Genomic and Phylogenetic Analysis of a Multidrug-Resistant bla_NDM-carrying Klebsiella michiganensis in China

References

• Logan LK, Weinstein RA. The epidemiology of carbapenem-resistant Enterobacteriaceae: the impact and evolution of a global menace. J Infect Dis. 2017;215(suppl_1):S28–s36. doi:10.1093/infdis/jiw282
   PubMed Web of Science ®Google Scholar
• Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol. 2018;45:131–139. doi:10.1016/j.mib.2018.04.004
   PubMed Web of Science ®Google Scholar
• Saha R, Farrance CE, Verghese B, Hong S, Donofrio RS. Klebsiella michiganensis sp. nov., a new bacterium isolated from a tooth brush holder. Curr Microbiol. 2013;66(1):72–78. doi:10.1007/s00284-012-0245-x
   PubMed Web of Science ®Google Scholar
• Zhang N, Liu X, Qi L, et al. A clinical KPC-producing Klebsiella michiganensis strain carrying IncFII/IncFIA (HI1)/IncFIB (K) multiple replicon plasmid. Front Microbiol. 2022;13:1086296. doi:10.3389/fmicb.2022.1086296
   PubMed Web of Science ®Google Scholar
• Mollenkopf DF, Stull JW, Mathys DA, et al. Carbapenemase-producing Enterobacteriaceae recovered from the environment of a Swine Farrow-to-Finish Operation in the United States. Antimicrob Agents Chemother. 2017;61(2). doi:10.1128/AAC.01298-16
   PubMed Web of Science ®Google Scholar
• Woodford N, Wareham DW, Guerra B, Teale C. Carbapenemase-producing Enterobacteriaceae and non-Enterobacteriaceae from animals and the environment: an emerging public health risk of our own making? J Antimicrob Chemother. 2014;69(2):287–291. doi:10.1093/jac/dkt392
   PubMed Web of Science ®Google Scholar
• David S, Reuter S, Harris SR, et al. Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread. Nat Microbiol. 2019;4(11):1919–1929. doi:10.1038/s41564-019-0492-8
   PubMed Web of Science ®Google Scholar
• Abed JY, Déraspe M, Bérubé È, et al. Complete genome sequences of Klebsiella michiganensis and Citrobacter farmeri, KPC-2-producers serially isolated from a single patient. Antibiotics. 2021;10(11):1408. doi:10.3390/antibiotics10111408
   Google Scholar
• Simoni S, Leoni F, Veschetti L, et al. The emerging nosocomial pathogen Klebsiella michiganensis: genetic analysis of a KPC-3 producing strain isolated from Venus clam. Microbiol Spectr. 2022;11(1):e0423522. doi:10.1128/spectrum.04235-22
   PubMed Web of Science ®Google Scholar
• Campos-Madueno EI, Sigrist T, Flückiger UM, Risch L, Bodmer T, Endimiani A. First report of a bla(VIM-1) metallo-β-lactamase-possessing Klebsiella michiganensis. J Glob Antimicrob Resist. 2021;25:310–314. doi:10.1016/j.jgar.2021.03.027
   PubMed Web of Science ®Google Scholar
• Prah I, Nukui Y, Yamaoka S, Saito R. Emergence of a high-risk Klebsiella michiganensis clone disseminating carbapenemase genes. Front Microbiol. 2022;13:880248. doi:10.3389/fmicb.2022.880248
   PubMed Web of Science ®Google Scholar
• Founou RC, Founou LL, Allam M, Ismail A, Essack SY. Genomic characterisation of Klebsiella michiganensis co-producing OXA-181 and NDM-1 carbapenemases isolated from a cancer patient in uMgungundlovu District, KwaZulu-Natal Province, South Africa. S Afr Med J. 2018;109(1):7–8. doi:10.7196/SAMJ.2018.v109i1.13696
   PubMed Web of Science ®Google Scholar
• Wick RR, Judd LM, Gorrie CL, Holt KE, Phillippy AM. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13(6):e1005595. doi:10.1371/journal.pcbi.1005595
