Convergent evolution and adaptation of Pseudomonas aeruginosa within patients with cystic fibrosis (original) (raw)
Marvig, R.L., Johansen, H.K., Molin, S. & Jelsbak, L. Genome analysis of a transmissible lineage of Pseudomonas aeruginosa reveals pathoadaptive mutations and distinct evolutionary paths of hypermutators. PLoS Genet.9, e1003741 (2013). ArticleCASPubMedPubMed Central Google Scholar
Smith, E.E. et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. USA103, 8487–8492 (2006). ArticleCASPubMedPubMed Central Google Scholar
Cramer, N. et al. Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs. Environ. Microbiol.13, 1690–1704 (2011). ArticleCASPubMed Google Scholar
Holt, K.E. et al. Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proc. Natl. Acad. Sci. USA110, 17522–17527 (2013). ArticleCASPubMedPubMed Central Google Scholar
Eyre, D.W. et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N. Engl. J. Med.369, 1195–1205 (2013). ArticleCASPubMed Google Scholar
Comas, I. et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat. Genet.45, 1176–1182 (2013). ArticleCASPubMedPubMed Central Google Scholar
Mather, A.E. et al. Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts. Science341, 1514–1517 (2013). ArticleCASPubMedPubMed Central Google Scholar
Grad, Y.H. et al. Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study. Lancet Infect. Dis.14, 220–226 (2014). ArticlePubMedPubMed Central Google Scholar
Sokurenko, E.V., Hasty, D.L. & Dykhuizen, D.E. Pathoadaptive mutations: gene loss and variation in bacterial pathogens. Trends Microbiol.7, 191–195 (1999). ArticleCASPubMed Google Scholar
Folkesson, A. et al. Adaptation of Pseudomonas aeruginosa to the cystic fibrosis airway: an evolutionary perspective. Nat. Rev. Microbiol.10, 841–851 (2012). ArticleCASPubMed Google Scholar
Johansen, H.K., Moskowitz, S.M., Ciofu, O., Pressler, T. & Hoiby, N. Spread of colistin resistant non-mucoid Pseudomonas aeruginosa among chronically infected Danish cystic fibrosis patients. J. Cyst. Fibros.7, 391–397 (2008). ArticlePubMed Google Scholar
Jelsbak, L. et al. Molecular epidemiology and dynamics of Pseudomonas aeruginosa populations in lungs of cystic fibrosis patients. Infect. Immun.75, 2214–2224 (2007). ArticleCASPubMedPubMed Central Google Scholar
Zimakoff, J., Hoiby, N., Rosendal, K. & Guilbert, J.P. Epidemiology of Pseudomonas aeruginosa infection and the role of contamination of the environment in a cystic fibrosis clinic. J. Hosp. Infect.4, 31–40 (1983). ArticleCASPubMed Google Scholar
Worby, C.J., Lipsitch, M. & Hanage, W.P. Within-host bacterial diversity hinders accurate reconstruction of transmission networks from genomic distance data. PLoS Comput. Biol.10, e1003549 (2014). ArticlePubMedPubMed CentralCAS Google Scholar
Oliver, A., Canton, R., Campo, P., Baquero, F. & Blazquez, J. High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection. Science288, 1251–1254 (2000). ArticleCASPubMed Google Scholar
Winsor, G.L. et al. Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res.39, D596–D600 (2011). ArticleCASPubMed Google Scholar
Luzar, M.A. & Montie, T.C. Avirulence and altered physiological properties of cystic fibrosis strains of Pseudomonas aeruginosa. Infect. Immun.50, 572–576 (1985). CASPubMedPubMed Central Google Scholar
Damkiær, S., Yang, L., Molin, S. & Jelsbak, L. Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts. Proc. Natl. Acad. Sci. USA110, 7766–7771 (2013). ArticlePubMedPubMed Central Google Scholar
Pai, H. et al. Carbapenem resistance mechanisms in Pseudomonas aeruginosa clinical isolates. Antimicrob. Agents Chemother.45, 480–484 (2001). ArticleCASPubMedPubMed Central Google Scholar
Ballestero, S. et al. Carbapenem resistance in Pseudomonas aeruginosa from cystic fibrosis patients. J. Antimicrob. Chemother.38, 39–45 (1996). ArticleCASPubMed Google Scholar
