1887
  1. Home
  2. Publications
  3. Microbial Genomics
  4. Volume 5, Issue 2
  5. Article

oa Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii

HTML
98.98 Kb
PDF
743.24 Kb
  • Authors: Christine J. Boinett1​,2​,3​ ,  Amy K. Cain1​,4​ ,  Jane Hawkey5​,6​,7​ ,  Nhu Tran Do Hoang2​ ,  Nhu Nguyen Thi Khanh8​ ,  Duy Pham Thanh2​ ,  Janina Dordel1​,9​ ,  James I. Campbell2​,3​ ,  Nguyen Phu Huong Lan2​,10​ ,  Matthew Mayho1​ ,  Gemma C. Langridge1​,11​ ,  James Hadfield1​ ,  Nguyen Van Vinh Chau10​ ,  Guy E. Thwaites2​,3​ ,  Julian Parkhill1​ ,  Nicholas R. Thomson1​,12​ ,  Kathryn E. Holt5​,6​ , Stephen Baker2​,3​,13​,*
    • VIEW AFFILIATIONS
    • 1​ 1​Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK 2​ 2​Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam 3​ 3​Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK 4​ 4​Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi 5​ 5​Centre for Systems Genomics, University of Melbourne, Melbourne, Victoria, Australia 6​ 6​Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia 7​ 7​Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia 8​ 8​School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia 9​ 9​Department of Biology, Drexel University, Philadelphia 19104, PA, USA 10​ 10​Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam 11​ 11​Norwich Medical School, University of East Anglia, Norwich, UK 12​ 12​Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK 13​ 13​Medicine, The University of Cambridge, Cambridge, UK
  • *Correspondence: Stephen Baker [email protected]
  • First Published Online: 05 February 2019, Microbial Genomics , 2019 5, doi: 10.1099/mgen.0.000246
  • Subject: Research Article - Responses to Human Interventions - Antibiotics
  • Received:
  • Accepted:
  • Cover date:
Preview this:
Free Preview thumbnail Magnify
Zoom in
Zoomout

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii, Page 1 of 1

| /docserver/preview/fulltext/mgen/5/2/mgen000246-1.gif

  • The increasing incidence and emergence of multi-drug resistant (MDR) Acinetobacter baumannii has become a major global health concern. Colistin is a historic antimicrobial that has become commonly used as a treatment for MDR A. baumannii infections. The increase in colistin usage has been mirrored by an increase in colistin resistance. We aimed to identify the mechanisms associated with colistin resistance in A. baumannii using multiple high-throughput-sequencing technologies, including transposon-directed insertion site sequencing (TraDIS), RNA sequencing (RNAseq) and whole-genome sequencing (WGS) to investigate the genotypic changes of colistin resistance in A. baumannii . Using TraDIS, we found that genes involved in drug efflux (adeIJK), and phospholipid (mlaC, mlaF and mlaD) and lipooligosaccharide synthesis (lpxC and lpsO) were required for survival in sub-inhibitory concentrations of colistin. Transcriptomic (RNAseq) analysis revealed that expression of genes encoding efflux proteins (adeI, adeC, emrB, mexB and macAB) was enhanced in in vitro generated colistin-resistant strains. WGS of these organisms identified disruptions in genes involved in lipid A (lpxC) and phospholipid synthesis (mlaA), and in the baeS/R two-component system (TCS). We additionally found that mutations in the pmrB TCS genes were the primary colistin-resistance-associated mechanisms in three Vietnamese clinical colistin-resistant A. baumannii strains. Our results outline the entire range of mechanisms employed in A. baumannii for resistance against colistin, including drug extrusion and the loss of lipid A moieties by gene disruption or modification.

  • All supporting data, code and protocols have been provided within the article or through supplementary data files. Eight supplementary tables and one supplementary figure are available with the online version of this article.

