摘要
      水上通勤是泰国一种主要的城市交通方式。然而，城市船只通勤者有暴露于微生物污染的生物气溶胶或飞溅物的风险。我们的目的是调查微生物群落结构，识别细菌和病毒病原体，并使用下一代测序（NGS）在Saen Saep运河18公里运输船路线上的10个采样点评估抗微生物耐药性基因（ARGs）的丰度，该运河横跨文化、商业和郊区陆地区域。霰弹枪宏基因组（Illumina HiSeq）和16S rRNA基因扩增子（V4区）（Illumina-MiSeq）测序平台显示，不同的微生物集群与这些区域对齐，在文化和郊区之间有明显的分离。霰弹枪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%）是洋葱伯克霍尔德菌复合体、布兹勒里Arcobacter、越南伯克霍尔德氏菌、肺炎克雷伯菌和阴沟肠杆菌复合体。病毒（在所有微生物序列中的丰度为0.28%-0.67%）主要包括脊椎动物病毒和噬菌体，在人类病毒病原体中有脑心肌炎病毒（在病毒序列中的丰富度为33.3%-58.2%）、丙型肝炎病毒基因型1、人类α疱疹病毒1和人类β疱疹病毒6A。15种ARG类型包含611种ARG亚型，包括对β-内酰胺耐药的ARG亚类，这是最多样化和最丰富的组（206种亚型；17.0%-27.5%）、氨基糖苷类（94种亚型，9.6%-15.3%）、四环素类（80种亚型）、15.6%-20.2%和大环内酯类（79种亚型、14.5%-32.1%）。有趣的是，在培养位点，与β-内酰胺、甲氧苄啶和磺酰胺以及A.butzleri和crAssphage耐药性相关的ARGs的丰度与其他位点显著不同（p<0.05）。我们证明了使用NGS深入了解微生物群落和抗微生物耐药性的好处，这两者都对人类健康构成风险。使用NGS可以促进城市用水通勤者和附近居民的微生物风险缓解和管理。
Abstract
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.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722047507