Comparison of pulsed-field gel electrophoresis and whole-genome-sequencing-based typing confirms the accuracy of pulsed-field gel electrophoresis for the investigation of local Pseudomonas aeruginosa outbreaks

• Published in: The Journal of hospital infection 2020-08, Vol.105 (4), p.643-647
• Main Authors: Martak, D., Meunier, A., Sauget, M., Cholley, P., Thouverez, M., Bertrand, X., Valot, B., Hocquet, D.
• Format: Article
• Language: English
• Subjects: Bacterial typing; cgMLST; Life Sciences; Microbiology and Parasitology; Outbreaks; Pseudomonas aeruginosa; Pulsed-field gel electrophoresis; Whole-genome sequencing
• ISSN: 0195-6701; 1532-2939
• DOI: 10.1016/j.jhin.2020.06.013

To determine whether pulsed-field gel electrophoresis (PFGE) accurately recognizes isolates belonging to clusters defined by techniques based on whole-genome sequencing (WGS) using Pseudomonas aeruginosa as a model. We selected 65 isolates of ST395 P. aeruginosa isolated in seven European hospitals between 1998 and 2012. Isolates were typed by PFGE and sequenced by WGS. A core genome multi-locus sequence typing (cgMLST) analysis based on 3831 genes was performed with a homemade pipeline. PFGE identified eight pulsotypes and cgMLST differentiated nine clusters and nine singletons. Five cgMLST clusters and pulsotypes (31/65 isolates) coincided perfectly. Isolates without evident epidemiological links grouped by PFGE were separated by cgMLST (16/65 isolates) differentiating cities, suggesting that PFGE should be kept for the investigation of local outbreaks. Importantly, hypermutator isolates still shared the pulsotype with their parents (16/65 isolates), whereas they were not recognized by cgMLST. This shows that PFGE was less affected than WGS-based typing by the accelerated genetic drift that occurs in epidemic P. aeruginosa. although WGS-based typing has logically become the new reference standard, we show here that the PFGE can be used with confidence for the investigation of local outbreaks caused by P. aeruginosa.