Revisiting the heterogeneous global genomic population structure of Leishmania infantum

Abstract

Leishmania infantum is the main causative agent responsible for visceral leishmaniasis (VL), a disease with global distribution. The genomic structure and genetic variation of this species have been widely studied in different parts of the world. However, in some countries, this information is still yet unknown, as is the genomic behaviour of the main antigens used in VL diagnosis (rK39 and rK28), which have demonstrated variable sensitivity and specificity in a manner dependent on the geographic region analysed. The objective of this study was to explore the genomic architecture and diversity of four Colombian L. infantum isolates obtained in this study and to compare these results with the genetic analysis of 183 L. infantum isolates from across the world (obtained from public databases), as well as to analyse the whole rK39 and rK28 antigen sequences in our dataset. The results showed that, at the global level, L. infantum has high genetic homogeneity and extensive aneuploidy. Furthermore, we demonstrated that there are distinct populations of L. infantum circulating in various countries throughout the globe and that populations of distant countries have close genomic relationships. Additionally, this study demonstrated the high genetic variability of the rK28 antigen worldwide. In conclusion, our study allowed us to (i) expand our knowledge of the genomic structure of global L. infantum; (ii) describe the intra-specific genomic variability of this species; and (iii) understand the genomic characteristics of the main antigens used in the diagnosis of VL. Additionally, this is the first study to report whole-genome sequences of Colombian L. infantum isolates.

Impact of Genetic Diversity and Genome Plasticity of Leishmania spp. in Treatment and the Search for Novel Chemotherapeutic Targets

“…Variations in the parasite genome can be associated with its geographical distribution and clinical manifestations, which can influence leishmaniasis management. Interestingly, large-scale research involving a large number of samples and wide geographic range has revealed that genetic diversity is significantly higher than that previously reported ( Bussotti et al., 2018 ; Zackay et al., 2018 ; Franssen et al., 2020 ; Imamura et al., 2020 ; Patino et al., 2020 ; Salloum et al., 2020 ; Zheng et al., 2020 ; Patino et al., 2021 ; Schwabl et al., 2021 ). Recently, single-cell sequencing has demonstrated the presence of several distinct karyotypes within the same Leishmania clone ( Imamura et al., 2020 ; Negreira et al., 2020 ), and multiple-genotype infections have been demonstrated to occur even within the same host and tissue ( Cupolillo et al., 2020 ).…”

Genetic variability of Leishmania (Leishmania) infantum causing human visceral leishmaniasis in the Southeastern Brazil

“…These findings also contrast with different screening targets, such as hsp70, maxicircle, and microsatellite panel that distinguished distinct profiles and dispersal routes. However, they showed aneuploidy and low variability among isolates 7,9,18,19 . Few studies presented some distinction and characterization of these populations present in L. infantum; however, they were based on culture isolates 5,7,10,12 .…”

A Landscape of the Genomic Structure of Cryptococcus neoformans in Colombian Isolates

“…An identity threshold of y = 0.8 prevented the mapping of non- Cryptococcus reads to the reference sequences. The read file merging, sorting, and elimination of PCR duplicates was implemented with SAMtools (version 0.1.18) and Picard (version 1.85) [ 32 ]…”