Bayesian spatio-temporal distributed lag modeling for delayed climatic effects on sparse malaria incidence data

Background In many areas of the Greater Mekong Subregion (GMS), malaria endemic regions have shrunk to patches of predominantly low-transmission. With a regional goal of elimination by 2030, it is important to use appropriate methods to analyze and predict trends in incidence in these remaining transmission foci to inform planning efforts. Climatic variables have been associated with malaria incidence to varying degrees across the globe but the relationship is less clear in the GMS and standard methodologies may not be appropriate to account for the lag between climate and incidence and for locations with low numbers of cases. Methods In this study, a methodology was developed to estimate the spatio-temporal lag effect of climatic factors on malaria incidence in Thailand within a Bayesian framework. A simulation was conducted based on ground truth of lagged effect curves representing the delayed relation with sparse malaria cases as seen in our study population. A case study to estimate the delayed effect of environmental variables was used with malaria incidence at a fine geographic scale of sub-districts in a western province of Thailand. Results From the simulation study, the model assumptions which accommodated both delayed effects and excessive zeros appeared to have the best overall performance across evaluation metrics and scenarios. The case study demonstrated lagged climatic effect estimation of the proposed modeling with real data. The models appeared to be useful to estimate the shape of association with malaria incidence. Conclusions A new method to estimate the spatiotemporal effect of climate on malaria trends in low transmission settings is presented. The developed methodology has potential to improve understanding and estimation of past and future trends in malaria incidence. With further development, this could assist policy makers with decisions on how to more effectively distribute resources and plan strategies for malaria elimination

Spatial heterogeneity and temporal trends in Malaria on the Thai–Myanmar Border (2012–2017): a retrospective observational study

Malaria infections remain an important public health problem for the Thai-Myanmar border population, despite a plan for the elimination by the end of 2026 (Thailand) and 2030 (Myanmar). This study aimed to explore spatiotemporal patterns in Plasmodium falciparum and Plasmodium vivax incidence along the Thai-Myanmar border. Malaria cases among Thai citizens in 161 sub-districts in Thailand's Kanchanaburi and Tak Provinces (2012-2017) were analyzed to assess the cluster areas and temporal trends. Based on reported incidence, 65.22% and 40.99% of the areas studied were seen to be at elimination levels for P. falciparum and P. vivax already, respectively. There were two clear clusters of malaria in the region: One in the northern part (Cluster I), and the other in the central part (Cluster II). In Cluster I, the malaria season exhibited two peaks, while there was only one peak seen for Cluster II. Malaria incidence decreased at a faster rate in Cluster I, with 5% and 4% reductions compared with 4% and 3% reductions in P. falciparum and P. vivax incidence per month, respectively, in Cluster II. The decreasing trends reflect the achievements of malaria control efforts on both sides of the Thai-Myanmar border. However, these clusters could act as reservoirs. Perhaps one of the main challenges facing elimination programs in this low transmission setting is maintaining a strong system for early diagnosis and treatment, even when malaria cases are very close to zero, whilst preventing re-importation of cases

Molecular characterization of Plasmodium falciparum antifolate resistance markers in Thailand between 2008 and 2016

Background Resistance to anti-malarials is a major threat to the control and elimination of malaria. Sulfadoxine–pyrimethamine (SP) anti-malarial treatment was used as a national policy for treatment of uncomplicated falciparum malaria in Thailand from 1973 to 1990. In order to determine whether withdrawal of this antifolate drug has led to restoration of SP sensitivity, the prevalence of genetic markers of SP resistance was assessed in historical Thai samples. Methods Plasmodium falciparum DNA was collected from the Thailand–Myanmar, Thailand–Malaysia and Thailand–Cambodia borders during 2008–2016 (N = 233). Semi-nested PCR and nucleotide sequencing were used to assess mutations in Plasmodium falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthase (pfdhps). Gene amplification of Plasmodium falcipaurm GTP cyclohydrolase-1 (pfgch1) was assessed by quantitative real-time PCR. The association between pfdhfr/pfdhps mutations and pfgch1 copy numbers were evaluated. Results Mutations in pfdhfr/pfdhsp and pfgch1 copy number fluctuated overtime through the study period. Altogether, 14 unique pfdhfr–pdfhps haplotypes collectively containing quadruple to octuple mutations were identified. High variation in pfdhfr–pfdhps haplotypes and a high proportion of pfgch1 multiple copy number (51% (73/146)) were observed on the Thailand–Myanmar border compared to other parts of Thailand. Overall, the prevalence of septuple mutations was observed for pfdhfr–pfdhps haplotypes. In particular, the prevalence of pfdhfr–pfdhps, septuple mutation was observed in the Thailand–Myanmar (50%, 73/146) and Thailand–Cambodia (65%, 26/40) border. In Thailand–Malaysia border, majority of the pfdhfr–pfdhps haplotypes transaction from quadruple (90%, 9/10) to quintuple (65%, 24/37) during 2008–2016. Within the pfdhfr–pfdhps haplotypes, during 2008–2013 the pfdhps A/S436F mutation was observed only in Thailand–Myanmar border (9%, 10/107), while it was not identified later. In general, significant correlation was observed between the prevalence of pfdhfr I164L (ϕ = 0.213, p-value = 0.001) or pfdhps K540E/N (ϕ = 0.399, p-value ≤ 0.001) mutations and pfgch1 gene amplification. Conclusions Despite withdrawal of SP as anti-malarial treatment for 17 years, the border regions of Thailand continue to display high prevalence of antifolate and anti-sulfonamide resistance markers in falciparum malaria. Significant association between pfgch1 amplification and pfdhfr (I164L) or pfdhps (K540E) resistance markers were observed, suggesting a compensatory mutation

