1887

Abstract

We recently reported a dramatic increase in the prevalence of carbapenem-resistant Acinetobacter baumannii infections in the intensive care unit (ICU) of a Vietnamese hospital. This upsurge was associated with a specific oxa23-positive clone that was identified by multilocus VNTR analysis. Here, we used whole-genome sequence analysis to dissect the emergence of carbapenem-resistant A. baumannii causing ventilator-associated pneumonia (VAP) in the ICU during 2009–2012. To provide historical context and distinguish microevolution from strain introduction, we compared these genomes with those of A. baumannii asymptomatic carriage and VAP isolates from this same ICU collected during 2003–2007. We identified diverse lineages co-circulating over many years. Carbapenem resistance was associated with the presence of oxa23, oxa40, oxa58 and ndm1 genes in multiple lineages. The majority of resistant isolates were oxa23-positive global clone GC2; fine-scale phylogenomic analysis revealed five distinct GC2 sublineages within the ICU that had evolved locally via independent chromosomal insertions of oxa23 transposons. The increase in infections caused by carbapenem-resistant A. baumannii was associated with transposon-mediated transmission of a carbapenemase gene, rather than clonal expansion or spread of a carbapenemase-harbouring plasmid. Additionally, we found evidence of homologous recombination creating diversity within the local GC2 population, including several events resulting in replacement of the capsule locus. We identified likely donors of the imported capsule locus sequences amongst the A. baumannii isolated on the same ward, suggesting that diversification was largely facilitated via reassortment and sharing of genetic material within the localized A. baumannii population.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000050
2016-03-02
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/mgen/2/3/mgen000050.html?itemId=/content/journal/mgen/10.1099/mgen.0.000050&mimeType=html&fmt=ahah

References

  1. Adams-Haduch J. M., Paterson D. L., Sidjabat H. E., Pasculle A. W., Potoski B. A., Muto C. A., Harrison L. H., Doi Y. 2008; Genetic basis of multidrug resistance in Acinetobacter baumannii clinical isolates at a tertiary medical center in Pennsylvania. Antimicrob Agents Chemother 52:3837–3843 [View Article][PubMed]
    [Google Scholar]
  2. Akaike H. 1974; A new look at statistical-model identification. IEEE Trans Autom Control 19:716–723 [View Article]
    [Google Scholar]
  3. Alqasim A., Scheutz F., Zong Z., McNally A. 2014; Comparative genome analysis identifies few traits unique to the Escherichia coli ST131 H30Rx clade and extensive mosaicism at the capsule locus. BMC Genomics 15:830 [View Article][PubMed]
    [Google Scholar]
  4. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. 1990; Basic local alignment search tool. J Mol Biol 215:403–410 [View Article][PubMed]
    [Google Scholar]
  5. Antunes L. C., Visca P., Towner K. J. 2014; Acinetobacter baumannii: evolution of a global pathogen. Pathog Dis 71:292–301 [View Article][PubMed]
    [Google Scholar]
  6. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S., other authors. 2012; SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477 [View Article][PubMed]
    [Google Scholar]
  7. Bergogne-Bérézin E., Towner K. J. 1996; Acinetobacter spp. as nosocomial pathogens: microbiological, clinical, and epidemiological features. Clin Microbiol Rev 9:148–165[PubMed]
    [Google Scholar]
  8. Bouvet P. J., Grimont P. A. 1987; Identification and biotyping of clinical isolates of Acinetobacter . Ann Inst Pasteur Microbiol 138:569–578 [View Article][PubMed]
    [Google Scholar]
