References:

MLST, rMLST and cgMLST typing, and sublineage / clonal group nomenclatures

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• MLST

  • Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S. Multilocus Sequence Typing of Klebsiella pneumoniae nosocomial isolates. J Clin Microbiol 2005, 43:4178-82. PMID 16081970

  • Brisse S, Fevre C, Passet V, Issenhuth-Jeanjean S, Tournebize R, Diancourt L, Grimont P. Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS One 2009, 4(3):e4982. PMID 19319196

• ribosomal MLST

  • Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MC. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012, 158(Pt 4):1005-15. PMID 22282518

• core genome MLST

  • Bialek-Davenet S, Criscuolo A, Ailloud F, Passet V, Jones L, Delannoy-Vieillard AS, Garin B, Le Hello S, Arlet G, Nicolas-Chanoine MH, Decré D, Brisse S. Genomic definition of Hypervirulent and Multidrug-Resistant Klebsiella pneumoniae Clonal Groups. Emerging Infectious Diseases 2014, 20(11):1812-20. PMID 25341126 Technical appendix

  • Hennart M, Guglielmini J, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S. A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains. Molecular Biology and Evolution 2022, 39(7):msac135. PMID 35700230

• sublineage and clonal group nomenclatures

  • Hennart M, Guglielmini J, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S. A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains. Molecular Biology and Evolution 2022,39(7):msac135. PMID 35700230

Capsule typing

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• wzi sequencing

  • Brisse S, Passet V, Haugaard AB, Babosan A, Kassis-Chikhani N, Struve C, Decré D. wzi gene sequencing, a rapid method to determine the capsular type of Klebsiella strains. J Clin Microbiol 2013, 51:4073-8. PMID 24088853

• wzc sequencing

  • Pan YJ, Lin TL, Chen YH, Hsu CR, Hsieh PF, Wu MC, Wang JT. Capsular types of Klebsiella pneumoniae revisited by wzc sequencing. PLoS One 2013, 8(12):e80670. PMID 24349011

Virulence typing

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• AbST & SmST

  • Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, Holt KE. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome Medicine 2018, 10(1):77. PMID 30371343

• YbST & CbST

  • Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM, Jenney A, Brisse S, Holt KE. Genetic diversity, mobilisation and spread of the yersiniabactin- encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microbial Genomics 2018, 4(9):e000196. PMID 29985125

Resistance genes nomenclature

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• OKP Beta-lactamases

  • Fevre C, Passet V, Weill F-X, Grimont PAD, Brisse S. Variants of the Klebsiella pneumoniae OKP Chromosomal Beta-Lactamase Are Divided into Two Main Groups, OKP-A and OKP-B. Antimicrob Agents Chemother 2005, 49(12):5149-52. PMID 16304190

  • Hæggman S, Löfdahl S, Paauw A, Verhoef J, Brisse. Diversity and Evolution of the Class A Chromosomal Beta-Lactamase Gene in Klebsiella pneumoniae. Antimicrob Agents Chemoter 2004, 48(7):2400-8. PMID 15215087

• OXY Beta-lactamases

  • Fevre C, Jbel M, Passet V, Weill F-X, Grimont PAD, Brisse S. Six groups of the OXY beta-Lactamase evolved over millions of years in Klebsiella oxytoca. Antimicrob Agents Chemother 2005, 49(8):3453-62. PMID 16048960