Molecular characterization of Plasmodium falciparum antifolate resistance markers in Thailand between 2008 and 2016

Background Resistance to anti-malarials is a major threat to the control and elimination of malaria. Sulfadoxine–pyrimethamine (SP) anti-malarial treatment was used as a national policy for treatment of uncomplicated falciparum malaria in Thailand from 1973 to 1990. In order to determine whether withdrawal of this antifolate drug has led to restoration of SP sensitivity, the prevalence of genetic markers of SP resistance was assessed in historical Thai samples. Methods Plasmodium falciparum DNA was collected from the Thailand–Myanmar, Thailand–Malaysia and Thailand–Cambodia borders during 2008–2016 (N = 233). Semi-nested PCR and nucleotide sequencing were used to assess mutations in Plasmodium falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthase (pfdhps). Gene amplification of Plasmodium falcipaurm GTP cyclohydrolase-1 (pfgch1) was assessed by quantitative real-time PCR. The association between pfdhfr/pfdhps mutations and pfgch1 copy numbers were evaluated. Results Mutations in pfdhfr/pfdhsp and pfgch1 copy number fluctuated overtime through the study period. Altogether, 14 unique pfdhfr–pdfhps haplotypes collectively containing quadruple to octuple mutations were identified. High variation in pfdhfr–pfdhps haplotypes and a high proportion of pfgch1 multiple copy number (51% (73/146)) were observed on the Thailand–Myanmar border compared to other parts of Thailand. Overall, the prevalence of septuple mutations was observed for pfdhfr–pfdhps haplotypes. In particular, the prevalence of pfdhfr–pfdhps, septuple mutation was observed in the Thailand–Myanmar (50%, 73/146) and Thailand–Cambodia (65%, 26/40) border. In Thailand–Malaysia border, majority of the pfdhfr–pfdhps haplotypes transaction from quadruple (90%, 9/10) to quintuple (65%, 24/37) during 2008–2016. Within the pfdhfr–pfdhps haplotypes, during 2008–2013 the pfdhps A/S436F mutation was observed only in Thailand–Myanmar border (9%, 10/107), while it was not identified later. In general, significant correlation was observed between the prevalence of pfdhfr I164L (ϕ = 0.213, p-value = 0.001) or pfdhps K540E/N (ϕ = 0.399, p-value ≤ 0.001) mutations and pfgch1 gene amplification. Conclusions Despite withdrawal of SP as anti-malarial treatment for 17 years, the border regions of Thailand continue to display high prevalence of antifolate and anti-sulfonamide resistance markers in falciparum malaria. Significant association between pfgch1 amplification and pfdhfr (I164L) or pfdhps (K540E) resistance markers were observed, suggesting a compensatory mutation

Genetic population of Plasmodium knowlesi during pre-malaria elimination in Thailand

