831
Views
5
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo

ORCID Icon, , , , & ORCID Icon
Pages 4763-4777 | Published online: 23 Aug 2022

References

  • World Health Organization. Global Antimicrobial Resistance Surveillance System: Manual for Early Implementation. Geneva S; 2016:1–4
  • Amos GC, Hawkey PM, Gaze WH, Wellington EM. Waste water effluent contributes to the dissemination of CTX-M-15 in the natural environment. J Antimicrob Chemother. 2014;69(7):1785–1791. doi:10.1093/jac/dku079
  • Marti E, Jofre J, Balcazar JL. Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant. PLoS One. 2013;8(10):e78906. doi:10.1371/journal.pone.0078906
  • Mukherjee M, Laird E, Gentry TJ, Brooks JP, Karthikeyan R. Increased antimicrobial and multidrug resistance downstream of wastewater treatment plants in an urban watershed. Front Microbiol. 2021;12:657353. doi:10.3389/fmicb.2021.657353
  • Che Y, Xu X, Yang Y, et al. High-resolution genomic surveillance elucidates a multilayered hierarchical transfer of resistance between WWTP- and human/animal-associated bacteria. Microbiome. 2022;10(1):16. doi:10.1186/s40168-021-01192-w
  • Khan FA, Soderquist B, Jass J. Prevalence and diversity of antibiotic resistance genes in Swedish aquatic environments impacted by household and hospital wastewater. Front Microbiol. 2019;10:688. doi:10.3389/fmicb.2019.00688
  • ECDC. Antimicrobial consumption in the EU/EEA, Annual epidemiological report for 2018; 2018. Available from: https://wwwecdceuropaeu/sites/default/files/documents/Antimicrobial-consumption-EU-EEApdf. Accessed August 10, 2022.
  • Higa S, Sarassari R, Hamamoto K, et al. Characterization of CTX-M type ESBL-producing Enterobacteriaceae isolated from asymptomatic healthy individuals who live in a community of the Okinawa Prefecture, Japan. J Infect Chemother. 2019;25(4):314–317. doi:10.1016/j.jiac.2018.09.005
  • Nakane K, Kawamura K, Goto K, Arakawa Y. Long-term colonization by bla(CTX-M)-harboring Escherichia coli in healthy Japanese people engaged in food handling. Appl Environ Microbiol. 2016;82(6):1818–1827. doi:10.1128/aem.02929-15
  • Manaia CM. Assessing the risk of antibiotic resistance transmission from the environment to humans: non-direct proportionality between abundance and risk. Trends Microbiol. 2017;25(3):173–181. doi:10.1016/j.tim.2016.11.014
  • Hendriksen RS, Munk P, Njage P, et al. Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage. Nat Commun. 2019;10(1):1124. doi:10.1038/s41467-019-08853-3
  • Breitwieser FP, Baker DN, Salzberg SL. KrakenUniq: confident and fast metagenomics classification using unique k-mer counts. Genome Biol. 2018;19(1):198. doi:10.1186/s13059-018-1568-0
  • Breitwieser FP, Salzberg SL. Pavian: interactive analysis of metagenomics data for microbiome studies and pathogen identification. Bioinformatics. 2020;36(4):1303–1304. doi:10.1093/bioinformatics/btz715
  • Segata N, Izard J, Waldron L, et al. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12(6):R60. doi:10.1186/gb-2011-12-6-r60
  • Zankari E, Hasman H, Cosentino S, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640–2644. doi:10.1093/jac/dks261
  • Quast C, Pruesse E, Yilmaz P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590–D596. doi:10.1093/nar/gks1219
  • Pal C, Bengtsson-Palme J, Rensing C, Kristiansson E, Larsson DG. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res. 2014;42(Databaseissue):D737–D743. doi:10.1093/nar/gkt1252
  • Mitchell AL, Attwood TK, Babbitt PC, et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019;47(D1):D351–D360. doi:10.1093/nar/gky1100
  • Ye Y, Choi JH, Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinform. 2011;12:159. doi:10.1186/1471-2105-12-159
  • Rognes T, Flouri T, Nichols B, Quince C, Mahe F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584. doi:10.7717/peerj.2584
  • Hao L, Bize A, Conteau D, et al. New insights into the key microbial phylotypes of anaerobic sludge digesters under different operational conditions. Water Res. 2016;102:158–169. doi:10.1016/j.watres.2016.06.014
  • Fang H, Cai L, Yu Y, Zhang T. Metagenomic analysis reveals the prevalence of biodegradation genes for organic pollutants in activated sludge. Bioresour Technol. 2013;129:209–218. doi:10.1016/j.biortech.2012.11.054
  • Gillings MR. Integrons: past, present, and future. Microbiol Mol Biol Rev. 2014;78(2):257–277. doi:10.1128/MMBR.00056-13
  • Singh NS, Singhal N, Kumar M, Virdi JS. High prevalence of drug resistance and class 1 integrons in Escherichia coli isolated from river Yamuna, India: a serious public health risk. Front Microbiol. 2021;12:621564. doi:10.3389/fmicb.2021.621564
