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Background  Cystic fibrosis (CF) affects >70,000 people worldwide, yet the microbiologic trigger for pulmonary exacerbations (PExs) remains unknown. The objective of this study was to identify changes in bacterial metabolic pathways associated with clinical status.    Methods  Respiratory samples were collected at hospital admission for PEx, end of intravenous (IV) antibiotic treatment, and follow-up from 27 hospitalized children with CF. Bacterial DNA was extracted and shotgun DNA sequencing was performed. MetaPhlAn2 and HUMAnN2 were used to evaluate bacterial taxonomic and pathway relative abundance, while DESeq2 was used to evaluate differential abundance based on clinical status.    Results  The mean age of study participants was 10 years; 85% received combination IV antibiotic therapy (beta-lactam plus a second agent). Long-chain fatty acid (LCFA) biosynthesis pathways were upregulated in follow-up samples compared to end of treatment: gondoate ( p  = 0.012), oleate ( p  = 0.048), palmitoleate ( p  = 0.043), and pathways of fatty acid elongation ( p  = 0.012).  Achromobacter xylosoxidans  and  Escherichia  sp. were also more prevalent in follow-up compared to PEx ( p  < 0.001).    Conclusions  LCFAs may be associated with persistent infection of opportunistic pathogens. Future studies should more closely investigate the role of LCFA production by lung bacteria in the transition from baseline wellness to PEx in persons with CF.    ImpactIncreased levels of LCFAs are found after IV antibiotic treatment in persons with CF.    LCFAs have previously been associated with increased lung inflammation in asthma.    This is the first report of LCFAs in the airway of persons with CF.    This research provides support that bacterial production of LCFAs may be a contributor to inflammation in persons with CF.    Future studies should evaluate LCFAs as predictors of future PExs.

Inflammation in children with cystic fibrosis: contribution of bacterial production of long-chain fatty acids