Selective sweep and phylogenetic models for the emergence and spread of pyrimethamine resistance mutations inPlasmodium vivax

Abstract

Pyrimethamine resistance is a major concern for the control of human haemoprotozoa, especially Plasmodium species. Currently, there is little understanding of how pyrimethamine resistance developed in Plasmodium vivax in the natural field conditions. Here, we present first time the evidence of positive selection pressure on a dihydrofolate reductase locus and its consequences on the emergence and the spread of pyrimethamine resistance in P. vivax in the Punjab province of Pakistan. First, we examined the pyrimethamine resistance locus in 38 P. vivax populations to look for evidence of positive selection pressure in human patients. The S58R (AGA)/S117N (AAC) double mutation was most common, being detected in 10/38 populations. Single mutation S117N (AAC), I173L (CTT) and S58R (AGA) SNPs were detected in 8/38, 2/38 and 1/38 populations, respectively. The F57L/I (TTA/ATA) and T61M (ATG) SNPs were not detected in any population examined. Although both soft and hard selective sweeps have occurred with striking differences between populations, there was a predominance of hard sweeps. A single resistance haplotype was present at high frequency in 9/14 populations, providing a strong evidence for the single emergence of these mutations. In contrast, 5/14 populations carried multiple resistance haplotypes at high frequencies, providing an evidence of the emergence of resistance by recurrent mutations, characteristics of soft selective sweeps. Our phylogenetic relationship analysis suggests that S58R (AGA)/S117N (AAC) and S117N (AAC) mutations arose multiple times from a single origin and spread to multiple different cities in the Punjab province through gene flow. Interestingly, the I173L (CTT) mutation was present on a single haplotype, suggesting that it arises rarely and has not spread between cities. Our work shows the need for responsible use of exiting and new antimicrobial drugs and their combinations, control the movement of infected patients and mosquito vector control strategies.

Genetic characterisation of the Theileria annulata cytochrome b locus and its impact on buparvaquone resistance in ruminants

“…Overall, buparvaquone resistance-associated SNPs were reported for the first time in buffalo-and cattle-derived T. annulata field isolates and their impact on positive selection pressure. Our results are consistent with the study of the pyrimethamine resistance mutations in the protozoan parasite Plasmodium vivax (Auliff et al, 2006;Brega et al, 2004;de Pecoulas et al, 1998;Hastings et al, 2005;Imwong et al, 2003;Kaur et al, 2006;Kuesap et al, 2011;Lu et al, 2012;Mint Lekweiry et al, 2012;Ranjitkar et al, 2011;Schunk et al, 2006;Shaukat et al, 2019) and diminazene resistance in the Trypanosoma brucei (Carter et al, 1999;Mäser et al, 1999;Matovu et al, 2001). A possible explanation for the differences in the frequency of buparvaquone-conferring mutations with positive selection pressure may be variable drug doses, for example, if the 262S (TCA), 253S (TCT) and 129G (GGC)/253S (TCT) resistance mutations may be selected at low doses of buparvaquone, while 129G (GGC) may occur at higher doses.…”

“…The selective sweep on these individual isolates was effectively softer and a genetic footprint of selection was also detected by significant departures from the neutrality test. The results are consistent with the hypothesis that single and multiple mutations in dhfr locus emerged in the human protozoan parasite P. vivax (Shaukat et al, 2019). Overall, the data provide novel information on single and or multiple emergences of resistance mutations in this group of parasites that may have implications for targeted selective treatment, or use of different drug combinations, including new drugs or the modification of current compounds in resistance mitigation strategies.…”

“…This scenario would likely be a consequence of the gene flow of drug resistance alleles through host movement. In contrast, resistance mutations could repeatedly arise from multiple origins, become fixed by selection and migrate between parasites as a result of host movement (Chaudhry et al, 2016a; Chaudhry et al, 2015; Shaukat et al, 2019; Shaukat et al, 2021).…”

“…High throughput deep amplicon sequencing using the Illumina Mi-Seq platform is an accurate and relatively low-cost method for the identification of amplicon sequence variants in parasites. The method has transformed the study of benzimidazole resistance in nematode parasites (Ali et al, 2019; Sargison et al, 2019), and pyrimethamine resistance in Plasmodium (Shaukat et al, 2019; Shaukat et al, 2021) and has the potential to open new areas of research to improve understanding of buparvaquone resistance in Theileria . The method can generate sequence reads up to 600 bp in length by targeting primer binding to conserved sites.…”

“…Selective sweep models could potentially explain how resistance mutations emerge in parasites; whereby the use of antiparasitic drugs provides positive selection pressure for adaptive mutations in the resistance candidate loci of the parasite (Chaudhry and Gilleard, 2015). A hard selective sweep is characterised by a single resistance haplotype rising from a recent mutation at a high frequency in each parasite isolate (Chaudhry et al, 2020; Chaudhry et al, 2015; Shaukat et al, 2019). A soft selective sweep is characterised by the presence of multiple resistance haplotypes at a high frequency in each isolate, derived from either recurrent mutations appearing after the onset of selection, or pre-existing mutations before the onset of selection (Chaudhry et al, 2016a; Chaudhry et al, 2020; Shaukat et al, 2019).…”