  9. Brañas P., Villa J., Viedma E., Mingorance J., Orellana M. A., Chaves F. 2015; Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in a hospital in Madrid: successful establishment of an OXA-48 ST11 clone. Int J Antimicrob Agents 46:111–116 [View Article][PubMed]
    [Google Scholar]
  10. Cai Y., Chai D., Wang R., Liang B., Bai N. 2012; Colistin resistance of Acinetobacter baumannii: clinical reports, mechanisms and antimicrobial strategies. J Antimicrob Chemother 67:1607–1615 [View Article][PubMed]
    [Google Scholar]
  11. Carver T. J., Rutherford K. M., Berriman M., Rajandream M. A., Barrell B. G., Parkhill J. 2005; act: the Artemis comparison tool. Bioinformatics 21:3422–3423 [View Article][PubMed]
    [Google Scholar]
  12. Chastre J., Fagon J.-Y. 2002; Ventilator-associated pneumonia. Am J Respir Crit Care Med 165:867–903 [View Article][PubMed]
    [Google Scholar]
  13. CLSI 2012 Performance Standards for Antimicrobial Susceptibility Testing 22nd Informational Supplement Wayne, PA: Clinical and Laboratory Standards Institute;
    [Google Scholar]
  14. Corvec S., Poirel L., Naas T., Drugeon H., Nordmann P. 2007; Genetics and expression of the carbapenem-hydrolyzing oxacillinase gene bla OXA-23 in Acinetobacter baumannii . Antimicrob Agents Chemother 51:1530–1533 [View Article][PubMed]
    [Google Scholar]
  15. Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S. R. 2015; Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 43:e15[PubMed] [CrossRef]
    [Google Scholar]
  16. 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]
  17. Didelot X., Wilson D. J. 2015; ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 11:e1004041 [View Article][PubMed]
    [Google Scholar]
  18. Donald H. M., Scaife W., Amyes S. G., Young H. K. 2000; Sequence analysis of ARI-1, a novel OXA beta-lactamase, responsible for imipenem resistance in Acinetobacter baumannii 6B92. Antimicrob Agents Chemother 44:196–199 [View Article][PubMed]
    [Google Scholar]
  19. Drummond A. J., Suchard M. A., Xie D., Rambaut A. 2012; Bayesian phylogenetics with BEAUti and the beast 1.7. Mol Biol Evol 29:1969–1973 [View Article][PubMed]
    [Google Scholar]
  20. Evans B. A., Hamouda A., Amyes S. G. 2013; The rise of carbapenem-resistant Acinetobacter baumannii . Curr Pharm Des 19:223–238 [View Article][PubMed]
    [Google Scholar]
  21. Garonzik S. M., Li J., Thamlikitkul V., Paterson D. L., Shoham S., Jacob J., Silveira F. P., Forrest A., Nation R. L. 2011; Population pharmacokinetics of colistin methanesulfonate and formed colistin in critically ill patients from a multicenter study provide dosing suggestions for various categories of patients. Antimicrob Agents Chemother 55:3284–3294 [View Article][PubMed]
    [Google Scholar]
  22. Geisinger E., Isberg R. R. 2015; Antibiotic modulation of capsular exopolysaccharide and virulence in Acinetobacter baumannii . PLoS Pathog 11:e1004691 [View Article][PubMed]
    [Google Scholar]
  23. Gupta S. K., Padmanabhan B. R., Diene S. M., Lopez-Rojas R., Kempf M., Landraud L., Rolain J. M. 2014; arg-annot, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 58:212–220 [View Article][PubMed]
    [Google Scholar]
  24. Guy L., Kultima J. R., Andersson S. G. 2010; genoPlotR: comparative gene and genome visualization in r . Bioinformatics 26:2334–2335 [View Article][PubMed]
    [Google Scholar]
  25. Hamidian M., Kenyon J. J., Holt K. E., Pickard D., Hall R. M. 2014; A conjugative plasmid carrying the carbapenem resistance gene bla OXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate. J Antimicrob Chemother 69:2625–2628 [View Article][PubMed]
    [Google Scholar]