Background Thailand is committed to eliminating malaria by 2024. From 2013 to 2020, the total number of malaria cases have decreased, from 37,741 to 4474 (an 88.1% reduction). However, infections with Plasmodium knowlesi, a monkey malarial pathogen that can also infect humans, have been increasingly observed. This study focused on the molecular analysis of P. knowlesi parasites causing malaria in Thailand. Methods Under Thailand’s integrated Drug Efficacy Surveillance (iDES), which includes drug-resistance monitoring as part of routine case-based surveillance and responses, specimens were collected from malaria patients (n = 966) between 2018 and 2020. Thirty-one mono P. knowlesi infections (3.1%), most of which were from eastern and southern Thailand, were observed and confirmed by nested PCR assay and DNA sequencing. To evaluate whether these pathogens were from different lineages, cluster analysis based on seven microsatellite genotyping markers and the merozoite surface protein 1 (pkmsp1) gene was carried out. The P. knowlesi pyrimethamine resistance gene dihydrofolate reductase (pkdhfr) was sequenced and homology modelling was constructed. Results The results of analysing the seven microsatellite markers and pkmsp1 sequence demonstrated that P. knowlesi parasites from eastern Thailand were of the same lineage as those isolated in Cambodia, while the parasites causing malaria in southern Thailand were the same lineage as those isolated from Malaysia. The sequencing results for the pkdhfr genes indicated the presence of two mutations, Arg34Leu and a deletion at position 105. On analysis with homology modelling, the two mutations were not associated with anti-malarial drug resistance. Conclusions This report compared the genetic populations of P. knowlesi parasites in Thailand from 2018 to 2020 and have shown similar lineages as those isolated in Cambodia and Malaysia of P. knowlesi infection in Thailand and demonstrated that the P. knowlesi parasites were of the same lineages as those isolated in Cambodia and Malaysia. The parasites were also shown to be sensitive to pyrimethamine

Low parasite connectivity among three malaria hotspots in Thailand

Identifying sources and sinks of malaria transmission is critical for designing effective intervention strategies particularly as countries approach elimination. The number of malaria cases in Thailand decreased 90% between 2012 and 2020, yet elimination has remained a major public health challenge with persistent transmission foci and ongoing importation. There are three main hotspots of malaria transmission in Thailand: Ubon Ratchathani and Sisaket in the Northeast; Tak in the West; and Yala in the South. However, the degree to which these hotspots are connected via travel and importation has not been well characterized. Here, we develop a metapopulation model parameterized by mobile phone call detail record data to estimate parasite flow among these regions. We show that parasite connectivity among these regions was limited, and that each of these provinces independently drove the malaria transmission in nearby provinces. Overall, our results suggest that due to the low probability of domestic importation between the transmission hotspots, control and elimination strategies can be considered separately for each region

Molecular characterization of Plasmodium falciparum antifolate resistance markers in Thailand between 2008 and 2016

Background: Resistance to anti-malarials is a major threat to the control and elimination of malaria. Sulfadoxine-pyrimethamine (SP) anti-malarial treatment was used as a national policy for treatment of uncomplicated falciparum malaria in Thailand from 1973 to 1990. In order to determine whether withdrawal of this antifolate drug has led to restoration of SP sensitivity, the prevalence of genetic markers of SP resistance was assessed in historical Thai samples. Methods: Plasmodium falciparum DNA was collected from the Thailand-Myanmar, Thailand-Malaysia and Thailand-Cambodia borders during 2008-2016 (N = 233). Semi-nested PCR and nucleotide sequencing were used to assess mutations in Plasmodium falciparum dihydrofolate reductase (pfdhfr), P. falciparum dihydropteroate synthase (pfdhps). Gene amplification of Plasmodium falcipaurm GTP cyclohydrolase-1 (pfgch1) was assessed by quantitative real-time PCR. The association between pfdhfr/pfdhps mutations and pfgch1 copy numbers were evaluated. Results: Mutations in pfdhfr/pfdhsp and pfgch1 copy number fluctuated overtime through the study period. Altogether, 14 unique pfdhfr-pdfhps haplotypes collectively containing quadruple to octuple mutations were identified. High variation in pfdhfr-pfdhps haplotypes and a high proportion of pfgch1 multiple copy number (51% (73/146)) were observed on the Thailand-Myanmar border compared to other parts of Thailand. Overall, the prevalence of septuple mutations was observed for pfdhfr-pfdhps haplotypes. In particular, the prevalence of pfdhfr-pfdhps, septuple mutation was observed in the Thailand-Myanmar (50%, 73/146) and Thailand-Cambodia (65%, 26/40) border. In Thailand-Malaysia border, majority of the pfdhfr-pfdhps haplotypes transaction from quadruple (90%, 9/10) to quintuple (65%, 24/37) during 2008-2016. Within the pfdhfr-pfdhps haplotypes, during 2008-2013 the pfdhps A/S436F mutation was observed only in Thailand-Myanmar border (9%, 10/107), while it was not identified later. In general, significant correlation was observed between the prevalence of pfdhfr I164L (φ = 0.213, p-value = 0.001) or pfdhps K540E/N (φ = 0.399, p-value ≤ 0.001) mutations and pfgch1 gene amplification. Conclusions: Despite withdrawal of SP as anti-malarial treatment for 17 years, the border regions of Thailand continue to display high prevalence of antifolate and anti-sulfonamide resistance markers in falciparum malaria. Significant association between pfgch1 amplification and pfdhfr (I164L) or pfdhps (K540E) resistance markers were observed, suggesting a compensatory mutation

Assessing the acceptability and feasibility of reactive drug administration for malaria elimination in a Plasmodium vivax predominant setting: a qualitative study in two provinces in Thailand.