  • Ahmed MB, Zhou JL, Ngo HH, Guo W, Thomaidis NS, Xu J. Progress in the biological and chemical treatment technologies for emerging contaminant removal from wastewater: a critical review. J Hazard Mater. 2017;323(Pt A):274–298. doi:10.1016/j.jhazmat.2016.04.045
  • Rout PR, Zhang TC, Bhunia P, Surampalli RY. Treatment technologies for emerging contaminants in wastewater treatment plants: a review. Sci Total Environ. 2021;753:141990. doi:10.1016/j.scitotenv.2020.141990
  • Azuma T, Usui M, Hayashi T. Inactivation of antibiotic-resistant bacteria in wastewater by ozone-based advanced water treatment processes. Antibiotics. 2022;11(2). doi:10.3390/antibiotics11020210
  • Su HC, Pan CG, Ying GG, et al. Contamination profiles of antibiotic resistance genes in the sediments at a catchment scale. Sci Total Environ. 2014;490:708–714. doi:10.1016/j.scitotenv.2014.05.060
  • Wistrand-Yuen E, Knopp M, Hjort K, Koskiniemi S, Berg OG, Andersson DI. Evolution of high-level resistance during low-level antibiotic exposure. Nat Commun. 2018;9(1):1599. doi:10.1038/s41467-018-04059-1
  • Martin C, Stebbins B, Ajmani A, et al. Nanopore-based metagenomics analysis reveals prevalence of mobile antibiotic and heavy metal resistome in wastewater. Ecotoxicology. 2021;30(8):1572–1585. doi:10.1007/s10646-020-02342-w
  • Zhu YG, Johnson TA, Su JQ, et al. Diverse and abundant antibiotic resistance genes in Chinese swine farms. Proc Natl Acad Sci U S A. 2013;110(9):3435–3440. doi:10.1073/pnas.1222743110
  • Xu Y, Xu J, Mao D, Luo Y. Effect of the selective pressure of sub-lethal level of heavy metals on the fate and distribution of ARGs in the catchment scale. Environ Pollut. 2017;220(Pt B):900–908. doi:10.1016/j.envpol.2016.10.074
  • Biswas R, Halder U, Kabiraj A, Mondal A, Bandopadhyay R. Overview on the role of heavy metals tolerance on developing antibiotic resistance in both Gram-negative and Gram-positive bacteria. Arch Microbiol. 2021;203(6):2761–2770. doi:10.1007/s00203-021-02275-w
  • Kang W, Zhang YJ, Shi X, He JZ, Hu HW. Short-term copper exposure as a selection pressure for antibiotic resistance and metal resistance in an agricultural soil. Environ Sci Pollut Res Int. 2018;25(29):29314–29324. doi:10.1007/s11356-018-2978-y
  • Rizzo L, Manaia C, Merlin C, et al. Urban wastewater treatment plants as hotspots for antibiotic resistant bacteria and genes spread into the environment: a review. Sci Total Environ. 2013;447:345–360. doi:10.1016/j.scitotenv.2013.01.032
  • Karkman A, Do TT, Walsh F, Virta MPJ. Antibiotic-resistance genes in waste water. Trends Microbiol. 2018;26(3):220–228. doi:10.1016/j.tim.2017.09.005
  • Andersson DI, Hughes D. Microbiological effects of sublethal levels of antibiotics. Nat Rev Microbiol. 2014;12(7):465–478. doi:10.1038/nrmicro3270
  • Pribis JP, Garcia-Villada L, Zhai Y, et al. Gamblers: an antibiotic-induced evolvable cell subpopulation differentiated by reactive-oxygen-induced general stress response. Mol Cell. 2019;74(4):785–800 e7. doi:10.1016/j.molcel.2019.02.037
  • Gao H, Zhang L, Lu Z, He C, Li Q, Na G. Complex migration of antibiotic resistance in natural aquatic environments. Environ Pollut. 2018;232:1–9. doi:10.1016/j.envpol.2017.08.078
  • Vaz-Moreira I, Nunes OC, Manaia CM. Bacterial diversity and antibiotic resistance in water habitats: searching the links with the human microbiome. FEMS Microbiol Rev. 2014;38(4):761–778. doi:10.1111/1574-6976.12062
  • Sekizuka T, Inamine Y, Segawa T, Hashino M, Yatsu K, Kuroda M. Potential KPC-2 carbapenemase reservoir of environmental Aeromonas hydrophila and Aeromonas caviae isolates from the effluent of an urban wastewater treatment plant in Japan. Environ Microbiol Rep. 2019;11(4):589–597. doi:10.1111/1758-2229.12772
  • Makowska N, Bresa K, Koczura R, Philips A, Nowis K, Mokracka J. Urban wastewater as a conduit for pathogenic Gram-positive bacteria and genes encoding resistance to beta-lactams and glycopeptides. Sci Total Environ. 2021;765:144176. doi:10.1016/j.scitotenv.2020.144176
  • Osinska A, Harnisz M, Korzeniewska E. Prevalence of plasmid-mediated multidrug resistance determinants in fluoroquinolone-resistant bacteria isolated from sewage and surface water. Environ Sci Pollut Res Int. 2016;23(11):10818–10831. doi:10.1007/s11356-016-6221-4
  • Hultman J, Tamminen M, Parnanen K, Cairns J, Karkman A, Virta M. Host range of antibiotic resistance genes in wastewater treatment plant influent and effluent. FEMS Microbiol Ecol. 2018;94(4). doi:10.1093/femsec/fiy038