Background
Malaria continues being a worldwide problem; it is a vector-born disease (VBD) transmitted by parasites from the genus
Plasmodium [
1]. About 40% of the world’s population (around three billion people) are currently at risk of suffering from this disease. Malaria causes more than 200 million clinical cases and about 400,000 deaths each year [
1]. The climatic and geographical conditions in Colombia enable the transmission of this infection [
2], and both
Plasmodium vivax and
Plasmodium falciparum are prevalent.
There are three large
Plasmodium endemic foci in Colombia: Urabá–lower Cauca–southern Córdoba, the Pacific coast and the Orinoquía–Amazonía transition region; such regions favour malarial incidence and dispersion due to their environmental conditions and social, political and cultural variables [
1,
3]. The main difficulty in controlling
P. vivax lies in the need for treating both blood stage and latent liver forms (hypnozoites), the latter causing relapses months or years after initial infection [
4].
First-line treatment for uncomplicated
P. vivax malaria in Colombia is currently based on a combination of chloroquine (CQ) for eliminating blood stages (schizonts) and primaquine (PQ) for liver stages (hypnozoites) [
5]. In other countries, treatment is also based on the use of sulfadoxine–pyrimethamine (SP) [
6]. Although these drugs remain effective overall, cases of resistance have been recorded during the last few years, making this one of the greatest problems in controlling and eliminating malaria. The first report of CQ-resistant
P. vivax strains in Latin-America was published in 1989 (including Colombia and Brazil) [
7]; however, resistance targets have not been clearly established. Regarding
P. falciparum, parasite genes associated with resistance to anti-malarial drugs have been established with greater certainty. Simple, double or quadruple mutations in different genes enable the parasite to cope with anti-malarial drugs. Mutations in
pfcrt,
pfmdr1,
pfdhfr and
pfdhps genes have arisen/been fixed in several parasite populations and, since they confer drug resistance, this facilitates their dispersion.
There may be a clear association between
pfcrt,
pfmdr1,
pfdhfr and
pfdhps allele variants and drug resistance, but such association is not clear regarding
P. vivax. Nevertheless, genetic studies of
P. vivax drug susceptibility in different parts of the world [
8‐
13] have identified point mutations in orthologous genes (
pvcrt-
o,
pvmdr1,
pvdhfr and
pvdhps) to those associated with resistance in
P. falciparum, providing potential markers of resistance to
P. vivax anti-malarial drugs [
14‐
16]. Molecular biology techniques provide a valid alternative for identifying resistance-associated mutations regarding anti-malarial drug therapy in different populations and could therefore be used as a tool for surveillance of
P. vivax drug resistance.
Very few studies have been made in Colombia regarding the search for polymorphisms in these genes. A 2015 evaluation in Colombia’s Córdoba department [
17] stated that the
P. vivax population was more genetically diverse than it had been thought. However, some genome regions had low diversity due to a selective sweep associated with the PvDHPS A383G allele [
17] which, in turn, has been associated with sulfadoxine resistance [
18]. The region surrounding PvDHFR did not have a loss of genetic diversity, as with PvDHPS; nevertheless, two alleles (S58R and S117N) [
17] were reported to be associated with SP resistance [
11]. Five non-synonymous mutations have been reported in
pvdmr1; the mutation triggering change Y976F has been associated with reduced sensitivity to CQ [
19]. However, other studies have not found susceptibility to CQ, despite Y976F being present. This phenotype has been reported in the north of Colombia [
17], although such marker’s role in resistance has not been completely clarified [
16]. The Colombian Amazon region is another focus for malaria as the people inhabiting the area live far away from city centres (i.e. lacking basic services and sanitation), their insecticide use is infrequent and access to healthcare centres is limited, making them more vulnerable to acquiring the disease and putting them at greater risk of not receiving timely treatment. Bewilderingly, there have been no studies regarding the presence of genotypes associated with resistance to the anti-malarial drugs used against
P. vivax in this region. This study was thus aimed at evaluating the genetic diversity of
pvmdr1,
pvdhfr,
pvdhps and
pvcrt-
o fragments in
P. vivax parasites from Colombia’s Amazonian region, thereby providing significant information for the molecular surveillance of drug-resistant
P. vivax.
Discussion
Plasmodium vivax genetic diversity is an important challenge which must be overcome in attempts to control this infection [
34]. Such diversity could enable the parasite to evade host immune responses and confer an adaptive advantage for resisting anti-malarial drugs [
35].
