{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T20:13:21Z","timestamp":1790108001667,"version":"4.0.1"},"reference-count":31,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,3,15]],"date-time":"2026-03-15T00:00:00Z","timestamp":1773532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pathogens"],"abstract":"<jats:p>The threat of antimicrobial resistance in aquatic environments, particularly riverine systems, is escalating, in part due to effluents discharged from healthcare facilities. This issue has been recognized not only in Japan but also in other Asian countries such as Indonesia and Nepal. Nevertheless, existing research remains limited, prompting an investigation into the prevalence of antimicrobial-resistant bacteria in the upstream and downstream sites of environmental rivers. In 2024, six samples were collected from three rivers in Hyogo Prefecture, Japan; five samples from five river sites in Indonesia; and three samples from downstream sites of rivers in Kathmandu, Nepal. These samples were subjected to selective culture\u2013based Next Generation Sequencing and resistome analyses, based exclusively on the selective culture of bacteria propagated on CHROMagar ESBL plates. In Japan and Indonesia, Pseudomonas, Stenotrophomonas and Acinetobacter were frequently detected, whereas Klebsiella was overwhelmingly predominant in Nepal. Significant differences in the similarity of bacterial community composition among sampling sites across the three countries were observed (p &lt; 0.001). Notably, Nepal exhibited the highest abundance level of antimicrobial resistance genes among the three countries, largely consisting of \u03b2-lactam resistance genes. In conclusion, these analyses elucidated substantial differences in bacterial community composition and degrees of environmental contamination.<\/jats:p>","DOI":"10.3390\/pathogens15030317","type":"journal-article","created":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T10:10:43Z","timestamp":1773655843000},"page":"317","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Survey of Antimicrobial-Resistant Bacteria Isolated from Rivers in Japan, Indonesia and Nepal"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4787-4333","authenticated-orcid":false,"given":"Kayo","family":"Osawa","sequence":"first","affiliation":[{"name":"Department of Medical Technology, Kobe Tokiwa University, Kobe 653-0838, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5024-9520","authenticated-orcid":false,"given":"Ryohei","family":"Nomoto","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Kobe Institute of Health, Kobe 650-0046, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4697-8392","authenticated-orcid":false,"given":"Takashi","family":"Suzuki","sequence":"additional","affiliation":[{"name":"Department of Medical Technology, Kobe Tokiwa University, Kobe 653-0838, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taishi","family":"Maeda","sequence":"additional","affiliation":[{"name":"Department of Medical Technology, Kobe Tokiwa University, Kobe 653-0838, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ganesh","family":"Rai","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu 44600, Nepal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shouhiro","family":"Kinoshita","sequence":"additional","affiliation":[{"name":"Division of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe 650-0017, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3088-1254","authenticated-orcid":false,"given":"Noriko","family":"Nakanishi","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Kobe Institute of Health, Kobe 650-0046, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dadik","family":"Raharjo","sequence":"additional","affiliation":[{"name":"Institute of Tropical Disease, Airlangga University, Surabaya 60286, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5525-9915","authenticated-orcid":false,"given":"Masanori","family":"Kameoka","sequence":"additional","affiliation":[{"name":"Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe 654-0142, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Masato","family":"Fujisawa","sequence":"additional","affiliation":[{"name":"Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiba Kumar","family":"Rai","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Shi-Gan International College of Science and Technology, Kathmandu 44600, Nepal"},{"name":"Department of Microbiology, Nepal Medical College Teaching Hospital, Kathmandu 44600, Nepal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4897-8879","authenticated-orcid":false,"given":"Kuntaman","family":"Kuntaman","sequence":"additional","affiliation":[{"name":"Institute of Tropical Disease, Airlangga University, Surabaya 60286, Indonesia"},{"name":"Department of Microbiology, Faculty of Medicine, Airlangga University, Surabaya 60132, Indonesia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3925-8730","authenticated-orcid":false,"given":"Toshiro","family":"Shirakawa","sequence":"additional","affiliation":[{"name":"Division of Advanced Medical Science, Kobe University Graduate School of Science, Technology and Innovation, Kobe 650-0017, Japan"},{"name":"Division of Urology, Department of Organ Therapeutics, Faculty of Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/microbiolspec.ARBA-0009-2017","article-title":"Antimicrobial resistance: A One Health perspective","volume":"6","author":"McEwen","year":"2018","journal-title":"Microbiol. Spectr."