Combining Standard Molecular Typing and Whole Genome Sequencing to Investigate Pseudomonas aeruginosa Epidemiology in Intensive Care Units

Frontiers in Public Health

Benoit Valot¹  Gilbert Greub²  Guy Prod'hom²  Bárbara Magalhães³  Dominique S. Blanc³  Laurence Senn³  Mohamed M. H. Abdelbary³ 

[1] Chrono-Environment, Franche-Comté University, Besançon, France;Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland;Service of Hospital Preventive Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland;

关键词: whole genome sequencing;    Pseudomonas aeruginosa;    molecular typing;    molecular epidemiology;    double locus sequence typing;    genomic epidemiology;   

DOI  :  10.3389/fpubh.2020.00003

来源: DOAJ

【 摘 要 】

Pseudomonas aeruginosa is one of the main pathogens responsible for nosocomial infections, particularly in Intensive Care Units (ICUs). Due to the complexity of P. aeruginosa ecology, only powerful typing methods can efficiently allow its surveillance and the detection during expanding outbreaks. An increase in P. aeruginosa incidence was observed in the ICUs of the Lausanne University Hospital between 2010 and 2014. All clinical and environmental isolates retrieved during this period were typed with Double locus sequence typing (DLST), which detected the presence of three major genotypes: DLST 1–18, DLST 1–21, and DLST 6–7. DLST 1–18 (ST1076) isolates were previously associated with an epidemiologically well-described outbreak in the burn unit. Nevertheless, DLST 1–21 (ST253) and DLST 6–7 (ST17) showed sporadic occurrence with only few cases of possible transmission between patients. Whole genome sequencing (WGS) was used to further investigate the epidemiology of these three major P. aeruginosa genotypes in the ICUs. WGS was able to differentiate between outbreak and non-outbreak isolates and confirm suspected epidemiological links. Additionally, whole-genome single nucleotide polymorphisms (SNPs) results considered isolates as closely related for which no epidemiological links were suspected, expanding the epidemiological investigation to unsuspected links. The combination of a first-line molecular typing tool (DLST) with a more discriminatory method (WGS) proved to be an accurate and cost-efficient typing strategy for the investigation of P. aeruginosa epidemiology in the ICUs.

【 授权许可】

Unknown