Tiling 16S rRNA Gene Amplicon Sequencing Identifies Bacterial Species Soon After Lung Transplant That Predict Acute...

The lung bacteriome is increasingly recognized as consequential in lung transplant (LTx) outcomes; however, most studies are limited to genus-level taxonomic resolution.

LTx recipients at Ohio State University Wexner Medical Center were recruited for this study. By protocol, bronchoscopy is performed in patients shortly after LTx during their index intubation to obtain microbiologic samples and longitudinally at 1, 3, 6, 9, and 12 mo posttransplant to evaluate for rejection. We used a novel tiling amplicon sequencing method targeting the 16S ribosomal RNA V1-V9 regions for species-level characterization of both a mock microbial community and the initial posttransplant bronchoalveolar lavage fluid. Digital polymerase chain reaction of the 16S ribosomal RNA gene was performed to assess bacterial load. To identify associations between the early lung bacteriome and the risk of acute lung allograft rejection within 1 y after LTx, our primary outcome was histologic evidence of acute cellular rejection (≥A2). A secondary analysis investigated a composite outcome of acute cellular rejection (≥A2) or clinically suspected rejection requiring treatment initiation.

We first demonstrated accuracy by recapitulating a mock community (8/8 genera, 5/8 species). Bronchoalveolar lavage were collected from 23 participants, with an average of 0.96 ± 1.11 d post-LTx. Adjusting for transplant type (single versus bilateral LTx), acute cellular rejection by 1 y was associated with reduced relative abundance of Corynebacterium species ( P  = 0.002) and greater abundance of oral anaerobes, including Prevotella species ( P  = 0.002), Schaalia odontolytica ( P  = 0.012), and Streptococcus salivarius ( P  = 0.021).

Species-level characterization of the pulmonary bacteriome early post-LTx offers greater taxonomic resolution for microbial associations with transplant outcomes.