  26. Hawkey J., Hamidian M., Wick R. R., Edwards D. J., Billman-Jacobe H., Hall R. M., Holt K. E. 2015; ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 16:667 [View Article][PubMed]
    [Google Scholar]
  27. Heled J., Bouckaert R. R. 2013; Looking for trees in the forest: summary tree from posterior samples. BMC Evol Biol 13:221 [View Article][PubMed]
    [Google Scholar]
  28. Holt K. E., Baker S., Weill F. X., Holmes E. C., Kitchen A., Yu J., Sangal V., Brown D. J., Coia J. E., other authors. 2012; Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet 44:1056–1059 [View Article][PubMed]
    [Google Scholar]
  29. Hu D., Liu B., Dijkshoorn L., Wang L., Reeves P. R. 2013; Diversity in the major polysaccharide antigen of Acinetobacter baumannii assessed by DNA sequencing, and development of a molecular serotyping scheme. PLoS One 8:e70329 [View Article][PubMed]
    [Google Scholar]
  30. Huson D. H., Bryant D. 2006; Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23:254–267 [View Article][PubMed]
    [Google Scholar]
  31. Inouye M., Dashnow H., Raven L. A., Schultz M. B., Pope B. J., Tomita T., Zobel J., Holt K. E. 2014; srst2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 6:90 [View Article][PubMed]
    [Google Scholar]
  32. Kalanuria A. A., Zai W., Mirski M. 2014; Ventilator-associated pneumonia in the ICU. Crit Care 18:208 [View Article][PubMed]
    [Google Scholar]
  33. Katoh K., Standley D. M. 2013; mafft multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772–780 [View Article][PubMed]
    [Google Scholar]
  34. Kenyon J. J., Hall R. M. 2013; Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes. PLoS One 8:e62160 [View Article][PubMed]
    [Google Scholar]
  35. Kenyon J. J., Marzaioli A. M., Hall R. M., De Castro C. 2014; Structure of the K2 capsule associated with the KL2 gene cluster of Acinetobacter baumannii . Glycobiology 24:554–563 [View Article][PubMed]
    [Google Scholar]
  36. Kenyon J. J., Marzaioli A. M., De Castro C., Hall R. M. 2015; 5,7-Di-N-acetyl-acinetaminic acid: a novel non-2-ulosonic acid found in the capsule of an Acinetobacter baumannii isolate. Glycobiology 25:644–654 [View Article][PubMed]
    [Google Scholar]
  37. Langmead B., Salzberg S. L. 2012; Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359 [View Article][PubMed]
    [Google Scholar]
  38. Madsen J. S., Burmølle M., Hansen L. H., Sørensen S. J. 2012; The interconnection between biofilm formation and horizontal gene transfer. FEMS Immunol Med Microbiol 65:183–195 [View Article][PubMed]
    [Google Scholar]
  39. Mathers A. J., Cox H. L., Kitchel B., Bonatti H., Brassinga A. K., Carroll J., Scheld W. M., Hazen K. C., Sifri C. D. 2011; Molecular dissection of an outbreak of carbapenem-resistant enterobacteriaceae reveals Intergenus KPC carbapenemase transmission through a promiscuous plasmid. MBio 2:e00204–e00e11 [View Article][PubMed]
    [Google Scholar]
  40. Mathers A. J., Stoesser N., Sheppard A. E., Pankhurst L., Giess A., Yeh A. J., Didelot X., Turner S. D., Sebra R., other authors. 2015; Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae at a single institution: insights into endemicity from whole-genome sequencing. Antimicrob Agents Chemother 59:1656–1663 [View Article][PubMed]
    [Google Scholar]
  41. McQueary C. N., Kirkup B. C., Si Y., Barlow M., Actis L. A., Craft D. W., Zurawski D. V. 2012; Extracellular stress and lipopolysaccharide modulate Acinetobacter baumannii surface-associated motility. J Microbiol 50:434–443 [View Article][PubMed]
    [Google Scholar]
  42. Melsen W. G., Rovers M. M., Groenwold R. H., Bergmans D. C., Camus C., Bauer T. T., Hanisch E. W., Klarin B., Koeman M., other authors. 2013; Attributable mortality of ventilator-associated pneumonia: a meta-analysis of individual patient data from randomised prevention studies. Lancet Infect Dis 13:665–671 [View Article][PubMed]