© 2019 The Authors | Published by the Microbiology Society

  • 1. Perez F, Hujer AM, Hujer KM, Decker BK, Rather PN et al. Global challenge of multidrug-resistant Acinetobacter baumannii. Antimicrob Agents Chemother 2007;51:3471–3484 [CrossRef][PubMed]
     [Google Scholar]
  • 2. Chen Z, Chen Y, Fang Y, Wang X, Chen Y et al. Meta-analysis of colistin for the treatment of Acinetobacter baumannii infection. Sci Rep 2015;5:17091 [CrossRef][PubMed]
     [Google Scholar]
  • 3. Garnacho-Montero J, Ortiz-Leyba C, Jiménez-Jiménez FJ, Barrero-Almodóvar AE, García-Garmendia JL et al. Treatment of multidrug-resistant Acinetobacter baumannii ventilator-associated pneumonia (VAP) with intravenous colistin: a comparison with imipenem-susceptible VAP. Clin Infect Dis 2003;36:1111–1118 [CrossRef][PubMed]
     [Google Scholar]
  • 4. Petrosillo N, Chinello P, Proietti MF, Cecchini L, Masala M et al. Combined colistin and rifampicin therapy for carbapenem-resistant Acinetobacter baumannii infections: clinical outcome and adverse events. Clin Microbiol Infect 2005;11:682–683 [CrossRef][PubMed]
     [Google Scholar]
  • 5. Cai Y, Chai D, Wang R, Liang B, Bai N. Colistin resistance of Acinetobacter baumannii: clinical reports, mechanisms and antimicrobial strategies. J Antimicrob Chemother 2012;67:1607–1615 [CrossRef][PubMed]
     [Google Scholar]
  • 6. Li J, Nation RL, Owen RJ, Wong S, Spelman D et al. Antibiograms of multidrug-resistant clinical Acinetobacter baumannii: promising therapeutic options for treatment of infection with colistin-resistant strains. Clin Infect Dis 2007;45:594–598 [CrossRef][PubMed]
     [Google Scholar]
  • 7. Adams MD, Nickel GC, Bajaksouzian S, Lavender H, Murthy AR et al. Resistance to colistin in Acinetobacter baumannii associated with mutations in the PmrAB two-component system. Antimicrob Agents Chemother 2009;53:3628–3634 [CrossRef][PubMed]
     [Google Scholar]
  • 8. Arroyo LA, Herrera CM, Fernandez L, Hankins JV, Trent MS et al. The pmrCAB operon mediates polymyxin resistance in Acinetobacter baumannii ATCC 17978 and clinical isolates through phosphoethanolamine modification of lipid A. Antimicrob Agents Chemother 2011;55:3743–3751 [CrossRef][PubMed]
     [Google Scholar]
  • 9. Lee H, Hsu FF, Turk J, Groisman EA. The PmrA-regulated pmrC gene mediates phosphoethanolamine modification of lipid A and polymyxin resistance in Salmonella enterica. J Bacteriol 2004;186:4124–4133 [CrossRef][PubMed]
     [Google Scholar]
  • 10. Vaara M, Vaara T, Sarvas M. Decreased binding of polymyxin by polymyxin-resistant mutants of Salmonella typhimurium. J Bacteriol 1979;139:664–667[PubMed]
     [Google Scholar]
  • 11. Moffatt JH, Harper M, Harrison P, Hale JD, Vinogradov E et al. Colistin resistance in Acinetobacter baumannii is mediated by complete loss of lipopolysaccharide production. Antimicrob Agents Chemother 2010;54:4971–4977 [CrossRef][PubMed]
     [Google Scholar]
  • 12. Lim TP, Ong RT, Hon PY, Hawkey J, Holt KE et al. Multiple genetic mutations associated with polymyxin resistance in Acinetobacter baumannii. Antimicrob Agents Chemother 2015;59:7899–7902 [CrossRef][PubMed]
     [Google Scholar]
  • 13. Moffatt JH, Harper M, Adler B, Nation RL, Li J et al. Insertion sequence ISAba11 is involved in colistin resistance and loss of lipopolysaccharide in Acinetobacter baumannii. Antimicrob Agents Chemother 2011;55:3022–3024 [CrossRef][PubMed]
     [Google Scholar]
  • 14. Falagas ME, Kasiakou SK. Colistin: the revival of polymyxins for the management of multidrug-resistant gram-negative bacterial infections. Clin Infect Dis 2005;40:1333–1341 [CrossRef][PubMed]
     [Google Scholar]
  • 15. Schultz MB, Pham Thanh D, Tran do Hoan N, Wick RR, Ingle DJ et al. Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward. Microb Genom 2016;2:mgen.0.000050 [CrossRef]
     [Google Scholar]
  • 16. Nhu NTK, Lan NPH, Campbell JI, Parry CM, Thompson C et al. 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 2014;63:1386–1394 [CrossRef][PubMed]
     [Google Scholar]
  • 17. Thi Khanh Nhu N, Riordan DW, do Hoang Nhu T, Thanh DP, Thwaites G et al. The induction and identification of novel colistin resistance mutations in Acinetobacter baumannii and their implications. Sci Rep 2016;6:28291
     [Google Scholar]
  • 18. Andrews JM. Determination of minimum inhibitory concentrations. J Antimicrob Chemother 2001;48:5–16 [CrossRef][PubMed]
     [Google Scholar]
  • 19. CLSI Performance Standards for Antimicrobial Susceptibility Testing, M100-S20 Wayne, PA: Clinical and Laboratory Standards Institute; 2010
