Molecular characterization by using next-generation sequencing of plasmids containing blaNDM-7in Enterobacteriaceae from Calgary, Canada

Antimicrobial Agents and Chemotherapy

Volumn 60, Issue 3, 2016, Pages 1258-1263

  Chen, L ^a   Peirano, G ^b   Lynch, T ^b   Chavda, K D ^a   Gregson, D B ^b,c   Church, D L ^b,c   Conly, J ^b,c   Kreiswirth, B N ^a   Pitout, J D ^b,d  

^a PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF CALGARY   (Canada)

^c UNIVERSITY OF CALGARY   (Canada)

^d UNIVERSITY OF PRETORIA   (South Africa)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL TRANSMISSION; CANADA; CASE REPORT; ENTEROBACTER; ENTEROBACTER HORMAECHEI; ENTEROBACTERIACEAE; ESCHERICHIA COLI; HUMAN; KLEBSIELLA PNEUMONIAE; MALE; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SERRATIA MARCESCENS; ALBERTA; DRUG EFFECTS; ENTEROBACTERIACEAE INFECTIONS; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; HOSPITAL; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; PLASMID; PROCEDURES;

BACTERIAL PROTEIN; BETA LACTAMASE; CARBAPENEMASE;

ALBERTA; BACTERIAL PROTEINS; BETA-LACTAMASES; ENTEROBACTERIACEAE; ENTEROBACTERIACEAE INFECTIONS; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HOSPITALS; HUMANS; KLEBSIELLA PNEUMONIAE; MALE; MICROBIAL SENSITIVITY TESTS; PLASMIDS;

EID: 84960154884     PISSN: 00664804     EISSN: 10986596     Source Type: Journal    
DOI: 10.1128/AAC.02661-15     Document Type: Article

References (44)