    [Google Scholar]
  43. Mutreja A., Kim D. W., Thomson N. R., Connor T. R., Lee J. H., Kariuki S., Croucher N. J., Choi S. Y., Harris S. R., other authors. 2011; Evidence for several waves of global transmission in the seventh cholera pandemic. Nature 477:462–465 [View Article][PubMed]
    [Google Scholar]
  44. Nhu N. T., Lan N. P., Campbell J. I., Parry C. M., Thompson C., Tuyen H. T., Hoang N. V., Tam P. T., Le V. M., other authors. 2014; Emergence of carbapenem-resistant Acinetobacter baumannii as the major cause of ventilator-associated pneumonia in intensive care unit patients at an infectious disease hospital in southern Vietnam. J Med Microbiol 63:1386–1394 [View Article][PubMed]
    [Google Scholar]
  45. Okoro C. K., Kingsley R. A., Connor T. R., Harris S. R., Parry C. M., Al-Mashhadani M. N., Kariuki S., Msefula C. L., Gordon M. A., other authors. 2012; Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet 44:1215–1221 [View Article][PubMed]
    [Google Scholar]
  46. Ordooei Javan A., Shokouhi S., Sahraei Z. 2015; A review on colistin nephrotoxicity. Eur J Clin Pharmacol 71:801–810 [View Article][PubMed]
    [Google Scholar]
  47. Pagel M., Meade A., Barker D. 2004; Bayesian estimation of ancestral character states on phylogenies. Syst Biol 53:673–684 [View Article][PubMed]
    [Google Scholar]
  48. Papp-Wallace K. M., Endimiani A., Taracila M. A., Bonomo R. A. 2011; Carbapenems: past, present, and future. Antimicrob Agents Chemother 55:4943–4960 [View Article][PubMed]
    [Google Scholar]
  49. Paton R., Miles R. S., Hood J., Amyes S. G., Miles R. S., Amyes S. G. 1993; ARI 1: beta-lactamase-mediated imipenem resistance in Acinetobacter baumannii . Int J Antimicrob Agents 2:81–87 [View Article][PubMed]
    [Google Scholar]
  50. Perez F., Hujer A. M., Hujer K. M., Decker B. K., Rather P. N., Bonomo R. A. 2007; Global challenge of multidrug-resistant Acinetobacter baumannii . Antimicrob Agents Chemother 51:3471–3484 [View Article][PubMed]
    [Google Scholar]
  51. Perez F., Ponce-Terashima R., Adams M. D., Bonomo R. A. 2011; Are we closing in on an “elusive enemy”? The current status of our battle with Acinetobacter baumannii . Virulence 2:86–90 [View Article][PubMed]
    [Google Scholar]
  52. Poirel L., Figueiredo S., Cattoir V., Carattoli A., Nordmann P. 2008; Acinetobacter radioresistens as a silent source of carbapenem resistance for Acinetobacter spp. Antimicrob Agents Chemother 52:1252–1256 [View Article][PubMed]
    [Google Scholar]
  53. Qureshi Z. A., Hittle L. E., O'Hara J. A., Rivera J. I., Syed A., Shields R. K., Pasculle A. W., Ernst R. K., Doi Y. 2015; Colistin-resistant Acinetobacter baumannii: beyond carbapenem resistance. Clin Infect Dis 60:1295–1303[PubMed]
    [Google Scholar]
  54. Rice L. B. 2008; Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis 197:1079–1081 [View Article][PubMed]
    [Google Scholar]
  55. Schultsz C., Bootsma M. C., Loan H. T., Nga T. T., Thao T. P., Thuy T. T., Campbell J., Vien M., Hoa N. T., other authors. 2013; Effects of infection control measures on acquisition of five antimicrobial drug-resistant microorganisms in a tetanus intensive care unit in Vietnam. Intensive Care Med 39:661–671 [View Article][PubMed]
    [Google Scholar]
  56. Seemann T. 2014; Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  57. Senchenkova S. N., Shashkov A. S., Shneider M. M., Arbatsky N. P., Popova A. V., Miroshnikov K. A., Volozhantsev N. V., Knirel Y. A. 2014; Structure of the capsular polysaccharide of Acinetobacter baumannii ACICU containing di-N-acetylpseudaminic acid. Carbohydr Res 391:89–92 [View Article][PubMed]
