Development and application of a MLST panel for the identification of informative polymorphisms in Leishmania infantum strains in the Mediterranean region

Background. Leishmaniasis is a zoonotic disease endemic in the Mediterranean region, where the causative agent of human and canine infection is Leishmania infantum. The spread of leishmaniasis is associated with population movements, ecology of phlebotomine vectors, and reservoir host. We used multilocus sequence typing (MLST) to explore the genetic variability of L. infantum strains in the Mediterranean region, including the borderline territory of Pantelleria island, and identify informative polymorphisms for rapid identification of genotypes through high-resolution melt (HRM)-based assays.

Material and Methods. A customized sequencing panel targeting 14 housekeeping genes was designed and MLST analysis was performed using the Ion Torrent S5 on 9 L. infantum strains/isolates: 5 canine isolates (3 from Pantelleria Island and 2 from central Italy), and 4 human isolates/strains from Tunisia, France, central and southern Italy. MLST results and in silico analysis of sequences available in Genbank allowed to select two informative polymorphisms on ME and GPI genes (390T/G and 1834A/G, respectively) used to develop two HRM-based assays for fast screening of 28 clinical samples.

Results. The MLST analysis identified a single L. infantum clonal complex regardless of the geographic origin or host (human or canine), except for the human isolate from central Italy that showed polymorphisms in 11 out of 14 housekeeping genes, and clustered independently in a molecular phylogenetic analysis. Successively, the screening through HRM-based assays of 28 clinical samples from central/south Italy and Pantelleria island allowed to identify 6 diploid sequence types (DSTs). Interestingly, the sequence type 390T/1834A was found only in Pantelleria island (prevalence 75%).

Conclusion. This study represents a description of the genetic variability of L. infantum through a first approach based on MLST and then by HRM analysis on selected polymorphisms. The HRM assays could be used as fast and cheap tools for epidemiological surveillance of L. infantum.