RAPID RESPONSE: TRANSLATING MULTI-OMICS DATA ON CF EXACERBATIONS IN CLINICALLY RELEVANT TIME FRAMES

Current diagnostics of CF exacerbations are based on clinical culturing of microbial isolates from sputum samples followed by antibiotic susceptibility testing. Despite this established gold standard, studies have shown that antimicrobial susceptibility profiles frequently do not correlate with clinical outcomes. In some instances, antibiotic treatment still results in patient recovery despite highly reported resistance. This underlies the incomplete understanding of the microbial basis of CF exacerbations and the best methods for treatment. The likely cause of this discrepancy is that many pathogens in CF lungs are not identified in standard clinical labs. Bacterial 16S rRNA gene profiling has shown that CF lung infections are much more diverse than that revealed by clinical culture. Thus, we have begun to implement a “Rapid Response” pipeline for CF exacerbations that employs multi-omics data including transcriptome, metabolome and 16S rRNA gene sequencing to provide a timely, comprehensive assessment to clinicians. Sputum samples are collected and then DNA, RNA and metabolites extracted, followed by nucleic acid sequencing and mass spectrometry, and finally, data analysis.