Figure 6. Sequence-based bacterial identification generally agrees with culture but can produce false positives.

A. Sequencing and culture results of 18 BALs (i.e. BAL-4 samples) that were studied by both approaches. Taxa relative abundance (from sequencing) are shown at left, dashed boxes indicate taxa detected by culture. Culture results are listed at right, pathogens indicated in red were not detected by sequencing at appreciable levels (<1% relative abundance). We investigated the Bordetella results (indicated by †) by subjecting the Bordetella reference sequence in the Silva database to BLAST analysis in the NCBI 16S rRNA database, and found the Bordetella reference highly similar to Achromobacter sp. Thus, reads mapping to Bordetella may have originated from Achromobacter, as indicated by culture results. M. abscessus (indicated by *) may not have been detected by sequencing because procedures used may not have lysed mycobacterial cells. B. CF pathogens were detected in culture-negative BALs. Stacked bar graphs show relative abundance of CF pathogens (colored bars) and non-conventional organisms (black bars) in 3 culture negative BALs and their subject-paired instrument control samples. The percentage of bacterial DNA mapping to CF pathogens is listed below each bar.