The transmission of
Plasmodium species in Colombia varies according to each geographical area, enabling several of them to cohabit in the same area.
Plasmodium falciparum/P. vivax multiple infections could go unnoticed during diagnosis [
6,
20] and thus the attending doctor cannot prescribe suitable treatment for patients; in turn, this could exercise selective pressure on parasite populations. Choosing the right treatment is thus crucial for preventing the appearance and propagation of resistance [
1]. The samples analysed here came from a tri-border region involving Colombia, Peru and Brazil. First-line treatment for uncomplicated
P. vivax infections is similar for the three countries, where a combination of CQ and PQ is used [
5,
36,
37]. Previous studies have reported polymorphisms associated with resistance to anti-malarial drugs in South and Central America [
7,
10].
Polymorphisms have been found in Central America in
pvmdr1 and
pvdhfr which may be related to a loss of
P. vivax susceptibility to anti-malarial drugs [
10]. Nevertheless, no in vitro susceptibility studies have been reported so far to support such association. Cases of CQ therapeutic failure concerning treating
P. vivax malaria have been documented in South America. Around 12% of therapeutic failure due to CQ-resistant parasites and 6.4% due to mefloquine-resistant parasites have been reported in Brazil’s Amazon region [
38]. Taking into account that the sampling site in this study was near the tri-border area, the interchange of parasite strains carrying resistance mutations was likely and such haplotypes would become dispersed throughout neighbouring endemic areas. Although,
P. vivax CQ resistance mechanisms have not been fully elucidated, they could involve various genetic loci.
Plasmodium falciparum pfcrt-
o and
pfmdr1 variants have been identified as being associated with CQ resistance; these genes’ orthologues in
P. vivax have thus been evaluated for determining whether they might be associated with resistance [
39].
Previous studies have found that PvMDR1 Y976F and F1076L variants seem to have been associated with CQ resistance [
40]. One such polymorphism (variant Y976F) has been found to occur frequently in the east of the Brazilian Amazonian region [
7]. Nevertheless, the role of Y976F in CQ resistance is not yet clear [
16]. Neither Y976F nor F1076L have been observed in the Colombian Amazonian region’s population. Even so, other PvMDR1 polymorphisms were found in this population which have not been reported previously and could thus be substitutions in the strains circulating in the Colombian Amazon region. This suggested that haplotypes segregating in the Brazilian Amazonian region are different to those segregating in the Colombian equivalent and, therefore, gene flow between the Brazilian and Colombian Amazon regions seems to be limited or restricted. Further analysis is required to corroborate whether additional substitutions found in Colombia are related to clinical-resistance phenotypes.
Various mutations in
pvdhfr and
pvdhps have been associated with resistance to SP [
41]. SP in Colombia and Brazil is not currently used as first-line treatment for
P. vivax infection, even though having been included in Colombian Ministry of Health guidelines towards the end of the 1990s [
5]. However, SP is used as the drug of choice for treating
P. falciparum in Colombia [
37,
42] and in northern Perú [
43]. Diagnosis in the three countries is by thick smear; however, several reports have highlighted under-recording of cases by this method and a high rate of coinfection on the Colombia–Brazil–Perú frontier [
20,
44]. This diagnostic technique’s inherent limitations and the large amount of misdiagnosed co-infections could affect selecting the proper treatment, thereby creating selective pressure on the parasite, leading to the fixing of SP resistance in
P. vivax strains [
45], even if SP may not be being used for treating vivax malaria. Polymorphisms found in PvDHFR (F57L/I, S58R, T61M and S117T/N) usually appear in patients having therapeutic failure [
46]. Parasites having double substitutions (F57L–S117N), triple substitutions (5F7L–5S8R–S117N) and quadruple substitutions (F57L–S58R–T61M–S117T) have thus been associated with SP resistance [
10,
47,
48]. Ten different polymorphisms were found in the Amazon region evaluated in this work; double substitutions (S58R–S117N) were observed in 59% of them. It has been proposed that the current use of SP in Colombia has exercised selective pressure on both
P. falciparum and
P. vivax [
49]; validation follow-up is thus recommended to observe its efficacy as treatment. A triple mutation haplotype was observed (S58R–S117N–I173L) in 17% of samples; however, it is not clear whether this haplotype could be associated with resistance.
