1887

Abstract

Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in and isolates associated with transposon Tn commonly located in plasmids. has become an important multidrug-resistant nosocomial pathogen. KPC-producing has been reported to date only in Puerto Rico. The objective of this study was to determine the whole genomic sequence of a KPC-producing in order to (i) define its allelic diversity, (ii) identify the location and genetic environment of the and (iii) detect additional mechanisms of antimicrobial resistance. Next-generation sequencing, Southern blot, PFGE, multilocus sequence typing and bioinformatics analysis were performed. The organism was assigned to the international ST2 clone. The was identified on a novel truncated version of Tn (tentatively named Tn), located in the chromosome within an IncA/C plasmid fragment derived from an , probably owing to insertion sequence IS. A chromosomally located truncated Tn transposon harbouring a was found in a novel genetic environment within an antimicrobial resistance cluster. Additional resistance mechanisms included efflux pumps, non-β-lactam antibiotic inactivating enzymes within and outside a resistance island, two class 1 integrons, In and the novel In, as well as mutations in the topoisomerase and DNA gyrase genes which confer resistance to quinolones. The presence of the in an already globally disseminated ST2 presents a serious threat of further dissemination.

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2016-08-01
2021-08-01
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References

  1. Ardebili A., Lari A. R., Talebi M. 2014; Correlation of ciprofloxacin resistance with the AdeABC efflux system in Acinetobacter baumannii clinical isolates. Ann Lab Med 34:433–438 [View Article][PubMed]
    [Google Scholar]
  2. Bakour S., Alsharapy S. A., Touati A., Rolain J. M. 2014; Characterization of Acinetobacter baumannii clinical isolates carrying bla(OXA-23) carbapenemase and 16S rRNA methylase armA genes in Yemen. Microb Drug Resist 20:604–609 [View Article][PubMed]
    [Google Scholar]
  3. Barrios H., Garza-Ramos U., Ochoa-Sanchez L. E., Reyna-Flores F., Rojas-Moreno T., Morfin-Otero R., Rodriguez-Noriega E., Garza-Gonzalez E., Gonzalez G. et al. 2012; A plasmid-encoded class 1 integron contains GES-type extended-spectrum β-lactamases in Enterobacteriaceae clinical isolates in Mexico. Antimicrob Agents Chemother 56:4032–4034 [View Article][PubMed]
    [Google Scholar]
  4. Barton B. M., Harding G. P., Zuccarelli A. J. 1995; A general method for detecting and sizing large plasmids. Anal Biochem 226:235–240 [View Article][PubMed]
    [Google Scholar]
  5. Bertini A., Poirel L., Mugnier P. D., Villa L., Nordmann P., Carattoli A. 2010; Characterization and PCR-based replicon typing of resistance plasmids in Acinetobacter baumannii. Antimicrob Agents Chemother 54:4168–4177 [View Article][PubMed]
    [Google Scholar]
  6. Carattoli A., Bertini A., Villa L., Falbo V., Hopkins K. L., Threlfall E. J. 2005; Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63:219–228 [View Article][PubMed]
    [Google Scholar]
  7. Chen L., Chavda K. D., Fraimow H. S., Mediavilla J. R., Melano R. G., Jacobs M. R., Bonomo R. A., Kreiswirth B. N. 2013; Complete nucleotide sequences of blaKPC-4-and blaKPC-5-harboring IncN and IncX plasmids from Klebsiella pneumoniae strains isolated in New Jersey. Antimicrob Agents Chemother 57:269–276 [View Article][PubMed]
    [Google Scholar]
  8. Chen L., Chavda K. D., DeLeo F. R., Bryant K. A., Jacobs M. R., Bonomo R. A., Kreiswirth B. N. 2015; Genome sequence of a Klebsiella pneumoniae sequence type 258 isolate with prophage-encoded K. pneumoniae carbapenemase. Genome Announc 3:e00659-15 [View Article][PubMed]
    [Google Scholar]
  9. Chmelnitsky I., Shklyar M., Leavitt A., Sadovsky E., Navon-Venezia S., Ben Dalak M., Edgar R., Carmeli Y. 2014; Mix and match of KPC-2 encoding plasmids in Enterobacteriaceae-comparative genomics. Diagn Microbiol Infect Dis 79:255–260 [View Article][PubMed]
