Tracking a hospital outbreak of KPC-producing ST11 Klebsiella pneumoniae with whole genome sequencing

Clinical Microbiology and Infection

Volumn 21, Issue 11, 2015, Pages 1001-1007

  Jiang, Y ^a   Wei, Z ^b   Wang, Y ^a   Hua, X ^a   Feng, Y ^a,c   Yu, Y ^a,b  

^a ZHEJIANG UNIVERSITY   (China)

^b ZHEJIANG UNIVERSITY   (China)

^c ZHEJIANG UNIVERSITY   (China)

Author keywords

Carbapenem resistance; Outbreak; Plasmid; SNP; Whole genome sequencing

Indexed keywords

ANTIBIOTIC AGENT; ANTIINFECTIVE AGENT; BETA LACTAMASE;

ADULT; AGED; ANTIBIOTIC SENSITIVITY; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATION; CHOLECYSTITIS; CLINICAL ARTICLE; DIGESTION; FEMALE; GENE SEQUENCE; HOSPITAL SUBDIVISIONS AND COMPONENTS; HUMAN; KLEBSIELLA PNEUMONIAE; LUNG INFECTION; MALE; MIDDLE AGED; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR TYPING; MULTIDRUG RESISTANCE; NONHUMAN; PHYLOGENY; PLASMID; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; SINGLE NUCLEOTIDE POLYMORPHISM; VERY ELDERLY; CLASSIFICATION; CROSS INFECTION; DNA SEQUENCE; ENZYMOLOGY; EPIDEMIC; GENETIC VARIATION; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; KLEBSIELLA INFECTIONS; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MOLECULAR EPIDEMIOLOGY; PROCEDURES; SECRETION (PROCESS);

AGED; AGED, 80 AND OVER; ANTI-BACTERIAL AGENTS; BETA-LACTAMASES; CROSS INFECTION; DISEASE OUTBREAKS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ELECTROPHORESIS, GEL, PULSED-FIELD; FEMALE; GENETIC VARIATION; GENOME, BACTERIAL; GENOTYPE; HUMANS; KLEBSIELLA INFECTIONS; KLEBSIELLA PNEUMONIAE; MALE; MICROBIAL SENSITIVITY TESTS; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR TYPING; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84945495879     PISSN: 1198743X     EISSN: 14690691     Source Type: Journal    
DOI: 10.1016/j.cmi.2015.07.001     Document Type: Article

References (20)

1. Munoz-Price L.S., Poirel L., Bonomo R.A., Schwaber M.J., Daikos G.L., Cormican M., et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect Dis 2013, 13:785-796.
2. Qi Y., Wei Z., Ji S., Du X., Shen P., Yu Y. St11, the dominant clone of KPC-producing Klebsiella pneumoniae in China. J Antimicrob Chemother 2011, 66:307-312.
3. Parkhill J., Wren B.W. Bacterial epidemiology and biology-lessons from genome sequencing. Genome Biol 2011, 12:230.
4. Pallen M.J., Loman N.J. Are diagnostic and public health bacteriology ready to become branches of genomic medicine?. Genome Med 2011, 3:53.
5. Harris S.R., Feil E.J., Holden M.T., Quail M.A., Nickerson E.K., Chantratita N., et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327:469-474.
6. Mutreja A., Kim D.W., Thomson N.R., Connor T.R., Lee J.H., Kariuki S., et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 2011, 477:462-465.
7. Chin C.S., Sorenson J., Harris J.B., Robins W.P., Charles R.C., Jean-Charles R.R., et al. The origin of the Haitian cholera outbreak strain. N Engl J Med 2011, 364:33-42.
8. Beres S.B., Carroll R.K., Shea P.R., Sitkiewicz I., Martinez-Gutierrez J.C., Low D.E., et al. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics. Proc Natl Acad Sci USA 2010, 107:4371-4376.
9. Gardy J.L., Johnston J.C., Ho Sui S.J., Cook V.J., Shah L., Brodkin E., et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N Engl J Med 2011, 364:730-739.
10. Lienau E.K., Strain E., Wang C., Zheng J., Ottesen A.R., Keys C.E., et al. Identification of a salmonellosis outbreak by means of molecular sequencing. N Engl J Med 2011, 364:981-982.
11. Rasko D.A., Webster D.R., Sahl J.W., Bashir A., Boisen N., Scheutz F., et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011, 365:709-717.
12. Rasko D.A., Worsham P.L., Abshire T.G., Stanley S.T., Bannan J.D., Wilson M.R., et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc Natl Acad Sci USA 2011, 108:5027-5032.
13. Clinical and Laboratory Standards Institute Performance standards for antimicrobial susceptibility testing; 23rd informational supplement 2013, CLSI, Wayne, PA.
14. EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 3.1 2013, European Committee on Antimicrobial Susceptibility Testing.
15. Hunter S.B., Vauterin P., Lambert-Fair M.A., Van Duyne M.S., Kubota K., Graves L., et al. Establishment of a universal size standard strain for use with the Pulsenet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard. J Clin Microbiol 2005, 43:1045-1050.
16. Larsen M.V., Cosentino S., Rasmussen S., Friis C., Hasman H., Marvig R.L., et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 2012, 50:1355-1361.
17. Zankari E., Hasman H., Cosentino S., Vestergaard M., Rasmussen S., Lund O., et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012, 67:2640-2644.
18. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. Mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
19. Tenover F.C., Arbeit R.D., Goering R.V., Mickelsen P.A., Murray B.E., Persing D.H., et al. Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 1995, 33:2233-2239.
20. Snitkin E.S., Zelazny A.M., Thomas P.J., Stock F., Group N.C.S.P., Henderson D.K., et al. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 2012, 4:148ra16.