常见。在过去十年中，已发现并鉴定了几个qnr基因家族，但它们的真实流行情况和多样性仍不清楚。特别是，据推测环境和宿主相关细菌群落中存在大量未知的qnr基因，这些基因可能会转移到病原体中。
在本研究中，我们使用计算方法在基因组和宏基因组中筛选新型qnr基因。与之前的研究不同，我们分析了一个几乎大20倍的数据集，包含近13万亿碱基的序列数据。总共鉴定出362,843个潜在的qnr基因片段，从中重建了611个假定的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。611个已鉴定的qnr基因中有52个是从宏基因组中重建的，其中20个是先前未描述的。所有新型qnr基因均从与水生环境相关的宏基因组中组装而来。选择了9个新型基因进行验证，其中6个测试基因在大肠杆菌中表达时对环丙沙星的敏感性持续降低。
本研究结果为环境微生物群落中qnr基因的普遍存在提供了更多证据，扩大了已知qnr基因变体的数量，并进一步阐明了这类耐药基因的多样性。本研究还强化了环境细菌群落是先前未鉴定的qnr基因来源的假设。
