1887

Abstract

Carbapenem resistance in is due to , which is endemic in India. Recently, the sporadic presence of as well as the occurrence of dual carbapenemases were observed. The mobility as well as the dissemination of these resistance genes were mainly mediated by various mobile genetic elements. The present study was aimed at characterizing the genetic arrangement of and identified in two complete genomes of carbapenem-resistant (CRAB). Complete genomes obtained using a hybrid-assembly approach revealed the accurate arrangement of Tn with IS with and IS with In addition, the association of 1 integrase with the gene and several virulence factors required for type-IV pili assembly, motility and biofilm formation have been identified. The current study provided deeper insight into the complete characterization of insertion sequences and transposons associated with the carbapenem-resistant genes using short reads of IonTorrent PGM and long reads of MinIon in .

Funding
This study was supported by the:
  • Balaji Veeraraghavan , Indian Council of Medical Research , (Award AMR/TF/54/13ECDHIII)
Loading

Article metrics loading...

/content/journal/acmi/10.1099/acmi.0.000140
2020-06-05
2020-09-18
Loading full text...

Full text loading...

/deliver/fulltext/acmi/2/8/acmi000140.html?itemId=/content/journal/acmi/10.1099/acmi.0.000140&mimeType=html&fmt=ahah

References

  1. Poirel L, Nordmann P. Carbapenem resistance in Acinetobacter baumannii: mechanisms and epidemiology. Clin Microbiol Infect 2006; 12:826–836 [CrossRef][PubMed]
    [Google Scholar]
  2. Dijkshoorn L, Nemec A, Seifert H. An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii . Nat Rev Microbiol 2007; 5:939–951 [CrossRef][PubMed]
    [Google Scholar]
  3. Peleg AY, Seifert H, Paterson DL. Acinetobacter baumannii: emergence of a successful pathogen. Clin Microbiol Rev 2008; 21:538–582 [CrossRef][PubMed]
    [Google Scholar]
  4. Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VH et al. β-Lactamases and β-lactamase inhibitors in the 21st century. J Mol Biol 2019; 18:3472–3500
    [Google Scholar]
  5. Vijayakumar S, Gopi R, Gunasekaran P, Bharathy M, Walia K et al. Molecular characterization of invasive carbapenem-resistant Acinetobacter baumannii from a tertiary care hospital in South India. Infect Dis Ther 2016; 5:379–387 [CrossRef][PubMed]
    [Google Scholar]
  6. Martinez T, Martinez I, Vazquez GJ, Aquino EE, Robledo IE. Genetic environment of the KPC gene in Acinetobacter baumannii ST2 clone from Puerto Rico and genomic insights into its drug resistance. J Med Microbiol 2016; 65:784–792 [CrossRef][PubMed]
    [Google Scholar]
  7. Hammoudi D, Moubareck CA, Hakime N, Houmani M, Barakat A et al. Spread of imipenem-resistant Acinetobacter baumannii co-expressing OXA-23 and GES-11 carbapenemases in Lebanon. Int J Infect Dis 2015; 36:56–61 [CrossRef][PubMed]
    [Google Scholar]
  8. Nordmann P, Poirel L. Epidemiology and diagnostics of carbapenem resistance in gram-negative bacteria. Clin Infect Dis 2019; 69:S521–S528 [CrossRef][PubMed]
    [Google Scholar]
  9. Hsu L-Y, Apisarnthanarak A, Khan E, Suwantarat N, Ghafur A et al. Carbapenem-resistant Acinetobacter baumannii and Enterobacteriaceae in South and Southeast Asia. Clin Microbiol Rev 2017; 30:1–22 [CrossRef][PubMed]
    [Google Scholar]
  10. Vijayakumar S, Anandan S, Ms DP, Kanthan K, Vijayabaskar S et al. Insertion sequences and sequence types profile of clinical isolates of carbapenem-resistant A. baumannii collected across India over four year period. J Infect Public Health 2019; 19:30361–30362 [CrossRef][PubMed]
    [Google Scholar]
  11. Roca I, Espinal P, Vila-Farrés X, Vila J, Subir R I. The Acinetobacter baumannii oxymoron: commensal Hospital dweller turned pan-drug-resistant menace. Front Microbiol 2012; 3:148 [CrossRef][PubMed]
    [Google Scholar]
  12. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11:3146 [CrossRef][PubMed]
    [Google Scholar]
  13. Bentley SD, Parkhill J. Genomic perspectives on the evolution and spread of bacterial pathogens. Proc Biol Sci 2015; 282:20150488 [CrossRef][PubMed]
    [Google Scholar]
  14. Turton JF, Woodford N, Glover J, Yarde S, Kaufmann ME et al. Identification of Acinetobacter baumannii by detection of the blaOXA-51-like carbapenemase gene intrinsic to this species. J Clin Microbiol 2006; 44:2974–2976 [CrossRef][PubMed]
    [Google Scholar]
