1887

Abstract

Pseudomonas aeruginosa chronic infections of cystic fibrosis (CF) airways are a paradigm for within-host evolution with abundant evidence for rapid evolutionary adaptation and diversification. Recently emerged transmissible strains have spread globally, with the Liverpool Epidemic Strain (LES) the most common strain infecting the UK CF population. Previously we have shown that highly divergent lineages of LES can be found within a single infection, consistent with super-infection among a cross-sectional cohort of patients. However, despite its clinical importance, little is known about the impact of transmission on the genetic structure of these infections over time. To characterize this, we longitudinally sampled a meta-population of 15 genetic lineages within the LES over 13 months among seven chronically infected CF patients by genome sequencing. Comparative genome analyses of P. aeruginosa populations revealed that the presence of coexisting lineages contributed more to genetic diversity within an infection than diversification in situ. We observed rapid and substantial shifts in the relative abundance of lineages and replacement of dominant lineages, likely to represent super-infection by repeated transmissions. Lineage dynamics within patients led to rapid changes in the frequencies of mutations across suites of linked loci carried by each lineage. Many loci were associated with important infection phenotypes such as antibiotic resistance, mucoidy and quorum sensing, and were repeatedly mutated in different lineages. These findings suggest that transmission leads to rapid shifts in the genetic structure of CF infections, including in clinically important phenotypes such as antimicrobial resistance, and is likely to impede accurate diagnosis and treatment.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000167
2018-03-16
2019-12-07
Loading full text...

Full text loading...

/deliver/fulltext/mgen/4/3/mgen000167.html?itemId=/content/journal/mgen/10.1099/mgen.0.000167&mimeType=html&fmt=ahah