    [Google Scholar]
  10. Cuzon G., Naas T., Villegas M. V., Correa A., Quinn J. P., Nordmann P. 2011; Wide dissemination of Pseudomonas aeruginosa producing beta-lactamase blaKPC-2 gene in Colombia. Antimicrob Agents Chemother 55:5350–5353 [View Article][PubMed]
    [Google Scholar]
  11. Darling A. C., Mau B., Blattner F. R., Perna N. T. 2004; Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14:1394–1403 [View Article][PubMed]
    [Google Scholar]
  12. Doublet B., Boyd D., Douard G., Praud K., Cloeckaert A., Mulvey M. R. 2012; Complete nucleotide sequence of the multidrug resistance IncA/C plasmid pR55 from Klebsiella pneumoniae isolated in 1969. J Antimicrob Chemother 67:2354–2360 [View Article][PubMed]
    [Google Scholar]
  13. Durmaz R., Otlu B., Koksal F., Hosoglu S., Ozturk R., Ersoy Y., Aktas E., Gursoy N. C., Caliskan A. 2009; The optimization of a rapid pulsed-field gel electrophoresis protocol for the typing of Acinetobacter baumannii, Escherichia coli and Klebsiella spp. Jpn J Infect Dis 62:372–377[PubMed]
    [Google Scholar]
  14. Fricke W. F., Welch T. J., McDermott P. F., Mammel M. K., LeClerc J. E., White D. G., Cebula T. A., Ravel J. 2009; Comparative genomics of the IncA/C multidrug resistance plasmid family. J Bacteriol 191:4750–4757 [View Article][PubMed]
    [Google Scholar]
  15. Getchell-White S. I., Donowitz L. G., Gröschel D. H. 1989; The inanimate environment of an intensive care unit as a potential source of nosocomial bacteria: evidence for long survival of Acinetobacter calcoaceticus. Infect Control Hosp Epidemiol 10:402–407 [View Article][PubMed]
    [Google Scholar]
  16. Giannouli M., Cuccurullo S., Crivaro V., Di Popolo A., Bernardo M., Tomasone F., Amato G., Brisse S., Triassi M. et al. 2010; Molecular epidemiology of multidrug-resistant Acinetobacter baumannii in a tertiary care hospital in Naples, Italy, shows the emergence of a novel epidemic clone. J Clin Microbiol 48:1223–1230 [View Article][PubMed]
    [Google Scholar]
  17. Goering R. V. 2010; Pulsed field gel electrophoresis: a review of application and interpretation in the molecular epidemiology of infectious disease. Infect Genet Evol 10:866–875 [View Article][PubMed]
    [Google Scholar]
  18. He S., Hickman A. B., Varani A. M., Siguier P., Chandler M., Dekker J. P., Dyda F. 2015; Insertion sequence IS 26 reorganizes plasmids in clinically isolated multidrug-resistant bacteria by replicative transposition. MBio 6:1–14 [View Article]
    [Google Scholar]
  19. Héritier C., Poirel L., Nordmann P. 2006; Cephalosporinase over-expression resulting from insertion of ISAba1 in Acinetobacter baumannii. Clin Microbiol Infect 12:123–130 [View Article][PubMed]
    [Google Scholar]
  20. Hornsey M., Loman N., Wareham D. W., Ellington M. J., Pallen M. J., Turton J. F., Underwood A., Gaulton T., Thomas C. P. et al. 2011; Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. J Antimicrob Chemother 66:1499–1503 [View Article][PubMed]
    [Google Scholar]
  21. Hyatt D., Chen G. L., Locascio P. F., Land M. L., Larimer F. W., Hauser L. J. 2010; Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11:119 [View Article][PubMed]
    [Google Scholar]
  22. Jiang Y., Yu D., Wei Z., Shen P., Zhou Z., Yu Y. 2010; Complete nucleotide sequence of Klebsiella pneumoniae multidrug resistance plasmid pKP048, carrying blaKPC-2, blaDHA-1, qnrB4, and armA. Antimicrob Agents Chemother 54:3967–3969 [View Article][PubMed]
    [Google Scholar]
  23. Lean S. S., Yeo C. C., Suhaili Z., Thong K. L. 2015; Whole-genome analysis of an extensively drug-resistant clinical isolate of Acinetobacter baumannii AC12: insights into the mechanisms of resistance of an ST195 clone from Malaysia. Int J Antimicrob Agents 45:178–182 [View Article][PubMed]
    [Google Scholar]
