Genome sequencing of an extended series of NDM-producing Klebsiella pneumoniae isolates from neonatal infections in a Nepali hospital characterizes the extent of community- Versus hospital- associated transmission in an endemic setting

Antimicrobial Agents and Chemotherapy

Volumn 58, Issue 12, 2014, Pages 7347-7357

  Stoesser, N ^a   Giess, A ^a   Batty, E M ^b   Sheppard, A E ^a   Walker, A S ^c   Wilson, D J ^a,b   Didelot, X ^d   Bashir, A ^e   Sebra, R ^e   Kasarskis, A ^e   Sthapit, B ^f   Shakya, M ^f   Kelly, D ^c,g   Pollard, A J ^c,g   Peto, T E A ^a   Crook, D W ^a   Donnelly, P ^b   Thorson, S ^f   Amatya, P ^f   Joshi, S ^f  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d IMPERIAL COLLEGE LONDON   (United Kingdom)

^e MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^f PATAN HOSPITAL   (Nepal)

^g UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARSENIC; COPPER; IRON; KANAMYCIN; MERCURY; NEOMYCIN; SILVER; STREPTOMYCIN; ANTIINFECTIVE AGENT; BETA LACTAMASE;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL MUTATION; BACTERIUM ISOLATE; BLOOD CULTURE; BLOODSTREAM INFECTION; CEREBROSPINAL FLUID; COMMUNITY ACQUIRED INFECTION; DISEASE TRANSMISSION; ENTEROBACTER CLOACAE; ESCHERICHIA COLI; GENETIC PROCEDURES; HOSPITAL BUILDING; HOSPITAL INFECTION; HUMAN; INFECTION CONTROL; KLEBSIELLA OXYTOCA; KLEBSIELLA PNEUMONIAE; KLEBSIELLA PNEUMONIAE INFECTION; MAJOR CLINICAL STUDY; MORTALITY; MULTIDRUG RESISTANCE; NEPAL; NEWBORN; NEWBORN INFECTION; NONHUMAN; PHYLOGENETIC TREE; PLASMID; WHOLE GENOME SEQUENCING; BACTERIAL CHROMOSOME; BACTERIAL GENOME; CHEMISTRY; CHROMOSOME MAP; COMMUNITY-ACQUIRED INFECTIONS; CROSS INFECTION; DRUG EFFECTS; ENDEMIC DISEASE; ENZYMOLOGY; GENE EXPRESSION; GENETICS; HIGH THROUGHPUT SEQUENCING; HOSPITAL; INFANT; ISOLATION AND PURIFICATION; KLEBSIELLA INFECTIONS; METABOLISM; MICROBIOLOGY; NEWBORN INTENSIVE CARE;

ANTI-BACTERIAL AGENTS; BETA-LACTAMASES; CHROMOSOME MAPPING; CHROMOSOMES, BACTERIAL; COMMUNITY-ACQUIRED INFECTIONS; CROSS INFECTION; DRUG RESISTANCE, BACTERIAL; ENDEMIC DISEASES; GENE EXPRESSION; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOSPITALS; HUMANS; INFANT; INFANT, NEWBORN; INTENSIVE CARE UNITS, NEONATAL; KLEBSIELLA INFECTIONS; KLEBSIELLA PNEUMONIAE; NEPAL; PLASMIDS;

EID: 84912084358     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.03900-14     Document Type: Article

References (40)

