Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile

Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol [Internet]. The Authors. 2018;45:131–9. https://doi.org/10.1016/j.mib.2018.04.004.

Clegg S, Murphy CN. Epidemiology and virulence of Klebsiella pneumoniae. Microbiol Spectr. 2016;4.

Choby JE, Howard-Anderson J, Weiss DS. Hypervirulent Klebsiella pneumoniae – clinical and molecular perspectives. J Intern Med. 2020;287:283–300.

Article  PubMed  Google Scholar 

Lan P, Jiang Y, Zhou J, Yu Y. A global perspective on the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae. J Glob Antimicrob Resist [Internet]. Elsevier Ltd. 2021;25:26–34. https://doi.org/10.1016/j.jgar.2021.02.020.

Han YL, Wen XH, Zhao W, Cao XS, Wen JX, Wang JR, et al. Epidemiological characteristics and molecular evolution mechanisms of carbapenem-resistant hypervirulent Klebsiella pneumoniae. Front Microbiol. 2022;13:1–13.

Article  Google Scholar 

Tang M, Kong X, Hao J, Liu J. Epidemiological characteristics and formation mechanisms of Multidrug-Resistant Hypervirulent Klebsiella pneumoniae. Front Microbiol. 2020;11:1–10.

Article  Google Scholar 

Lam MMC, Wyres KL, Duchêne S, Wick RR, Judd LM, Gan YH et al. Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nat Commun. 2018;9.

Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae. Nat Rev Microbiol [Internet]. Springer: US.;2020.https://doi.org/10.1038/s41579-019-0315-1.

Russo TA, Marr CM. Hypervirulent Klebsiella pneumoniae. 2019;32:1–42.

Google Scholar 

Chen YT, Chang HY, Lai YC, Pan CC, Tsai SF, Peng HL. Sequencing and analysis of the large virulence plasmid pLVPK of Klebsiella pneumoniae CG43. Gene. 2004;337:189–98.

Article  PubMed  Google Scholar 

Marcoleta AE, Berríos-Pastén C, Nuñez G, Monasterio O, Lagos R. Klebsiella pneumoniae asparagine tDNAs are integration hotspots for different genomic islands encoding microcin E492 production determinants and other putative virulence factors present in hypervirulent strains. Front Microbiol. 2016;7.

Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM, Jenney AWJ et al. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microb Genomics [Internet]. 2018;1–14. Available from: http://www.microbiologyresearch.org/content/journal/mgen/https://doi.org/10.1099/mgen.0.000196.v1.

Zhang R, Lin D, Chan EW, Gu D, Chen G, Chen S. Emergence of Carbapenem-Resistant Serotype K1 Hypervirulent Klebsiella pneumoniae Strains in China. Antimicrob Agents Chemother [Internet]. 2016;60:709–11. https://doi.org/10.1128/AAC.02173-15.

Chen Y, Marimuthu K, Teo J, Venkatachalam I, Pei B, Cherng Z, et al. Acquisition of plasmid with Carbapenem-Resistance Gene blaKPC2 in Hypervirulent Klebsiella pneumoniae, Singapore. Clin Infect Dis. 2020;26:549–59.

Google Scholar 

Becker L, Kaase M, Pfeifer Y, Fuchs S, Reuss A, von Laer A, et al. Genome-based analysis of carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008–2014. Antimicrob Resist Infect Control Antimicrob Resist Infect Control. 2018;7:1–12.

Google Scholar 

Karlsson M, Stanton RA, Ansari U, McAllister G, Chan MY, Sula E et al. Identification of a carbapenemase-producing hypervirulent klebsiella pneumoniae isolate in the United States. Antimicrob Agents Chemother. 2019;63.

Cejas D, Canigia LF, Cruz GR, Elena AX, Maldonado I, Gutkind GO, et al. First isolate of KPC-2-producing Klebsiella pneumonaie sequence type 23 from the Americas. J Clin Microbiol. 2014;52:3483–5.

Article  PubMed  PubMed Central  Google Scholar 

Morales-León F, Matus-Köhler M, Araya-Vega P, Aguilera F, Torres I, Vera R et al. Molecular Characterization of the Convergent Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae Strain K1-ST23, Collected in Chile during the COVID-19 Pandemic. Lincopan N, editor. Microbiol Spectr [Internet]. American Society for Microbiology; 2023;2019:1–7. https://doi.org/10.1128/spectrum.00540-23.