References

  1. Driscoll JA, Brody SL, Kollef MH. The epidemiology, pathogenesis and treatment of Pseudomonas aeruginosa infections. Drugs 2007;67:351–368 [CrossRef][PubMed]
    [Google Scholar]
  2. Murray TS, Egan M, Kazmierczak BI. Pseudomonas aeruginosa chronic colonization in cystic fibrosis patients. Curr Opin Pediatr 2007;19:83–88 [CrossRef][PubMed]
    [Google Scholar]
  3. Folkesson A, Jelsbak L, Yang L, Johansen HK, Ciofu O et al. Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat Rev Microbiol 2012;10:841–851 [CrossRef][PubMed]
    [Google Scholar]
  4. Cramer N, Klockgether J, Wrasman K, Schmidt M, Davenport CF et al. Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ Microbiol 2011;13:1690–1704 [CrossRef][PubMed]
    [Google Scholar]
  5. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci USA 2006;103:8487–8492 [CrossRef][PubMed]
    [Google Scholar]
  6. Winstanley C, O'Brien S, Brockhurst MA. Pseudomonas aeruginosa evolutionary adaptation and diversification in cystic fibrosis chronic lung infections. Trends Microbiol 2016;24:327–337 [CrossRef][PubMed]
    [Google Scholar]
  7. Jelsbak L, Johansen HK, Frost AL, Thøgersen R, Thomsen LE et al. Molecular epidemiology and dynamics of Pseudomonas aeruginosa populations in lungs of cystic fibrosis patients. Infect Immun 2007;75:2214–2224 [CrossRef][PubMed]
    [Google Scholar]
  8. Martin K, Baddal B, Mustafa N, Perry C, Underwood A et al. Clusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK. J Med Microbiol 2013;62:988–1000 [CrossRef][PubMed]
    [Google Scholar]
  9. Fothergill JL, Walshaw MJ, Winstanley C. Transmissible strains of Pseudomonas aeruginosa in cystic fibrosis lung infections. Eur Respir J 2012;40:227–238 [CrossRef][PubMed]
    [Google Scholar]
  10. Parkins MD, Glezerson BA, Sibley CD, Sibley KA, Duong J et al. Twenty-five-year outbreak of Pseudomonas aeruginosa infecting individuals with cystic fibrosis: identification of the prairie epidemic strain. J Clin Microbiol 2014;52:1127–1135 [CrossRef][PubMed]
    [Google Scholar]
  11. Dingemans J, Ye L, Hildebrand F, Tontodonati F, Craggs M et al. The deletion of TonB-dependent receptor genes is part of the genome reduction process that occurs during adaptation of Pseudomonas aeruginosa to the cystic fibrosis lung. Pathog Dis 2014;71:26–38 [CrossRef][PubMed]
    [Google Scholar]
  12. Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C et al. Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the liverpool epidemic strain of Pseudomonas aeruginosa. Genome Res 2009;19:12–23 [CrossRef][PubMed]
    [Google Scholar]
  13. Aaron SD, Vandemheen KL, Ramotar K, Giesbrecht-Lewis T, Tullis E et al. Infection with transmissible strains of Pseudomonas aeruginosa and clinical outcomes in adults with cystic fibrosis. JAMA 2010;304:2145–2153 [CrossRef][PubMed]
    [Google Scholar]
  14. O'Brien S, Williams D, Fothergill JL, Paterson S, Winstanley C et al. High virulence sub-populations in Pseudomonas aeruginosa long-term cystic fibrosis airway infections. BMC Microbiol 2017;17:S75 [CrossRef][PubMed]
    [Google Scholar]
  15. Al-Aloul M, Crawley J, Winstanley C, Hart CA, Ledson MJ et al. Increased morbidity associated with chronic infection by an epidemic Pseudomonas aeruginosa strain in CF patients. Thorax 2004;59:334–336 [CrossRef][PubMed]
    [Google Scholar]
  16. Mowat E, Paterson S, Fothergill JL, Wright EA, Ledson MJ et al. Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections. Am J Respir Crit Care Med 2011;183:1674–1679 [CrossRef][PubMed]
    [Google Scholar]
  17. Fothergill JL, Mowat E, Ledson MJ, Walshaw MJ, Winstanley C. Fluctuations in phenotypes and genotypes within populations of Pseudomonas aeruginosa in the cystic fibrosis lung during pulmonary exacerbations. J Med Microbiol 2010;59:472–481 [CrossRef][PubMed]
    [Google Scholar]
  18. Williams D, Evans B, Haldenby S, Walshaw MJ, Brockhurst MA et al. Divergent, coexisting Pseudomonas aeruginosa lineages in chronic cystic fibrosis lung infections. Am J Respir Crit Care Med 2015;191:775–785 [CrossRef][PubMed]
    [Google Scholar]
  19. Workentine ML, Sibley CD, Glezerson B, Purighalla S, Norgaard-Gron JC et al. Phenotypic heterogeneity of Pseudomonas aeruginosa populations in a cystic fibrosis patient. PLoS One 2013;8:e60225 [CrossRef][PubMed]
    [Google Scholar]
  20. Burke MK. How does adaptation sweep through the genome? Insights from long-term selection experiments. Proc Biol Sci 2012;279:5029–5038 [CrossRef][PubMed]
    [Google Scholar]
  21. Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal 2011;17:10 [CrossRef]
    [Google Scholar]
  22. Joshi NA, Fass JN. 2011; Sickle: A sliding-window, adaptive, quality-based trimming tool for FastQ files. Available fromhttps://github.com/najoshi/sickle
  23. Mckenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297–1303 [CrossRef][PubMed]
    [Google Scholar]
  24. Cingolani P, Platts A, Wang L, Coon M, Nguyen T et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012;6:80–92 [CrossRef][PubMed]
    [Google Scholar]
  25. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32:268–274 [CrossRef][PubMed]
    [Google Scholar]
  26. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017;14:587–589 [CrossRef][PubMed]
