Selective Sweeps and Parallel Pathoadaptation Drive Pseudomonas aeruginosa Evolution in the Cystic Fibrosis Lung.
Pulmonary infections caused by Pseudomonas aeruginosa are a recalcitrant problem in cystic fibrosis (CF) patients. While the clinical implications and long-term evolutionary patterns of these infections are well studied, we know little about the short-term population dynamics that enable this pathogen to persist despite aggressive antimicrobial therapy. Here, we describe a short-term population genomic analysis of 233 P. aeruginosa isolates collected from 12 sputum specimens obtained over a 1-year period from a single patient. Whole-genome sequencing and antimicrobial susceptibility profiling identified the expansion of two clonal lineages. The first lineage originated from the coalescence of the entire sample less than 3 years before the end of the study and gave rise to a high-diversity ancestral population. The second expansion occurred 2 years later and gave rise to a derived population with a strong signal of positive selection. These events show characteristics consistent with recurrent selective sweeps. While we cannot identify the specific mutations responsible for the origins of the clonal lineages, we find that the majority of mutations occur in loci previously associated with virulence and resistance. Additionally, approximately one-third of all mutations occur in loci that are mutated multiple times, highlighting the importance of parallel pathoadaptation. One such locus is the gene encoding penicillin-binding protein 3, which received three independent mutations. Our functional analysis of these alleles shows that they provide differential fitness benefits dependent on the antibiotic under selection. These data reveal that bacterial populations can undergo extensive and dramatic changes that are not revealed by lower-resolution analyses.


OBJECTIVE
Pseudomonas aeruginosa is a bacterial opportunistic pathogen responsible for significant morbidity and mortality in cystic fibrosis (CF) patients. Once it has colonized the lung in CF, it is highly resilient and rarely eradicated. This study presents a deep sampling examination of the fine-scale evolutionary dynamics of P. aeruginosa in the lungs of a chronically infected CF patient. We show that diversity of P. aeruginosa is driven by recurrent clonal emergence and expansion within this patient and identify potential adaptive variants associated with these events. This high-resolution sequencing strategy thus reveals important intraspecies dynamics that explain a clinically important phenomenon not evident at a lower-resolution analysis of community structure.
Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
Julio
J
Diaz Caballero
Latner Thoracic Surgery Research Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
Shawn T
ST
Clark
Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada.
Bryan
B
Coburn
Latner Thoracic Surgery Research Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada.
Yu
Y
Zhang
Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
Pauline W
PW
Wang
Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada.
Sylva L
SL
Donaldson
Adult Cystic Fibrosis Clinic, St. Michael's Hospital, Toronto, Ontario, Canada.
D Elizabeth
DE
Tullis
Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Department of Pediatric Laboratory Medicine, Division of Microbiology, The Hospital for Sick Children, Toronto, Ontario, Canada.
Yvonne C W
YC
Yau
Department of Pediatrics, Division of Infectious Diseases, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
Valerie J
VJ
Waters
Latner Thoracic Surgery Research Laboratories, University Health Network, University of Toronto, Toronto, Ontario, Canada Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada Department of Pathology, University Health Network, Toronto, Ontario, Canada.
David M
DM
Hwang
Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada david.guttman@utoronto.ca.
David S
DS
Guttman
D000220:Adaptation, Biological; D058448:Biota; D016000:Cluster Analysis; D003550:Cystic Fibrosis / Q000150:complications*; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D016680:Genome, Bacterial; D005838:Genotype; D006801:Humans; D008168:Lung / Q000382:microbiology*; D011552:Pseudomonas Infections / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification / Q000502:physiology*; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D013183:Sputum / Q000382:microbiology
D004269:DNA, Bacterial