A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens

Songzhe Fu; Yixiang Zhang; Rui Wang; Zhiguang Qiu; Weizhi Song; Qian Yang; Lixin Shen

doi:10.1016/j.jenvman.2023.118737

A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens

J Environ Manage. 2023 Nov 1:345:118737. doi: 10.1016/j.jenvman.2023.118737. Epub 2023 Aug 30.

Authors

Songzhe Fu¹, Yixiang Zhang², Rui Wang³, Zhiguang Qiu⁴, Weizhi Song⁵, Qian Yang⁶, Lixin Shen⁷

Affiliations

¹ Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 116023, China. Electronic address: fusongzhe@dlou.edu.cn.
² CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences. Shanghai, China; University of Chinese Academy of Sciences, Shanghai, China.
³ Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 116023, China.
⁴ School of Environment and Energy, Shenzhen Graduate School, Peking University, Shenzhen, 518055, China.
⁵ School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, SAR, Hong Kong, China.
⁶ Center for Microbial Ecology and Technology, Ghent University, Ghent, Belgium.
⁷ Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi'an, 710069, China. Electronic address: shenlx@nwu.edu.cn.

PMID: 37657296
DOI: 10.1016/j.jenvman.2023.118737

Abstract

Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.

Keywords: Antibiotic resistance genes; Drinking water; Metagenome-assembled genomes; Mobile genetic elements; Oxford nanopore technology.

MeSH terms

Anti-Bacterial Agents
Drinking Water*
Metagenome*
Phylogeny
Risk Management

Substances

Drinking Water
Anti-Bacterial Agents