Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok, Thailand.
Research Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand.
Sci Total Environ. 2022 Nov 20;848:157652. doi: 10.1016/j.scitotenv.2022.157652. Epub 2022 Jul 26.
Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %-0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %-58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %-27.5 %), aminoglycoside (94 subtypes; 9.6 %-15.3 %), tetracycline (80 subtypes; 15.6 %-20.2 %), and macrolide (79 subtypes; 14.5 %-32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.
水上通勤是泰国主要的城市交通方式。然而，城市乘船通勤者有暴露于微生物污染的生物气溶胶或飞沫的风险。我们的目的是使用下一代测序（NGS）在贯穿文化、商业和郊区陆地区域的 18 公里水上交通船航线的 10 个采样点调查微生物群落结构、鉴定细菌和病毒病原体，并评估抗生素耐药基因（ARGs）的丰度。 shotgun 宏基因组（Illumina HiSeq）和 16S rRNA 基因扩增子（V4 区）（Illumina MiSeq）测序平台揭示了与区域相匹配的多样化微生物群聚类，文化区和郊区区站点之间有明显的隔离。 shotgun 宏基因组测序进一步鉴定了细菌和病毒病原体以及 ARGs。主要的细菌病原体（相对丰度>0.5%）为伯克霍尔德氏菌复合群、弯曲杆菌、越氏伯克霍尔德菌、肺炎克雷伯菌和阴沟肠杆菌复合群。病毒（所有微生物序列中的丰度为 0.28%-0.67%）主要由脊椎动物病毒和噬菌体组成，其中脑炎心肌炎病毒（病毒序列中的丰度为 33.3%-58.2%）、丙型肝炎病毒 1 型、人单纯疱疹病毒 1 型和人疱疹病毒 6A 为人类病毒病原体。15 种 ARG 类型包含 611 种 ARG 亚型，包括对β-内酰胺类、氨基糖苷类、四环素类和大环内酯类具有耐药性的亚型，其中β-内酰胺类是最多样和最丰富的组（206 种亚型；17.0%-27.5%）。有趣的是，文化区与β-内酰胺类、甲氧苄啶和磺胺类药物以及弯曲杆菌和 crAssphage 耐药相关的 ARG 丰度与其他站点显著不同（p<0.05）。我们展示了使用 NGS 提供对微生物群落和抗生素耐药性的深入了解的好处，这两者都对人类健康构成威胁。使用 NGS 可能有助于减轻城市水上通勤者和周边居民的微生物风险并进行管理。