Schurek, K.N. et al. Involvement of pmrAB and phoPQ in polymyxin B adaptation and inducible resistance in non-cystic fibrosis clinical isolates of Pseudomonas aeruginosa. Antimicrob. Agents Chemother.53, 4345–4351 (2009). ArticleCASPubMedPubMed Central Google Scholar
Cabot, G. et al. Genetic markers of widespread extensively drug-resistant Pseudomonas aeruginosa high-risk clones. Antimicrob. Agents Chemother.56, 6349–6357 (2012). ArticleCASPubMedPubMed Central Google Scholar
Juan, C. et al. Molecular mechanisms of β-lactam resistance mediated by AmpC hyperproduction in Pseudomonas aeruginosa clinical strains. Antimicrob. Agents Chemother.49, 4733–4738 (2005). ArticleCASPubMedPubMed Central Google Scholar
Mahenthiralingam, E., Campbell, M.E. & Speert, D.P. Nonmotility and phagocytic resistance of Pseudomonas aeruginosa isolates from chronically colonized patients with cystic fibrosis. Infect. Immun.62, 596–605 (1994). CASPubMedPubMed Central Google Scholar
Sobel, M.L., Hocquet, D., Cao, L., Plesiat, P. & Poole, K. Mutations in PA3574 (nalD) lead to increased MexAB-OprM expression and multidrug resistance in laboratory and clinical isolates of Pseudomonas aeruginosa. Antimicrob. Agents Chemother.49, 1782–1786 (2005). ArticleCASPubMedPubMed Central Google Scholar
Hancock, R.E. Resistance mechanisms in Pseudomonas aeruginosa and other nonfermentative Gram-negative bacteria. Clin. Infect. Dis.27 (suppl. 1), S93–S99 (1998). ArticleCASPubMed Google Scholar
Strateva, T. & Yordanov, D. _Pseudomonas aeruginosa_—a phenomenon of bacterial resistance. J. Med. Microbiol.58, 1133–1148 (2009). ArticleCASPubMed Google Scholar
Pasca, M.R. et al. Evaluation of fluoroquinolone resistance mechanisms in Pseudomonas aeruginosa multidrug resistance clinical isolates. Microb. Drug Resist.18, 23–32 (2012). ArticleCASPubMed Google Scholar
Huse, H.K. et al. Pseudomonas aeruginosa enhances production of a non-alginate exopolysaccharide during long-term colonization of the cystic fibrosis lung. PLoS ONE8, e82621 (2013). ArticlePubMedPubMed CentralCAS Google Scholar
Kuchma, S.L. et al. BifA, a cyclic-Di-GMP phosphodiesterase, inversely regulates biofilm formation and swarming motility by Pseudomonas aeruginosa PA14. J. Bacteriol.189, 8165–8178 (2007). ArticleCASPubMedPubMed Central Google Scholar
Davies, D.G. et al. The involvement of cell-to-cell signals in the development of a bacterial biofilm. Science280, 295–298 (1998). ArticleCASPubMed Google Scholar
Choy, W.K., Zhou, L., Syn, C.K., Zhang, L.H. & Swarup, S. MorA defines a new class of regulators affecting flagellar development and biofilm formation in diverse Pseudomonas species. J. Bacteriol.186, 7221–7228 (2004). ArticleCASPubMedPubMed Central Google Scholar
An, S., Wu, J. & Zhang, L.H. Modulation of Pseudomonas aeruginosa biofilm dispersal by a cyclic-Di-GMP phosphodiesterase with a putative hypoxia-sensing domain. Appl. Environ. Microbiol.76, 8160–8173 (2010). ArticleCASPubMedPubMed Central Google Scholar
Goodman, A.L. et al. A signaling network reciprocally regulates genes associated with acute infection and chronic persistence in Pseudomonas aeruginosa. Dev. Cell7, 745–754 (2004). ArticleCASPubMed Google Scholar
Hickman, J.W., Tifrea, D.F. & Harwood, C.S. A chemosensory system that regulates biofilm formation through modulation of cyclic diguanylate levels. Proc. Natl. Acad. Sci. USA102, 14422–14427 (2005). ArticleCASPubMedPubMed Central Google Scholar
Behrends, V. et al. Metabolite profiling to characterize disease-related bacteria: gluconate excretion by Pseudomonas aeruginosa mutants and clinical isolates from cystic fibrosis patients. J. Biol. Chem.288, 15098–15109 (2013). ArticleCASPubMedPubMed Central Google Scholar
