Secondary metabolite profiling of Pseudomonas aeruginosa isolates reveals rare genomic traits

Pseudomonas aeruginosa is a ubiquitous gram-negative opportunistic pathogen with remarkable phylogenetic and phenotypic variability. In this work, we applied classical molecular networking analysis to secondary metabolite profiling data from seven Pseudomonas aeruginosa strains, including five clinical isolates from the lung secretions of people with cystic fibrosis. Combined with whole-genome sequencing, we show that some P. aeruginosa isolates, including nmFLRO1, produce a previously unreported class of acyl putrescines, isolate SH3A does not produce di-rhamnolipids because its genome belongs to phylogenetic clade 5, and the secondary metabolite profile of isolate SH1B reflects a frame-shift mutation in the quorum sensing regulator rhlR. This study highlights for the first time that secondary metabolite profiling provides unique insight into genetic variation of P. aeruginosa.