Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen

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Adaptation is likely to be an important determinant of the success of many pathogens, for example when colonizing a new host species, when challenged by antibiotic treatment, or in governing the establishment and progress of long-term chronic infection. Yet, the genomic basis of adaptation is poorly understood in general, and for pathogens in particular. We investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen Pseudomonas aeruginosa. Whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. While the level of antibiotic resistance was largely determined by these known resistance genes, the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. Notably, stereotypical quinolone resistance mutations in DNA gyrase often co-occurred with other mutations that, together, conferred high levels of resistance but no consistent cost of resistance. This result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. In addition, genes involved in cyclic-di-GMP signalling were repeatedly mutated in populations evolved in viscous culture media, suggesting a shared mechanism of adaptation to this CF–like growth environment. Experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates.

Vyšlo v časopise: Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen. PLoS Genet 8(9): e32767. doi:10.1371/journal.pgen.1002928
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002928

Souhrn

Zdroje

1. PasteurL (1878) La Theorie des Germes. Comptes Rendus l'Academie des Sciences 86: 1037–1043.

2. BrownSA, PalmerKL, WhiteleyM (2008) Revisiting the host as a growth medium. Nat Rev Microbiol 6: 657–666.

3. GarberED (1960) The host as a growth medium. Ann NY Acad Sci 88: 1187–1194.

4. AnderssonDI (2003) Persistence of antibiotic resistant bacteria. Curr Opin Microbiol l6: 452–456.

5. SalyersAA, Amábile-CuevasCF (1997) Why are antibiotic resistance genes so resistant to elimination? Antimicrob Agents Chemother 41: 2321–2325.

6. LivermoreDM (2004) The need for new antibiotics. Clin Microbiol Infect 10 Suppl 4: 1–9.

7. PingJ, KeletaL, ForbesNE, DankarS, StechoW, et al. (2011) Genomic and Protein Structural Maps of Adaptive Evolution of Human Influenza A Virus to Increased Virulence in the Mouse. PLoS ONE 6: e21740 doi:10.1371/journal.pone.0021740..

8. HolmesEC, ZhangLQ, SimmondsP, LudlamCA, BrownAJ (1992) Convergent and divergent sequence evolution in the surface envelope glycoprotein of human immunodeficiency virus type 1 within a single infected patient. Proc Natl Acad Sci USA 89: 4835–4839.

9. MwangiMM, WuSW, ZhouY, SieradzkiK, de LencastreH, et al. (2007) Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proc Natl Acad Sci USA 104: 9451–9456.

10. SmithEE, BuckleyDG, WuZ, SaenphimmachakC, HoffmanLR, et al. (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 103: 8487–8492.

11. ElenaSF, LenskiRE (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4: 457–469.

12. BucklingA, Craig MacleanR, BrockhurstMA, ColegraveN (2009) The Beagle in a bottle. Nature 457: 824–829.

13. HallAR, MacLeanRC (2011) Epistasis buffers the fitness effects of rifampicin- resistance mutations in Pseudomonas aeruginosa. Evolution 65: 2370–2379.

14. KassenR (2009) Toward a general theory of adaptive radiation: insights from microbial experimental evolution. Ann NY Acad Sci 1168: 3–22.

15. PerronGG, LeeAEG, WangY, HuangWE, BarracloughTG (2011) Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations. Proc Biol Sci 279: 1477–1484.

16. KugelbergE, LöfmarkS, WretlindB, AnderssonDI (2005) Reduction of the fitness burden of quinolone resistance in Pseudomonas aeruginosa. J Antimicrob Chemother 55: 22–30.

17. CounagoR, ChenS, ShamooY (2006) In vivo molecular Evolution Reveals Biophysical Origins of Organismal Fitness. Mol Cell 22: 441–449.

18. MarxCJ (2011) Evolution as an experimental tool in microbiology: ‘Bacterium, improve thyself!’. Environ Microbiol Rep 3: 12–14.

19. BrockhurstMA, ColegraveN, RozenDE (2011) Next-generation sequencing as a tool to study microbial evolution. Mol Ecol 20: 972–980.

20. SilbyMW, WinstanleyC, GodfreySAC, LevySB, JacksonRW (2011) Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Lett 35: 652–680.

21. Stephenson A (2008) Canadian Cystic Fibrosis Patient Data Registry Report 2008. Toronto.

22. HuseHK, KwonT, ZlosnikJEA, SpeertDP, MarcotteEM, et al. (2010) Parallel evolution in Pseudomonas aeruginosa over 39,000 generations in vivo. mBio 1: e00199–10.

23. WongA, KassenR (2011) Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa. Microbiology 157: 937–944.

24. CiofuO, MandsbergLF, BjarnsholtT, WassermannT, HøibyN (2010) Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants. Microbiology 156: 1108–1119.

