Whole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China

References

• Nordmann P, Dortet L, Poirel L. Carbapenem resistance in Enterobacteriaceae: here is the storm! Trends Mol Med. 2012;18(5):263–272. doi:10.1016/j.molmed.2012.03.00322480775
   PubMed Web of Science ®Google Scholar
• van Duin D, Doi Y. The global epidemiology of carbapenemase-producing Enterobacteriaceae. Virulence. 2017;8(4):460–469. doi:10.1080/21505594.2016.122234327593176
   PubMed Web of Science ®Google Scholar
• Partridge SR. Resistance mechanisms in Enterobacteriaceae. Pathology. 2015;47(3):276–284. doi:10.1097/pat.000000000000023725764207
   PubMed Web of Science ®Google Scholar
• Wu W, Feng Y, Tang G, Qiao F, McNally A, Zong Z. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin Microbiol Rev. 2019;32(2):e00115–18. doi:10.1128/CMR30700432
   PubMed Web of Science ®Google Scholar
• 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.2017.09.00529033338
   PubMed Web of Science ®Google Scholar
• Sun P, Bi Z, Nilsson M, et al. Occurrence of blaKPC-2, blaCTX-M, and mcr-1 in Enterobacteriaceae from well water in rural China. Antimicrob Agents Chemother. 2017;61(4). doi:10.1128/AAC.02569-16
   Google Scholar
• Xu G, Jiang Y, An W, Wang H, Zhang X. Emergence of KPC-2-producing Escherichia coli isolates in an urban river in Harbin, China. World J Microbiol Biotechnol. 2015;31(9):1443–1450. doi:10.1007/s11274-015-1897-z26149956
   PubMed Web of Science ®Google Scholar
• Yang F, Huang L, Li L, Yang Y, Mao D, Luo Y. Discharge of KPC-2 genes from the WWTPs contributed to their enriched abundance in the receiving river. Sci Total Environ. 2017;581-582:136–143. doi:10.1016/j.scitotenv.2016.12.06328065546
   PubMed Web of Science ®Google Scholar
• Yang F, Gu Y, Zhou J, Zhang K. Swine waste: a reservoir of high-risk blaNDM and mcr-1. Sci Total Environ. 2019;683:308–316. doi:10.1016/j.scitotenv.2019.05.25131132710
   PubMed Web of Science ®Google Scholar
• Yang F, Mao D, Zhou H, Wang X, Luo Y. Propagation of New Delhi Metallo-β-lactamase genes (blaNDM-1) from a wastewater treatment plant to its receiving river. Environ Sci Tech Let. 2016;3(4):138–143. doi:10.1021/acs.estlett.6b00036
   Google Scholar
• Zhang R, Li J, Wang Y, Shen J, Shen Z, Wang S. Presence of NDM in non-E. coli Enterobacteriaceae in the poultry production environment. J Antimicrob Chemother. 2019;74(8):2209–2213. doi:10.1093/jac/dkz19331102511
   PubMed Web of Science ®Google Scholar
• Bleichenbacher S, Stevens MJA, Zurfluh K, et al. Environmental dissemination of carbapenemase-producing Enterobacteriaceae in rivers in Switzerland. Environ Pollut. 2020;265:115081. doi:10.1016/j.envpol.2020.11508132806462
   PubMed Web of Science ®Google Scholar
• Yang J, Wang H, Roberts DJ, et al. Persistence of antibiotic resistance genes from river water to tap water in the Yangtze River Delta. Sci Total Environ. 2020;742:140592. doi:10.1016/j.scitotenv.2020.14059232629269
   PubMed Web of Science ®Google Scholar
• Zhao Q, Berglund B, Zou H, et al. Dissemination of blaNDM-5 via IncX3 plasmids in carbapenem-resistant Enterobacteriaceae among humans and in the environment in an intensive vegetable cultivation area in eastern China. Environ Pollut. 2021;273:116370. doi:10.1016/j.envpol.2020.11637033460870
   PubMedGoogle Scholar
• Suzuki Y, Nazareno PJ, Nakano R, et al. Environmental presence and genetic characteristics of carbapenemase-producing Enterobacteriaceae from hospital sewage and river water in the Philippines. Appl Environ Microbiol. 2020;86(2). doi:10.1128/AEM.01906-19
   Web of Science ®Google Scholar
