Bacterial pathogens evolve during the infection of their human host1,2,3,4,5,6,7,8, but separating adaptive and neutral mutations remains challenging9,10,11. Here we identify bacterial genes under adaptive evolution by tracking recurrent patterns of mutations in the same pathogenic strain during the infection of multiple individuals. We conducted a retrospective study of a Burkholderia dolosa outbreak among subjects with cystic fibrosis, sequencing the genomes of 112 isolates collected from 14 individuals over 16 years. We find that 17 bacterial genes acquired nonsynonymous mutations in multiple individuals, which indicates parallel adaptive evolution. Mutations in these genes affect important pathogenic phenotypes, including antibiotic resistance and bacterial membrane composition and implicate oxygen-dependent regulation as paramount in lung infections. Several genes have not previously been implicated in pathogenesis and may represent new therapeutic targets. The identification of parallel molecular evolution as a pathogen spreads among multiple individuals points to the key selection forces it experiences within human hosts.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $18.75 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Suerbaum, S. & Josenhans, C. Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat. Rev. Microbiol. 5, 441–452 (2007).
Smith, E.E. et al. Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. USA 103, 8487–8492 (2006).
Musher, D.M. et al. Emergence of macrolide resistance during treatment of pneumococcal pneumonia. N. Engl. J. Med. 346, 630–631 (2002).
Wong, A. & Kassen, R. Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa. Microbiology 157, 937–944 (2011).
Zdziarski, J. et al. Host imprints on bacterial genomes—rapid divergent evolution in individual patients. PLoS Pathog. 6, e1001078 (2010).
Yang, L. et al. Evolutionary dynamics of a bacteria in a human host environment. Proc. Natl. Acad. Sci. USA 108, 7481–7486 (2011).
Kennemann, L. et al. Helicobacter pylori genome evolution during human infection. Proc. Natl. Acad. Sci. USA 108, 5033–5038 (2011).
Mwangi, M.M. et al. Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing. Proc. Natl. Acad. Sci. USA 104, 9451–9456 (2007).
Harris, S.R. et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327, 469–474 (2010).
Goodarzi, H., Hottes, A.K. & Tavazoie, S. Global discovery of adaptive mutations. Nat. Methods 6, 581–583 (2009).
Pleasance, E.D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191–196 (2010).
Moxon, E.R., Rainey, P.B., Nowak, M.A. & Lenski, R.E. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4, 24–33 (1994).
van der Woude, M.W. & Bäumler, A.J. Phase and antigenic variation in bacteria. Clin. Microbiol. Rev. 17, 581–611 (2004).
Croucher, N.J. et al. Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430–434 (2011).
Holt, K.E. et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat. Genet. 40, 987–993 (2008).
Pallen, M.J. & Wren, B.W. Bacterial pathogenomics. Nature 449, 835–842 (2007).
Elena, S.F. & Lenski, R.E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4, 457–469 (2003).
Woods, R. et al. Tests of parallel molecular evolution in long-term experiment with Escherichia coli. Proc. Natl. Acad. Sci. USA 103, 9107–9112 (2006).
Barrick, J.E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243–1247 (2009).
Lipuma, J.J. The changing microbial epidemiology in cystic fibrosis. Clin. Microbiol. Rev. 23, 299–323 (2010).
Vermis, K. et al. Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov. Int. J. Syst. Evol. Microbiol. 54, 689–691 (2004).
Lipuma, J.J. Update on the Burkholderia cepacia complex. Curr. Opin. Pulm. Med. 11, 528–533 (2005).
LiPuma, J.J., Dasen, S.E., Nielson, D.W., Stern, R.C. & Stull, T.L. Person-to-person transmission of Pseudomonas cepacia between patients with cystic fibrosis. Lancet 336, 1094–1096 (1990).
Biddick, R., Spilker, T., Martin, A. & LiPuma, J.J. Evidence of transmission of Burkholderia cepacia, Burkholderia multivorans and Burkholderia dolosa among persons with cystic fibrosis. FEMS Microbiol. Lett. 228, 57–62 (2003).
Kalish, L.A. et al. Impact of Burkholderia dolosa on lung function and survival in cystic fibrosis. Am. J. Respir. Crit. Care Med. 173, 421–425 (2006).
