Su Zhiguo, Gu April Z, Wen Donghui, Li Feifei, Huang Bei, Mu Qinglin, Chen Lyujun
School of Environment, Tsinghua University, Beijing, 100084, China.
School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14853, United States.
Environ Sci Ecotechnol. 2024 Oct 29;23:100502. doi: 10.1016/j.ese.2024.100502. eCollection 2025 Jan.
Effective risk assessment and control of environmental antibiotic resistance depend on comprehensive information about antibiotic resistance genes (ARGs) and their microbial hosts. Advances in sequencing technologies and bioinformatics have enabled the identification of ARG hosts using metagenome-assembled contigs and genomes. However, these approaches often suffer from information loss and require extensive computational resources. Here we introduce a bioinformatic strategy that identifies ARG hosts by prescreening ARG-like reads (ALRs) directly from total metagenomic datasets. This ALR-based method offers several advantages: (1) it enables the detection of low-abundance ARG hosts with higher accuracy in complex environments; (2) it establishes a direct relationship between the abundance of ARGs and their hosts; and (3) it reduces computation time by approximately 44-96% compared to strategies relying on assembled contigs and genomes. We applied our ALR-based strategy alongside two traditional methods to investigate a typical human-impacted environment. The results were consistent across all methods, revealing that ARGs are predominantly carried by Gammaproteobacteria and Bacilli, and their distribution patterns may indicate the impact of wastewater discharge on coastal resistome. Our strategy provides rapid and accurate identification of antibiotic-resistant bacteria, offering valuable insights for the high-throughput surveillance of environmental antibiotic resistance. This study further expands our knowledge of ARG-related risk management in future.
有效的环境抗生素抗性风险评估和控制取决于有关抗生素抗性基因(ARGs)及其微生物宿主的全面信息。测序技术和生物信息学的进步使得能够使用宏基因组组装的重叠群和基因组来鉴定ARG宿主。然而,这些方法常常存在信息丢失的问题,并且需要大量的计算资源。在此,我们介绍一种生物信息学策略,该策略通过直接从总宏基因组数据集中预筛选类ARG读数(ALRs)来鉴定ARG宿主。这种基于ALR的方法具有几个优点:(1)它能够在复杂环境中以更高的准确性检测低丰度ARG宿主;(2)它建立了ARG丰度与其宿主之间的直接关系;(3)与依赖组装重叠群和基因组的策略相比,它将计算时间减少了约44%-96%。我们将基于ALR的策略与两种传统方法一起应用于研究一个典型的受人类影响的环境。所有方法的结果都是一致的,表明ARGs主要由γ-变形菌和芽孢杆菌携带,并且它们的分布模式可能表明废水排放对沿海抗性组的影响。我们的策略提供了对抗生素抗性细菌的快速准确鉴定,为环境抗生素抗性的高通量监测提供了有价值的见解。这项研究进一步扩展了我们对未来ARG相关风险管理的认识。