1887

Abstract

Acinetobacter baumannii is a common causative agent of hospital-acquired infections and a leading cause of infection in burns patients. Carbapenem-resistant A. baumannii is considered a major public-health threat and has been identified by the World Health Organization as the top priority organism requiring new antimicrobials. The most common mechanism for carbapenem resistance in A. baumannii is via horizontal acquisition of carbapenemase genes. In this study, we sampled 20 A. baumannii isolates from a patient with extensive burns, and characterized the evolution of carbapenem resistance over a 45 day period via Illumina and Oxford Nanopore sequencing. All isolates were multidrug resistant, carrying two genomic islands that harboured several antibiotic-resistance genes. Most isolates were genetically identical and represented a single founder genotype. We identified three novel non-synonymous substitutions associated with meropenem resistance: F136L and G288S in AdeB (part of the AdeABC efflux pump) associated with an increase in meropenem MIC to ≥8 µg ml; and A515V in FtsI (PBP3, a penicillin-binding protein) associated with a further increase in MIC to 32 µg ml. Structural modelling of AdeB and FtsI showed that these mutations affected their drug-binding sites and revealed mechanisms for meropenem resistance. Notably, one of the adeB mutations arose prior to meropenem therapy but following ciprofloxacin therapy, suggesting exposure to one drug whose resistance is mediated by the efflux pump can induce collateral resistance to other drugs to which the bacterium has not yet been exposed.

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2018-03-16
2019-09-15
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References

  1. Rice LB. Federal funding for the study of antimicrobial resistance in nosocomial pathogens: no ESKAPE. J Infect Dis 2008;197:1079–1081 [CrossRef][PubMed]
    [Google Scholar]
  2. Maragakis LL, Perl TM. Acinetobacter baumannii: epidemiology, antimicrobial resistance, and treatment options. Clin Infect Dis 2008;46:1254–1263 [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. Nigro SJ, Farrugia DN, Paulsen IT, Hall RM. A novel family of genomic resistance islands, AbGRI2, contributing to aminoglycoside resistance in Acinetobacter baumannii isolates belonging to global clone 2. J Antimicrob Chemother 2013;68:554–557 [CrossRef][PubMed]
    [Google Scholar]
  5. Post V, White PA, Hall RM. Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii. J Antimicrob Chemother 2010;65:1162–1170 [CrossRef][PubMed]
    [Google Scholar]
  6. Hamidian M, Holt KE, Pickard D, Dougan G, Hall RM. A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid. JAntimicrob Chemother 2014;69:955–958 [CrossRef][PubMed]
    [Google Scholar]
  7. Holt K, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ et al. Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. Microb Genom 2016;2::e000052 [CrossRef][PubMed]
    [Google Scholar]
  8. Hornsey M, Loman N, Wareham DW, Ellington MJ, Pallen MJ et al. Whole-genome comparison of two Acinetobacter baumannii isolates from a single patient, where resistance developed during tigecycline therapy. J Antimicrob Chemother 2011;66:1499–1503 [CrossRef][PubMed]
    [Google Scholar]
  9. Bergogne-Bérézin E, Towner KJ. Acinetobacter spp. as nosocomial pathogens: microbiological, clinical, and epidemiological features. Clin Microbiol Rev 1996;9:148–165[PubMed]
    [Google Scholar]
  10. Hamidian M, Hall RM. ISAba1 targets a specific position upstream of the intrinsic ampC gene of Acinetobacter baumannii leading to cephalosporin resistance. J Antimicrob Chemother 2013;68:2682–2683 [CrossRef][PubMed]
    [Google Scholar]
  11. Hamidian M, Hancock DP, Hall RM. Horizontal transfer of an ISAba125-activated ampC gene between Acinetobacter baumannii strains leading to cephalosporin resistance. J Antimicrob Chemother 2013;68:244–245 [CrossRef][PubMed]
    [Google Scholar]
  12. Hamidian M, Hall RM. Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii. J Antimicrob Chemother 2014;69:77–80 [CrossRef][PubMed]
    [Google Scholar]
  13. Seward RJ, Towner KJ. Molecular epidemiology of quinolone resistance in Acinetobacter spp. Clin Microbiol Infect 1998;4:248–254 [CrossRef][PubMed]
    [Google Scholar]
  14. Hamouda A, Amyes SG. Novel gyrA and parC point mutations in two strains of Acinetobacter baumannii resistant to ciprofloxacin. J Antimicrob Chemother 2004;54:695–696 [CrossRef][PubMed]
    [Google Scholar]