     [Google Scholar]
  • 20. Boinett CJ, Harris SR, Langridge GC, Trainor EA, Merkel TJ et al. Complete genome sequence of Bordetella pertussis D420. Genome Announc 2015;3:e0065715 [CrossRef][PubMed]
     [Google Scholar]
  • 21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30:2068–2069 [CrossRef][PubMed]
     [Google Scholar]
  • 22. Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF et al. Optimal enzymes for amplifying sequencing libraries. Nat Meth 2011;9:10–11 [CrossRef][PubMed]
     [Google Scholar]
  • 23. Harris SR, Feil EJ, Holden MT, Quail MA, Nickerson EK et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010;327:469–474 [CrossRef][PubMed]
     [Google Scholar]
  • 24. Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H et al. ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. BMC Genomics 2015;16:667 [CrossRef][PubMed]
     [Google Scholar]
  • 25. Vergara-Irigaray M, Fookes MC, Thomson NR, Tang CM. RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC Genomics 2014;15:438 [CrossRef][PubMed]
     [Google Scholar]
  • 26. Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010;11:R106 [CrossRef][PubMed]
     [Google Scholar]
  • 27. Hassan KA, Cain AK, Huang T, Liu Q, Elbourne LD et al. Fluorescence-based flow sorting in parallel with transposon insertion site sequencing identifies multidrug efflux systems in Acinetobacter baumannii. mBio 2016;7:e01200–16 [CrossRef][PubMed]
     [Google Scholar]
  • 28. Langridge GC, Phan MD, Turner DJ, Perkins TT, Parts L et al. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res 2009;19:2308–2316 [CrossRef][PubMed]
     [Google Scholar]
  • 29. Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ et al. The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. Bioinformatics 2016;32:1109–1111 [CrossRef][PubMed]
     [Google Scholar]
  • 30. Dembek M, Barquist L, Boinett CJ, Cain AK, Mayho M et al. High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. mBio 2015;6:e02383 [CrossRef][PubMed]
     [Google Scholar]
  • 31. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010;26:139–140 [CrossRef][PubMed]
     [Google Scholar]
  • 32. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006;22:2688–2690 [CrossRef][PubMed]
     [Google Scholar]
  • 33. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2015;43:e15e15 [CrossRef][PubMed]
     [Google Scholar]
  • 34. Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 2017;34:292–293 [CrossRef][PubMed]
     [Google Scholar]
  • 35. Barquist L, Boinett CJ, Cain AK. Approaches to querying bacterial genomes with transposon-insertion sequencing. RNA Biol 2013;10:1161–1169 [CrossRef][PubMed]
     [Google Scholar]
  • 36. Hood MI, Becker KW, Roux CM, Dunman PM, Skaar EP. Genetic determinants of intrinsic colistin tolerance in Acinetobacter baumannii. Infect Immun 2013;81:542–551 [CrossRef][PubMed]
     [Google Scholar]
  • 37. Cao M, Helmann JD. The Bacillus subtilis extracytoplasmic-function sigmaX factor regulates modification of the cell envelope and resistance to cationic antimicrobial peptides. J Bacteriol 2004;186:1136–1146 [CrossRef][PubMed]
     [Google Scholar]
  • 38. Jana B, Cain AK, Doerrler WT, Boinett CJ, Fookes MC et al. The secondary resistome of multidrug-resistant Klebsiella pneumoniae. Sci Rep 2017;7:42483 [CrossRef][PubMed]
     [Google Scholar]
  • 39. Malinverni JC, Silhavy TJ. An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Proc Natl Acad Sci USA 2009;106:8009–8014 [CrossRef][PubMed]
     [Google Scholar]
  • 40. Henry R, Vithanage N, Harrison P, Seemann T, Coutts S et al. Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-β-1,6-N-acetylglucosamine. Antimicrob Agents Chemother 2012;56:59–69 [CrossRef][PubMed]
     [Google Scholar]
  • 41. Rosenfeld N, Bouchier C, Courvalin P, Périchon B. Expression of the resistance-nodulation-cell division pump AdeIJK in Acinetobacter baumannii is regulated by AdeN, a TetR-type regulator. Antimicrob Agents Chemother 2012;56:2504–2510 [CrossRef][PubMed]
     [Google Scholar]
  • 42. Raffa RG, Raivio TL. A third envelope stress signal transduction pathway in Escherichia coli. Mol Microbiol 2002;45:1599–1611 [CrossRef][PubMed]
     [Google Scholar]
  • 43. Lin MF, Lin YY, Lan CY. The role of the two-component system BaeSR in disposing chemicals through regulating transporter systems in Acinetobacter baumannii. PLoS One 2015;10:e013284315 [CrossRef][PubMed]
     [Google Scholar]
