MLST-based inference of genetic diversity and population structure of clinical Klebsiella pneumoniae, China

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Guo, Chenyi ^a   Yang, Xianwei ^b   Wu, Yarong ^b   Yang, Huiying ^b   Han, Yanping ^b   Yang, Ruifu ^b   Hu, Liangping ^a   Cui, Yujun ^b   Zhou, Dongsheng ^b  

^a Beijing Consulting Centre of Biomedical Statistics   (China)

^b BEIJING INSTITUTE OF MICROBIOLOGY AND EPIDEMIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CYTOCHROME P450; ISOMERASE; PROSTACYCLIN SYNTHASE; STOP CODON;

ALLELE; BACTERIAL GENE; CHINA; CLASSIFICATION; GENE LOCUS; GENETIC LINKAGE; GENETIC VARIABILITY; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; KLEBSIELLA PNEUMONIAE; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; STOP CODON;

ALLELES; BACTERIAL PROTEINS; CHINA; CODON, NONSENSE; CYTOCHROME P-450 ENZYME SYSTEM; GENES, BACTERIAL; GENETIC LINKAGE; GENETIC LOCI; GENETIC VARIATION; GENOTYPE; INTRAMOLECULAR OXIDOREDUCTASES; KLEBSIELLA PNEUMONIAE; MULTILOCUS SEQUENCE TYPING; PHYLOGENY;

EID: 84940831657     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep07612     Document Type: Article

References (40)

