Epidemiological investigation of Pseudomonas aeruginosa isolates including multidrug-resistant serogroup O12 isolates, by use of a rapid and simplified multiple-locus variable-number of tandem repeats analysis and whole genome sequencing

Abstract

Clustered cases of Pseudomonas aeruginosa infection in immunocompromised patients' wards require rapid characterization of a potential epidemic to guide investigations and identify the potential source of contamination. To design and evaluate a rapid and simple typing method for P.aeruginosa in comparison to whole genome sequencing (WGS). A simplified polymerase chain reaction based on multiple-locus variable-number of tandem repeats analysis (MLVA) was designed and used to investigate cases of P.aeruginosa infection and colonization in a paediatric haematology department. The method was compared to WGS by using the Illumina method. On the 17 isolates recovered from 15 children (eight from blood cultures, three from urinary tract infections, one from sputum and five stool isolates), MLVA distinguished 10 different profiles, and seven isolates from six children shared the same profile. Analysis by WGS revealed that these seven isolates belonged to sequence type ST111 and serotype O12, allowing at least three different genotypes to be distinguished among them. Five environmental strains had three MLVA profiles; one was shared with a clinical isolate but WGS excluded any relationship. The simplified and inexpensive MLVA method enabled the exclusion, in less than 5h, of most of the unrelated isolates and thus to focus investigations on a small number of cases, whereas WGS, taking several days of work, drew definitive conclusions concerning the outbreak and the genetic relationships of the ST111 isolates circulating in the department. We conclude that sequential use of both methods is the optimal strategy to investigate clustered cases of P.aeruginosa infections.