   PubMed Web of Science ®Google Scholar
• Feng Y, Zou S, Chen H, Yu Y, Ruan Z. BacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking. Nucleic Acids Res. 2021;49(D1):D644–d650. doi:10.1093/nar/gkaa821
   PubMed Web of Science ®Google Scholar
• Feldgarden M, Brover V, Gonzalez-Escalona N, et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021;11(1):12728. doi:10.1038/s41598-021-91456-0
   PubMed Web of Science ®Google Scholar
• Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27(7):1009–1010. doi:10.1093/bioinformatics/btr039
   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:10.1186/1471-2164-12-402
   PubMed Web of Science ®Google Scholar
• Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol. 2013;30(5):1224–1228. doi:10.1093/molbev/mst028
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. Interactive Tree of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 2019;47(W1):W256–w259. doi:10.1093/nar/gkz239
   PubMed Web of Science ®Google Scholar
• Papp-Wallace KM, Endimiani A, Taracila MA, Bonomo RA. Carbapenems: past, present, and future. Antimicrob Agents Chemother. 2011;55(11):4943–4960. doi:10.1128/AAC.00296-11
   PubMed Web of Science ®Google Scholar
• Sun Q, Dai Y, Chen J, et al. Coexistence of two bla(KPC-2) genes in a bla(NDM-1)-carrying multidrug-resistant ST15 Klebsiella pneumoniae isolate recovered from cerebrospinal fluid in China. J Glob Antimicrob Resist. 2022;29:232–235. doi:10.1016/j.jgar.2022.04.006
   PubMed Web of Science ®Google Scholar
• Acman M, Wang R, van Dorp L, et al. Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene bla(NDM). Nat Commun. 2022;13(1):1131. doi:10.1038/s41467-022-28819-2
   PubMed Web of Science ®Google Scholar
• Wang Y, Tong MK, Chow KH, et al. Occurrence of Highly Conjugative IncX3 Epidemic Plasmid Carrying bla (NDM) in Enterobacteriaceae Isolates in Geographically Widespread Areas. Front Microbiol. 2018;9:2272. doi:10.3389/fmicb.2018.02272
   PubMed Web of Science ®Google Scholar
• Lopes R, Furlan JPR, Dos Santos LDR, Stehling EG. Detection of CTX-M-27-positive endophytic Escherichia coli ST131 lineage C1/H30R subclade carrying bla(KPC-2) on an IncX3-IncU plasmid in a fresh vegetable. J Glob Antimicrob Resist. 2022;30:178–179. doi:10.1016/j.jgar.2022.06.012
   PubMed Web of Science ®Google Scholar
• Yang M, Xu G, Ruan Z, Wang Y. Genomic characterization of a multidrug-resistant Escherichia coli isolate co-carrying bla (NDM-5) and bla (CTX-M-14) genes recovered from a pediatric patient in China. Infect Drug Resist. 2022;15:6405–6412. doi:10.2147/IDR.S388797
   PubMed Web of Science ®Google Scholar
• Li P, Lin Y, Hu X, et al. Characterization of blaNDM-1- and blaSHV-12-positive IncX3 plasmid in an Enterobacter hormaechei new sequence type 1000 from China. Infect Drug Resist. 2020;13:145–153. doi:10.2147/IDR.S231366
   PubMed Web of Science ®Google Scholar
• Miethke M, Marahiel MA. Siderophore-based iron acquisition and pathogen control. Microbiol Mol Biol Rev. 2007;71(3):413–451. doi:10.1128/MMBR.00012-07
   PubMed Web of Science ®Google Scholar
• Dallman TJ, Byrne L, Ashton PM, et al. Whole-genome sequencing for national surveillance of Shiga toxin-producing Escherichia coli O157. Clin Infect Dis. 2015;61(3):305–312.
   PubMed Web of Science ®Google Scholar