  15. Vila J, Ruiz J, Goñi P, Jimenez de Anta T. Quinolone-resistance mutations in the topoisomerase IV parC gene of Acinetobacter baumannii. J Antimicrob Chemother 1997;39:757–762 [CrossRef][PubMed]
    [Google Scholar]
  16. Fernández-Cuenca F, Martínez-Martínez L, Conejo MC, Ayala JA, Perea EJ et al. Relationship between β-lactamase production, outer membrane protein and penicillin-binding protein profiles on the activity of carbapenems against clinical isolates of Acinetobacter baumannii. J Antimicrob Chemother 2003;51:565–574 [CrossRef][PubMed]
    [Google Scholar]
  17. Héritier C, Poirel L, Lambert T, Nordmann P. Contribution of acquired carbapenem-hydrolyzing oxacillinases to carbapenem resistance in Acinetobacter baumannii. Antimicrob Agents Chemother 2005;49:3198–3202 [CrossRef][PubMed]
    [Google Scholar]
  18. Lee Y, Yum JH, Kim C-K, Yong D, Jeon EH et al. Role of OXA-23 and AdeABC efflux pump for acquiring carbapenem resistance in an Acinetobacter baumannii strain carrying the bla OXA-66 gene. Ann Clin Lab Sci 2010;40:43–48[PubMed]
    [Google Scholar]
  19. Ardebili A, Lari AR, Talebi M. Correlation of ciprofloxacin resistance with the AdeABC efflux system in Acinetobacter baumannii clinical isolates. Ann Lab Med 2014;34:433–438 [CrossRef][PubMed]
    [Google Scholar]
  20. Lim CJ, Cheng AC, Kennon J, Spelman D, Hale D et al. Prevalence of multidrug-resistant organisms and risk factors for carriage in long-term care facilities: a nested case-control study. J Antimicrob Chemother 2014;69:1972–1980 [CrossRef][PubMed]
    [Google Scholar]
  21. Ruzin A, Keeney D, Bradford PA. AdeABC multidrug efflux pump is associated with decreased susceptibility to tigecycline in Acinetobacter calcoaceticus-Acinetobacter baumannii complex. J Antimicrob Chemother 2007;59:1001–1004 [CrossRef][PubMed]
    [Google Scholar]
  22. Peleg AY, Adams J, Paterson DL. Tigecycline efflux as a mechanism for nonsusceptibility in Acinetobacter baumannii. Antimicrob Agents Chemother 2007;51:2065–2069 [CrossRef][PubMed]
    [Google Scholar]
  23. WHO Global Priority List of Antibiotic-Resistant Bacteria to Guide Research, Discovery, and Development of New Antibiotics. Geneva:: World Health Organization; 2017
    [Google Scholar]
  24. Zarrilli R, Pournaras S, Giannouli M, Tsakris A. Global evolution of multidrug-resistant Acinetobacter baumannii clonal lineages. Int J Antimicrob Agents 2013;41:11–19 [CrossRef][PubMed]
    [Google Scholar]
  25. 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::e000050 [CrossRef][PubMed]
    [Google Scholar]
  26. Young BC, Golubchik T, Batty EM, Fung R, Larner-Svensson H et al. Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease. Proc Natl Acad Sci USA 2012;109:4550–4555 [CrossRef][PubMed]
    [Google Scholar]
  27. Kennemann L, Didelot X, Aebischer T, Kuhn S, Drescher B et al. Helicobacter pylori genome evolution during human infection. Proc Natl Acad Sci USA 2011;108:5033–5038 [CrossRef][PubMed]
    [Google Scholar]
  28. Price EP, Sarovich DS, Mayo M, Tuanyok A, Drees KP et al. Within-host evolution of Burkholderia pseudomallei over a twelve-year chronic carriage infection. mBio 2013;4:e00388-13 [CrossRef][PubMed]
    [Google Scholar]
  29. Wright MS, Iovleva A, Jacobs MR, Bonomo RA, Adams MD. Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. Genome Med 2016;8:26 [CrossRef][PubMed]
    [Google Scholar]
  30. 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]
  31. Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microb Genom 2017;3:e000132 [CrossRef][PubMed]
    [Google Scholar]
  32. 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]
  33. 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]
  34. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75 [CrossRef][PubMed]
    [Google Scholar]
  35. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ et al. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014;6:90 [CrossRef][PubMed]
    [Google Scholar]
  36. Gupta SK, Padmanabhan BR, Diene SM, Lopez-Rojas R, Kempf M et al. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 2014;58:212–220 [CrossRef][PubMed]
    [Google Scholar]
  37. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009;10:421 [CrossRef][PubMed]
    [Google Scholar]
  38. Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG et al. ACT: the Artemis Comparison Tool. Bioinformatics 2005;21:3422–3423 [CrossRef][PubMed]
    [Google Scholar]
  39. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Meth 2012;9:357–359 [CrossRef][PubMed]
    [Google Scholar]
