Comprehensive Genomic Survey of Antimicrobial-Resistance Bacteria in the Sewage Tank Replacement with Hospital Relocation

References

• World Health Organization. Global action plan on antimicrobial resistance; 2016. Available from: https://www.who.int/publications/i/item/9789241509763. Accessed August 24, 2021.
   Google Scholar
• Gekenidis MT, Qi W, Hummerjohann J, Zbinden R, Walsh F, Drissner D. Antibiotic-resistant indicator bacteria in irrigation water: high prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli. PLoS One. 2018;13(11):e0207857. doi:10.1371/journal.pone.020785730475879
   PubMed Web of Science ®Google Scholar
• Nascimento T, Cantamessa R, Melo L, et al. International high-risk clones of Klebsiella pneumoniae KPC-2/CC258 and Escherichia coli CTX-M-15/CC10 in urban lake waters. Sci Total Environ. 2017;598:910–915. doi:10.1016/j.scitotenv.2017.03.20728458208
   PubMed Web of Science ®Google Scholar
• Proia L, Anzil A, Borrego C, et al. Occurrence and persistence of carbapenemases genes in hospital and wastewater treatment plants and propagation in the receiving river. J Hazard Mater. 2018;358:33–43. doi:10.1016/j.jhazmat.2018.06.05829960932
   PubMed Web of Science ®Google Scholar
• Makowska N, Philips A, Dabert M, et al. Metagenomic analysis of beta-lactamase and carbapenemase genes in the wastewater resistome. Water Res. 2020;170:115277. doi:10.1016/j.watres.2019.11527731756613
   PubMed Web of Science ®Google Scholar
• Ng C, Tay M, Tan B, et al. Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters. Front Microbiol. 2017;8:2200. doi:10.3389/fmicb.2017.0220029201017
   PubMed Web of Science ®Google Scholar
• Sekizuka T, Yatsu K, Inamine Y, et al. Complete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan. mSphere. 2018;3(5). doi:10.1128/mSphere.00314-18.
   Web of Science ®Google Scholar
• Sekizuka T, Inamine Y, Segawa T, Kuroda M. Characterization of NDM-5- and CTX-M-55-coproducing Escherichia coli GSH8M-2 isolated from the effluent of a wastewater treatment plant in Tokyo Bay. Infect Drug Resist. 2019;12:2243–2249. doi:10.2147/IDR.S21527331413601
   PubMed Web of Science ®Google Scholar
• Lien TQ, Lan PT, Chuc NTK, et al. Antibiotic Resistance and Antibiotic Resistance Genes in Escherichia coli Isolates from Hospital Wastewater in Vietnam. Int J Environ Res Public Health. 2017;14(7):699. doi:10.3390/ijerph14070699
   Web of Science ®Google Scholar
• Kummerer K, Henninger A. Promoting resistance by the emission of antibiotics from hospitals and households into effluent. Clin Microbiol Infect. 2003;9(12):1203–1214. doi:10.1111/j.1469-0691.2003.00739.x14686985
   PubMed Web of Science ®Google Scholar
• Jager T, Hembach N, Elpers C, et al. Reduction of antibiotic resistant bacteria during conventional and advanced wastewater treatment, and the disseminated loads released to the environment. Front Microbiol. 2018;9:2599. doi:10.3389/fmicb.2018.0259930425704
   PubMed Web of Science ®Google Scholar
• Paulus GK, Hornstra LM, Alygizakis N, Slobodnik J, Thomaidis N, Medema G. The impact of on-site hospital wastewater treatment on the downstream communal wastewater system in terms of antibiotics and antibiotic resistance genes. Int J Hyg Environ Health. 2019;222(4):635–644. doi:10.1016/j.ijheh.2019.01.00430737165
   PubMed Web of Science ®Google Scholar
• Takeuchi F, Sekizuka T, Yamashita A, Ogasawara Y, Mizuta K, Kuroda M. MePIC, metagenomic pathogen identification for clinical specimens. Jpn J Infect Dis. 2014;67(1):62–65. doi:10.7883/yoken.67.6224451106
   PubMed Web of Science ®Google Scholar
• Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinform. 2011;12:385. doi:10.1186/1471-2105-12-385
   PubMed Web of Science ®Google Scholar
• Huson DH, Beier S, Flade I, et al. MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PLoS Comput Biol. 2016;12(6):e1004957. doi:10.1371/journal.pcbi.100495727327495
   PubMed Web of Science ®Google Scholar
• Larsen MV, Cosentino S, Rasmussen S, et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355–1361. doi:10.1128/JCM.06094-1122238442
   PubMed Web of Science ®Google Scholar
• 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/dks26122782487
