Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Klebsiella pneumoniae

Frontiers in Microbiology

Volumn 8, Issue MAR, 2017, Pages

  Zhou, Haijian ^a,b   Liu, Wenbing ^c   Qin, Tian ^a,b   Liu, Chen ^c   Ren, Hongyu ^a  

^a CHINESE CENTER FOR DISEASE CONTROL AND PREVENTION   (China)

^b Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases ^*  (China)

^c Beijing Novogene Bioinformatics Technology   (China)

Author keywords

Core genome multilocus sequence typing; Klebsiella pneumoniae; Outbreak investigation; Population structure analysis; Whole genome sequence

Indexed keywords

CONTIG;

ARTICLE; BACTERIAL GENOME; DNA SEQUENCE; EPIDEMIC; GENE CLUSTER; HOSPITAL INFECTION; HUMAN; KLEBSIELLA PNEUMONIAE; MULTILOCUS SEQUENCE TYPING; NONHUMAN; OVERLAPPING GENE; PHYLOGENETIC TREE; PULSED FIELD GEL ELECTROPHORESIS; RETROSPECTIVE STUDY; SANGER SEQUENCING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; START CODON; STOP CODON; SURGICAL INTENSIVE CARE UNIT; TRANSPOSON; WHOLE GENOME SEQUENCING;

EID: 85016617283     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2017.00371     Document Type: Article

References (34)