1. Downie L, Armiento R, Subhi R, Kelly J, Clifford V, Duke T. 2013. Community-acquired neonatal and infant sepsis in developing countries: efficacy of WHO's currently recommended antibiotics-systematic review and meta-analysis. Arch. Dis. Child. 98:146-154. http://dx.doi.org /10.1136/archdischild-2012-302033.
2. Giske CG, Monnet DL, Cars O, Carmeli Y, ReAct-Action on Antibiotic Resistance. 2008. Clinical and economic impact of common multidrugresistant gram-negative bacilli. Antimicrob. Agents Chemother. 52:813-821. http://dx.doi.org/10.1128/AAC.01169-07.
3. Gupta N, Limbago BM, Patel JB, Kallen AJ. 2011. Carbapenem-resistant Enterobacteriaceae: epidemiology and prevention. Clin. Infect. Dis. 53: 60-67. http://dx.doi.org/10.1093/cid/cir202.
4. Munoz-Price LS, Quinn JP. 2013. Deconstructing the infection control bundles for the containment of carbapenem-resistant Enterobacteriaceae. Curr. Opin. Infect. Dis. 26:378-387. http://dx.doi.org/10.1097/01.qco .0000431853.71500.77.
5. Tofteland S, Naseer U, Lislevand JH, Sundsfjord A, Samuelsen O. 2013. A long-term low-frequency hospital outbreak of KPC-producing Klebsiella pneumoniae involving intergenus plasmid diffusion and a persisting environmental reservoir. PLoS One 8:e59015. http://dx.doi.org/10.1371 /journal.pone.0059015.
6. Jean SS, Hsueh PR. 2011. High burden of antimicrobial resistance in Asia. Int. J. Antimicrob. Agents 37:291-295. http://dx.doi.org/10.1016/j .ijantimicag.2011.01.009.
7. Pfeifer Y, Cullik A, Witte W. 2010. Resistance to cephalosporins and carbapenems in Gram-negative bacterial pathogens. Int. J. Med. Microbiol. 300:371-379. http://dx.doi.org/10.1016/j.ijmm.2010.04.005.
8. Yigit H, Queenan AM, Anderson GJ, Domenech-Sanchez A, Biddle JW, Steward CD, Alberti S, Bush K, Tenover FC. 2001. Novel carbapenemhydrolyzing beta-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob. Agents Chemother. 45: 1151-1161. http://dx.doi.org/10.1128/AAC.45.4.1151-1161.2001.
9. Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR. 2009. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob. Agents Chemother. 53:5046-5054. http://dx.doi.org/10 .1128/AAC.00774-09.
10. Johnson AP, Woodford N. 2013. Global spread of antibiotic resistance: the example of New Delhi metallo-beta-lactamase (NDM)-mediated carbapenem resistance. J. Med. Microbiol. 62:499-513. http://dx.doi.org/10 .1099/jmm.0.052555-0.
11. Woodford N, Wareham DW, Guerra B, Teale C. 2014. Carbapenemaseproducing Enterobacteriaceae and non-Enterobacteriaceae from animals and the environment: an emerging public health risk of our own making? J. Antimicrob. Chemother. 69:287-291. http://dx.doi.org/10.1093/jac /dkt392.
12. Doyle D, Peirano G, Lascols C, Lloyd T, Church DL, Pitout JD. 2012. Laboratory detection of Enterobacteriaceae that produce carbapenemases. J. Clin. Microbiol. 50:3877-3880. http://dx.doi.org/10.1128/JCM .02117-12.
13. Didelot X, Bowden R, Wilson DJ, Peto TE, Crook DW. 2012. Transforming clinical microbiology with bacterial genome sequencing. Nat. Rev. Genet. 13:601-612. http://dx.doi.org/10.1038/nrg3226.
14. Eyre DW, Cule ML, Wilson DJ, Griffiths D, Vaughan A, O'Connor L, Ip CL, Golubchik T, Batty EM, Finney JM, Wyllie DH, Didelot X, Piazza P, Bowden R, Dingle KE, Harding RM, Crook DW, Wilcox MH, Peto TE, Walker AS. 2013. Diverse sources of C. difficile infection identified on whole-genome sequencing. N. Engl. J. Med. 369:1195-1205. http: //dx.doi.org/10.1056/NEJMoa1216064.
15. Walker TM, Ip CL, Harrell RH, Evans JT, Kapatai G, Dedicoat MJ, Eyre DW, Wilson DJ, Hawkey PM, Crook DW, Parkhill J, Harris D, Walker AS, Bowden R, Monk P, Smith EG, Peto TE. 2013. Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect. Dis. 13:137-146. http://dx.doi .org/10.1016/S1473-3099(12)70277-3.
16. Epson EE, Pisney LM, Wendt JM, MacCannell DR, Janelle SJ, Kitchel B, Rasheed JK, Limbago BM, Gould CV, Kallen AJ, Barron MA, Bamberg WM. 2014. Carbapenem-resistant Klebsiella pneumoniae producing New Delhi metallo-beta-lactamase at an acute care hospital, Colorado, 2012. Infect. Control Hosp. Epidemiol. 35:390-397. http://dx.doi .org/10.1086/675607.
17. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, NISC Comparative Sequencing Program Group, Henderson DK, Palmore TN, Segre JA. 2012. Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci. Transl. Med. 4(148): 148ra116. http://dx.doi.org/10.1126/scitranslmed.3004129.
18. st informational supplement, vol 31, no 1. M100-S21. National Committee for Clinical Laboratory Standards, Wayne, PA.
