Profiling of antibiotic resistance genes and their hosts in drinking water distribution systems by Oxford Nanopore MinION sequencing

Abstract

Drinking water safety is critical to public health and the stability of drinking water quality is highly related with drinking water distribution systems (DWDSs). Antibiotic resistance genes (ARGs) and their hosts are the two major concerns in drinking water, however, the knowledge of fate of ARGs and their hosts were limited due to the current short-read length based sequencing technologies. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) is expected to overcome the challenges on ARGs and ARB characterization owing to its ultra-long reads generated. In this study, therefore, direct gDNA Nanopore sequencing was performed on treated water, distributed water and biofilm samples in two different DWDSs located at Kamerik and Lekkerkerk to explore its potential on ARGs and ARB characterization in drinking water systems. Additionally, the performances of taxonomy classification and ARGs profiling with Oxford Nanopore gDNA sequencing with different thresholds were assessed using an artificial microbial community. However, the conflict between the high requirements of input DNA quality and quantity with Nanopore sequencing and extremely low microbial biomass content in drinking water samples led to a challenge for our research. Therefore, evaluation on different sample preparation methods was conducted to meet the requirements of the input DNA.