Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways

Abstract

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 Prevotella . Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of Prevotella species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid Prevotella species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of Prevotella and non- Prevotella 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 Prevotella species, P. histicola , P. melaninogenica , P. nanceiensis , P. salivae and P. denticola 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 tetQ presence and decreased doxycycline susceptibility, and ermF 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 Prevotella isolates were tobramycin-resistant, providing a potential selection method to improve Prevotella culture retrieval rates. Our addition of 35 airway-derived Prevotella genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.

Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis

“…The treatment-induced decrease in richness and phylogenetic diversity of the LRT microbiota was linked to a compositional change 15,16 mainly driven by a mutually exclusive increase in relative abundance of the two predominant genera in IPF lung, Streptococcus (Gram-positive Firmicutes) and Prevotella (Gram-negative Bacteroidetes). Enrichment of these genera was consistent with the development of macrolide resistance previously described in cystic fibrosis (30,31). The difference we observed with the increase in ARG carriage during AZT treatment when either of these genera predominated suggests that different mechanisms may be present 15 .…”

Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis

“…These reported alterations were mainly driven by a mutually exclusive increase in relative abundance of the two predominant genera of LRT microbiota in IPF, Streptococcus (Gram-positive Firmicutes) and Prevotella (Gram-negative Bacteroidetes). Enrichment of these genera was consistent with the development of macrolide resistance previously described in fibrosis 30,31 . The difference we observed with the increase in ARG carriage during AZT treatment when either of these genera predominated suggests that different mechanisms may be present.…”

Antibiotic Susceptibility and Resistance Genes in Oral Clinical Isolates of Prevotella intermedia, Prevotella nigrescens, and Prevotella melaninogenica

“…This resistance is likely mediated by other genes or allelic variants of the cfx gene, such as cfxA3 or cfxA6 [ 17 ], or other mechanisms that were not evaluated here. The antimicrobial resistance (AMR) phenotypic profiles with identified AMR genes also have been reported between the presence of ermF , and decreased susceptibility to azithromycin and resistance to clindamycin [ 18 ]. Isolates 3, 6, and 9 of P. nigrescens , presented a direct genotype–phenotype relationship due to the presence of the ermF gene and phenotypic resistance to clindamycin.…”