  • 44. Nagakubo S, Nishino K, Hirata T, Yamaguchi A. The putative response regulator BaeR stimulates multidrug resistance of Escherichia coli via a novel multidrug exporter system, MdtABC. J Bacteriol 2002;184:4161–4167
     [Google Scholar]
  • 45. Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M et al. Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.. Sci Rep 2018;8:9868
     [Google Scholar]
  • 46. Band VI, Crispell EK, Napier BA, Herrera CM, Tharp GK et al. Antibiotic failure mediated by a resistant subpopulation in Enterobacter cloacae. Nat Microbiol 2016;1:16053 [CrossRef][PubMed]
     [Google Scholar]
  • 47. Makarova KS, Grishin NV. The Zn-peptidase superfamily: functional convergence after evolutionary divergence. J Mol Biol 1999;292:11–17 [CrossRef][PubMed]
     [Google Scholar]
  • 48. Kooi C, Sokol PA. Burkholderia cenocepacia zinc metalloproteases influence resistance to antimicrobial peptides. Microbiology 2009;155:2818–2825 [CrossRef][PubMed]
     [Google Scholar]
  • 49. Geisinger E, Isberg RR. Antibiotic modulation of capsular exopolysaccharide and virulence in Acinetobacter baumannii. PLoS Pathog 2015;11:e100469127 [CrossRef][PubMed]
     [Google Scholar]
  • 50. Kenyon JJ, Hall RM. Variation in the complex carbohydrate biosynthesis loci of Acinetobacter baumannii genomes. PLoS One 2013;8:e62160 [CrossRef][PubMed]
     [Google Scholar]
  • 51. Snitkin ES, Zelazny AM, Montero CI, Stock F, Mijares LNISC Comparative Sequence Program et al. Genome-wide recombination drives diversification of epidemic strains of Acinetobacter baumannii. Proc Natl Acad Sci USA 2011;108:13758–13763 [CrossRef][PubMed]
     [Google Scholar]
  • 52. Snitkin ES, Zelazny AM, Gupta J, Palmore TN, Murray PRNISC Comparative Sequencing Program et al. Genomic insights into the fate of colistin resistance and Acinetobacter baumannii during patient treatment. Genome Res 2013;23:1155–1162 [CrossRef][PubMed]
     [Google Scholar]
  • 53. Beceiro A, Moreno A, Fernández N, Vallejo JA, Aranda J et al. Biological cost of different mechanisms of colistin resistance and their impact on virulence in Acinetobacter baumannii. Antimicrob Agents Chemother 2014;58:518–526 [CrossRef][PubMed]
     [Google Scholar]
  • 54. Bender RA. Regulation of the histidine utilization (hut) system in bacteria. Microbiol Mol Biol Rev 2012;76:565–584 [CrossRef][PubMed]
     [Google Scholar]
  • 55. Krell T, Lacal J, Busch A, Silva-Jiménez H, Guazzaroni ME et al. Bacterial sensor kinases: diversity in the recognition of environmental signals. Annu Rev Microbiol 2010;64:539–559 [CrossRef][PubMed]
     [Google Scholar]
  • 56. Ramos JL, Martínez-Bueno M, Antonio J, Terán W, Watanabe K et al. The TetR family of transcriptional repressors the TetR family of transcriptional repressors. Microbiol Mol Biol Rev 2005;69:326–356
     [Google Scholar]
  • 57. Piddock LJ. Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria. Clin Microbiol Rev 2006;19:382–402 [CrossRef][PubMed]
     [Google Scholar]
  • 58. Cheah SE, Johnson MD, Zhu Y, Tsuji BT, Forrest A et al. Polymyxin resistance in Acinetobacter baumannii: genetic mutations and transcriptomic changes in response to clinically relevant dosage regimens. Sci Rep 2016;6:26233 [CrossRef]
     [Google Scholar]
  • 59. Henry R, Crane B, Powell D, Deveson Lucas D, Li Z et al. The transcriptomic response of Acinetobacter baumannii to colistin and doripenem alone and in combination in an in vitro pharmacokinetics/pharmacodynamics model. J Antimicrob Chemother 2015;70:1303–1313 [CrossRef][PubMed]
     [Google Scholar]
  • 60. Lin MF, Lin YY, Lan CY. Contribution of EmrAB efflux pumps to colistin resistance in Acinetobacter baumannii. J Microbiol 2017;55:130–136 [CrossRef][PubMed]
     [Google Scholar]
  • 61. Ni W, Li Y, Guan J, Zhao J, Cui J et al. Effects of efflux pump inhibitors on colistin resistance in multidrug-resistant gram-negative bacteria. Antimicrob Agents Chemother 2016;60:3215–3218 [CrossRef][PubMed]
     [Google Scholar]
http://sgm.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000246
Loading

Supplementary Data

 Data loading....

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000246
2019-02-05
2019-07-22
Loading full text...

Full text loading...

/deliver/fulltext/mgen/5/2/mgen000246.html?itemId=/content/journal/mgen/10.1099/mgen.0.000246&mimeType=html&fmt=ahah

Author and Article Information

 Figure data loading....

Footnotes:

Validated antibodies in this article

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error