Eschbach, M. et al. Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J. Bacteriol.186, 4596–4604 (2004). ArticleCASPubMedPubMed Central Google Scholar
Aires, J.R., Kohler, T., Nikaido, H. & Plesiat, P. Involvement of an active efflux system in the natural resistance of Pseudomonas aeruginosa to aminoglycosides. Antimicrob. Agents Chemother.43, 2624–2628 (1999). ArticleCASPubMedPubMed Central Google Scholar
Westbrock-Wadman, S. et al. Characterization of a Pseudomonas aeruginosa efflux pump contributing to aminoglycoside impermeability. Antimicrob. Agents Chemother.43, 2975–2983 (1999). ArticleCASPubMedPubMed Central Google Scholar
Sobel, M.L., McKay, G.A. & Poole, K. Contribution of the MexXY multidrug transporter to aminoglycoside resistance in Pseudomonas aeruginosa clinical isolates. Antimicrob. Agents Chemother.47, 3202–3207 (2003). ArticleCASPubMedPubMed Central Google Scholar
Islam, S., Jalal, S. & Wretlind, B. Expression of the MexXY efflux pump in amikacin-resistant isolates of Pseudomonas aeruginosa. Clin. Microbiol. Infect.10, 877–883 (2004). ArticleCASPubMed Google Scholar
Yu, H., Schurr, M.J. & Deretic, V. Functional equivalence of Escherichia coli σE and Pseudomonas aeruginosa AlgU: E. coli rpoE restores mucoidy and reduces sensitivity to reactive oxygen intermediates in algU mutants of P. aeruginosa. J. Bacteriol.177, 3259–3268 (1995). ArticleCASPubMedPubMed Central Google Scholar
DeVries, C.A. & Ohman, D.E. Mucoid-to-nonmucoid conversion in alginate-producing Pseudomonas aeruginosa often results from spontaneous mutations in algT, encoding a putative alternate sigma factor, and shows evidence for autoregulation. J. Bacteriol.176, 6677–6687 (1994). ArticleCASPubMedPubMed Central Google Scholar
Schurr, M.J., Martin, D.W., Mudd, M.H. & Deretic, V. Gene cluster controlling conversion to alginate-overproducing phenotype in Pseudomonas aeruginosa: functional analysis in a heterologous host and role in the instability of mucoidy. J. Bacteriol.176, 3375–3382 (1994). ArticleCASPubMedPubMed Central Google Scholar
Ciofu, O. et al. Investigation of the algT operon sequence in mucoid and non-mucoid Pseudomonas aeruginosa isolates from 115 Scandinavian patients with cystic fibrosis and in 88 in vitro non-mucoid revertants. Microbiology154, 103–113 (2008). ArticleCASPubMed Google Scholar
Heeb, S. et al. Functional analysis of the post-transcriptional regulator RsmA reveals a novel RNA-binding site. J. Mol. Biol.355, 1026–1036 (2006). ArticleCASPubMed Google Scholar
Yang, L. et al. In situ growth rates and biofilm development of Pseudomonas aeruginosa populations in chronic lung infections. J. Bacteriol.190, 2767–2776 (2008). ArticleCASPubMed Google Scholar
Barrick, J.E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature461, 1243–1247 (2009). ArticleCASPubMed Google Scholar
Lieberman, T.D. et al. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat. Genet.46, 82–87 (2014). ArticleCASPubMed Google Scholar
Ciofu, O., Riis, B., Pressler, T., Poulsen, H.E. & Hoiby, N. Occurrence of hypermutable Pseudomonas aeruginosa in cystic fibrosis patients is associated with the oxidative stress caused by chronic lung inflammation. Antimicrob. Agents Chemother.49, 2276–2282 (2005). ArticleCASPubMedPubMed Central Google Scholar
Waine, D.J., Honeybourne, D., Smith, E.G., Whitehouse, J.L. & Dowson, C.G. Association between hypermutator phenotype, clinical variables, mucoid phenotype, and antimicrobial resistance in Pseudomonas aeruginosa. J. Clin. Microbiol.46, 3491–3493 (2008). ArticleCASPubMedPubMed Central Google Scholar
Hoiby, N. & Frederiksen, B. in Cystic Fibrosis (eds. Hodson, M. & Geddes, D.) 83–107 (Arnold, London, 2000).
DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet.43, 491–498 (2011). CASPubMedPubMed Central Google Scholar