Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents

IF 4.5 2区 医学 Q1 INFECTIOUS DISEASES
Thobela Conco-Biyela , Muneer Ahmad Malla , Oluyemi Olatunji Awolusi , Mushal Allam , Arshad Ismail , Thor A. Stenström , Faizal Bux , Sheena Kumari
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Abstract

Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.

Abstract Image

元基因组学对含氯废水中自由生活阿米巴微生物组和抗生素耐药性基因的深入研究
自由生活阿米巴(FLA)是废水中常见的生物之一,也是多种微生物群落的既定宿主。尽管FLA具有重要的临床意义,但人们对其微生物组和抗药性组的了解却很少,以往的研究大多依赖于传统方法。在这项研究中,我们利用霰弹枪元基因组学全面分析了从两家污水处理厂(WWTP)最终处理出水中分离出的 FLA 微生物组、抗生素耐药性组和毒力因子(VFs)。结果表明,棘阿米巴是最常见的 FLA,其次是恩塔米巴。从两个污水处理厂获得的 FLA 微生物组中,细菌多样性无明显差异(p > 0.05)。在门一级,最主要的类群是变形菌,其次是固着菌和放线菌。鉴定出的最多的菌属是肠杆菌属,其次是柠檬杆菌属、白杆菌属和杯状杆菌属。后三个属是首次在棘阿米巴中发现。我们总共发现了 43 种 ARG,它们对头孢菌素、苯酚、链霉素、三甲氧苄啶、喹诺酮类、头孢菌素、替加环素、利福平和卡那霉素具有耐药性。同样,在 FLA 元基因组中也检测到了多种 VFs,包括鞭毛蛋白、IV 型纤毛抽动运动蛋白(pilH 和 rpoN)、藻酸盐生物合成基因 AlgI、AlgG、藻酸盐生物合成基因 AlgI、AlggG、AlgD 和 AlgW 以及 VI 型分泌系统蛋白和一般分泌途径蛋白(tssM、tssA、tssL、tssK、tssJ、fha、tssG、tssF、tssC 和 tssB、gspC、gspE、gspD、gspF、gspG、gspH、gspI、gspJ、gspK 和 gspM)。据我们所知,这是首次对 FLA 中的微生物组和抗药性组及其在处理过的污水中的潜在致病性进行研究。此外,这项研究还表明,FLA 可以寄生多种潜在的致病菌,包括以前未曾报道过的拟杆菌(Paenibacillus)和杯形拟杆菌(Cupriavidus),这表明它们之间的关系可能在抗生素耐药菌(ARBs)和抗生素耐药基因(ARGs)的传播和持久性以及新型病原体的进化中发挥作用。
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来源期刊
CiteScore
11.50
自引率
5.00%
发文量
151
审稿时长
22 days
期刊介绍: The International Journal of Hygiene and Environmental Health serves as a multidisciplinary forum for original reports on exposure assessment and the reactions to and consequences of human exposure to the biological, chemical, and physical environment. Research reports, short communications, reviews, scientific comments, technical notes, and editorials will be peer-reviewed before acceptance for publication. Priority will be given to articles on epidemiological aspects of environmental toxicology, health risk assessments, susceptible (sub) populations, sanitation and clean water, human biomonitoring, environmental medicine, and public health aspects of exposure-related outcomes.
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