  24. Liu S. L., Hessel A., Sanderson K. E. 1993; Genomic mapping with I-Ceu I, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A 90:6874–6878 [View Article][PubMed]
    [Google Scholar]
  25. Lockhart S. R., Abramson M. A., Beekmann S. E., Gallagher G., Riedel S., Diekema D. J., Quinn J. P., Doern G. V. 2007; Antimicrobial resistance among gram-negative bacilli causing infections in intensive care unit patients in the United States between 1993 and 2004. J Clin Microbiol 45:3352–3359 [View Article][PubMed]
    [Google Scholar]
  26. Mammeri H., Poirel L., Mangeney N., Nordmann P., Central L., Chenevier A. 2003; Chromosomal integration of a cephalosporinase gene from Acinetobacter baumannii into Oligella urethralis as a source of acquired resistance to beta-lactams. Antimicrob Agents Chemother 47:1536–1542 [View Article][PubMed]
    [Google Scholar]
  27. Mammina C., Bonura C., Aleo A., Calà C., Caputo G., Cataldo M. C., Benedetto A. D., Distefano S., Fasciana T. et al. 2011; Characterization of Acinetobacter baumannii from intensive care units and home care patients in Palermo, Italy. Clin Microbiol Infect 17:E12E15 [View Article][PubMed]
    [Google Scholar]
  28. Manchanda V., Sanchaita S., Singh N. 2010; Multidrug resistant acinetobacter. J Glob Infect Dis 2:291 [View Article][PubMed]
    [Google Scholar]
  29. Martínez T., Vazquez G. J., Aquino E. E., Goering R. V., Robledo I. E. 2012; Two novel class I integron arrays containing IMP-18 metallo-β-lactamase gene in Pseudomonas aeruginosa clinical isolates from Puerto Rico. Antimicrob Agents Chemother 56:2119–2121 [View Article][PubMed]
    [Google Scholar]
  30. Martínez T., Vázquez G. J., Aquino E. E., Martínez I., Robledo I. E. 2014; ISEcp1-mediated transposition of blaKPC into the chromosome of a clinical isolate of Acinetobacter baumannii from Puerto Rico. J Med Microbiol 63:1644–1648 [View Article][PubMed]
    [Google Scholar]
  31. Martínez T., Ropelewski A. J., González-Mendez R., Vázquez G. J., Robledo I. E. 2015; Draft genome sequence of Klebsiella pneumoniae carbapenemase-producing Acinetobacter baumannii strain M3AC9-7, isolated from Puerto Rico. Genome Announc 3:e00274-15 [View Article][PubMed]
    [Google Scholar]
  32. Moland E. S., Hanson N. D., Black J. A., Hossain A., Song W., Thomson K. S. 2006; Prevalence of newer beta-lactamases in gram-negative clinical isolates collected in the United States from 2001 to 2002. J Clin Microbiol 44:3318–3324 [View Article][PubMed]
    [Google Scholar]
  33. Moura A., Soares M., Pereira C., Leitão N., Henriques I., Correia A. 2009; INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 25:1096–1098 [View Article][PubMed]
    [Google Scholar]
  34. Naas T., Cuzon G., Villegas M. V., Lartigue M. F., Quinn J. P., Nordmann P. 2008; Genetic structures at the origin of acquisition of the beta-lactamase bla KPC gene. Antimicrob Agents Chemother 52:1257–1263 [View Article][PubMed]
    [Google Scholar]
  35. Nigro S. J., Farrugia D. N., Paulsen I. T., Hall R. M. 2013; A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii isolates belonging to global clone 2. J Antimicrob Chemother 68:554–557 [View Article][PubMed]
    [Google Scholar]
  36. Nordmann P., Cuzon G., Naas T. 2009; The real threat of Klebsiella pneumoniae carbapenemase-producing bacteria. Lancet Infect Dis 9:228–236 [View Article][PubMed]
    [Google Scholar]
  37. Pecora N. D., Li N., Allard M., Li C., Albano E., Delaney M., Dubois A., Onderdonk A. B., Bry L. 2015; Genomically informed surveillance for carbapenem-resistant Enterobacteriaceae in a health care system. MBio 6:e0103001015 [View Article][PubMed]
    [Google Scholar]
  38. Robledo I. E., Aquino E. E., Santé M. I., Santana J. L., Otero D. M., León C. F., Vázquez G. J. 2010; Detection of KPC in Acinetobacter spp. in Puerto Rico. Antimicrob Agents Chemother 54:1354–1357 [View Article][PubMed]
    [Google Scholar]
