In order to assist the annotation of variants selected in the CF host, sequence variants against the PAO1 reference genome that were also found in PA14 were treated as “neutral” changes for study strains, with the assumption that they would not result in major MIC discrepancies or in other CF P. aeruginosa phenotypic characteristics (Table 4 and 5; see also Table S1,  to , S4 in the supplemental material). Here, SMOX is linked to cystic fibrosis.