1. Podschun, R., Ullmann, U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin. Microbiol. Rev. 11, 589-603 (1998).
2. Paterson, D. L. et al. International prospective study of Klebsiella pneumoniae bacteremia: implications of extended-spectrum beta-lactamase production in nosocomial Infections. Ann. Intern. Med. 140, 26-32 (2004).
3. Keynan, Y., Rubinstein, E. The changing face of Klebsiella pneumoniae infections in the community. Int. J. Antimicrob. Agents 30, 385-389 (2007).
4. Siu, L. K., Yeh, K.M., Lin, J. C., Fung, C. P., Chang, F. Y. Klebsiella pneumoniae liver abscess: a new invasive syndrome. Lancet Infect. Dis. 12, 881-887 (2012).
5. Shon, A. S., Russo, T. A. Hypervirulent Klebsiella pneumoniae: the next superbug Future Microbiol. 7, 669-671 (2012).
6. Shon, A. S., Bajwa, R. P., Russo, T. A. Hypervirulent (hypermucoviscous) Klebsiella pneumoniae: a new and dangerous breed. Virulence 4, 107-118, DOI: 10.4161/viru.22718 (2013).
7. Turton, J. F., Perry, C., Elgohari, S., Hampton, C. V. PCR characterization and typing of Klebsiella pneumoniae using capsular type-specific, variable number tandem repeat and virulence gene targets. J. Med. Microbiol. 59, 541-547 (2010).
8. Diancourt, L., Passet, V., Verhoef, J., Grimont, P. A., Brisse, S. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43, 4178-4182 (2005).
9. Wang, Q. et al. Genotypic Analysis of Klebsiella pneumoniae Isolates in a Beijing Hospital Reveals High Genetic Diversity and Clonal Population Structure of Drug-Resistant Isolates. PLoS One 8, e57091, DOI:10.1371/journal.pone.0057091 (2013).
10. Brisse, S. et al. 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 (2009).
11. Harada, S. et al. Familial spread of a virulent clone of Klebsiella pneumoniae causing primary liver abscess. J. Clin. Microbiol. 49, 2354-2356 (2011).
12. Siu, L. K. et al. Molecular typing and virulence analysis of serotype K1 Klebsiella pneumoniae strains isolated from liver abscess patients and stool samples from noninfectious subjects in Hong Kong, Singapore, and Taiwan. J. Clin. Microbiol. 49, 3761-3765 (2011).
13. Lin, J. C. et al.Genotypes and virulence in serotype K2 Klebsiella pneumoniae from liver abscess and non-infectious carriers in Hong Kong, Singapore and Taiwan. Gut. Pathog. 6, 21, DOI:10.1186/1757-4749-6-21 (2014).
14. Luo, Y.,Wang, Y., Ye, L., Yang, J. Molecular epidemiology and virulence factors of pyogenic liver abscess causing Klebsiella pneumoniae in China. Clin.Microbiol. Infect., DOI:10.1111/1469-0691.12664 (2014).
15. Chen, L., Mathema, B., Pitout, J. D., DeLeo, F. R., Kreiswirth, B. N. Epidemic Klebsiella pneumoniae ST258 is a hybrid strain. MBio 5, e01355-14, DOI: 10.1128/mBio.01355-14 (2014).
16. Chen, Z. et al. A novel PCR-based genotyping scheme for clinical Klebsiella pneumoniae. Future Microbiol. 9, 21-32 (2014).
17. Feil, E. J., Li, B. C., Aanensen, D. M., Hanage, W. P., Spratt, B. G. eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol. 186, 1518-1530 (2004).
18. Matic, I., Radman, M., Rayssiguier, C. Structure of recombinants from conjugational crosses between Escherichia coli donor and mismatch-repair deficient Salmonella typhimurium recipients. Genetics 136, 17-26 (1994).
19. Charusanti, P. et al. Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene. PLoS Genet. 6, e1001186, DOI:10.1371/journal.pgen.1001186 (2010).
20. Spratt, B. G., Hanage, W. P., Feil, E. J. The relative contributions of recombination and point mutation to the diversification of bacterial clones. Curr. Opin. Microbiol. 4, 602-606 (2001).
21. Salerno, A. et al. Recombining population structure of Plesiomonas shigelloides (Enterobacteriaceae) revealed by multilocus sequence typing. J. Bacteriol. 189, 7808-7818 (2007).
22. Yu,W. L. et al.Association between rmpA and magA genes and clinical syndromes caused by Klebsiella pneumoniae in Taiwan. Clin. Infect. Dis. 42, 1351-1358 (2006).
23. Hsu, C. R., Lin, T. L., Chen, Y. C., Chou, H. C.,Wang, J. T. The role of Klebsiella pneumoniae rmpA in capsular polysaccharide synthesis and virulence revisited. Microbiology, 157, 3446-3457 (2011).
24. Wu, K. M. et al. Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis. J. Bacteriol. 191, 4492-4501 (2009).
25. Xiao, X. et al. Two methods for extraction of high-purity genomic DNA from mucoid Gram-negative bacteria. Afric. J. Microbiol. Res. 5, 4013-4018 (2011).
26. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
27. Librado, P., Rozas, J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25, 1451-1452 (2009).
28. Wang, D., Zhang, Y., Zhang, Z., Zhu, J., Yu, J. KaKs-Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics, Proteomics & Bioinformatics 8, 77-80 (2010).
29. Saitou, N., Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987).
30. Pritchard, J. K., Stephens, M., Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000).
31. Falush, D., Stephens, M., Pritchard, J. K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567-1587 (2003).
32. Falush, D., Stephens, M., Pritchard, J. K. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol. Ecol. Notes 7, 574-578 (2007).
33. Hubisz, M. J., Falush, D., Stephens, M.& Pritchard, J. K. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour. 9, 1322-1332 (2009).
34. Bryant, D., Moulton, V. Neighbor-Net: an agglomerative method for the construction of phylogenetic networks. in Algorithms in Bioinformatics, 375-391 (Springer, 2002).
35. Bruen, T. C., Philippe, H., Bryant, D. A simple and robust statistical test for detecting the presence of recombination. Genetics 172, 2665-2681 (2006).
36. Francisco, A. P. et al. PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics 13, 87 (2012).
37. Haubold, B., Hudson, R. R. LIAN 3.0: detecting linkage disequilibrium in multilocus data. Linkage Analysis. Bioinformatics 16, 847-848 (2000).
38. McVean,G. A. et al. The fine-scale structure of recombination rate variation in the human genome. Science 304, 581-584 (2004).
39. Auton, A., McVean, G. Recombination rate estimation in the presence of hotspots. Genome Res. 17, 1219-1227 (2007).
40. Martin, D. P. et al. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26, 2462-2463 (2010).