    [Google Scholar]
  27. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: Improving the Ultrafast Bootstrap Approximation. Mol Biol Evol 2018;35:518–522 [CrossRef][PubMed]
    [Google Scholar]
  28. Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 1981;78:454–458 [CrossRef][PubMed]
    [Google Scholar]
  29. Fothergill JL, Ledson MJ, Walshaw MJ, Mcnamara PS, Southern KW et al. Comparison of real time diagnostic chemistries to detect Pseudomonas aeruginosa in respiratory samples from cystic fibrosis patients. J Cyst Fibros 2013;12:675–681 [CrossRef][PubMed]
    [Google Scholar]
  30. Mccallum SJ, Corkill J, Gallagher M, Ledson MJ, Hart CA et al. Superinfection with a transmissible strain of Pseudomonas aeruginosa in adults with cystic fibrosis chronically colonised by P aeruginosa. Lancet 2001;358:558–560 [CrossRef][PubMed]
    [Google Scholar]
  31. Marvig RL, Johansen HK, Molin S, Jelsbak L. Genome analysis of a transmissible lineage of pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators. PLoS Genet 2013;9:e1003741 [CrossRef][PubMed]
    [Google Scholar]
  32. Williams D, Paterson S, Brockhurst MA, Winstanley C. Refined analyses suggest that recombination is a minor source of genomic diversity in Pseudomonas aeruginosa chronic cystic fibrosis infections. Microb Genom 2016;2:e000051 [CrossRef][PubMed]
    [Google Scholar]
  33. Winstanley C, Fothergill JL. The role of quorum sensing in chronic cystic fibrosis Pseudomonas aeruginosa infections. FEMS Microbiol Lett 2009;290:1–9 [CrossRef][PubMed]
    [Google Scholar]
  34. Lee J, Zhang L. The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 2015;6:26–41 [CrossRef][PubMed]
    [Google Scholar]
  35. Flemming HC, Wingender J. The biofilm matrix. Nat Rev Microbiol 2010;8:623–633 [CrossRef][PubMed]
    [Google Scholar]
  36. Nguyen AT, O'Neill MJ, Watts AM, Robson CL, Lamont IL et al. Adaptation of iron homeostasis pathways by a Pseudomonas aeruginosa pyoverdine mutant in the cystic fibrosis lung. J Bacteriol 2014;196:2265–2276 [CrossRef][PubMed]
    [Google Scholar]
  37. Marvig RL, Damkiær S, Khademi SM, Markussen TM, Molin S et al. Within-host evolution of Pseudomonas aeruginosa reveals adaptation toward iron acquisition from hemoglobin. MBio 2014;5:e00966-14 [CrossRef][PubMed]
    [Google Scholar]
  38. Hirakata Y, Srikumar R, Poole K, Gotoh N, Suematsu T et al. Multidrug efflux systems play an important role in the invasiveness of Pseudomonas aeruginosa. J Exp Med 2002;196:109–118 [CrossRef][PubMed]
    [Google Scholar]
  39. Li XZ, Nikaido H, Poole K. Role of mexA-mexB-oprM in antibiotic efflux in Pseudomonas aeruginosa. Antimicrob Agents Chemother 1995;39:1948–1953[PubMed]
    [Google Scholar]
  40. Hilliam Y, Moore MP, Lamont IL, Bilton D, Haworth CS et al. Pseudomonas aeruginosa adaptation and diversification in the non-cystic fibrosis bronchiectasis lung. Eur Respir J 2017;49:1602108 [CrossRef][PubMed]
    [Google Scholar]
  41. Winstanley C, O'Brien S, Brockhurst MA. Pseudomonas aeruginosa evolutionary adaptation and diversification in cystic fibrosis chronic lung infections. Trends Microbiol 2016;24:327–337 [CrossRef][PubMed]
    [Google Scholar]
  42. Marvig RL, Sommer LM, Jelsbak L, Molin S, Johansen HK. Evolutionary insight from whole-genome sequencing of Pseudomonas aeruginosa from cystic fibrosis patients. Future Microbiol 2015;10:599–611 [CrossRef][PubMed]
    [Google Scholar]
  43. Chung JC, Becq J, Fraser L, Schulz-Trieglaff O, Bond NJ et al. Genomic variation among contemporary Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis patients. J Bacteriol 2012;194:4857–4866 [CrossRef][PubMed]
    [Google Scholar]
  44. Feliziani S, Marvig RL, Luján AM, Moyano AJ, di Rienzo JA et al. Coexistence and within-host evolution of diversified lineages of hypermutable Pseudomonas aeruginosa in long-term cystic fibrosis infections. PLoS Genet 2014;10:e1004651 [CrossRef][PubMed]
    [Google Scholar]
  45. Markussen T, Marvig RL, Gómez-Lozano M, Aanæs K, Burleigh AE et al. Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa. MBio 2014;5:e01592-14 [CrossRef][PubMed]
    [Google Scholar]
  46. Jorth P, Staudinger BJ, Wu X, Hisert KB, Hayden H et al. Regional isolation drives bacterial diversification within cystic fibrosis lungs. Cell Host Microbe 2015;18:307–319 [CrossRef][PubMed]
    [Google Scholar]
  47. Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. The dynamics of molecular evolution over 60,000 generations. Nature 2017;551:45–50 [CrossRef][PubMed]
    [Google Scholar]
  48. Corander J, Fraser C, Gutmann MU, Arnold B, Hanage WP et al. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat Ecol Evol 2017;1:1950–1960 [CrossRef][PubMed]
    [Google Scholar]
  49. Hibbing ME, Fuqua C, Parsek MR, Peterson SB. Bacterial competition: surviving and thriving in the microbial jungle. Nat Rev Microbiol 2010;8:15–25 [CrossRef][PubMed]
    [Google Scholar]
  50. Marvig RL, Sommer LM, Molin S, Johansen HK. Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis. Nat Genet 2015;47:57–64 [CrossRef][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000167
Loading
/content/journal/mgen/10.1099/mgen.0.000167
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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