1. 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.
2. 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.
3. Netikul T, Sidjabat HE, Paterson DL, Kamolvit W, Tantisiriwat W, Steen JA, Kiratisin P. 2014. Characterization of an IncN2-type blaNDM-1-carrying plasmid in Escherichia coli ST131 and Klebsiella pneumoniae ST11 and ST15 isolates in Thailand. J Antimicrob Chemother 69:3161-3163. http://dx.doi.org/10.1093/jac/dku275.
4. Rimrang B, Chanawong A, Lulitanond A, Wilailuckana C, Charoensri N, Sribenjalux P, Phumsrikaew W, Wonglakorn L, Kerdsin A, Chetchotisakd P. 2012. Emergence of NDM-1- and IMP-14a-producing Enterobacteriaceae in Thailand. J Antimicrob Chemother 67:2626-2630. http://dx.doi.org/10.1093/jac/dks267.
5. Nordmann P, Poirel L, Walsh TR, Livermore DM. 2011. The emerging NDM carbapenemases. Trends Microbiol 19:588-595. http://dx.doi.org/10.1016/j.tim.2011.09.005.
6. van der Bij AK, Pitout JD. 2012. The role of international travel in the worldwide spread of multiresistant Enterobacteriaceae. J Antimicrob Chemother 67:2090-2100. http://dx.doi.org/10.1093/jac/dks214.
7. Poirel L, Dortet L, Bernabeu S, Nordmann P. 2011. Genetic features of blaNDM-1-positive Enterobacteriaceae. Antimicrob Agents Chemother 55:5403-5407. http://dx.doi.org/10.1128/AAC.00585-11.
8. Walsh TR, Weeks J, Livermore DM, Toleman MA. 2011. Dissemination of NDM-1 positive bacteria in the New Delhi environment and its implications for human health: an environmental point prevalence study. Lancet Infect Dis 11:355-362. http://dx.doi.org/10.1016/S1473-3099 (11) 70059-7.
9. Nordmann P, Naas T, Poirel L. 2011. Global spread of carbapenemaseproducing Enterobacteriaceae. Emerg Infect Dis 17:1791-1798. http://dx.doi.org/10.3201/eid1710.110655.
10. Nordmann P, Poirel L. 2014. The difficult-to-control spread of carbapenemase producers among Enterobacteriaceae worldwide. Clin Microbiol Infect 20:821-830. http://dx.doi.org/10.1111/1469-0691.12719.
11. Andrade LN, Novais A, Branquinho R, Peixe L. 2015. Species reassignment of Enterobacter cloacae complex isolates by in silico phylogenetic analysis, abstr 2692. FEMS 2015, Maastricht, The Netherlands, 7 to 11 June 2015.
12. Clinical and Laboratory Standards Institute. 2014. Performance standards for antimicrobial susceptibility testing; 22nd informational supplement. CLSI M100-S24. Clinical and Laboratory Standards Institute, Wayne, PA.
13. 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.
14. Boyd DA, Tyler S, Christianson S, McGeer A, Muller MP, Willey BM, Bryce E, Gardam M, Nordmann P, Mulvey MR. 2004. Complete nucleotide sequence of a 92-kilobase plasmid harboring the CTX-M-15 extended-spectrum beta-lactamase involved in an outbreak in long-term-care facilities in Toronto, Canada. Antimicrob Agents Chemother 48:3758-3764. http://dx.doi.org/10.1128/AAC.48.10.3758-3764.2004.
15. Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ. 2005. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63:219-228. http://dx.doi.org/10.1016/j.mimet.2005.03.018.
16. Villa L, Garcia-Fernandez A, Fortini D, Carattoli A. 2010. Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. J Antimicrob Chemother 65:2518-2529. http://dx.doi.org/10.1093/jac/dkq347.
17. Johnson TJ, Bielak EM, Fortini D, Hansen LH, Hasman H, Debroy C, Nolan LK, Carattoli A. 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae. Plasmid 68:43-50. http://dx.doi.org/10.1016/j.plas mid.2012.03.001.
18. 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.
19. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MC, Ochman H, Achtman M. 2006. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 60:1136-1151. http://dx.doi.org/10.1111/j.1365-2958.2006.05172.x.
20. Miyoshi-Akiyama T, Hayakawa K, Ohmagari N, Shimojima M, Kirikae T. 2013. Multilocus sequence typing (MLST) for characterization of Enterobacter cloacae. PLoS One 8:e66358. http://dx.doi.org/10.1371/journal.pone.0066358.
21. Chen L, Hu H, Chavda KD, Zhao S, Liu R, Liang H, Zhang W, Wang X, Jacobs MR, Bonomo RA, Kreiswirth BN. 2014. Complete sequence of a KPC-producing IncN multidrug-resistant plasmid from an epidemic Escherichia coli sequence type 131 strain in China. Antimicrob Agents Chemother 58:2422-2425. http://dx.doi.org/10.1128/AAC.02587-13.
22. 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.
23. Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Moller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895-3903. http://dx.doi.org/10.1128/AAC.02412-14.
24. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O'Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The comprehensive antibiotic resistance database. Antimicrob Agents Chemother 57:3348-3357. http://dx.doi.org/10.1128/AAC.00419-13.
25. Sullivan MJ, Petty NK, Beatson SA. 2011. Easyfig: a genome comparison visualizer. Bioinformatics 27:1009-1010. http://dx.doi.org/10.1093/bioin formatics/btr039.