  15. Clinical and Laboratory Standards Institute Performance Standards for Antimicrobial Susceptibility Testing: Twenty second Informational Supplement M100-S28 USA: CLSI, Wayne, PA; 2018
    [Google Scholar]
  16. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [CrossRef][PubMed]
    [Google Scholar]
  17. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [CrossRef][PubMed]
    [Google Scholar]
  18. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  19. Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 2016; 32:2103–2110 [CrossRef][PubMed]
    [Google Scholar]
  20. Vaser R, Sović I, Nagarajan N. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 2017; 27:737–746 [CrossRef][PubMed]
    [Google Scholar]
  21. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [CrossRef][PubMed]
    [Google Scholar]
  22. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [CrossRef][PubMed]
    [Google Scholar]
  23. Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 2014; 42:D581–D591 [CrossRef][PubMed]
    [Google Scholar]
  24. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 2012; 67:2640–2644 [CrossRef][PubMed]
    [Google Scholar]
  25. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–D328 [CrossRef][PubMed]
    [Google Scholar]
  26. Siguier P, Pérochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–D36 [CrossRef][PubMed]
    [Google Scholar]
  27. Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS. PHAST: a fast phage search tool. Nucleic Acids Res 2011; 39:W347–W352 [CrossRef][PubMed]
    [Google Scholar]
  28. Bertelli C, Laird MR, Williams KP, Lau BY et al. Simon Fraser University Research Computing Group IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [CrossRef][PubMed]
    [Google Scholar]
  29. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 2012; 50:1355–1361 [CrossRef][PubMed]
    [Google Scholar]
  30. Hamidian M, Wick RR, Hartstein RM, Judd LM, Holt KE et al. Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2. Microb Genom 2019; 5: [CrossRef][PubMed]
    [Google Scholar]
  31. Ramoul A, Loucif L, Bakour S, Amiri S, Dekhil M et al. Co-Occurrence of blaNDM-1 with blaOXA-23 or blaOXA-58 in clinical multidrug-resistant Acinetobacter baumannii isolates in Algeria. J Glob Antimicrob Resist 2016; 6:136–141 [CrossRef][PubMed]
    [Google Scholar]
  32. Regeen H, Al-Sharafa-Kittaneh D, Kattan R, Al-Dawodi R, Marzouqa H et al. First report of blaNDM and blaOXA-58 coexistence in Acinetobacter junii . J Clin Microbiol 2014; 52:3492–3493 [CrossRef][PubMed]
    [Google Scholar]
  33. Zhou S, Chen X, Meng X, Zhang G, Wang J et al. "Roar" of blaNDM-1 and "silence" of blaOXA-58 co-exist in Acinetobacter pittii . Sci Rep 2015; 5:8976 [CrossRef][PubMed]
    [Google Scholar]
  34. Chen Y, Guo P, Huang H, Huang Y, Wu Z et al. Detection of co-harboring OXA-58 and NDM-1 carbapenemase producing genes resided on a same plasmid from an Acinetobacter pittii clinical isolate in China. Iran J Basic Med Sci 2019; 22:106–111 [CrossRef][PubMed]
    [Google Scholar]
  35. Principe L, Piazza A, Giani T, Bracco S, Caltagirone MS et al. Epidemic diffusion of OXA-23-producing Acinetobacter baumannii isolates in Italy: results of the first cross-sectional countrywide survey. J Clin Microbiol 2014; 52:3004–3010 [CrossRef][PubMed]
    [Google Scholar]
  36. El Bannah AMS, Nawar NN, Hassan RMM, Salem STB. Molecular epidemiology of carbapenem-resistant Acinetobacter baumannii in a tertiary care hospital in Egypt: clonal spread of bla OXA-23. Microb Drug Resist 2018; 24:269–277 [CrossRef]
    [Google Scholar]
  37. Turton JF, Ward ME, Woodford N, Kaufmann ME, Pike R et al. The role of ISAba1 in expression of OXA carbapenemase genes in Acinetobacter baumannii . FEMS Microbiol Lett 2006; 258:72–77 [CrossRef][PubMed]
    [Google Scholar]
  38. Poirel L, Lebessi E, Héritier C, Patsoura A, Foustoukou M et al. Nosocomial spread of OXA-58-positive carbapenem-resistant Acinetobacter baumannii isolates in a paediatric hospital in Greece. Clin Microbiol Infect 2006; 12:1138–1141 [CrossRef][PubMed]
    [Google Scholar]
  39. Lopes BS, Evans BA, Amyes SGB. Disruption of the blaOXA-51-like gene by ISAba16 and activation of the blaOXA-58 gene leading to carbapenem resistance in Acinetobacter baumannii Ab244. J Antimicrob Chemother 2012; 67:59–63 [CrossRef][PubMed]
    [Google Scholar]
