In vitro single nucleotide variability applied in vivo: drain to patient transmission of multidrug-resistant Pseudomonas aeruginosa

Whole genome sequencing (WGS) is increasingly used to study bacterial outbreak epidemiology such as hospital-acquired Pseudomonas aeruginosa, although optimal single nucleotide polymorphism (SNP) cut-off values for clonality are unknown. Weperformed in vitro subculture experiments of three clinical P. aeruginosa strains to define a SNP cut-off value. The dataset contains (A) three different generations of each strain, and (B)five different colonies of one generation of each strain.Additionally, SNP analysis was applied during a multidrug-resistant P. aeruginosa (MDR-P) outbreak. Isolates were cultured from three patients and from environmental samples. Clonal relationship between patients and sink and shower drain isolates, with previous negativesurveillance cultures in two patients, and prior positive drain cultures, made acquisition of the MDR-P strain through transmission from drain to patient plausible. In conclusion, based on subculture experiments, we defined objective SNP cut-off values for our WGS pipeline to detect clonality of P. aeruginosa, and applied these during outbreak investigations.