摘要

        抗生素耐药性（AMR）的传播是一个日益严重的问题，也是对公众健康的威胁。采用比较基因组学方法研究了新加坡城市污水和城市地表水环境中抗生素耐药基因（ARGs）的发生情况。医院和城市污水（n=6）的ARGs多样性和平均丰度（303个ARG亚型，197816x/Gb）高于处理污水（n=2，58个ARG亚型，2692x/Gb）和地表水（n=5，35个亚型，7985x/Gb）。聚类分析表明，废水的分类组成非常相似，其细菌群落组成富含肠道细菌（类杆菌、粪大肠杆菌、双歧杆菌、Blautia、Roseburia、瘤胃球菌）、肠杆菌科菌群（Klebsiella、气单胞菌、肠杆菌）和条件致病菌（Prevotella，小孢子虫，奈瑟菌）。废水、处理后的废水和地表水共有21个ARGs，编码耐多药外排泵或对氨基糖苷、大环内酯类林可酰胺链球菌（MLS）、喹诺酮类、磺胺类和四环素类的耐药性，这表明这些基因在不同的环境中广泛传播。废水中抗β-内酰胺酶a类临床相关基因（即blaKPC、blaCTX-M、blaSHV、blaTEM）的平均丰度明显较高。尤其是来自临床隔离病房的废水中，blaKPC-2基因（142200x/Gb）含量极高，编码碳青霉烯类抗生素耐药性。从隔离病房废水样本中组装的支架（16和30kbp）表明该基因位于Tn3基转座子（Tn4401）上，该转座子是在肺炎克雷伯菌质粒中发现的一种动员元件。在较长的支架中，转座因子被毒素-抗毒素（TA）系统和其他金属抗性基因所包围，这些基因可能在胁迫条件下增加质粒在宿主中的持久性、适应性和繁殖。在CHROMagar培养基上从隔离病房废水中培养的几种细菌（阴沟肠杆菌、肺炎克雷伯杆菌、弗劳迪柠檬酸杆菌、铜绿假单胞菌）含有blaKPC-2基因。提示临床专科病房废水是AMR传播的热点。在废水样品中回收了含有喹诺酮类耐药基因（qnrS1，qnrS2）和β-内酰胺酶基因（blaTEM-1）的IncQ和IncF质粒等其他流动基因元件的组装支架，有助于AMR的转移。

        The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb). A cluster analysis showed that the taxonomic composition of wastewaters was highly similar and had a bacterial community composition enriched in gut bacteria (Bacteroides, Faecalibacterium, Bifidobacterium, Blautia, Roseburia, Ruminococcus), the Enterobacteriaceae group (Klebsiella, Aeromonas, Enterobacter) and opportunistic pathogens (Prevotella, Comamonas, Neisseria). Wastewater, treated effluents and surface waters had a shared resistome of 21 ARGs encoding multidrug resistant efflux pumps or resistance to aminoglycoside, macrolide-lincosamide-streptogramins (MLS), quinolones, sulfonamide, and tetracycline resistance which suggests that these genes are wide spread across different environments. Wastewater had a distinctively higher average abundance of clinically relevant, class A beta-lactamase resistant genes (i.e., bla_KPC, bla_CTX-M, bla_SHV, bla_TEM). The wastewaters from clinical isolation wards, in particular, had a exceedingly high levels of bla_KPC-2 genes (142,200 x/Gb), encoding for carbapenem resistance. Assembled scaffolds (16 and 30 kbp) from isolation ward wastewater samples indicated this gene was located on a Tn3-based transposon (Tn4401), a mobilization element found in Klebsiella pneumonia plasmids. In the longer scaffold, transposable elements were flanked by a toxin-antitoxin (TA) system and other metal resistant genes that likely increase the persistence, fitness and propagation of the plasmid in the bacterial host under conditions of stress. A few bacterial species (Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, Pseudomonas aeruginosa) that were cultured from the isolation ward wastewaters on CHROMagar media harbored the bla_KPC-2 gene. This suggests that hospital wastewaters derived from clinical specialty wards are hotspots for the spread of AMR. Assembled scaffolds of other mobile genetic elements such as IncQ and IncF plasmids bearing quinolone resistance genes (qnrS1, qnrS2) and the class A beta-lactamase gene (bla_TEM-1) were recovered in wastewater samples which may aid the transfer of AMR.

         https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5696577/