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

• Published in: Frontiers in public health Vol. 8; p. 3
• Main Authors: Magalhães, Bárbara, Valot, Benoit, Abdelbary, Mohamed M H, Prod'hom, Guy, Greub, Gilbert, Senn, Laurence, Blanc, Dominique S
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 28.01.2020
• Subjects: Bacterial Typing Techniques; Bacteriology; Biochemistry, Molecular Biology; double locus sequence typing; genomic epidemiology; Genomics; Humans; Intensive Care Units; Life Sciences; Microbiology and Parasitology; Molecular Epidemiology; Molecular Typing; Pseudomonas aeruginosa; Pseudomonas aeruginosa - classification; Pseudomonas aeruginosa - genetics; Pseudomonas Infections - epidemiology; Pseudomonas Infections - microbiology; Public Health; Santé publique et épidémiologie; Whole Genome Sequencing; molecular epidemiology; whole genome sequencing; Pseudomonas aeruginosa; genomic epidemiology; double locus sequence typing; molecular typing
• ISSN: 2296-2565; 2296-2565
• DOI: 10.3389/fpubh.2020.00003

is one of the main pathogens responsible for nosocomial infections, particularly in Intensive Care Units (ICUs). Due to the complexity of ecology, only powerful typing methods can efficiently allow its surveillance and the detection during expanding outbreaks. An increase in 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 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 epidemiology in the ICUs.