25. StarkeyM, HickmanJH, MaL, ZhangN, De LongS, et al. (2009) Pseudomonas aeruginosa rugose small-colony variants have adaptations that likely promote persistence in the cystic fibrosis lung. J Bacteriol 191: 3492–3503.

26. WorlitzschD, TarranR, UlrichM, SchwabU, CekiciA, et al. (2002) Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J Clin Invest 109: 317–325.

27. MeissnerA, WildV, SimmR, RohdeM, ErckC, et al. (2007) Pseudomonas aeruginosa cupA-encoded fimbriae expression is regulated by a GGDEF and EAL domain-dependent modulation of the intracellular level of cyclic diguanylate. Environ Microbiol 9: 2475–2485.

28. HickmanJW, TifreaDF, HarwoodCS (2005) A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels. Proc Natl Acad Sci USA 102: 14422–14427.

29. WolfeAJ, VisickKL (2008) Get the message out: cyclic-Di-GMP regulates multiple levels of flagellum-based motility. J Bacteriol 190: 463–475.

30. PalmerKL, AyeLM, WhiteleyM (2007) Nutritional cues control Pseudomonas aeruginosa multicellular behavior in cystic fibrosis sputum. J Bacteriol 189: 8079–8087.

31. PedersenSS, JensenT, HvidbergEF (1987) Comparative pharmacokinetics of ciprofloxacin and ofloxacin in cystic fibrosis patients. J Antimicrob Chemother 20: 575–583.

32. FungC, NaughtonS, TurnbullL, TingpejP, RoseB, et al. (2010) Gene expression of Pseudomonas aeruginosa in a mucin-containing synthetic growth medium mimicking CF lung sputum. J Med Microbiol 1089–1100.

33. SriramuluDD, LünsdorfH, LamJS, RömlingU (2005) Microcolony formation: a novel biofilm model of Pseudomonas aeruginosa for the cystic fibrosis lung. J Med Microbiol 54: 667–676.

34. HassettDJ, SuttonMD, SchurrMJ, HerrAB, CaldwellCC, et al. (2009) Pseudomonas aeruginosa hypoxic or anaerobic biofilm infections within cystic fibrosis airways. Trends Microbiol 17: 130–138.

35. SibleyCD, ParkinsMD, RabinHR, DuanK, NorgaardJC, et al. (2008) A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc Natl Acad Sci USA 105: 15070–15075.

36. MowatE, PatersonS, FothergillJL, WrightEA, LedsonMJ, et al. (2011) Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections. Am J Respir Crit Care Med 183: 1674–1679.

37. SmithDR, QuinlanAR, PeckhamHE, MakowskyK, TaoW, et al. (2008) Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18: 1638–1642.

38. BarrickJE, YuDS, YoonSH, JeongH, OhTK, et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243–1247.

39. SchaaperRM, DunnRL (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc Natl Acad Sci USA 84: 6220–6224.

40. DettmanJR, RodrigueN, MelnykAH, WongA, BaileySF, et al. (2012) Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol Ecol epub Feb. 2012

41. DesaiMM, FisherDS (2007) Beneficial mutation selection balance and the effect of linkage on positive selection. Genetics 176: 1759–1798.

42. SchoustraSE, BataillonT, GiffordDR, KassenR (2009) The properties of adaptive walks in evolving populations of fungus. PLoS Biol 7: e1000250 doi:10.1371/journal.pbio.1000250.

43. LynchM (2010) Evolution of the mutation rate. Trends Genet 26: 345–352.

44. YoshidaH, BogakiM, NakamuraM, NakamuraS (1990) Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli. Antimicrob Agents Chemother 34: 1271–1272.

45. YoshidaH, NakamuraM, BogakiM, NakamuraS (1990) Proportion of DNA gyrase mutants among quinolone-resistant strains of Pseudomonas aeruginosa. Antimicrob Agents Chemother 34: 1273–1275.

46. PooleK (2005) Efflux-mediated antimicrobial resistance. J Antimicrob Chemother 56: 20–51.

47. SchirmM, AroraSK, VermaA, VinogradovE, ThibaultP, et al. (2004) Structural and genetic characterization of glycosylation of type a flagellin in Pseudomonas aeruginosa. J Bacteriol 186: 2523–2531.

48. BreidensteinEBM, KhairaBK, WiegandI, OverhageJ, HancockREW (2008) Complex ciprofloxacin resistome revealed by screening a Pseudomonas aeruginosa mutant library for altered susceptibility. Antimicrob Agents Chemother 52: 4486–4491.

49. HooperDC (2001) Emerging Mechanisms of Fluoroquinolone Resistance. Emerg Infect Dis 7: 337–341.

50. YoshidaH, BogakiM, NakamuraM, YamanakaLM, NakamuraS (1991) Quinolone resistance-determining region in the DNA gyrase gyrB gene of Escherichia coli. Antimicrob Agents Chemother 35: 1647–1650.