PvDHPS polymorphisms in aa 382, 383, 512, 553 and 585 (homologues for
P. falciparum positions 436, 437, 540, 581 and 613, respectively) [
26] seem to be involved in resistance to sulfadoxine. A high S382C mutation prevalence in chloroquine and mefloquine-resistant parasites has been observed in Brazil’s Amazon region [
38,
50]. A383G substitution prevalence was 41.6%, the most prevalent in this study, unlike S382C and K462R mutations; this could have been related to changes in aa position 382 and 383 which are frequent in regions having high SP use [
51]. In addition to the aforementioned polymorphisms, new
pvdhfr and
pvdhps variants and haplotypes were found in
P. vivax strains from the Colombian Amazonian region.
pvcrt is an orthologue of
pfcrt whose association with resistance to CQ is controversial [
52]; CRT has shown no contribution whatsoever to resistance to chloroquine regarding
P. vivax, even though sensitive or resistant
P. vivax parasites cause substitution 76K [
53]. Concerning the Colombian Amazonian region this gene fragment was seen to be highly conserved, having 100% identity with the
P. vivax Sal-1 strain which is susceptible to anti-malarial drugs.
Selective sweep could be taking place, fixing advantageous variants
Point mutations or determined haplotypes in
P. falciparum that alter
dhfr,
dhps,
mdr1 and
crt-
o protein products, enable the parasite to resist several drugs. Such mutations are usually fixed rapidly in populations due to a selective advantage causing DNA regions containing such genes to have low genetic diversity (such effect is known as selective sweep). The
pvdhfr,
pvdhps,
pvmdr1 and
pvcrt-
o fragments analysed in the population from Colombia’s southern Amazon region had low genetic diversity; such polymorphisms seemed to be neutral according to Tajima, Fu and Li and d
N–d
S tests. However, the Fay and Wu H estimator gave significant
pvdhfr and
pvmdr1 values, suggesting a selective sweep. A candidate-resistant gene (
pvdhps) having this pattern has been recorded previously in Colombia’s Córdoba department [
17] according to information regarding the complete genome of
P. vivax clinical isolates. Some mutations found in these
P. vivax genes could have been fixed by conferring an advantage, in turn fixing neutral variants and thus reducing genetic diversity. As Fay and Wu tests gave statistically significant values, the southern Colombian Amazonian region’s parasite population might be under selective pressure, probably exerted by anti-malarial drugs; a selective sweep might thereby be fixing mutations enabling the appearance of resistant phenotypes. However, genes involved in selective sweep were different between Tierra Alta and the Colombian Amazonian region, probably due to differential treatment in these populations or populations in Colombia being structured with low gene flow between them, as seen in previous studies [
54‐
56]. Further analysis is required to assess the selective sweep hypothesis regarding these genes in the Colombian Amazonian region.
Conclusions
Even though studies in malaria-endemic regions have focused on the search for alternatives for improving the available treatment against malaria, the impact of these strategies on the evolution of
P. vivax populations must be evaluated, due to the appearance and dispersion of resistance in such regions. Although, resistance is not fully understood concerning
P. vivax and resistance-markers have not been clearly defined yet [
16],
dhfr,
dhps,
mdr1 and
crt-
o genes have mutations which (in some cases) seem to provide resistance or at least reduced susceptibility to anti-malarial drugs [
57]. Even though not all four genes have confirmed roles regarding
P. vivax drug susceptibility, they are potential targets for
P. vivax resistance. These four genes have low genetic diversity in the Colombian Amazon region. However, some of the mutations found were associated with resistance, i.e. the F1070L mutation in PvMDR1, S117N and S58R/K in PvDHFR and A383G and A382C in PvDHPS, whilst other new variants were also found in these genes.
pvmdr1 and
pvdhfr fragments’ diversity pattern could be the consequence of a selective sweep, indicating that these genes’ variants might be becoming fixed in the population due to an adaptive advantage; these mutations could endow the parasite population with lower sensitivity to anti-malarial drugs. However, additional sequence analysis and in vitro assays are needed to confirm whether these variants are associated with resistance and/or therapeutic failures. The results reported here could be taken as a base tool for advising on how malaria control measures are implemented in Colombia and avoid the dispersion of haplotypes associated with resistance in this region.
Authors’ contributions
JRC conceived and designed the experiments. JRC, PAC-A, CHN, AO-O, EO-C and MFO-D performed the experiments. DG-O performed the evolutionary analysis. JRC, CHN, PAC-A, DG-O, MAP analysed the data. JRC, DG-O, PAC-A, CHN, MEP, MAP wrote the paper. All authors read and approved the final manuscript.