Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.
Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
Microbiome. 2017 Oct 12;5(1):134. doi: 10.1186/s40168-017-0353-8.
Metallo-β-lactamases are bacterial enzymes that provide resistance to carbapenems, the most potent class of antibiotics. These enzymes are commonly encoded on mobile genetic elements, which, together with their broad substrate spectrum and lack of clinically useful inhibitors, make them a particularly problematic class of antibiotic resistance determinants. We hypothesized that there is a large and unexplored reservoir of unknown metallo-β-lactamases, some of which may spread to pathogens, thereby threatening public health. The aim of this study was to identify novel metallo-β-lactamases of class B1, the most clinically important subclass of these enzymes.
Based on a new computational method using an optimized hidden Markov model, we analyzed over 10,000 bacterial genomes and plasmids together with more than 5 terabases of metagenomic data to identify novel metallo-β-lactamase genes. In total, 76 novel genes were predicted, forming 59 previously undescribed metallo-β-lactamase gene families. The ability to hydrolyze imipenem in an Escherichia coli host was experimentally confirmed for 18 of the 21 tested genes. Two of the novel B1 metallo-β-lactamase genes contained atypical zinc-binding motifs in their active sites, which were previously undescribed for metallo-β-lactamases. Phylogenetic analysis showed that B1 metallo-β-lactamases could be divided into five major groups based on their evolutionary origin. Our results also show that, except for one, all of the previously characterized mobile B1 β-lactamases are likely to have originated from chromosomal genes present in Shewanella spp. and other Proteobacterial species.
This study more than doubles the number of known B1 metallo-β-lactamases. The findings have further elucidated the diversity and evolutionary history of this important class of antibiotic resistance genes and prepare us for some of the challenges that may be faced in clinics in the future.
金属β-内酰胺酶是一种对碳青霉烯类抗生素（最有效的抗生素之一）具有抗性的细菌酶。这些酶通常编码在移动遗传元件上，这些元件与其广泛的底物谱和缺乏临床有用的抑制剂一起，使它们成为一种特别成问题的抗生素耐药决定因素。我们假设存在大量尚未开发的未知金属β-内酰胺酶，其中一些可能传播到病原体，从而威胁公共健康。本研究的目的是鉴定新型 B1 类金属β-内酰胺酶，这是这些酶中最具临床意义的亚类。
基于一种使用优化隐马尔可夫模型的新计算方法，我们分析了超过 10000 个细菌基因组和质粒以及超过 5 太字节的宏基因组数据，以鉴定新型金属β-内酰胺酶基因。总共预测了 76 个新基因，形成了 59 个以前未描述的金属β-内酰胺酶基因家族。在大肠杆菌宿主中水解亚胺培南的能力在 21 个测试基因中的 18 个基因中得到了实验证实。两个新型 B1 金属β-内酰胺酶基因在其活性位点含有不典型的锌结合基序，这是以前在金属β-内酰胺酶中未描述的。系统发育分析表明，B1 金属β-内酰胺酶可以根据其进化起源分为五个主要组。我们的研究结果还表明，除了一个之外，所有以前表征的移动 B1 内酰胺酶都可能起源于希瓦氏菌属和其他变形菌门物种中存在的染色体基因。
本研究使已知的 B1 金属β-内酰胺酶数量增加了一倍以上。研究结果进一步阐明了这一重要抗生素耐药基因类别的多样性和进化历史，并为我们未来在临床中可能面临的一些挑战做好了准备。