26. Cuzon G, Bonnin RA, Nordmann P. 2013. First identification of novel NDM carbapenemase, NDM-7, in Escherichia coli in France. PLoS One 8:e61322. http://dx.doi.org/10.1371/journal.pone.0061322.
27. Gottig S, Hamprecht AG, Christ S, Kempf VA, Wichelhaus TA. 2013. Detection of NDM-7 inGermany, anew variantof the New Delhi metallobeta-lactamase with increased carbapenemase activity. J Antimicrob Chemother 68:1737-1740. http://dx.doi.org/10.1093/jac/dkt088.
28. Rahman M, Shukla SK, Prasad KN, Ovejero CM, Pati BK, Tripathi A, Singh A, Srivastava AK, Gonzalez-Zorn B. 2014. Prevalence and molecular characterisation of New Delhi metallo-beta-lactamases NDM-1, NDM-5, NDM-6 and NDM-7 in multidrug-resistant Enterobacteriaceae from India. Int J Antimicrob Agents 44:30-37. http://dx.doi.org/10.1016/j.ijantimicag.2014.03.003.
29. Lee CS, Vasoo S, Hu F, Patel R, Doi Y. 2014. Klebsiella pneumoniae ST147 coproducing NDM-7 carbapenemase and RmtF 16S rRNA methyltransferase in Minnesota. J Clin Microbiol 52:4109-4110. http://dx.doi.org/10.1128/JCM.01404-14.
30. Mizuno Y, Yamaguchi T, Matsumoto T. 2014. A first case of New Delhi metallo-beta-lactamase-7 in an Escherichia coli ST648 isolate in Japan. J Infect Chemother 20:814-816. http://dx.doi.org/10.1016/j.jiac.2014.08.009.
31. Seara N, Oteo J, Carrillo R, Perez-Blanco V, Mingorance J, Gomez-Gil R, Herruzo R, Perez-Vazquez M, Astray J, Garcia-Rodriguez J, Ruiz-Velasco LM, Campos J, de Burgos C, Ruiz-Carrascoso G. 2015. Interhospital spread of NDM-7-producing Klebsiella pneumoniae belonging to ST437 in Spain. IntJ Antimicrob Agents 46:169-173. http://dx.doi.org/10.1016/j.ijantimicag.2015.04.001.
32. Hammerum AM, Littauer P, Hansen F. 2015. Detection of Klebsiella pneumoniaeco-producing NDM-7 and OXA-181, Escherichia coliproducing NDM-5 and Acinetobacter baumannii producing OXA-23 in a single patient. Int J Antimicrob Agents 46:597-598. http://dx.doi.org/10.1016/j.ijantimicag.2015.07.008.
33. Yang Q, Fang L, Fu Y, Du X, Shen Y, Yu Y. 2015. Dissemination of NDM-1-producing Enterobacteriaceae mediated by the IncX3-type plasmid. PLoS One 10:e0129454. http://dx.doi.org/10.1371/journal.pone.0129454.
34. Krishnaraju M, Kamatchi C, Jha AK, Devasena N, Vennila R, Sumathi G, Vaidyanathan R. 2015. Complete sequencing of an IncX3 plasmid carrying blaNDM-5 allele reveals an early stage in the dissemination of the blaNDM gene. Indian J Med Microbiol 33:30-38. http://dx.doi.org/10.4103/0255-0857.148373.
35. Espedido BA, Dimitrijovski B, van Hal SJ, Jensen SO. 2015. The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae. J Clin Pathol 68:835-838. http://dx.doi.org/10.1136/jclinpath-2015-203044.
36. Ho PL, Li Z, Lo WU, Cheung YY, Lin CH, Sham PC, Cheng VC, Ng TK, Que TL, Chow KH. 2012. Identification and characterization of a novel incompatibility group X3 plasmid carrying blaNDM-1 in Enterobacteriaceae isolates with epidemiological links to multiple geographical areas in China. Emerg Microbes Infect 1:e39. http://dx.doi.org/10.1038/emi.2012.37.
37. Wailan AM, Paterson DL, Kennedy K, Ingram PR, Bursle E, Sidjabat HE. 19October2015. Genomic characteristics of NDM-producing Enterobacteriaceae in Australia and their blaNDM genetic contexts. Antimicrob Agents Chemother http://dx.doi.org/10.1128/AAC.01243-15.
38. Ho PL, Cheung YY, Lo WU, Li Z, Chow KH, Lin CH, Chan JF, Cheng VC. 2013. Molecular characterization of an atypical IncX3 plasmid pKPC-NY79 carrying blaKPC-2 in a Klebsiella pneumoniae. Curr Microbiol 67:493-498. http://dx.doi.org/10.1007/s00284-013-0398-2.
39. Zurfluh K, Poirel L, Nordmann P, Klumpp J, Stephan R. 2015. First detection of Klebsiella variicola producing OXA-181 carbapenemase in fresh vegetable imported from Asia to Switzerland. Antimicrob Resist Infect Control 4:38. http://dx.doi.org/10.1186/s13756-015-0080-5.
40. Liu Y, Feng Y, Wu W, Xie Y, Wang X, Zhang X, Chen X, Zong Z. 2015. First report of OXA-181-producing Escherichia coli in China and characterization of the isolate using whole-genome sequencing. Antimicrob Agents Chemother 59:5022-5025. http://dx.doi.org/10.1128/AAC.00442-15.
41. Norman A, Hansen LH, She Q, Sorensen SJ. 2008. Nucleotide sequence of pOLA52: a conjugative IncX1 plasmid from Escherichia coli which enables biofilm formation and multidrug efflux. Plasmid 60:59-74. http://dx.doi.org/10.1016/j.plasmid.2008.03.003.
42. Avila P, Nunez B, de la Cruz F. 1996. Plasmid R6K contains two functional oriTs which can assemble simultaneously in relaxosomes in vivo. J Mol Biol 261:135-143. http://dx.doi.org/10.1006/jmbi.1996.0447.
43. Nunez B, Avila P, de la Cruz F. 1997. Genes involved in conjugative DNA processing of plasmid R6K. Mol Microbiol 24:1157-1168. http://dx.doi.org/10.1046/j.1365-2958.1997.4111778.x.
44. Feng J, Qiu Y, Yin Z, Chen W, Yang H, Yang W, Wang J, Gao Y, Zhou D. 2015. Coexistence of a novel KPC-2-encoding MDR plasmid and an NDM-1-encoding pNDM-HN380-like plasmid in a clinical isolate of Citrobacter freundii. J Antimicrob Chemother 70:2987-2991. http://dx.doi.org/10.1093/jac/dkv232.