Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi‐resistant P seudomonas aeruginosa isolates exposed to waste water and tap water

Summary The fitness of sensitive and resistant P seudomonas aeruginosa in different aquatic environments depends on genetic capacities and transcriptional regulation. Therefore, an antibiotic‐sensitive isolate PA 30 and a multi‐resistant isolate PA 49 originating from waste waters were compared via whole genome and transcriptome Illumina sequencing after exposure to municipal waste water and tap water. A number of different genomic islands (e.g. PAGIs , PAPIs ) were identified in the two environmental isolates beside the highly conserved core genome. Exposure to tap water and waste water exhibited similar transcriptional impacts on several gene clusters (antibiotic and metal resistance, genetic mobile elements, efflux pumps) in both environmental P . aeruginosa isolates. The MexCD ‐ OprJ efflux pump was overexpressed in PA 49 in response to waste water. The expression of resistance genes, genetic mobile elements in PA 49 was independent from the water matrix. Consistently, the antibiotic sensitive strain PA 30 did not show any difference in expression of the intrinsic resistance determinants and genetic mobile elements. Thus, the exposure of both isolates to polluted waste water and oligotrophic tap water resulted in similar expression profiles of mentioned genes. However, changes in environmental milieus resulted in rather unspecific transcriptional responses than selected and stimuli‐specific gene regulation.