  39. Shen P., Wei Z., Jiang Y., Du X., Ji S., Yu Y., Li L., Yu N. 2009; Novel genetic environment of the carbapenem-hydrolyzing beta-lactamase KPC-2 among Enterobacteriaceae in China. Antimicrob Agents Chemother 53:4333–4338 [View Article][PubMed]
    [Google Scholar]
  40. Siguier P., Perochon J., Lestrade L., Mahillon J., Chandler M. 2006; ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34:D32–D36 [View Article][PubMed]
    [Google Scholar]
  41. Sun C., Hao J., Dou M., Gong Y. 2015; Mutant prevention concentrations of levofloxacin, pazufloxacin and ciprofloxacin for A. baumannii and mutations in gyrA and parC genes. J Antibiot 68:313–317 [View Article][PubMed]
    [Google Scholar]
  42. Towns J., Cockerill T., Dahan M., Foster I., Gaither K., Grimshaw A., Hazlewood V., Lathrop S., Lifka D. et al. 2014; XSEDE: accelerating scientific discovery. Comput Sci Eng 16:62–74 [View Article]
    [Google Scholar]
  43. Turton J. F., Ward M. E., Woodford N., Kaufmann M. E., Pike R., Livermore D. M., Pitt T. L. 2006; The role of ISAba1 in expression of OXA carbapenemase genes in Acinetobacter baumannii. FEMS Microbiol Lett 258:72–77 [View Article][PubMed]
    [Google Scholar]
  44. Viedma E., Juan C., Acosta J., Zamorano L., Otero J. R., Sanz F., Chaves F., Oliver A. 2009; Nosocomial spread of colistin-only-sensitive sequence type 235 Pseudomonas aeruginosa isolates producing the extended-spectrum beta-lactamases GES-1 and GES-5 in Spain. Antimicrob Agents Chemother 53:4930–4933 [View Article][PubMed]
    [Google Scholar]
  45. Villegas M. V., Lolans K., Correa A., Kattan J. N., Lopez J. A., Quinn J. P.Colombian Nosocomial Resistance Study Group 2007; First identification of Pseudomonas aeruginosa isolates producing a KPC-type carbapenem-hydrolyzing beta-lactamase. Antimicrob Agents Chemother 51:1553–1555 [View Article][PubMed]
    [Google Scholar]
  46. Wolter D. J., Khalaf N., Robledo I. E., Vázquez G. J., Santé M. I., Aquino E. E., Goering R. V., Hanson N. D. 2009; Surveillance of carbapenem-resistant Pseudomonas aeruginosa isolates from Puerto Rican medical center hospitals: dissemination of KPC and IMP-18 beta-lactamases. Antimicrob Agents Chemother 53:1660–1664 [View Article][PubMed]
    [Google Scholar]
  47. Woodford N., Ellington M. J., Coelho J. M., Turton J. F., Ward M. E., Brown S., Amyes S. G., Livermore D. M. 2006; Multiplex PCR for genes encoding prevalent OXA carbapenemases in Acinetobacter spp. Int J Antimicrob Agents 27:351–353 [View Article][PubMed]
    [Google Scholar]
  48. Wright M. S., Haft D. H., Harkins D. M., Perez F., Hujer K. M., Bajaksouzian S., Benard M. F., Jacobs M. R., Bonomo R. A., Adams M. D. 2014; New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. MBio 5:e0096313 [View Article][PubMed]
    [Google Scholar]
  49. Yigit H., Queenan A. M., Anderson G. J., Domenech-Sanchez A., Biddle J. W., Steward C. D., Alberti S., Bush K., Tenover F. C. 2001; Novel carbapenem-hydrolyzing beta-lactamase, KPC-1, from a carbapenem-resistant strain of Klebsiella pneumoniae. Antimicrob Agents Chemother 45:1151–1161 [View Article][PubMed]
    [Google Scholar]
  50. Zankari E., Hasman H., Cosentino S., Vestergaard M., Rasmussen S., Lund O., Aarestrup F. M., Larsen M. V. 2012; Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644 [View Article][PubMed]
    [Google Scholar]
  51. Zarrilli R., Pournaras S., Giannouli M., Tsakris A. 2013; Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents 41:11–19 [View Article][PubMed]
    [Google Scholar]
  52. Zhang G. Q., Yao Y. H., Yu X. L., Niu J. J. 2014; A survey of five broad-host-range plasmids in gram-negative bacilli isolated from patients. Plasmid 74:9–14 [View Article][PubMed]
    [Google Scholar]
  53. Zhou Y., Liang Y., Lynch K. H., Dennis J. J., Wishart D. S. 2011; PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352 [View Article][PubMed]
    [Google Scholar]
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