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1432","DOI":"10.1038\/s41564-019-0503-9","article-title":"Defining and combating antibiotic resistance from One Health and global health perspectives","volume":"4","author":"Coque","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Aslam, B., Khurshid, M., Arshad, M.I., Muzammil, S., Rasool, M., Yasmeen, N., Shah, T., Chaudhry, T.H., Rasool, M.H., and Shahid, A. (2021). Antibiotic resistance: One Health one world outlook. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.771510"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1038\/s12276-021-00569-z","article-title":"Antibiotic resistome from the one-health perspective: Understanding and controlling antimicrobial resistance transmission","volume":"53","author":"Kim","year":"2021","journal-title":"Exp. Mol. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s12941-023-00638-3","article-title":"\u201cOne Health\u201d perspective on prevalence of co-existing extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae: A comprehensive systematic review and meta-analysis","volume":"22","author":"Ramatla","year":"2023","journal-title":"Ann. Clin. Microbiol. Antimicrob."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2225","DOI":"10.1093\/jac\/dkab169","article-title":"Rapid spread of critical priority carbapenemase-producing pathogens in companion animals: A One Health challenge for a post-pandemic world","volume":"76","author":"Sellera","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Teramae, M., Osawa, K., Shigemura, K., Kitagawa, K., Shirakawa, T., Fujisawa, M., and Miyara, T. (2019). Prevalence of quinolone resistance of extended-spectrum \u03b2-lactamase-producing Escherichia coli with ST131-fimH30 in a city hospital in Hyogo, Japan. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20205162"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1111\/iju.13818","article-title":"Molecular characteristics of carbapenem-resistant Pseudomonas aeruginosa isolated from urine in Hyogo, Japan","volume":"26","author":"Osawa","year":"2019","journal-title":"Int. J. Urol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"966","DOI":"10.1111\/iju.13787","article-title":"Occurrence and characterization of carbapenem-resistant Gram-negative bacilli: A collaborative study of antibiotic-resistant bacteria between Indonesia and Japan","volume":"25","author":"Kuntaman","year":"2018","journal-title":"Int. J. Urol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Takaichi, M., Osawa, K., Nomoto, R., Nakanishi, N., Kameoka, M., Miura, M., Shigemura, K., Kinoshita, S., Kitagawa, K., and Uda, A. (2022). Antibiotic resistance in non-typhoidal Salmonella enterica strains isolated from chicken meat in Indonesia. Pathogens, 11.","DOI":"10.3390\/pathogens11050543"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Nomoto, R., Osawa, K., Kinoshita, S., Kitagawa, K., Nakanishi, N., Sarassari, R., Raharjo, D., Fujisawa, M., Kuntaman, K., and Shirakawa, T. (2024). Metagenome and resistome analysis of beta-lactam-resistant bacteria isolated from river waters in Surabaya, Indonesia. Microorganisms, 12.","DOI":"10.3390\/microorganisms12010199"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s13071-020-04090-6","article-title":"Distribution and pyrethroid resistance status of Aedes aegypti and Aedes albopictus populations and possible phylogenetic reasons for the recent invasion of Aedes aegypti in Nepal","volume":"13","author":"Kawada","year":"2020","journal-title":"Parasit. Vectors"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"156232","DOI":"10.1016\/j.scitotenv.2022.156232","article-title":"Distribution and characteristics of carbapenem-resistant and extended-spectrum \u03b2-lactamase (ESBL) producing Escherichia coli in hospital effluents, sewage treatment plants, and river water in an urban area of Japan","volume":"839","author":"Azuma","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.jbiosc.2024.09.006","article-title":"Metagenomic profiling of antibiotic resistance genes and their associations with the bacterial community along the Kanda River, an urban river in Japan","volume":"139","author":"Xiao","year":"2025","journal-title":"J. Biosci. Bioeng."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"176109","DOI":"10.1016\/j.scitotenv.2024.176109","article-title":"Comparative performance of electronegative membrane filtration and automated concentrating pipette for detection of antibiotic resistance genes and microbial markers in river water samples","volume":"953","author":"Siri","year":"2024","journal-title":"Sci. Total Environ."