A Genome-Wide Association Analysis Reveals a Role for Recombination in the Evolution of Antimicrobial Resistance in Burkholderia multivorans

Abstract

24 25 26 Running title: B. multivorans GWAS reveals a role for recombination in the evolution of 27 antimicrobial resistance 28 29 30 Abstract (300 words) 33 34Cystic fibrosis (CF) lung infections caused by members of the Burkholderia cepacia complex, 35 such as Burkholderia multivorans, are associated with high rates of mortality and morbidity. We 36 performed a population genomic study of 111 B. multivorans sputum isolates from a single CF 37 patient through three stages of infection including the initial incident infection, deep sampling of 38 a one-year period of chronic infection, and deep sampling of a post-transplant recolonization. 39 We reconstructed the evolutionary history of the population and used a lineage-controlled 40 genome-wide association study (GWAS) approach to identify genetic variants associated with 41 antibiotic resistance. We found that the incident isolate was more susceptible to agents from 42 three antimicrobial classes (β-lactams, aminoglycosides, quinolones), while the chronic isolates 43 diversified into distinct genetic lineages with reduced antimicrobial susceptibility to the same 44 agents. The post-transplant reinfection isolates displayed genetic and phenotypic signatures 45 that were distinct from sputum isolates from all CF lung specimens. There were numerous 46 examples of parallel pathoadaptation, in which individual loci, or even the same codon, were 47 independently mutated multiple times. This set of loci was enriched for functions associated with 48 virulence and resistance. Our GWAS approach identified one variant in the ampD locus (which 49 was independently mutated four times in our dataset) associated with resistance to β-lactams, 50 and two non-synonymous polymorphisms associated with resistance to both aminoglycosides 51 and quinolones, affecting an araC family transcriptional regulator, which was independently 52 mutated three times, and an outer member porin, which was independently mutated twice. We 53 also performed recombination analysis and identified a minimum of 14 recombination events. 54 Parallel pathoadaptive loci and polymorphisms associated with β-lactam resistance were over-55 represented in these recombinogenic regions. This study illustrates the power of deep, 56 longitudinal sampling coupled with evolutionary and lineage-corrected GWAS analyses to reveal 57 how pathogens adapt to their hosts. 58 3 Author Summary 59 60 Cystic fibrosis (CF) is a common lethal genetic disorder that affects individuals of European 61 descent and predisposes them to chronic lung infections. Among the organisms involved in 62 these infections, bacteria from the Burkholderia cepacia complex (BCC) are often associated 63 with poor clinical prognosis. This study examines how the most prevalent BCC species among 64 CF patients, B. multivorans, evolves within a CF patient and identifies mutations underlying 65antibiotic resistance and adaptation to both the native CF lung and a non-CF lung allograft. We 66 demonstrate that B. multivorans can diversify phen...