• Teixeira P, Tacao M, Pureza L, et al. Occurrence of carbapenemase-producing Enterobacteriaceae in a Portuguese river: blaNDM, blaKPC and blaGES among the detected genes. Environ Pollut. 2020;260:113913. doi:10.1016/j.envpol.2020.11391331972417
   PubMed Web of Science ®Google Scholar
• Piedra-Carrasco N, Fabrega A, Calero-Caceres W, et al. Carbapenemase-producing Enterobacteriaceae recovered from a Spanish river ecosystem. PLoS One. 2017;12(4):e0175246. doi:10.1371/journal.pone.017524628380016
   PubMed Web of Science ®Google Scholar
• Almakki A, Maure A, Pantel A, et al. NDM-5-producing Escherichia coli in an urban river in Montpellier, France. Int J Antimicrob Agents. 2017;50(1):123–124. doi:10.1016/j.ijantimicag.2017.04.00328435018
   PubMed Web of Science ®Google Scholar
• Di DYW, Jang J, Unno T, Hur H-G. Emergence of Klebsiella variicola positive for NDM-9, a variant of New Delhi metallo-β-lactamase, in an urban river in South Korea. J Antimicrob Chemother. 2017;dkw547. doi:10.1093/jac/dkw547
   Web of Science ®Google Scholar
• Tafoukt R, Touati A, Leangapichart T, Bakour S, Rolain JM. Characterization of OXA-48-like-producing Enterobacteriaceae isolated from river water in Algeria. Water Res. 2017;120:185–189. doi:10.1016/j.watres.2017.04.07328486169
   PubMed Web of Science ®Google Scholar
• Zhang L, Ma X, Luo L, et al. The prevalence and characterization of Extended-Spectrum beta-Lactamase- and carbapenemase-producing bacteria from hospital sewage, treated effluents and receiving rivers. Int J Environ Res Public Health. 2020;17(4). doi:10.3390/ijerph17041183
   Web of Science ®Google Scholar
• Lane DJ. 16S/23S rRNA sequencing. Nucleic Acid Techniques Bacterial Syst. 1991;1:115–175.
   Google Scholar
• Poirel L, Walsh TR, Cuvillier V, Nordmann P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn Microbiol Infect Dis. 2011;70(1):119–123. doi:10.1016/j.diagmicrobio.2010.12.00221398074
   PubMed Web of Science ®Google Scholar
• Institute CLS. Performance Standards for Antimicrobial Susceptibility Testing. Clinical and Laboratory Standards Institute Wayne, PA, USA; 2017.
   Google Scholar
• Giske CG, Turnidge J, Canton R, Kahlmeter G. Update From The European Committee On Antimicrobial Susceptibility Testing (EUCAST). J Clin Microbiol. 2021;21:JCM0027621.
   Google Scholar
• Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. doi:10.1093/bioinformatics/btu15324642063
   PubMed Web of Science ®Google Scholar
• Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 2006;34(Databaseissue):D32–D36. doi:10.1093/nar/gkj01416381877
   PubMed Web of Science ®Google Scholar
• Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics. 2011;12:402. doi:10.1186/1471-2164-12-40221824423
   PubMed Web of Science ®Google Scholar
• Page AJ, Taylor B, Delaney AJ, et al. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microb Genom. 2016;2(4):e000056. doi:10.1099/mgen.0.00005628348851
   PubMed Web of Science ®Google Scholar
• Hu Y, Feng Y, Qin J, Zhang X, Zong Z. Acinetobacter chinensis, a novel Acinetobacter species, carrying blaNDM-1, recovered from hospital sewage. J Microbiol. 2019;57(5):350–355. doi:10.1007/s12275-019-8485-030806982
   PubMed Web of Science ®Google Scholar
• Johnson JR, Murray AC, Gajewski A, et al. Isolation and molecular characterization of nalidixic acid-resistant extraintestinal pathogenic Escherichia coli from retail chicken products. Antimicrob Agents Chemother. 2003;47(7):2161–2168. doi:10.1128/aac.47.7.2161-2168.200312821463
   PubMed Web of Science ®Google Scholar
• Rodriguez-Siek KE, Giddings CW, Doetkott C, Johnson TJ, Nolan LK. Characterizing the APEC pathotype. Vet Res. 2005;36(2):241–256. doi:10.1051/vetres:200405715720976
