The Genetic Structure of Leishmania infantum Populations in Brazil and Its Possible Association with the Transmission Cycle of Visceral Leishmaniasis

Leishmania infantum is the etiologic agent of visceral leishmaniasis (VL) in the Americas, Mediterranean basin and West and Central Asia. Although the geographic structure of L. infantum populations from the Old World have been described, few studies have addressed the population structure of this parasite in the Neotropical region. We employed 14 microsatellites to analyze the population structure of the L. infantum strains isolated from humans and dogs from most of the Brazilian states endemic for VL and from Paraguay. The results indicate a low genetic diversity, high inbreeding estimates and a depletion of heterozygotes, which together indicate a predominantly clonal breeding system, but signs of sexual events are also present. Three populations were identified from the clustering analysis, and they were well supported by F statistics inferences and partially corroborated by distance-based. POP1 (111 strains) was observed in all but one endemic area. POP2 (31 strains) is also well-dispersed, but it was the predominant population in Mato Grosso (MT). POP3 (31 strains) was less dispersed, and it was observed primarily in Mato Grosso do Sul (MS). Strains originated from an outbreak of canine VL in Southern Brazil were grouped in POP1 with those from Paraguay, which corroborates the hypothesis of dispersal from Northeastern Argentina and Paraguay. The distribution of VL in MS seems to follow the west-east construction of the Bolivia-Brazil pipeline from Corumbá municipality. This may have resulted in a strong association of POP3 and Lutzomyia cruzi, which is the main VL vector in Corumbá, and a dispersion of this population in this region that was shaped by human interference. This vector also occurs in MT and may influence the structure of POP2. This paper presents significant advances in the understanding of the population structure of L. infantum in Brazil and its association with eco-epidemiological aspects of VL

Neighbor-net constructed on SplitsTree software employing the chord distance values among the <i>Leishmania infantum</i> genotypes.

<p>Identical genotypes for the 14 microsatellite markers were grouped and are represented by “TYPEs” (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036242#pone.0036242.s003" target="_blank">Table S1</a>). The distribution of the splits shows the same populations that were determined by the STRUCTURE analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036242#pone-0036242-g002" target="_blank">Figure 2</a>); some genotypes from POP2 are closer to POP1, and others are closer to POP3.</p

The distribution of MLMT genotypes shared among <i>Leishmania infantum</i> strains by hosts and geographic origins.

<p>POP1, ‘TYPE1’ to ‘TYPE14’; POP2, ‘TYPE15’ to ‘TYPE19’; POP3, ‘TYPE20’ to ‘TYPE22’. Brazilian States: AM, Amazonas; BA, Bahia; CE, Ceará; DF, Distrito Federal; ES, Espírito Santo; MA, Maranhão; MG, Minas Gerais; MT, Mato Grosso; MS, Mato Grosso do Sul; PA, Pará; PE, Pernambuco; PI, Piauí; RJ, Rio de Janeiro; RN, Rio Grande do Norte; RS, Rio Grande do Sul; SE, Sergipe; SP, São Paulo. Paraguay: ASU, Asunción.</p><p>The number of strains per state for each genotype is shown in brackets.</p><p>See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036242#pone.0036242.s003" target="_blank">Table S1</a> for more details.</p

Factorial correspondence analysis (FCA) of the <i>Leishmania infantum</i> genotypes.

<p>Spacial distribution of strains after FCA of microsatellite genotypes. Blue dots, POP1; yellow dots, POP2; grey dots, POP3.</p

<i>Leishmania infantum</i> populations inferred from STRUCTURE analysis based on profiles of 14 microsatellites.

<p>The barplot was generated in Excel using the results of the aligned distribution of Q values from 10 for <i>K</i> = 3, which was generated using CLUMPP software. Evanno's method predicted that three was the most likely number of populations (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036242#pone.0036242.s001" target="_blank">Figure S1</a>). The POP1 (n = 111) is composed of strains from all of the foci (with the exception of PA), and most of the strains contain traces from POP2. POP2 (n = 31) includes strains from 10 states, but it is predominantly observed in MT. POP3 (n = 31) is composed primarily of MS strains and of four strains from other states of Northeast Brazil. Abbreviations: AM, Amazonas; BA, Bahia; CE, Ceará; DF, Distrito Federal; ES, Espírito Santo; MA, Maranhão; MG, Minas Gerais; MT, Mato Grosso; MS, Mato Grosso do Sul; PA, Pará; PE, Pernambuco; PI, Piauí; RJ, Rio de Janeiro; RN, Rio Grande do Norte; RS, Rio Grande do Sul; SE, Sergipe; SP, São Paulo; PY, Paraguay.</p

The geographic origin of <i>Leishmania infantum</i> strains and populations of STRUCTURE analysis.

<p>The yellow dots represent the locations of the collections of each analyzed strain. The graphics indicate the proportion numbers of the strains (Y axis) in each population (X axis). The assignment of the strains to a population was performed in the STRUCTURE analysis that was based on the profiles of 14 microsatellite markers. POP1 is a widespread population, and it is predominant in most of the foci. POP2 and POP3 are predominant in Central West Brazil where <i>Lutzomyia longipalpis</i> and <i>Lutzomyia cruzi</i> are involved in the transmission cycle of Visceral Leishmaniasis. The abbreviations for the Brazilian states are as follows (in bold): AM, Amazonas; BA, Bahia; CE, Ceará; DF, Distrito Federal; ES, Espírito Santo; MA, Maranhão; MG, Minas Gerais; MT, Mato Grosso; MS, Mato Grosso do Sul; PA, Pará; PE, Pernambuco; PI, Piauí; RJ, Rio de Janeiro; RN, Rio Grande do Norte; RS, Rio Grande do Sul; SE, Sergipe; SP, São Paulo. International country codes: AR, Argentina; BO, Bolivia; CL, Chile; CO, Colômbia; GF, French Guiana; GY, Guyana; PY, Paraguay; PE, Peru; SR, Suriname; UR, Uruguay; VE, Venezuela. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036242#pone.0036242.s003" target="_blank">Table S1</a> for more details.</p