Epidemiological typing of Pseudomonas aeruginosa – Pulsed-field gel electrophoresis versus next generation sequencing

Abstract

Bacterial infection with Pseudomonas aeruginosa is common in immunocompromised individuals, such as patients with cystic fibrosis. These infections are difficult to treat, due to thick mucus in the respiratory tract and antibiotic resistance among the bacterial population is common. This often leads to an increased morbidity and mortality for the colonized patients. During several years, the gold standard typing method pulsed-field gel electrophoresis was used for the epidemiological typing of P. aeruginosa within Västra Götalandsregionen (VGR). Here, P. aeruginosa bacterial strains have been whole genome sequenced with the Ion Torrent next generation sequencing technology (NGS), followed by single nucleotide polymorphism analysis or core genome/whole genome multi loci sequencing typing. Our results show that this is a highly discriminative method with an objective interpretation as well as being communicative interlaboratory. In conclusion, surveillance of the Cystic fibrosis patient community in VGR, as well as other immunocompromised patient groups, could be beneficiary by using NGS for bacterial strain typing.