Passet V, Brisse S. Association of tellurite resistance with hypervirulent clonal groups of Klebsiella pneumoniae. J Clin Microbiol. 2015;53:1380–2.

Article  PubMed  PubMed Central  Google Scholar 

Mikei LA, Starki AJ, Forsyth VS, Vornhagen J, Smith SN, Bachman MA et al. A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness [Internet]. PLoS Pathog. 2021. https://doi.org/10.1371/journal.ppat.1009376.

Tan YH, Chen Y, Chu WHW, Sham LT, Gan YH. Cell envelope defects of different capsule-null mutants in K1 hypervirulent Klebsiella pneumoniae can affect bacterial pathogenesis. Mol Microbiol. 2020;1–17.

Russo TA, Olson R, Fang C-T, Stoesser N, Miller M, MacDonald U et al. Identification of Biomarkers for Differentiation of Hypervirulent Klebsiella pneumoniae from Classical K. pneumoniae. Diekema DJ, editor. J Clin Microbiol [Internet]. 2018;56. https://doi.org/10.1128/JCM.00776-18.

Lee CH, Liu JW, Su LH, Chien CC, Li CC, Yang KD. Hypermucoviscosity associated with Klebsiella pneumoniae-mediated invasive syndrome: A prospective cross-sectional study in Taiwan. Int J Infect Dis [Internet]. International Society for Infectious Diseases; 2010;14:e688–92. https://doi.org/10.1016/j.ijid.2010.01.007.

Wozniak A, Figueroa C, Moya-Flores F, Guggiana P, Castillo C, Rivas L, et al. A multispecies outbreak of carbapenem-resistant bacteria harboring the bla KPC gene in a non-classical transposon element. BMC Microbiol BMC Microbiol. 2021;21:1–10.

Google Scholar 

Veloso M, Arros P, Acosta J, Rojas R, Berríos-Pastén C, Varas M et al. Antimicrobial resistance, pathogenic potential, and genomic features of carbapenem-resistant Klebsiella pneumoniae isolated in Chile: high-risk ST25 clones and novel mobile elements. Lincopan N, editor. Microbiol Spectr [Internet]. American Society for Microbiology; 2023;0. https://doi.org/10.1128/spectrum.00399-23.

Morales-León F, Matus-Köhler M, Araya-Vega P, Aguilera F, Torres I, Vera R et al. Molecular Characterization of the Convergent Carbapenem-Resistant and Hypervirulent Klebsiella pneumoniae Strain K1-ST23, Collected in Chile during the COVID-19 Pandemic. Lincopan N, editor. Microbiol Spectr [Internet]. American Society for Microbiology; 2023;11:1–7. https://doi.org/10.1128/spectrum.00540-23.

Coutinho RL, Visconde MF, Descio FJ, Nicoletti AG, Pinto FCL, da Silva ACR, et al. Community-acquired invasive liver abscess syndrome caused by a K1 serotype Klebsiella pneumoniae isolate in Brazil: a case report of hypervirulent ST23. Mem Inst Oswaldo Cruz. 2014;109:973–4.

Article  Google Scholar 

Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A et al. A dual Barcoding Approach to bacterial strain nomenclature: genomic taxonomy of Klebsiella pneumoniae strains. Mol Biol Evol. 2022;39.

Yong M, Chen Y, Oo G, Chang KC, Chu WHW, Teo J, et al. Dominant carbapenemase-encoding plasmids in clinical Enterobacterales isolates and Hypervirulent Klebsiella pneumoniae, Singapore. Emerg Infect Dis. 2022;28:1578–88.

Article  PubMed  PubMed Central  Google Scholar 

Shon AS, Bajwa RPS, Russo TA. Hypervirulent (hypermucoviscous) Klebsiella Pneumoniae: a new and dangerous breed. Virulence. 2013;4:107–18.

Article  PubMed  PubMed Central  Google Scholar 

Araya I, Roach-Poblete F, Tapia T, Rodas PI, Villamil A, Aguero R, et al. Caracterización fenotípica y molecular de cepas de Klebsiella pneumoniae productores de carbapenemasas tipo OXA-48 circulantes en Chile. Rev Chil infectología. 2022;39:551–8.