  40. Bertini A, Poirel L, Bernabeu S, Fortini D, Villa L et al. Multicopy blaOXA-58 gene as a source of high-level resistance to carbapenems in Acinetobacter baumannii . Antimicrob Agents Chemother 2007; 51:2324–2328 [CrossRef][PubMed]
    [Google Scholar]
  41. Ravasi P, Limansky AS, Rodriguez RE, Viale AM, Mussi MA. ISAba825, a functional insertion sequence modulating genomic plasticity and bla(OXA-58) expression in Acinetobacter baumannii . Antimicrob Agents Chemother 2011; 55:917–920 [CrossRef][PubMed]
    [Google Scholar]
  42. Huovinen P, Jacoby GA. Sequence of the PSE-1 -Lactamase Gene. Antimicrob Agents Chemother 1991; 35:2428–2430 [CrossRef]
    [Google Scholar]
  43. Kamolvit W, Derrington P, Paterson DL, Sidjabat HE. A case of IMP-4-, OXA-421-, OXA-96-, and CARB-2-producing Acinetobacter pittii sequence type 119 in Australia. J Clin Microbiol 2015; 53:727–730 [CrossRef][PubMed]
    [Google Scholar]
  44. Poirel L, Bonnin RA, Boulanger A, Schrenzel J, Kaase M et al. Tn125-related acquisition of blaNDM-like genes in Acinetobacter baumannii . Antimicrob Agents Chemother 2012; 56:1087–1089 [CrossRef][PubMed]
    [Google Scholar]
  45. Jones LS, Toleman MA, Weeks JL, Howe RA, Walsh TR et al. Plasmid carriage of bla NDM-1 in clinical Acinetobacter baumannii isolates from India. Antimicrob Agents Chemother 2014; 58:4211–4213 [CrossRef][PubMed]
    [Google Scholar]
  46. Mugnier PD, Poirel L, Nordmann P. Functional analysis of insertion sequence ISAba1, responsible for genomic plasticity of Acinetobacter baumannii . J Bacteriol 2009; 191:2414–2418 [CrossRef][PubMed]
    [Google Scholar]
  47. Chen T-L, Wu RC-C, Shaio M-F, Fung C-P, Cho W-L. Acquisition of a plasmid-borne blaOXA-58 gene with an upstream IS1008 insertion conferring a high level of carbapenem resistance to Acinetobacter baumannii . Antimicrob Agents Chemother 2008; 52:2573–2580 [CrossRef][PubMed]
    [Google Scholar]
  48. Choi AHK, Slamti L, Avci FY, Pier GB, Maira-Litrán T. The pgaABCD locus of Acinetobacter baumannii encodes the production of poly-beta-1-6-N-acetylglucosamine, which is critical for biofilm formation. J Bacteriol 2009; 191:5953–5963 [CrossRef][PubMed]
    [Google Scholar]
  49. Cerqueira GM, Peleg AY. Insights into Acinetobacter baumannii pathogenicity. IUBMB Life 2011; 63:1055–1060 [CrossRef][PubMed]
    [Google Scholar]
  50. Perez F, Ponce-Terashima R, Adams MD, Bonomo RA. Are we closing in on an "elusive enemy"? The current status of our battle with Acinetobacter baumannii . Virulence 2011; 2:86–90 [CrossRef][PubMed]
    [Google Scholar]
  51. Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M. Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog 2010; 6:e1000834 p. [CrossRef][PubMed]
    [Google Scholar]
  52. Sauer FG, Mulvey MA, Schilling JD, Martinez JJ, Hultgren SJ. Bacterial pili: molecular mechanisms of pathogenesis. Curr Opin Microbiol 2000; 3:65–72 [CrossRef][PubMed]
    [Google Scholar]
  53. Loehfelm TW, Luke NR, Campagnari AA. Identification and characterization of an Acinetobacter baumannii biofilm-associated protein. J Bacteriol 2008; 190:1036–1044 [CrossRef][PubMed]
    [Google Scholar]
  54. Saffari F, Monsen T, Karmostaji A, Azimabad FB, Widerström M. Significant spread of extensively drug-resistant Acinetobacter baumannii genotypes of clonal complex 92 among intensive care unit patients in a university hospital in southern Iran. J Med Microbiol 2017; 66:1656–1662 [CrossRef][PubMed]
    [Google Scholar]
  55. Uwingabiye J, Lemnouer A, Roca I, Alouane T, Frikh M et al. Clonal diversity and detection of carbapenem resistance encoding genes among multidrug-resistant Acinetobacter baumannii isolates recovered from patients and environment in two intensive care units in a Moroccan Hospital. Antimicrob Resist Infect Control 2017; 26: 6:99
    [Google Scholar]
  56. Rynga D, Shariff M, Deb M. Phenotypic and molecular characterization of clinical isolates of Acinetobacter baumannii isolated from Delhi, India. Ann Clin Microbiol Antimicrob 2015; 14:40 [CrossRef][PubMed]
    [Google Scholar]
  57. Vijayakumar S, Mathur P, Kapil A, Das BK, Ray P et al. Molecular characterization & epidemiology of carbapenem-resistant Acinetobacter baumannii collected across India. Indian J Med Res 2019; 2:240–246
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/acmi/10.1099/acmi.0.000140
Loading
/content/journal/acmi/10.1099/acmi.0.000140
Loading

Data & Media loading...

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error