19. Wood DE, Salzberg SL. 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15:R46. http://dx.doi .org/10.1186/gb-2014-15-3-r46.
20. Gladman S, Seemann T. 2008. VelvetOptimiser, v2.1.7. Victorian Bioinformatics Consortium, Monash University, Clayton, Australia.
21. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829. http://dx.doi .org/10.1101/gr.074492.107.
22. Stoesser N, Batty EM, Eyre DW, Morgan M, Wyllie DH, Del Ojo Elias C, Johnson JR, Walker AS, Peto TE, Crook DW. 2013. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J. Antimicrob. Chemother. 68:2234-2244. http://dx.doi.org/10.1093/jac/dkt180.
23. Diancourt L, Passet V, Verhoef J, Grimont PA, Brisse S. 2005. Multilocus sequence typing of Klebsiella pneumoniae nosocomial isolates. J. Clin. Microbiol. 43:4178-4182. http://dx.doi.org/10.1128/JCM.43.8 .4178-4182.2005.
24. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59:307-321. http://dx.doi.org/10.1093/sysbio/syq010.
25. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10:563-569. http://dx.doi.org/10 .1038/nmeth.2474.
26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410. http://dx.doi.org/10 .1016/S0022-2836(05)80360-2.
27. Delcher AL, Phillippy A, Carlton J, Salzberg SL. 2002. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30:2478-2483. http://dx.doi.org/10.1093/nar/30.11.2478.
28. Li H, Durbin R. 2009. Fast and accurate short read alignment with Bur-rows-Wheeler transform. Bioinformatics 25:1754-1760. http://dx.doi .org/10.1093/bioinformatics/btp324.
29. SeemannT. 2014. Prokka: rapid prokaryoticgenomeannotation. Bioinformatics 30:2068-2069. http://dx.doi.org/10.1093/bioinformatics/btu153.
30. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214. http://dx.doi.org/10.1186 /1471-2148-7-214.
31. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N. 2014. Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data. PLoS Comput. Biol. 10:e1003457. http://dx .doi.org/10.1371/journal.pcbi.1003457.
32. Gordon NC, Price JR, Cole K, Everitt R, Morgan M, Finney J, Kearns AM, Pichon B, Young B, Wilson DJ, Llewelyn MJ, Paul J, Peto TE, Crook DW, Walker AS, Golubchik T. 2014. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J. Clin. Microbiol. 52:1182-1191. http://dx.doi.org/10.1128/JCM.03117-13.
33. Iqbal Z, Turner I, McVean G. 2013. High-throughput microbial population genomics using the Cortex variation assembler. Bioinformatics 29: 275-276. http://dx.doi.org/10.1093/bioinformatics/bts673.
34. Peirano G, Ahmed-Bentley J, Fuller J, Rubin JE, Pitout JD. 2014. Travel-related carbapenemase-producing Gram-negative bacteria in Alberta, Canada: the first 3 years. J. Clin. Microbiol. 52:1575-1581. http://dx .doi.org/10.1128/JCM.00162-14.
35. Quinones D, Valverde A, Rodriguez-Banos M, Kobayashi N, Zayaz A, Abreu M, Canton R, del Campo R. 2014. High clonal diversity in a non-outbreak situation of clinical ESBL-producing Klebsiella pneumoniae isolates in the first national surveillance program in Cuba. Microb. Drug Resist. 20:45-51. http://dx.doi.org/10.1089/mdr.2013.0021.
36. Toth A, Kocsis B, Damjanova I, Kristof K, Janvari L, Paszti J, Csercsik R, Topf J, Szabo D, Hamar P, Nagy K, Fuzi M. 2014. Fitness cost associated with resistance to fluoroquinolones is diverse across clones of Klebsiella pneumoniae and may select for CTX-M-15 type extendedspectrum beta-lactamase. Eur. J. Clin. Microbiol. Infect. Dis. 33:837-843. http://dx.doi.org/10.1007/s10096-013-2022-6.
37. Villa L, Poirel L, Nordmann P, Carta C, Carattoli A. 2012. Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaCTX-M-15 and qnrB1 genes. J. Antimicrob. Chemother. 67:1645-1650. http://dx.doi .org/10.1093/jac/dks114.
38. Huang TW, Chen TL, Chen YT, Lauderdale TL, Liao TL, Lee YT, Chen CP, Liu YM, Lin AC, Chang YH, Wu KM, Kirby R, Lai JF, Tan MC, Siu LK, Chang CM, Fung CP, Tsai SF. 2013. Copy number change of the NDM-1 sequence in a multidrug-resistant Klebsiella pneumoniae clinical isolate. PLoS One 8:e62774. http://dx.doi.org/10.1371/journal.pone .0062774.
39. Reeves PR, Liu B, Zhou Z, Li D, Guo D, Ren Y, Clabots C, Lan R, Johnson JR, Wang L. 2011. Rates of mutation and host transmission for an Escherichia coli clone over 3 years. PLoS One 6:e26907. http://dx.doi .org/10.1371/journal.pone.0026907.
40. Maiden MC, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. 2013. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol. 11:728-736. http://dx .doi.org/10.1038/nrmicro3093.