BackgroundReactive case detection (RACD) or testing and treatment of close contacts of recent malaria cases, is commonly practiced in settings approaching malaria elimination, but standard diagnostics have limited sensitivity to detect low level infections. Reactive drug administration (RDA), or presumptive treatment without testing, is an alternative approach, but better understanding regarding community acceptability and operational feasibility are needed.MethodsA qualitative study was conducted as part of a two-arm cluster randomized-controlled trial evaluating the effectiveness of RDA targeting high-risk villages and forest workers for reducing Plasmodium vivax and P. falciparum malaria in Thailand. Key informant interviews (KIIs) and focus group discussions (FGDs) were conducted virtually among key public health staff, village health volunteers (VHVs), and household members that implemented or received RDA activities. Transcriptions were reviewed, coded, and managed manually using Dedoose qualitative data analysis software, then underwent qualitative content analysis to identify key themes.ResultsRDA was well accepted by household members and public health staff that implemented it. RDA participation was driven by fear of contracting malaria, eagerness to receive protection provided by malaria medicines, and the increased access to health care. Concerns were raised about the safety of taking malaria medicines without having an illness, particularly if underlying health conditions existed. Health promotion hospital (HPH) staff implementing RDA noted its operational feasibility, but highlighted difficulty in traveling to remote areas, and requested additional travel resources and hiring more VHVs. Other challenges were highlighted including the need for additional training for VHVs on malaria activities and the inability of HPH staff to conduct RDA due to other health priorities (e.g., Covid-19). More training and practice for VHVs were noted as ways to improve implementation of RDA.ConclusionsTo maximize uptake of RDA, regular education and sensitization campaigns in collaboration with village leaders on the purpose and rationale of RDA will be critical. To alleviate safety concerns and increase participant safety, a rigorous pharmacovigilance program will be important. To accelerate uptake of RDA, trust between HPH staff and VHVs and the communities they serve must continue to be strengthened to ensure acceptance of the intervention.Trial registrationThis study was approved by the Committee on Human Research at the University of California San Francisco (19-28,060) and the local Ethics Committee for Research in Human Subjects at Tak Provincial Health office (009/63) and Kanchanaburi Provincial health office (Kor Chor 0032.002/2185). Local authorities and health officers in the provinces, districts, and villages agreed upon and coordinated the implementation of the study. All methods in this study were carried out in accordance with relevant guidelines and regulations

Assessing the acceptability and feasibility of reactive drug administration for malaria elimination in a Plasmodium vivax predominant setting : a qualitative study in two provinces in Thailand

Background: Reactive case detection (RACD) or testing and treatment of close contacts of recent malaria cases, is commonly practiced in settings approaching malaria elimination, but standard diagnostics have limited sensitivity to detect low level infections. Reactive drug administration (RDA), or presumptive treatment without testing, is an alternative approach, but better understanding regarding community acceptability and operational feasibility are needed. Methods: A qualitative study was conducted as part of a two-arm cluster randomized-controlled trial evaluating the effectiveness of RDA targeting high-risk villages and forest workers for reducing Plasmodium vivax and P. falciparum malaria in Thailand. Key informant interviews (KIIs) and focus group discussions (FGDs) were conducted virtually among key public health staff, village health volunteers (VHVs), and household members that implemented or received RDA activities. Transcriptions were reviewed, coded, and managed manually using Dedoose qualitative data analysis software, then underwent qualitative content analysis to identify key themes. Results: RDA was well accepted by household members and public health staff that implemented it. RDA participation was driven by fear of contracting malaria, eagerness to receive protection provided by malaria medicines, and the increased access to health care. Concerns were raised about the safety of taking malaria medicines without having an illness, particularly if underlying health conditions existed. Health promotion hospital (HPH) staff implementing RDA noted its operational feasibility, but highlighted difficulty in traveling to remote areas, and requested additional travel resources and hiring more VHVs. Other challenges were highlighted including the need for additional training for VHVs on malaria activities and the inability of HPH staff to conduct RDA due to other health priorities (e.g., Covid-19). More training and practice for VHVs were noted as ways to improve implementation of RDA. Conclusions: To maximize uptake of RDA, regular education and sensitization campaigns in collaboration with village leaders on the purpose and rationale of RDA will be critical. To alleviate safety concerns and increase participant safety, a rigorous pharmacovigilance program will be important. To accelerate uptake of RDA, trust between HPH staff and VHVs and the communities they serve must continue to be strengthened to ensure acceptance of the intervention