Fig 1.
Geographical distribution of human, canine and sand fly Leishmania-positive samples, 2013–2017, Emilia-Romagna region (northeastern Italy).
Colors depict the subpopulations inferred by STRUCTURE analysis: yellow for subPopA1; orange for subPopA2; green for subPopB1; brown for subPopB2; light blue for subPopB3; white for samples not submitted to cluster analysis. More than one sample per area are shown by numbers inside the icon. Map generated with Quantum-GIS (https://www.qgis.org/it/site/).
Table 1.
Characteristics of Leishmania-positive samples and WHO reference strains included in the study.
Table 2.
Genetic characteristics and variation of the 15 microsatellite loci detected in the population of Leishmania infantum from the Emilia-Romagna region (northeastern Italy, N = 55).
Fig 2.
Estimated population structure for the 52 L. infantum strains from the Emilia-Romagna region (northeastern Italy), as inferred by STRUCTURE software on the basis of data for 15 microsatellite markers.
Each strain is represented by a single vertical line divided into K colors, where K is the number of populations that were assumed. Each color represents one population, and the length of the colored segment shows the strain’s estimated proportion of membership (Q) in that population. (A) The derived graph for ΔK shows a peak at K = 2, indicating the existence of two populations in the investigated strain set. (B) The derived graphs for ΔK indicated the existence of two subpopulations within PopA and three subpopulations within PopB.
Fig 3.
Spatial distribution of 52 L. infantum strains from the Emilia-Romagna region (northeastern Italy) by factorial correspondence analysis (FCA).
Each square represents one microsatellite profile. The designations PopA (red circle), PopB (blue circle), subPopA1 (yellow circle), subPopA2 (orange circle), subPopB1 (green circle), subPopB2 (brown circle) and subPopB3 (light blue circle) correspond to the populations and subpopulations defined by STRUCTURE analysis as shown in Fig 2.
Table 3.
Differentiation measures (Fst), probability (p-value) and migration rate (Nm) between populations/subpopulations of L. infantum strains (n = 52) from the Emilia-Romagna region (northeastern Italy) as assumed by STRUCTURE.
Table 4.
Population genetic characterization of the populations and subpopulations found for 52 L. infantum strains from the Emilia-Romagna region (northeastern Italy).
Fig 4.
Bayesian phylogenetic tree (cladogram) obtained by the Sainudiin model [29] using data of 14 coincident microsatellite loci for the 62 L. infantum strains from Italy, 49 MLMT profiles available in literature and 3 WHO reference strains.
Posterior probabilities > 0.75 are showed near the nodes. Strains representing the different microsatellite profiles are listed in S1 and S2 Tables. Strains designations specify, respectively, the laboratory code, the zymodeme (ND, not defined), the geographical origin (IT, Italy; ER, Emilia-Romagna; FR, France; SP, Spain; GR, Greece; PT, Portugal; DZ, Algeria; TN, Tunisia; KE, Kenia; SD, Sudan; ET, Ethiopia; IN, India; NP, Nepal). Italian samples are differentiated by the color of STRUCTURE designation (K = 2): PopA samples in red, PopB samples in blue.