Morelli, G. et al. Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet. 6, e1001036 (2010).
Sibley, C.D. et al. A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients. Proc. Natl. Acad. Sci. USA 105, 15070–15075 (2008).
Guss, A.M. et al. Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis. ISME J. 5, 20–29 (2011).
Mowat, E. et al. Psuedomonas aeruginosa population diversity and turnover in cystic fibrosis infections. Am. J. Respir. Crit. Care Med. 183, 1674–1679 (2011).
Wilder, C.N., Allada, G. & Schuster, M. Instantaneous within-patient diversity of Psuedomonas aeruginosa quorum-sensing populations from cystic fibrosis lung infections. Infect. Immun. 77, 5631–5639 (2009).
Weigel, L.M., Steward, C.D. & Tenover, F.C. gyrA mutations associated with fluoroquinolone resistance in eight species of Enterobacteriaceae. Antimicrob. Agents Chemother. 42, 2661–2667 (1998).
Reyna, F., Huesca, M., Gonzalez, V. & Fuchs, L.Y. Salmonella typhimurium gyrA mutations associated with fluoroquinolone resistance. Antimicrob. Agents Chemother. 39, 1621–1623 (1995).
Silhavy, T.J., Kahne, D. & Walker, S. The bacterial cell envelope. Cold Spring Harb. Perspect. Biol. 2, a000414 (2010).
Vinion-Dubiel, A.D. & Goldberg, J.B. Lipopolysaccharide of Burkholderia cepacia complex. J. Endotoxin Res. 9, 201–213 (2003).
Ortega, X. et al. Reconstitution of O-specific lipopolysaccharide expression in Burkholderia cenocepacia strain J2315, which is associated with transmissible infections in patients with cystic fibrosis. J. Bacteriol. 187, 1324–1333 (2005).
Crosson, S., McGrath, P.T., Stephens, C., McAdams, H.H. & Shapiro, L. Conserved modular design of an oxygen sensory/signaling network with species-specific output. Proc. Natl. Acad. Sci. USA 102, 8018–8023 (2005).
Worlitzsch, D. et al. Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. J. Clin. Invest. 109, 317–325 (2002).
Marteyn, B. et al. Modulation of Shigella virulence in response to available oxygen in vivo. Nature 465, 355–358 (2010).
We are grateful to M. Caimano, M. Cendron, P. Kokorowski, S. Lory, C. Marx, N. Delany, S. Walker, M. Waldor and R. Ward for insightful discussions and comments, to O. Iartchouk, A. Brown, M. Light and their team at Partners HealthCare Center for Personalized Genetic Medicine (PCPGM) for Illumina sequencing, to J. Deane and L. Williams for technical assistance, to S. Vargas for assistance with IRB protocols and to M. Baym, M. Ernebjerg, A. Palmer, E. Toprak, K. Vetsigian, Z. Yao and all of the Kishony lab members for helpful discussions and general support. J.B.M. was supported by the Foundational Questions in Evolutionary Biology Prize Fellowship and the Systems Biology PhD Program (Harvard Medical School). G.P.P. was supported in part by The Mannion Fund for Research of the Center for the Critically Ill Child of Children's Hospital Boston. J.J.L. was supported by the Cystic Fibrosis Foundation. This work was supported in part by US National Institutes of Health grants (GM080177 to the Systems Biology Department, Harvard Medical School and GM081617 to R.K.), by a grant from the New England Regional Center of Excellence for Biodefense and Emerging Infectious Diseases (NERCE; AI057159 to R.K.) and by a Harvard Catalyst grant (to R.K., A.J.M. and M. Cendron).
The authors declare no competing financial interests.
About this article
Trends in Microbiology (2019)
Philosophical Transactions of the Royal Society B: Biological Sciences (2019)
Nature Medicine (2019)
Experimental Evolution of Extreme Resistance to Ionizing Radiation in Escherichia coli after 50 Cycles of Selection
Journal of Bacteriology (2019)
Burkholderia cepacia Complex Species Differ in the Frequency of Variation of the Lipopolysaccharide O-Antigen Expression During Cystic Fibrosis Chronic Respiratory Infection
Frontiers in Cellular and Infection Microbiology (2019)