Metagenome and Resistome Analysis of Beta-Lactam-Resistant Bacteria Isolated from River Waters in Surabaya, Indonesia

Ryohei Nomoto, Kayo Osawa, Shohiro Kinoshita, Koichi Kitagawa, Noriko Nakanishi, Rosantia Sarassari, Dadik Raharjo, Masato Fujisawa, Kuntaman Kuntaman, Toshiro Shirakawa

Research output: Contribution to journalArticlepeer-review


Antimicrobial agents are administered to humans and livestock, and bacterial antimicrobial resistance (AMR) and antimicrobial agents are released into the environment. In this study, to investigate the trend of AMR in humans, livestock, and the environment, we performed a metagenomic analysis of multidrug-resistant bacteria with CHROMagar ESBL in environmental river water samples, which were collected using syringe filter units from waters near hospitals, downtown areas, residential areas, and water treatment plants in Surabaya, Indonesia. Our results showed that Acinetobacter, Pseudomonas, Aeromonas, Enterobacter, Escherichia, and Klebsiella grew in CHROMagar ESBL; they were most frequently detected in water samples from rivers surrounding hospitals contaminated with various AMR genes (ARGs) in high levels. These results identified bacteria as ARG reservoirs and revealed that hospitals could be sources for various ARGs disseminated into the environment. In conclusion, this study details a novel metagenomic analysis of collected bacteria in environmental water samples using a syringe filter unit for an AMR epidemiological study based on the One Health approach.

Original languageEnglish
Article number199
Issue number1
Publication statusPublished - Jan 2024


  • antimicrobial resistance genes (ARGs)
  • antimicrobial-resistant bacteria (AMR)
  • environmental river
  • public health
  • whole genome sequencing (WGS)


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