Genomic Diversity and Antimicrobial Resistance of Species Isolated from Chronic Lung Disease Airways

Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus . Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of and non- species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified species, , , , and overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between presence and decreased doxycycline susceptibility, and presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested isolates were tobramycin-resistant, providing a potential selection method to improve culture retrieval rates. Our addition of 35 airway-derived genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.