Genome sequencing of P. aeruginosa isolate

The isolate DHS01, the first isolate of the epidemic, was isolated in May 1997 from the nose of a 31-year-old male patient in the surgical intensive care unit in the University Hospital of Besançon (Eastern France). In our hospital, P. aeruginosa is searched for weekly in patients hospitalized in the intensive care unit. Microbiological records revealed that the patient was already colonized by P. aeruginosa 25 days before isolation of DHS01. DHS01 was identified at the species level by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with a Microflex LT (Bruker Daltonik), according to the manufacturer's procedures. Bacterial DNA was isolated from an overnight culture on Mueller-Hinton (MH) agar using a Genomic-tip kit (Qiagen) and further sequenced with Single Molecule Real-Time technology (Pacific Biosciences) [11 (link)]. The reads were assembled using Hgap3 into a circular complete genome [12 (link)]. The genome was annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (pgat) [13 (link)]. The genes were sorted as core or accessory genes of the species P. aeruginosa by comparing to previous pangenome analysis [14 (link)].