   PubMed Web of Science ®Google Scholar
• Murase K, Martin P, Porcheron G, et al. HlyF produced by extraintestinal pathogenic Escherichia coli is a virulence factor that regulates outer membrane vesicle biogenesis. J Infect Dis. 2016;213(5):856–865. doi:10.1093/infdis/jiv50626494774
   PubMed Web of Science ®Google Scholar
• Steenbergen SM, Vimr ER. Biosynthesis of the Escherichia coli K1 group 2 polysialic acid capsule occurs within a protected cytoplasmic compartment. Mol Microbiol. 2008;68(5):1252–1267. doi:10.1111/j.1365-2958.2008.06231.x18435708
   PubMed Web of Science ®Google Scholar
• Hao Y, Shao C, Bai Y, Jin Y. Genotypic and phenotypic characterization of IncX3 plasmid carrying blaNDM-7 in Escherichia coli sequence type 167 isolated from a patient with urinary tract infection. Front Microbiol. 2018;9:2468. doi:10.3389/fmicb.2018.0246830405550
   PubMed Web of Science ®Google Scholar
• Adefioye OJ, Weinreich J, Rodiger S, Schierack P, Olowe OA. Phylogenetic characterization and multilocus sequence typing of extended-spectrum beta lactamase-producing Escherichia coli from food-producing animals, beef, and humans in southwest Nigeria. Microb Drug Resist. 2020. doi:10.1089/mdr.2019.0397
   Web of Science ®Google Scholar
• Compain F, Frangeul L, Drieux L, et al. Complete nucleotide sequence of two multidrug-resistant IncR plasmids from Klebsiella pneumoniae. Antimicrob Agents Chemother. 2014;58(7):4207–4210. doi:10.1128/aac.02773-1324752259
   PubMed Web of Science ®Google Scholar
• Norman A, Hansen LH, She Q, Sorensen SJ. Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux. Plasmid. 2008;60(1):59–74. doi:10.1016/j.plasmid.2008.03.00318440636
   PubMed Web of Science ®Google Scholar
• Li X, Fu Y, Shen M, et al. Dissemination of blaNDM-5 gene via an IncX3-type plasmid among non-clonal Escherichia coli in China. Antimicrob Resist Infect Control. 2018;7:59. doi:10.1186/s13756-018-0349-629713466
   PubMed Web of Science ®Google Scholar
• Wang Y, Tong MK, Chow KH, et al. Occurrence of highly conjugative IncX3 epidemic plasmid carrying blaNDM in Enterobacteriaceae isolates in geographically widespread areas. Front Microbiol. 2018;9:2272. doi:10.3389/fmicb.2018.0227230294321
   PubMed Web of Science ®Google Scholar
• Tacconelli E, Carrara E, Savoldi A, et al. Discovery, research, and development of new antibiotics: the WHO priority list of antibiotic-resistant bacteria and tuberculosis. Lancet Infect Dis. 2018;18(3):318–327. doi:10.1016/S1473-3099(17)30753-329276051
   PubMed Web of Science ®Google Scholar
• Gomi R, Matsuda T, Yamamoto M, et al. Characteristics of carbapenemase-producing Enterobacteriaceae in wastewater revealed by genomic analysis. Antimicrob Agents Chemother. 2018;62(5). doi:10.1128/AAC.02501-17
   Web of Science ®Google Scholar
• Mahon BM, Brehony C, Cahill N, et al. Detection of OXA-48-like-producing Enterobacterales in Irish recreational water. Sci Total Environ. 2019;690:1–6. doi:10.1016/j.scitotenv.2019.06.48031299565
   PubMed Web of Science ®Google Scholar
• Magiorakos AP, Srinivasan A, Carey RB, et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect. 2012;18(3):268–281. doi:10.1111/j.1469-0691.2011.03570.x21793988
   PubMed Web of Science ®Google Scholar
• Rozwandowicz M, Brouwer MSM, Fischer J, et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother. 2018;73(5):1121–1137. doi:10.1093/jac/dkx48829370371
   PubMed Web of Science ®Google Scholar
• Pak-Leung Ho YW. IncX3 epidemic plasmid carrying blaNDM-5 in Escherichia coli from swine in multiple geographic areas in China. Antimicrob Agents Chemother. 2017;62(3):e02295–02217.