Article  Google Scholar 

Han R, Guo Y, Peng M, Shi Q, Wu S, Yang Y, et al. Evaluation of the Immunochromatographic NG-Test Carba 5, RESIST-5 O.O.K.N.V., and IMP K-SeT for Rapid Detection of KPC-, NDM-, IMP-, VIM-type, and OXA-48-like carbapenemase among Enterobacterales. Front Microbiol. 2021;11:1–7.

Article  Google Scholar 

Clinical and Laboratory Standards Institute (CLSI). Performance Standards for Antimicrobial Susceptibility Testing. 33rd ed. CLSI supplement M100. Clin. Lab. Stand. Institue. 2023.

Chen S, Zhou Y, Chen Y, Gu J. Fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90.

Article  PubMed  PubMed Central  Google Scholar 

Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G, Vezina B, et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol Genome Biology. 2021;22:1–17.

Google Scholar 

Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol [Internet]. Springer US; 2019;37:540–6. https://doi.org/10.1038/s41587-019-0072-8.

Vaser R, Šikić M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci [Internet]. Springer US; 2021;1:332–6. https://doi.org/10.1038/s43588-021-00073-4.

Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094–100.

Article  PubMed  PubMed Central  Google Scholar 

Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics. 2016;32:2103–10.

Article  PubMed  PubMed Central  Google Scholar 

Wick RR, Holt KE. Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000Research. 2019;8:1–23.

Article  Google Scholar 

Wick RR, Holt KE, Polypolish. Short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol [Internet]. 2022;18:1–13. https://doi.org/10.1371/journal.pcbi.1009802.

Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29:2669–77.

Article  PubMed  PubMed Central  Google Scholar 

Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: Quality assessment tool for genome assemblies. Bioinformatics. 2013;29:1072–5.

Article  PubMed  PubMed Central  Google Scholar 

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

Article  PubMed  PubMed Central  Google Scholar 

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A, Bakta. Rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. Microb Genomics. 2021;7.

Gilchrist CLM, Chooi YH. Clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics. 2021;37:2473–5.

Article  PubMed  Google Scholar 

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011;7:1–6.

Article  Google Scholar 

Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ. Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics. 2009;25:1189–91.

Article  PubMed  PubMed Central  Google Scholar 

Molton JS, Chan M, Kalimuddin S, Oon J, Young BE, Low JG, et al. Oral vs intravenous antibiotics for patients with klebsiella pneumoniae liver abscess: a randomized, controlled noninferiority study. Clin Infect Dis. 2020;71:952–9.

Article  PubMed  Google Scholar 

Wyres KL, Nguyen TNT, Lam MMC, Judd LM, Van Vinh Chau N, Dance DAB, et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Med Genome Med. 2020;12:1–16.

Google Scholar 

Baker KS, Burnett E, McGregor H, Deheer-Graham A, Boinett C, Langridge GC et al. The Murray collection of pre-antibiotic era Enterobacteriacae: A unique research resource. Genome Med [Internet]. Genome Medicine; 2015;7:1–7. https://doi.org/10.1186/s13073-015-0222-7.

Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL, Holt KE. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun [Internet]. Springer US; 2021;12. https://doi.org/10.1038/s41467-021-24448-3.

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol [Internet]. 1990;215:403–10. Available from: http://www.sciencedirect.com/science/article/pii/S0022283605803602.

Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.

Article  PubMed  PubMed Central  Google Scholar 

Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, Von Haeseler A, et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.

Article  PubMed  PubMed Central  Google Scholar 

Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS, ModelFinder. Fast model selection for accurate phylogenetic estimates. Nat Methods [Internet]. Nature Publishing Group; 2017;14:587–9. https://doi.org/10.1038/nmeth.4285.

Robertson J, Nash JHE. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genomics. 2018;4.

Feldgarden M, Brover V, Gonzalez-Escalona N, Frye JG, Haendiges J, Haft DH et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep [Internet]. Nature Publishing Group UK; 2021;11:1–9. https://doi.org/10.1038/s41598-021-91456-0.

Xie Z, Tang H. ISEScan: automated identification of insertion sequence elements in prokaryotic genomes. Bioinformatics. 2017;33:3340–7.

Article  PubMed  Google Scholar 

Néron B, Littner E, Haudiquet M, Perrin A, Cury J, Rocha EPC. IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella. Microorganisms. 2022;10.

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