    [Google Scholar]
  58. 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]
  59. Snitkin E. S., Zelazny A. M., Thomas P. J., Stock F., Henderson D. K., Palmore T. N., Segre J. A., NISC Comparative Sequencing Program Group. 2012; Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with whole-genome sequencing. Sci Transl Med 4:148ra116 [View Article][PubMed]
    [Google Scholar]
  60. Spapen H., Jacobs R., Van Gorp V., Troubleyn J., Honoré P. M. 2011; Renal and neurological side effects of colistin in critically ill patients. Ann Intensive Care 1:14 [View Article][PubMed]
    [Google Scholar]
  61. Stamatakis A. 2014; RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  62. Tomaras A. P., Dorsey C. W., Edelmann R. E., Actis L. A. 2003; Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system. Microbiology 149:3473–3484 [View Article][PubMed]
    [Google Scholar]
  63. van Hal S. J., Ip C. L. C., Anzari M. A., Wilson D. J., Espedido B., Jensen S. O., Bowden R. 2016; Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance. MGen2 [View Article] http://dx.doi.org/10.1099/mgen.0.000048
    [Google Scholar]
  64. Vinogradov E., Maclean L., Xu H. H., Chen W. 2014; The structure of the polysaccharide isolated from Acinetobacter baumannii strain LAC-4. Carbohydr Res 390:42–45 [View Article][PubMed]
    [Google Scholar]
  65. Wick R. R., Schultz M. B., Zobel J., Holt K. E. 2015; Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 31:3350–3352 [View Article][PubMed]
    [Google Scholar]
  66. Wilharm G., Piesker J., Laue M., Skiebe E. 2013; DNA uptake by the nosocomial pathogen Acinetobacter baumannii occurs during movement along wet surfaces. J Bacteriol 195:4146–4153 [View Article][PubMed]
    [Google Scholar]
  67. 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:e00963–e00e13 [View Article][PubMed]
    [Google Scholar]
  68. Wyres K. L., Gorrie C., Edwards D. J., Wertheim H. F., Hsu L. Y., Van Kinh N., Zadoks R., Baker S., Holt K. E. 2015; Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal group 258. Genome Biol Evol 7:1267–1279 [View Article][PubMed]
    [Google Scholar]
  69. 1. Schultz, M. B., Thanh, D. P., Hoang, N. T. D., Wick, R. R., Ingle, D. J., Hawkey, J., Edwards, D. J., Kenyon, J., Lan, N. P. H. & other authors (2015). GenBank accession number KT852971.
  70. 2. Schultz, M. B., Thanh, D. P., Hoang, N. T. D., Wick, R. R., Ingle, D. J., Hawkey, J., Edwards, D. J., Kenyon, J., Lan, N. P. H. & other authors (2015). GenBank accession number KT852972.
  71. 3. Schultz, M. B., Thanh, D. P., Hoang, N. T. D., Wick, R. R., Ingle, D. J., Hawkey, J., Edwards, D. J., Kenyon, J., Lan, N. P. H. & other authors (2015). GenBank accession number KT946773.
  72. 4. Schultz, M. B., Thanh, D. P., Hoang, N. T. D., Wick, R. R., Ingle, D. J., Hawkey, J., Edwards, D. J., Kenyon, J., Lan, N. P. H. & other authors (2015). GenBank accession number KT359615.
  73. 5. Schultz, M. B., Thanh, D. P., Hoang, N. T. D., Wick, R. R., Ingle, D. J., Hawkey, J., Edwards, D. J., Kenyon, J., Lan, N. P. H. & other authors (2015). GenBank accession number KT359616.
  74. 6. Schultz, M. B., Thanh, D. P., Hoang, N. T. D., Wick, R. R., Ingle, D. J., Hawkey, J., Edwards, D. J., Kenyon, J., Lan, N. P. H. & other authors (2015). GenBank accession number KT359617.
  75. 7. The Wellcome Trust Sanger Institute. European Nucleotide Archive project ERP001080 (pre-publication access).
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000050
Loading
/content/journal/mgen/10.1099/mgen.0.000050
Loading

Data & Media loading...

Supplements

Loading data from figshare Loading data from figshare
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