   PubMed Web of Science ®Google Scholar
• Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589–595. doi:10.1093/bioinformatics/btp69820080505
   PubMed Web of Science ®Google Scholar
• Koboldt DC, Chen K, Wylie T, et al. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009;25(17):2283–2285. doi:10.1093/bioinformatics/btp37319542151
   PubMed Web of Science ®Google Scholar
• Arndt D, Grant JR, Marcu A, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(W1):W16–21. doi:10.1093/nar/gkw38727141966
   PubMed Web of Science ®Google Scholar
• Kurtz S, Phillippy A, Delcher AL, et al. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12. doi:10.1186/gb-2004-5-2-r1214759262
   PubMed Web of Science ®Google Scholar
• Croucher NJ, Page AJ, Connor TR, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43(3):e15. doi:10.1093/nar/gku119625414349
   PubMed Web of Science ®Google Scholar
• Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biol. 2018;19(1):153. doi:10.1186/s13059-018-1540-z30286803
   PubMed Web of Science ®Google Scholar
• Joensen KG, Tetzschner AM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2015;53(8):2410–2426. doi:10.1128/JCM.00008-1525972421
   PubMed Web of Science ®Google Scholar
• Narumiya M, Nakada N, Yamashita N, Tanaka H. Phase distribution and removal of pharmaceuticals and personal care products during anaerobic sludge digestion. J Hazard Mater. 2013;260:305–312. doi:10.1016/j.jhazmat.2013.05.03223774781
   PubMed Web of Science ®Google Scholar
• Lee K, Izumiya H, Iyoda S, Ohnishi M. Effective surveillance using multilocus variable-number tandem-repeat analysis and whole-genome sequencing for enterohemorrhagic Escherichia coli O157. Appl Environ Microbiol. 2019;85:17. doi:10.1128/AEM.00728-19
   Web of Science ®Google Scholar
• Li D, Yang M, Hu J, Zhang Y, Chang H, Jin F. Determination of penicillin G and its degradation products in a penicillin production wastewater treatment plant and the receiving river. Water Res. 2008;42(1–2):307–317. doi:10.1016/j.watres.2007.07.01617675133
   PubMed Web of Science ®Google Scholar
• Zhou LJ, Ying GG, Liu S, et al. Occurrence and fate of eleven classes of antibiotics in two typical wastewater treatment plants in South China. Sci Total Environ. 2013;452–453:365–376. doi:10.1016/j.scitotenv.2013.03.010
   PubMed Web of Science ®Google Scholar
• Tang WHW, Li DY, Hazen SL. Dietary metabolism, the gut microbiome, and heart failure. Nat Rev Cardiol. 2019;16(3):137–154. doi:10.1038/s41569-018-0108-730410105
   PubMed Web of Science ®Google Scholar
• Kurokawa K, Itoh T, Kuwahara T, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 2007;14(4):169–181. doi:10.1093/dnares/dsm01817916580
   PubMed Web of Science ®Google Scholar
• Merga JY, Royden A, Pandey AK, Williams NJ. Arcobacter spp. isolated from untreated domestic effluent. Lett Appl Microbiol. 2014;59(1):122–126. doi:10.1111/lam.1225624666283
   PubMed Web of Science ®Google Scholar
• Ghaju Shrestha R, Sherchan SP, Kitajima M, Tanaka Y, Gerba CP, Haramoto E. Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA. Pathogens. 2019;8(4). doi:10.3390/pathogens8040175
   Web of Science ®Google Scholar
• Usami M, Miyoshi M, Yamashita H. Gut microbiota and host metabolism in liver cirrhosis. World J Gastroenterol. 2015;21(41):11597–11608. doi:10.3748/wjg.v21.i41.1159726556989
   PubMed Web of Science ®Google Scholar
• 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.2018.09.00530292768
   PubMed Web of Science ®Google Scholar
• Bevan ER, Jones AM, Hawkey PM. Global epidemiology of CTX-M beta-lactamases: temporal and geographical shifts in genotype. J Antimicrob Chemother. 2017;72(8):2145–2155. doi:10.1093/jac/dkx14628541467
   PubMed Web of Science ®Google Scholar
• Harris PNA, Ben Zakour NL, Roberts LW, et al. Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27. J Antimicrob Chemother. 2018;73(3):634–642. doi:10.1093/jac/dkx46629253152
   PubMed Web of Science ®Google Scholar
• Noguchi T, Matsumura Y, Kanahashi T, et al. Role of TEM-1 beta-lactamase in the predominance of ampicillin-sulbactam-nonsusceptible Escherichia coli in Japan. Antimicrob Agents Chemother. 2019;63(2). doi:10.1128/AAC.02366-18.
