Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
Microbiome. 2019 Jun 27;7(1):97. doi: 10.1186/s40168-019-0710-x.
Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases.
Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and bla. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli.
By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.
医院废水中含有大量个体的粪便物质，其中许多正在接受抗生素治疗。因此，医院废水有可能提供发现尚未在临床菌株中描述的新型碳青霉烯酶和其他耐药基因的机会。我们的目的是调查从印度孟买市收集的医院污水中的微生物群和抗生素抗性组，特别关注鉴定新型碳青霉烯酶。
shotgun 宏基因组学共揭示了 112 种不同的移动抗生素耐药基因类型，对几乎所有类别的抗生素都具有耐药性。β-内酰胺酶基因，包括编码临床上重要的碳青霉烯酶，如 NDM、VIM、IMP、KPC 和 OXA-48，非常丰富。NDM（相对于 16S rRNA 基因的 0.9%）是最常见的碳青霉烯酶基因，其次是 OXA-58（相对于 16S rRNA 基因的 0.84%）。在所研究的移动遗传元件中，1 类整合子（相对于 16S rRNA 基因的 11%）最为丰富。属不动杆菌占总 16S rRNA 读数的 30%之多，其中鲍曼不动杆菌估计占 2.5%。扩增整合子基因盒的高通量测序鉴定了一种新型的 IMP 型（拟议的 IMP-81）碳青霉烯酶基因（8 个 aa 取代）的功能变体，以及最近描述的新型耐药基因，如 sul4 和 bla。使用计算隐马尔可夫模型，我们在 shotgun 数据中检测到 27 种独特的金属-β-内酰胺酶（MBL）基因，其中 9 种是新型 B1 亚类基因，1 种新型 B2 亚类基因和 10 种新型 B3 亚类基因。在大肠杆菌中表达的七种新型 MBL 基因中有六种是有功能的。
通过探索来自印度的医院废水，我们对碳青霉烯酶的多样性有了更深入的了解。该研究还表明，医院废水的微生物群可以作为新型耐药基因的储库，包括以前未被描述的具有进一步传播潜力的碳青霉烯酶。
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