Detection of associated bacteria in aspiration pneumonia and lung abscesses using partial 16S rRNA gene amplicon...

Lower respiratory tract infections (LRTIs) are often caused by the patient's own oral commensal bacteria. Causative bacteria must be identified to select the appropriate antimicrobial agents; however, the pathogens are identified via routine culture methods in only approximately half of LRTI cases.

To investigate LRTI-associated bacteria, we conducted culture testing under aerobic and anaerobic conditions using culture-independent partial 16S rRNA gene amplicon sequencing analysis using a high-throughput sequencer in cases of aspiration pneumonia and lung abscesses.

Culture testing of 17 aspiration pneumonia cases revealed Streptococcus spp. (n = 13), Prevotella spp. (n = 9), and Veillonella spp. (n = 8); 16S rRNA analysis of these cases yielded Streptococcus spp. (n = 16), Veillonella spp. (n = 12), Haemophilus spp. (n = 12), Prevotella spp. (n = 11), and Rothia spp. (n = 11). Culture testing of 8 lung abscess cases revealed Streptococcus spp. (n = 7) and Fusobacterium spp. (n = 4); 16S rRNA analysis of these cases yielded Fusobacterium spp. (n = 8), Prevotella spp. (n = 7), Streptococcus spp. (n = 6), and Porphyromonas spp. (n = 5). All taxa with abundance ratios of ≥50% on the 16S rRNA analysis were also detected in the cultures. However, several taxa were either undetected in the cultures despite relatively high abundance ratios on the 16S rRNA analysis or negative on the 16S rRNA analysis and isolated only by culturing.

Our data provide a comprehensive list of bacterial taxa that may be associated with aspiration pneumonia and lung abscesses. In empirically treating LRTIs, this information will help determine the best treatment against the targeted anaerobes.