COMPARISON OF WHOLE GENOME SEQUENCING TYPING TOOLS FOR THE TYPING OF BELGIAN LEGIONELLA PNEUMOPHILA ISOLATES
The recent advances in whole genome sequencing (WGS) are currently making a big revolution for outbreak investigations for public health important microorganisms, like Legionella pneumophila (Lp). Here, we evaluated the available WGS tools for the typing of Legionella pneumophila strains of old Belgian outbreaks, as well as small groups of related and non-related isolates. One ATCC reference strain and 77 clinical and environmental isolates were selected for the evaluation. Seven and sixteen (including 4 non-related controls) isolates belong to 2 old outbreaks respectively. The remaining isolates belong to small groups of related and non-related isolates of diverse Sequence Types (ST). Sequencing was performed on the MiSeq or Hiseq sequencing system (Illumina) at the BRIGHTcore WGS platform of VUB-ULB universities. WGS data were further analysed using whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) with the available schemes: “Ridom SeqSphere+” (cgMLST) (v.5.1.1), “Applied Maths-Bionumerics” (wgMLST) (v.7.6.3) and the 50 loci cgMLST (CDC/ESGLI_ESCMID). Results of further analyses of WGS data were concordant with the results of traditional SBT method. The known outbreaks and small clusters could be detected and clear discrimination of ST1 non-related isolates was obtained. WGS analysis generated more accurate conclusions for outbreak investigations and simultaneous analysis of a large volume of samples compared to other typing methods due to its higher discriminatory power and throughput.