51. SticklandHG, DavenportPW, LilleyKS, GriffinJL, WelchM (2010) Mutation of nfxB Causes Global Changes in the Physiology and Metabolism of Pseudomonas aeruginosa. Journal of Proteome Research 2957–2967.

52. BagelS, HüllenV, WiedemannB, HeisigP (1999) Impact of gyrA and parC mutations on quinolone resistance, doubling time, and supercoiling degree of Escherichia coli. Antimicrob Agents Chemother 43: 868–875.

53. MarcussonLL, Frimodt-MøllerN, HughesD (2009) Interplay in the selection of fluoroquinolone resistance and bacterial fitness. PLoS Pathog 5: e1000541 doi:10.1371/journal.ppat.1000541..

54. TrindadeS, SousaA, XavierKB, DionisioF, FerreiraMG, et al. (2009) Positive epistasis drives the acquisition of multidrug resistance. PLoS Genet 5: e1000578 doi:10.1371/journal.pgen.1000578..

55. RozenDE, McGeeL, LevinBR, KlugmanKP (2007) Fitness costs of fluoroquinolone resistance in Streptococcus pneumoniae. Antimicrob Agents Chemother 51: 412–416.

56. WardH, PerronGG, MacleanRC (2009) The cost of multiple drug resistance in Pseudomonas aeruginosa. J Evol Biol 22: 997–1003.

57. GottesmanBS, CarmeliY, ShitritP, ChowersM (2009) Impact of quinolone restriction on resistance patterns of Escherichia coli isolated from urine by culture in a community setting. Clin Infect Dis 49: 869–875.

58. BarbosaTM, LevySB (2000) The impact of antibiotic use on resistance development and persistence. Drug Resist Updat 3: 303–311.

59. ChoyW-K, ZhouL, SynCK-C, ZhangL-H, SwarupS (2004) MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species. J Bacteriol 186: 7221–7228.

60. BantinakiE, KassenR, KnightCG, RobinsonZ, SpiersAJ, et al. (2007) Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176: 441–453.

61. FriedmanL, KolterR (2004) Genes involved in matrix formation in Pseudomonas aeruginosa PA14 biofilms. Mol Microbiol 51: 675–690.

62. MerrittJH, HaD-G, CowlesKN, LuW, MoralesDK, et al. (2010) Specific control of Pseudomonas aeruginosa surface-associated behaviors by two c-di-GMP diguanylate cyclases. mBio 1: e00183–10.

63. DietrichLEP, TealTK, Price-WhelanA, NewmanDK (2008) Redox-active antibiotics control gene expression and community behavior in divergent bacteria. Science 321: 1203–1206.

64. GovanJR, DereticV (1996) Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol Rev 60: 539–574.

65. MaloneJG, JaegerT, SpanglerC, RitzD, SpangA, et al. (2010) YfiBNR mediates cyclic di-GMP dependent small colony variant formation and persistence in Pseudomonas aeruginosa. PLoS Pathog 6: e1000804 doi:10.1371/journal.ppat.1000804..

66. CrozatE, WinkworthC, GafféJ, HallinPF, RileyMA, et al. (2010) Parallel genetic and phenotypic evolution of DNA superhelicity in experimental populations of Escherichia coli. Mol Biol Evol 27: 2113–2128.

67. WoodsR, SchneiderD, WinkworthCL, RileyMA, LenskiRE (2006) Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc Natl Acad Sci USA 103: 9107–9112.

68. CunninghamCW, JengK, HustiJ, BadgettM, MolineuxIJ, et al. (1997) Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. Mol Biol Evol 14: 113–116.

69. BullJJ, BadgettMR, WichmanHA, HuelsenbeckJP, HillisDM, et al. (1997) Exceptional convergent evolution in a virus. Genetics 147: 1497–1507.

70. WichmanHA, BrownCJ (2010) Experimental evolution of viruses: Microviridae as a model system. Philos Trans R Soc Lond B Biol Sci 365: 2495–2501.

71. WichmanHA, MillsteinJ, BullJJ (2005) Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170: 19–31.

72. RokytaDR, AbdoZ, WichmanHA (2009) The genetics of adaptation for eight microvirid bacteriophages. J Mol Evol 69: 229–239.

73. CooperVS, SchneiderD, BlotM, LenskiRF (2001) Mechanisms causing rapid and parallel losses of ribose catabolism in evolving populations of Escherichia coli B. J Bacteriol 183: 2834–2841.

74. ChevinL-M, MartinG, LenormandT (2010) Fisher's Model and the Genomics of Adaptation: Restricted Pleiotropy, Heterogenous Mutation, and Parallel Evolution. Evolution 64: 3213–3231.

75. LiH, HandsakerB, WysokerA, FennellT, RuanJ, et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078–2079.

76. McKennaA, HannaM, BanksE, SivachenkoA, CibulskisK, et al. (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297–1303.

77. R Core Development Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.