FIGURE 4.

Dominance of lung communities by pathogens or oral taxa was strongly associated with respiratory culture results. (A) Pathogen dominance (>50% abundance) was strongly associated with concordant pathogen culture-positivity [Fisher’s odds ratio (OR) with continuity correction and associated 95% confidence interval shown]. The reference standard here was chosen to be concordant pathogen positivity, as the sequencing diagnostic test would be clinically valid if able to detect the same organism as our current reference standard of cultures. (B) Oral taxa dominance (>50% abundance) practically eliminated the odds of culture-positivity by any pathogen (OR = 0.01). The reference standard here was defined as “any pathogen,” given that oral taxa are not generally considered as pathogens or speciated by routine microbiologic cultures, and this comparison aims to assess the negative predictive value of high oral abundance in a lung community for ruling out culture positivity by any pathogenic bacteria.