Single locus genotyping to track Leishmania donovani in the Indian subcontinent: Application in Nepal

Abstract

BackgroundWe designed a straightforward method for discriminating circulating Leishmania populations in the Indian subcontinent (ISC). Research on transmission dynamics of visceral leishmaniasis (VL, or Kala-azar) was recently identified as one of the key research priorities for elimination of the disease in the ISC. VL in Bangladesh, India, and Nepal is caused by genetically homogeneous populations of Leishmania donovani parasites, transmitted by female sandflies. Classical methods to study diversity of these protozoa in other regions of the world, such as microsatellite typing, have proven of little use in the area, as they are not able to discriminate most genotypes. Recently, whole genome sequencing (WGS) so far identified 10 different populations termed ISC001-ISC010.Methodology / Principle findingsAs an alternative to WGS for epidemiological or clinical studies, we designed assays based on PCR amplification followed by dideoxynucleotide sequencing for identification of the non-recombinant genotypes ISC001 up to ISC007. These assays were applied on 106 parasite isolates collected in Nepal between 2011 and 2014. Combined with data from WGS on strains collected in the period 2002–2011, we provide a proof-of-principle for the application of genotyping to study treatment outcome, and differential geographic distribution.Conclusions / SignificanceOur method can aid in epidemiological follow-up of visceral leishmaniasis in the Indian subcontinent, a necessity in the frame of the Kala-azar elimination initiative in the region.

The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh

“…This is different to several previous transmission models of VL [ 18 – 20 ], which assume that individuals who have recovered from symptomatic or asymptomatic infection return to being susceptible after a number of years, and thus can be reinfected. Whilst this may be true for asymptomatic infection, multiple VL episodes are relatively rare [ 25 ] and the limited available evidence suggests that the majority of these are due to relapse rather than reinfection [ 65 , 66 ]. PKDL cases are also not included, since there were only 4 confirmed cases of PKDL during the study period and no information was recorded on time of PKDL onset.…”

Drug resistance and treatment failure in leishmaniasis: A 21st century challenge

“…WGS offers unprecedented insight into the molecular epidemiology of Leishmania , in particular in the context of DR. As such, this method should be implemented in surveillance schemes, when and where it is available. Of course, molecular tracking could be simplified and new assays translated from this genomic knowledge, as seen with the single locus genotyping (SLG) for the detection of ISC groups [ 63 ] or a PCR assay for the detection of the 2-nt insertion in AQP1. However, such targeted assays do have limitations.…”

“…However, such targeted assays do have limitations. For example, when SLG was evaluated in Nepal, about 50% of the isolates could not be typed, possibly because other genotypes circulating in this region are not detected by SLG [ 63 ].…”

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent

“…donovani (called ISC1), which diverged much earlier than 1850 ( Imamura et al, 2016 ). Rai et al (2017) investigated the geographic spread of different L . donovani genotypes over a period of 12 years (2002–2014) in Nepal and showed that the frequency of ISC1 was increasing in the country and that this emerging genotype was also present in the lowlands.…”