   Web of Science ®Google Scholar
• Hornsey M, Phee L, Wareham DW. A novel variant, NDM-5, of the New Delhi metallo-beta-lactamase in a multidrug-resistant Escherichia coli ST648 isolate recovered from a patient in the United Kingdom. Antimicrob Agents Chemother. 2011;55(12):5952–5954. doi:10.1128/AAC.05108-1121930874
   PubMed Web of Science ®Google Scholar
• Zhu YQ, Zhao JY, Xu C, Zhao H, Jia N, Li YN. Identification of an NDM-5-producing Escherichia coli sequence type 167 in a neonatal patient in China. Sci Rep. 2016;6:29934. doi:10.1038/srep2993427406405
   PubMed Web of Science ®Google Scholar
• Xu L, Wang P, Cheng J, Qin S, Xie W. Characterization of a novel blaNDM-5-harboring IncFII plasmid and an mcr-1-bearing IncI2 plasmid in a single Escherichia coli ST167 clinical isolate. Infect Drug Resist. 2019;12:511–519. doi:10.2147/IDR.S19299830881056
   PubMed Web of Science ®Google Scholar
• Huang J, Ma S, Yu Q, et al. Whole genome sequence of an Escherichia coli ST410 isolate co-harbouring blaNDM-5, blaOXA-1, blaCTX-M-15, blaCMY-2, aac (3)-IIa and aac (6ʹ)-Ib-cr genes isolated from a patient with bloodstream infection in China. J Glob Antimicrob Resist. 2019;19:354–355. doi:10.1016/j.jgar.2019.10.02731698110
   PubMedGoogle Scholar
• Naha S, Sands K, Mukherjee S, Saha B, Dutta S, Basu S. OXA-181-Like carbapenemases in Klebsiella pneumoniae ST14, ST15, ST23, ST48, and ST231 from septicemic neonates: coexistence with NDM-5, resistome, transmissibility, and genome diversity. mSphere. 2021;6(1). doi:10.1128/mSphere.01156-20
   Web of Science ®Google Scholar
• Mei YF, Liu PP, Wan LG, et al. Virulence and genomic feature of a virulent Klebsiella pneumoniae sequence type 14 strain of serotype K2 harboring blaNDM-5 in China. Front Microbiol. 2017;8:335. doi:10.3389/fmicb.2017.0033528386246
   PubMed Web of Science ®Google Scholar
• Hammerum AM, Hansen F, Olesen B, et al. Investigation of a possible outbreak of NDM-5-producing ST16 Klebsiella pneumoniae among patients in Denmark with no history of recent travel using whole-genome sequencing. J Glob Antimicrob Resist. 2015;3(3):219–221. doi:10.1016/j.jgar.2015.05.00327873714
   PubMed Web of Science ®Google Scholar
• Zhang R, Liu L, Zhou H, et al. Nationwide surveillance of clinical carbapenem-resistant Enterobacteriaceae (CRE) strains in China. EBioMedicine. 2017;19:98–106. doi:10.1016/j.ebiom.2017.04.03228479289
   PubMed Web of Science ®Google Scholar
• Yuan Y, Li Y, Wang G, et al. blaNDM-5 carried by a hypervirulent Klebsiella pneumoniae with sequence type 29. Antimicrob Resist Infect Control. 2019;8:140. doi:10.1186/s13756-019-0596-131452874
   PubMedGoogle Scholar
• Zhu W, Wang X, Qin J, Liang W, Shen Z. Dissemination and stability of the blaNDM-5-carrying IncX3-type plasmid among multiclonal Klebsiella pneumoniae isolates. mSphere. 2020;5(6). doi:10.1128/mSphere.00917-20
   Google Scholar
• He T, Wang Y, Sun L, Pang M, Zhang L, Wang R. Occurrence and characterization of blaNDM-5-positive Klebsiella pneumoniae isolates from dairy cows in Jiangsu, China. J Antimicrob Chemother. 2017;72(1):90–94. doi:10.1093/jac/dkw35727621177
   PubMedGoogle Scholar