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Amarasiri, M., Takezawa, T., Malla, B., Furukawa, T., Sherchand, J.B., Haramoto, E., and Sei, K. (2022). Prevalence of antibiotic resistance genes in drinking and environmental water sources of the Kathmandu Valley, Nepal. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.894014"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"dlaf186","DOI":"10.1093\/jacamr\/dlaf186","article-title":"Antibiotic resistance and beta-lactam resistant genes among bacterial isolates from clinical, river water and poultry samples from Kathmandu, Nepal","volume":"7","author":"Shrestha","year":"2025","journal-title":"JAC Antimicrob. Resist."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"Fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"4908","DOI":"10.21105\/joss.04908","article-title":"Metagenomic classification with KrakenUniq on low-memory computers","volume":"7","author":"Pockrandt","year":"2022","journal-title":"J. Open Source Softw."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1101\/gr.213959.116","article-title":"metaSPAdes: A new versatile metagenomic assembler","volume":"27","author":"Nurk","year":"2017","journal-title":"Genome Res."},{"key":"ref_21","first-page":"000748","article-title":"ResFinder\u2014An open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes","volume":"8","author":"Florensa","year":"2022","journal-title":"Microb. Genom."},{"key":"ref_22","unstructured":"(2026, January 10). Nippon AMR One Health Report (NAOR) Highlights 2024. Available online: https:\/\/www.mhlw.go.jp\/content\/10900000\/001466661.pdf."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1016\/j.jgar.2019.07.001","article-title":"Whole-genome analysis of EC129, an NDM-5-, CTX-M-14-, OXA-10- and MCR-1-co-producing Escherichia coli ST167 strain isolated from Japan","volume":"18","author":"Nukui","year":"2019","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"14994","DOI":"10.1021\/acs.est.2c01570","article-title":"Antibiotic resistomes and microbiomes in the surface water along the Code River in Indonesia reflect drainage basin anthropogenic activities","volume":"56","author":"Muurinen","year":"2022","journal-title":"Environ. Sci. Technol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"e0116524","DOI":"10.1128\/aem.01165-24","article-title":"Citrobacter spp. and Enterobacter spp. as reservoirs of carbapenemase bla(NDM) and bla(KPC) resistance genes in hospital wastewater","volume":"90","author":"Schilmann","year":"2024","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"11786361231152220","DOI":"10.1177\/11786361231152220","article-title":"Multi-drug resistance, beta-lactamases production, and coexistence of bla (NDM-1) and mcr-1 in Escherichia coli clinical isolates from a referral hospital in Kathmandu, Nepal","volume":"16","author":"Bhusal","year":"2023","journal-title":"Microbiol. Insights"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Sharma, S., Devkota, M.D., Pokhrel, B.M., and Banjara, M.R. (2023). Detection of bla(NDM-1,)mcr-1 and MexB in multidrug resistant Pseudomonas aeruginosa isolated from clinical specimens in a tertiary care hospital of Nepal. BMC Microbiol., 23.","DOI":"10.1186\/s12866-023-02906-w"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"109765","DOI":"10.1016\/j.envres.2020.109765","article-title":"Prevalence of antibiotic resistance in the tropical rivers of Sri Lanka and India","volume":"188","author":"Kumar","year":"2020","journal-title":"Environ. Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"10622","DOI":"10.1007\/s11356-020-11329-3","article-title":"Antibiotic and antiparasitic residues in surface water of urban rivers in the Red River Delta (Hanoi, Vietnam): Concentrations, profiles, source estimation, and risk assessment","volume":"28","author":"Hoang","year":"2021","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"13808","DOI":"10.1038\/s41598-022-14781-y","article-title":"Antibiotic resistance genes of public health importance in livestock and humans in an informal urban community in Nepal","volume":"12","author":"Young","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"e2411919121","DOI":"10.1073\/pnas.2411919121","article-title":"Global trends in antibiotic consumption during 2016\u20132023 and future projections through 2030","volume":"121","author":"Klein","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/3\/317\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T05:44:39Z","timestamp":1773726279000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-0817\/15\/3\/317"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,15]]},"references-count":31,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,3]]}},"alternative-id":["pathogens15030317"],"URL":"https:\/\/doi.org\/10.3390\/pathogens15030317","relation":{},"ISSN":["2076-0817"],"issn-type":[{"value":"2076-0817","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,15]]}}}