1. Baraniak, A., Izdebski, R., Fiett, J., Gawryszewska, I., Bojarska, K., Herda, M., et al. (2016). NDM-producing Enterobacteriaceae in Poland, 2012-14: inter-regional outbreak of Klebsiella pneumoniae ST11 and sporadic cases. J. Antimicrob. Chemother. 71, 85-91. doi: 10.1093/jac/dkv282
2. Bialek-Davenet, S., Criscuolo, A., Ailloud, F., Passet, V., Jones, L., Delannoy-Vieillard, A. S., et al. (2014). Genomic definition of hypervirulent and multidrug-resistant Klebsiella pneumoniae clonal groups. Emerg. Infect. Dis. 20, 1812-1820. doi: 10.3201/eid2011.140206
3. Bratcher, H. B., Corton, C., Jolley, K. A., Parkhill, J., and Maiden, M. C. (2014). A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 15:1138. doi: 10.1186/1471-2164-15-1138
4. Brisse, S., Fevre, C., Passet, V., Issenhuth-Jeanjean, S., Tournebize, R., Diancourt, L., et al. (2009). Virulent clones of Klebsiella pneumoniae: identification and evolutionary scenario based on genomic and phenotypic characterization. PLoS ONE 4:e4982. doi: 10.1371/journal.pone.0004982
5. Campos, A. C., Albiero, J., Ecker, A. B., Kuroda, C. M., Meirelles, L. E., Polato, A., et al. (2016). Outbreak of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae: a systematic review. Am. J. Infect. Control. 44, 1374-1380. doi: 10.1016/j.ajic.2016.03.022
6. de Been, M., Pinholt, M., Top, J., Bletz, S., Mellmann, A., van Schaik, W., et al. (2015). Core genome multilocus sequence typing scheme for high-resolution typing of Enterococcus faecium. J. Clin. Microbiol. 53, 3788-3797. doi: 10.1128/JCM.01946-15
7. Diancourt, L., Passet, V., Verhoef, J., Grimont, P. A., and Brisse, S. (2005). Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43, 4178-4182. doi: 10.1128/JCM.43.8.4178-4182.2005
8. Jiang, Y., Wei, Z., Wang, Y., Hua, X., Feng, Y., and Yu, Y. (2015). Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing. Clin. Microbiol. Infect. 21, 1001-1007. doi: 10.1016/j.cmi.2015.07.001
9. Jin, Y., Shao, C., Li, J., Fan, H., Bai, Y., and Wang, Y. (2015). Outbreak of multidrug resistant NDM-1-producing Klebsiella pneumoniae from a neonatal unit in Shandong Province, China. PLoS ONE 10:e0119571. doi: 10.1371/journal.pone.0119571
10. Jolley, K. A., and Maiden, M. C. (2010). BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11:595. doi: 10.1186/1471-2105-11-595
11. Keynan, Y., and Rubinstein, E. (2007). The changing face of Klebsiella pneumoniae infections in the community. Int. J. Antimicrob. Agents 30, 385-389. doi: 10.1016/j.ijantimicag.2007.06.019
12. Kohl, T. A., Diel, R., Harmsen, D., Rothgänger, J., Walter, K. M., Merker, M., et al. (2014). Whole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach. J. Clin. Microbiol. 52, 2479-2486. doi: 10.1128/JCM.00567-14
13. Lee, C. R., Lee, J. H., Park, K. S., Kim, Y. B., Jeong, B. C., and Lee, S. H. (2016). Global dissemination of carbapenemase-producing Klebsiella pneumoniae: epidemiology, genetic context, treatment options, and detection methods. Front. Microbiol. 7:895. doi: 10.3389/fmicb.2016.00895
14. Lee, Y., Kim, B. S., Chun, J., Yong, J. H., Lee, Y. S., Yoo, J. S., et al. (2014). Clonality and Resistome analysis of KPC-producing Klebsiella pneumoniae strain isolated in Korea using whole genome sequencing. Biomed Res. Int. 2014:352862. doi: 10.1155/2014/352862
15. Leopold, S. R., Goering, R. V., Witten, A., Harmsen, D., and Mellmann, A. (2014). Bacterial whole-genome sequencing revisited: portable, scalable, and standardized analysis for typing and detection of virulence and antibiotic resistance genes. J. Clin. Microbiol. 52, 2365-2370. doi: 10.1128/JCM.00262-14
16. Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., et al. (2010). De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265-272. doi: 10.1101/gr.097261.109
17. Maiden, M. C., Bygraves, J. A., Feil, E., Morelli, G., Russell, J. E., Urwin, R., et al. (1998). Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. U.S.A. 95, 3140-3145
18. Maiden, M. C., Jansen van Rensburg, M. J., Bray, J. E., Earle, S. G., Ford, S. A., Jolley, K. A., et al. (2013). MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol. 11, 728-736. doi: 10.1038/nrmicro3093
19. Marsh, J. W., Krauland, M. G., Nelson, J. S., Schlackman, J. L., Brooks, A. M., Pasculle, A. W., et al. (2015). Genomic epidemiology of an endoscope-associated outbreak of Klebsiella pneumoniae carbapenemase(KPC)-producing K. pneumoniae. PLoS ONE 10:e0144310. doi: 10.1371/journal.pone.0144310
20. Mathers, A. J., Stoesser, N., Sheppard, A. E., Pankhurst, L., Giess, A., Yeh, A. J., et al. (2015). Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing. Antimicrob. Agents. Chemother. 59, 1656-1663. doi: 10.1128/AAC.04292-14
21. Moran-Gilad, J., Prior, K., Yakunin, E., Harrison, T. G., Underwood, A., Lazarovitch, T., et al. (2015). Design and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents. Euro. Surveill 20:21186. doi: 10.2807/1560-7917.ES2015.20.28.21186
22. Mshana, S. E., Fritzenwanker, M., Falgenhauer, L., Domann, E., Hain, T., Chakraborty, T., et al. (2015). Molecular epidemiology and characterization of an outbreak causing Klebsiella pneumoniae clone carrying chromosomally located bla(CTX-M-15) at a German University-Hospital. BMC Microbiol. 15:122. doi: 10.1186/s12866-015-0460-2
23. Onori, R., Gaiarsa, S., Comandatore, F., Pongolini, S., Brisse, S., Colombo, A., et al. (2015). Tracking nosocomial Klebsiella pneumoniae infections and outbreaks by whole-genome analysis: small-scale italian scenario within a single hospital. J. Clin. Microbiol. 53, 2861-2868. doi: 10.1128/JCM.00545-15
24. Pitout, J. D., Nordmann, P., and Poirel, L. (2015). Carbapenemase-producing Klebsiella pneumoniae, a key pathogen set for global nosocomial dominance. Antimicrob. Agents Chemother. 59, 5873-5884. doi: 10.1128/AAC.01019-15
25. Podschun, R., and Ullmann, U. (1998). Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin. Microbiol. Rev. 11, 589-603
26. Prokesch, B. C., TeKippe, M., Kim, J., Raj, P., TeKippe, E. M., and Greenberg, D. E. (2016). Primary osteomyelitis caused by hypervirulent Klebsiella pneumoniae. Lancet Infect. Dis. 16:e190-5. doi: 10.1016/S1473-3099(16)30021-4
27. Ruppitsch, W., Pietzka, A., Prior, K., Bletz, S., Fernandez, H. L., Allerberger, F., et al. (2015). Defining and evaluating a core genome multilocus sequence typing scheme for whole-genome sequence-based typing of Listeria monocytogenes. J. Clin. Microbiol. 53, 2869-2876. doi: 10.1128/JCM.01193-15
28. Snitkin, E. S., Zelazny, A. M., Thomas, P. J., Stock, F., NISC Comparative Sequencing Program Group, Henderson, D. K., et al. (2012). Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Transl. Med. 4:148ra116. doi: 10.1126/scitranslmed.3004129
29. Struelens, M. J. (1998). Molecular epidemiologic typing systems of bacterial pathogens: current issues and perspectives. Mem. Inst. Oswaldo. Cruz. 93, 581-585
30. Struve, C., Roe, C. C., Stegger, M., Stahlhut, S. G., Hansen, D. S., Engelthaler, D. M., et al. (2015). Mapping the evolution of hypervirulent Klebsiella pneumoniae. MBio 6:e00630. doi: 10.1128/mBio.00630-15
31. Swaminathan, B., Barrett, T. J., Hunter, S. B., and Tauxe, R. V., and CDC PulseNet Task Force (2001). PulseNet: the molecular subtyping network for foodborne bacterial disease surveillance, United States. Emerg Infect Dis. 7, 382-389. doi: 10.3201/eid0703.010303
32. Tenover, F. C., Arbeit, R. D., Goering, R. V., Mickelsen, P. A., Murray, B. E., Persing, D. H., et al. (1995). Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J. Clin. Microbiol. 33, 2233-2239
33. Zhou, K., Lokate, M., Deurenberg, R. H., Tepper, M., Arends, J. P., Raangs, E. G., et al. (2016). Use of whole-genome sequencing to trace, control and characterize the regional expansion of extended-spectrum β-lactamase producing ST15 Klebsiella pneumoniae. Sci. Rep. 6:20840. doi: 10.1038/srep20840
34. Zhu, J., Sun, L., Ding, B., Yang, Y., Xu, X., Liu, W., et al. (2016). Outbreak of NDM-1-producing Klebsiella pneumoniae ST76 and ST37 isolates in neonates. Eur. J. Clin. Microbiol. Infect. Dis. 35, 611-618. doi: 10.1007/s10096-016-2578-z