Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

Bacterial pathogens evolve during the infection of their human host, but separating adaptive and neutral mutations remains challenging. 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.

[1]  J. Goldberg,et al.  Lipopolysaccharide of Burkholderia cepacia complex. , 2003, Journal of endotoxin research.

[2]  M. Brockhurst,et al.  Pseudomonas aeruginosa population diversity and turnover in cystic fibrosis chronic infections. , 2011, American journal of respiratory and critical care medicine.

[3]  C. Josenhans,et al.  Helicobacter pylori evolution and phenotypic diversification in a changing host , 2007, Nature Reviews Microbiology.

[4]  J. Lipuma.  The Changing Microbial Epidemiology in Cystic Fibrosis , 2010, Clinical Microbiology Reviews.

[5]  M. Nowak,et al.  Adaptive evolution of highly mutable loci in pathogenic bacteria , 1994, Current Biology.

[6]  F. Tenover,et al.  gyrA Mutations Associated with Fluoroquinolone Resistance in Eight Species ofEnterobacteriaceae , 1998, Antimicrobial Agents and Chemotherapy.

[7]  Dominique Schneider,et al.  Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Craig Stephens,et al.  Conserved modular design of an oxygen sensory/signaling network with species-specific output , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[9]  J. A. Cole,et al.  Modulation of Shigella virulence in response to available oxygen in vivo , 2010, Nature.

[10]  Anders Folkesson,et al.  Evolutionary dynamics of bacteria in a human host environment , 2011, Proceedings of the National Academy of Sciences.

[11]  J. Burton,et al.  Rapid Pneumococcal Evolution in Response to Clinical Interventions , 2011, Science.

[12]  M. P. Cummings.  PHYLIP (Phylogeny Inference Package) , 2004 .

[13]  S. Lory,et al.  Phylogenetic and metabolic diversity of bacteria associated with cystic fibrosis , 2011, The ISME Journal.

[14]  D. Falush,et al.  Helicobacter pylori genome evolution during human infection , 2011, Proceedings of the National Academy of Sciences.

[15]  Mark J. Pallen,et al.  Bacterial pathogenomics , 2007, Nature.

[16]  T. Silhavy,et al.  The bacterial cell envelope. , 2010, Cold Spring Harbor perspectives in biology.

[17]  J. Goldberg,et al.  Review: Lipopolysaccharide of Burkholderia cepacia complex , 2003 .

[18]  M. Hecker,et al.  Host Imprints on Bacterial Genomes—Rapid, Divergent Evolution in Individual Patients , 2010, PLoS pathogens.

[19]  Alexander Tomasz,et al.  Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing , 2007, Proceedings of the National Academy of Sciences.

[20]  Richard C Boucher,et al.  Effects of reduced mucus oxygen concentration in airway Pseudomonas infections of cystic fibrosis patients. , 2002, The Journal of clinical investigation.

[21]  Joanna B. Goldberg,et al.  Reconstitution of O-Specific Lipopolysaccharide Expression in Burkholderia cenocepacia Strain J2315, Which Is Associated with Transmissible Infections in Patients with Cystic Fibrosis , 2005, Journal of bacteriology.

[22]  J. Lipuma,et al.  Evidence of transmission of Burkholderia cepacia, Burkholderia multivorans and Burkholderia dolosa among persons with cystic fibrosis. , 2003, FEMS microbiology letters.

[23]  A. Wong,et al.  Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa. , 2011, Microbiology.

[24]  P. Vandamme,et al.  Proposal to accommodate Burkholderia cepacia genomovar VI as Burkholderia dolosa sp. nov. , 2004, International journal of systematic and evolutionary microbiology.

[25]  Jeffrey E. Barrick,et al.  Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.

[26]  M. Schuster,et al.  Instantaneous Within-Patient Diversity of Pseudomonas aeruginosa Quorum-Sensing Populations from Cystic Fibrosis Lung Infections , 2009, Infection and Immunity.

[27]  Giovanna Morelli,et al.  Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families , 2010, PLoS genetics.

[28]  Julian Parkhill,et al.  Evolution of MRSA During Hospital Transmission and Intercontinental Spread , 2010, Science.

[29]  David A. D'Argenio,et al.  Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[30]  M. Huesca,et al.  Salmonella typhimurium gyrA mutations associated with fluoroquinolone resistance , 1995, Antimicrobial agents and chemotherapy.

[31]  R. Lenski,et al.  Microbial genetics: Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation , 2003, Nature Reviews Genetics.

[32]  J. Wain,et al.  High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi , 2008, Nature Genetics.

[33]  Tom Royce,et al.  A comprehensive catalogue of somatic mutations from a human cancer genome , 2010, Nature.

[34]  J. Lipuma.  Update on the Burkholderia cepacia complex , 2005, Current opinion in pulmonary medicine.

[35]  Alison K. Hottes,et al.  Global Discovery of Adaptive Mutations , 2009, Nature Methods.

[36]  R. Stern,et al.  Person-to-person transmission of Pseudomonas cepacia between patients with cystic fibrosis , 1990, The Lancet.

[37]  L. Kalish,et al.  Impact of Burkholderia dolosa on lung function and survival in cystic fibrosis. , 2006, American journal of respiratory and critical care medicine.

[38]  D. Musher,et al.  Emergence of macrolide resistance during treatment of pneumococcal pneumonia. , 2002, The New England journal of medicine.

[39]  M. Surette,et al.  A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients , 2008, Proceedings of the National Academy of Sciences.

[40]  M. W. van der Woude,et al.  Phase and Antigenic Variation in Bacteria , 2004, Clinical Microbiology Reviews.