  40. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009;25:2078–2079 [CrossRef][PubMed]
    [Google Scholar]
  41. Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol 2011;12:R30 [CrossRef][PubMed]
    [Google Scholar]
  42. 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]
  43. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000;16:276–277 [CrossRef][PubMed]
    [Google Scholar]
  44. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779–815 [CrossRef][PubMed]
    [Google Scholar]
  45. Jubb HC, Pandurangan AP, Turner MA, Ochoa-Montaño B, Blundell TL et al. Mutations at protein-protein interfaces: small changes over big surfaces have large impacts on human health. Prog Biophys Mol Biol 2017;128:3–13 [CrossRef][PubMed]
    [Google Scholar]
  46. Pires DEV, Chen J, Blundell TL, Ascher DB. In silico functional dissection of saturation mutagenesis: interpreting the relationship between phenotypes and changes in protein stability, interactions and activity. Sci Rep 2016;6:19848 [CrossRef][PubMed]
    [Google Scholar]
  47. Pandurangan AP, Ochoa-Montaño B, Ascher DB, Blundell TL. SDM: a server for predicting effects of mutations on protein stability. Nucleic Acids Res 2017;45:W229–W235 [CrossRef][PubMed]
    [Google Scholar]
  48. Pires DEV, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics 2014;30:335–342 [CrossRef][PubMed]
    [Google Scholar]
  49. Pires DEV, Ascher DB, Blundell TL. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res 2014;42:W314–W319 [CrossRef][PubMed]
    [Google Scholar]
  50. Pires DEV, Blundell TL, Ascher DB. mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Sci Rep 2016;6:29575 [CrossRef][PubMed]
    [Google Scholar]
  51. Pires DEV, Blundell TL, Ascher DB. Platinum: a database of experimentally measured effects of mutations on structurally defined protein-ligand complexes. Nucleic Acids Res 2015;43:D387–D391 [CrossRef][PubMed]
    [Google Scholar]
  52. Pires DEV, Ascher DB. CSM-lig: a web server for assessing and comparing protein-small molecule affinities. Nucleic Acids Res 2016;44:W557–W561 [CrossRef][PubMed]
    [Google Scholar]
  53. Huang H, Yang Z-L, Wu X-M, Wang Y, Liu Y-J et al. Complete genome sequence of Acinetobacter baumannii MDR-TJ and insights into its mechanism of antibiotic resistance. J Antimicrob Chemother 2012;67:2825–2832 [CrossRef][PubMed]
    [Google Scholar]
  54. Hamidian M, Hall RM. Origin of the AbGRI1 antibiotic resistance island found in the comM gene of Acinetobacter baumannii GC2 isolates. J Antimicrob Chemother 2017;72:2944–2947 [CrossRef][PubMed]
    [Google Scholar]
  55. Blackwell GA, Nigro SJ, Hall RM. Evolution of AbGRI2-0, the progenitor of the AbGRI2 resistance island in global clone 2 of Acinetobacter baumannii. Antimicrob Agents Chemother 2015;60:1421–1429 [CrossRef][PubMed]
    [Google Scholar]
  56. Lopes BS, Amyes SG. Insertion sequence disruption of adeR and ciprofloxacin resistance caused by efflux pumps and gyrA and parC mutations in Acinetobacter baumannii. Int J Antimicrob Agents 2013;41:117–121 [CrossRef][PubMed]
    [Google Scholar]
  57. Huang L, Sun L, Xu G, Xia T. Differential susceptibility to carbapenems due to the AdeABC efflux pump among nosocomial outbreak isolates of Acinetobacter baumannii in a Chinese hospital. Diagn Microbiol Infect Dis 2008;62:326–332 [CrossRef][PubMed]
    [Google Scholar]
  58. Cayô R, Rodríguez M-C, Espinal P, Fernández-Cuenca F, Ocampo-Sosa AA et al. Analysis of genes encoding penicillin-binding proteins in clinical isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 2011;55:5907–5913 [CrossRef][PubMed]
    [Google Scholar]
  59. Zhang T, Wang M, Xie Y, Li X, Dong Z et al. Active efflux pump adeB is involved in multidrug resistance of Acinetobacter baumannii induced by antibacterial agents. Exp Ther Med 2017;13:1538–1546 [CrossRef][PubMed]
    [Google Scholar]
  60. Higgins PG, Schneiders T, Hamprecht A, Seifert H. In vivo selection of a missense mutation in adeR and conversion of the novel blaOXA-164 gene into blaOXA-58 in carbapenem-resistant Acinetobacter baumannii isolates from a hospitalized patient. Antimicrob Agents Chemother 2010;54:5021–5027 [CrossRef][PubMed]
    [Google Scholar]
  61. Wright MS, Haft DH, Harkins DM, Perez F, Hujer KM et al. New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. mBio 2014;5:e00963-13 [CrossRef][PubMed]
    [Google Scholar]
  62. Rafla K, Tredget EE. Infection control in the burn unit. Burns 2011;37:5–15 [CrossRef][PubMed]
    [Google Scholar]
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