   Web of Science ®Google Scholar
• Luvsansharav UO, Hirai I, Niki M, et al. Prevalence of fecal carriage of extended-spectrum beta-lactamase-producing Enterobacteriaceae among healthy adult people in Japan. J Infect Chemother. 2011;17(5):722–725. doi:10.1007/s10156-011-0225-221359543
   PubMed Web of Science ®Google Scholar
• 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.02929-1526746714
   PubMed Web of Science ®Google Scholar
• Remold SK, Brown CK, Farris JE, Hundley TC, Perpich JA, Purdy ME. Differential habitat use and niche partitioning by Pseudomonas species in human homes. Microb Ecol. 2011;62(3):505–517. doi:10.1007/s00248-011-9844-521503776
   PubMed Web of Science ®Google Scholar
• Ocampo-Sosa AA, Guzman-Gomez LP, Fernandez-Martinez M, et al. Isolation of VIM-2-producing Pseudomonas monteilii clinical strains disseminated in a tertiary hospital in northern Spain. Antimicrob Agents Chemother. 2015;59(2):1334–1336. doi:10.1128/AAC.04639-1425421471
   PubMed Web of Science ®Google Scholar
• Scotta C, Juan C, Cabot G, et al. Environmental microbiota represents a natural reservoir for dissemination of clinically relevant metallo-beta-lactamases. Antimicrob Agents Chemother. 2011;55(11):5376–5379. doi:10.1128/AAC.00716-1121859934
   PubMed Web of Science ®Google Scholar
• Wiest L, Chonova T, Berge A, et al. Two-year survey of specific hospital wastewater treatment and its impact on pharmaceutical discharges. Environ Sci Pollut Res Int. 2018;25(10):9207–9218. doi:10.1007/s11356-017-9662-528718023
   PubMed Web of Science ®Google Scholar
• Le TH, Ng C, Chen H, et al. Occurrences and characterization of antibiotic-resistant bacteria and genetic determinants of hospital wastewater in a tropical country. Antimicrob Agents Chemother. 2016;60(12):7449–7456. doi:10.1128/AAC.01556-1627736769
   PubMed Web of Science ®Google Scholar
• Coutu S, Rossi L, Barry DA, Rudaz S, Vernaz N. Temporal variability of antibiotics fluxes in wastewater and contribution from hospitals. PLoS One. 2013;8(1):e53592. doi:10.1371/journal.pone.005359223320096
   PubMed Web of Science ®Google Scholar
• Gullberg E, Cao S, Berg OG, et al. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathog. 2011;7(7):e1002158. doi:10.1371/journal.ppat.100215821811410
   PubMed Web of Science ®Google Scholar
• Acuna V, Casellas M, Font C, Romero F, Sabater S. Nutrient attenuation dynamics in effluent dominated watercourses. Water Res. 2019;160:330–338. doi:10.1016/j.watres.2019.05.09331158615
   PubMed Web of Science ®Google Scholar
• Bengtsson-Palme J, Kristiansson E, Larsson DGJ. Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiol Rev. 2018;42(1). doi:10.1093/femsre/fux053
   Web of Science ®Google Scholar
• Goren MG, Carmeli Y, Schwaber MJ, Chmelnitsky I, Schechner V, Navon-Venezia S. Transfer of carbapenem-resistant plasmid from Klebsiella pneumoniae ST258 to Escherichia coli in patient. Emerg Infect Dis. 2010;16(6):1014–1017. doi:10.3201/eid1606.09167120507761
   PubMed Web of Science ®Google Scholar
• Krzeminski P, Schwermer C, Wennberg A, Langford K, Vogelsang C. Occurrence of UV filters, fragrances and organophosphate flame retardants in municipal WWTP effluents and their removal during membrane post-treatment. J Hazard Mater. 2017;323(Pt A):166–176. doi:10.1016/j.jhazmat.2016.08.00127566858
   PubMed Web of Science ®Google Scholar
• Hembach N, Alexander J, Hiller C, Wieland A, Schwartz T. Dissemination prevention of antibiotic resistant and facultative pathogenic bacteria by ultrafiltration and ozone treatment at an urban wastewater treatment plant. Sci Rep. 2019;9(1):12843. doi:10.1038/s41598-019-49263-131492933
   PubMed Web of Science ®Google Scholar
• Okubo T, Hasegawa T, Fukuda A, et al. Screening of hospital-manhole sewage using MacConkey agar with cefotaxime reveals extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. Int J Antimicrob Agents. 2019;54(6):831–833. doi:10.1016/j.ijantimicag.2019.08.00431398479
   PubMed Web of Science ®Google Scholar
• Azuma T, Otomo K, Kunitou M, et al. Environmental fate of pharmaceutical compounds and antimicrobial-resistant bacteria in hospital effluents, and contributions to pollutant loads in the surface waters in Japan. Sci Total Environ. 2019;657:476–484. doi:10.1016/j.scitotenv.2018.11.43330550911
   PubMed Web of Science ®Google Scholar