title: Water metagenomic analysis reveals low bacterial diversity and the presence of antimicrobial residues and resistance genes in a river containing wastewater from backyard aquacultures in the Mekong Delta, Vietnam.
abstract: The environmental pathways for the dissemination of antibiotic resistance have recently received increased attention. Aquatic environments act as reservoirs or sources of antimicrobial-resistant bacteria, antimicrobial residues, and antimicrobial resistance genes (ARGs). Therefore, it is imperative to identify the role of polluted water in the dissemination of antimicrobial resistance. The aim of this study was to evaluate the antimicrobial residues, ARGs, and microbiota in the freshwater systems of the Mekong Delta. We selected 12 freshwater sites from aquacultures and rivers in Can Tho, Vietnam and analyzed them for 45 antimicrobial residues and 8 ARGs by LC/MS/MS and real-time PCR, respectively. A 16S rDNA-based metagenomic analysis was conducted to characterize the water microbiota. Residues of sulfamethoxazole (10/12) and sulfadimidine (7/12) were widely detected, together with the sulfa-resistance genes sul1 (11/12) and sul2 (9/12). Additionally, sulfamethoxazole residues and the β-lactamase-resistance gene blaCTX-M-1were detected in eight freshwater systems (8/12), suggesting that these freshwater systems may have been polluted by human activity. The metagenomic analysis showed that all the tested freshwater systems contained the phyla Proteobacteria, Actinobacteria, and Bacteroidetes, representing 64% of the total microbiota. Moreover, the Cai Rang River site (Ri-E), which is located at the merge point of wastewaters from backyard-based aquacultures, contained the genera Polynucleobacter, Variovorax, and Limnohabitans, representing more than 78.4% of the total microbiota. Bacterial diversity analysis showed that the Ri-E exhibited the lowest diversity compared with other regions. Principal coordinate analysis showed that the differences among water microbiotas in backyard-based aquacultures could be explained by the farmers' aquaculture techniques. In conclusion, this study demonstrated a collapse of bacterial diversity at the merge point of wastewaters from backyard-based aquacultures in the Mekong Delta.
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku Ourai Kita, Izumisano, Osaka, 598-8531, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Tatsuya
authors.initials: T
authors.lastname: Nakayama
authors.affiliation: College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam.
authors.forename: Tran Thi
authors.initials: TT
authors.lastname: Tuyet Hoa
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan. Electronic address: harada6@phs.osaka-u.ac.jp.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Harada
authors.affiliation: Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Minae
authors.initials: M
authors.lastname: Warisaya
authors.affiliation: Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Megumi
authors.initials: M
authors.lastname: Asayama
authors.affiliation: Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58, Rinku Ourai Kita, Izumisano, Osaka, 598-8531, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Hinenoya
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Joon Won
authors.initials: JW
authors.lastname: Lee
authors.affiliation: College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam.
authors.forename: Tran Minh
authors.initials: TM
authors.lastname: Phu
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Shuhei
authors.initials: S
authors.lastname: Ueda
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Sumimura
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Graduate School of Pharmaceutical Science, Osaka University, 1-6, Yamadaoka, Suita, Osaka, 565-0871, Japan.
authors.forename: Kazumasa
authors.initials: K
authors.lastname: Hirata
authors.affiliation: College of Aquaculture and Fisheries, Can Tho University, Campus II, 3/2 Street, Ninh Kieu, Can Tho, Viet Nam.
authors.forename: Nguyen Thanh
authors.initials: NT
authors.lastname: Phuong
authors.affiliation: Global Collaboration Center, Osaka University, 2-7, Yamadaoka, Suita, Osaka, 565-0871, Japan; Osaka Prefectural Institute of Public Health, 1-3-69, Nakamichi, Higashinari-ku, Osaka, 537-0025, Japan.
authors.forename: Yoshimasa
authors.initials: Y
authors.lastname: Yamamoto
mesh_terms: D000900:Anti-Bacterial Agents / Q000032:analysis*; D017756:Aquaculture; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification; D004352:Drug Resistance, Microbial / Q000235:genetics*; D056186:Metagenomics; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D060888:Real-Time Polymerase Chain Reaction; D045483:Rivers / Q000737:chemistry* / Q000382:microbiology*; D013420:Sulfamethoxazole / Q000032:analysis; D053719:Tandem Mass Spectrometry; D014744:Vietnam; D062065:Wastewater / Q000737:chemistry / Q000382:microbiology; D014874:Water Pollutants, Chemical / Q000032:analysis
chemical_list: D000900:Anti-Bacterial Agents; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D013420:Sulfamethoxazole; D062065:Wastewater; D014874:Water Pollutants, Chemical
keywords: Antimicrobial residue; Antimicrobial resistance gene; Aquaculture; Waste water; Water microbiota