Dataset Information

A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

ABSTRACT: Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.

SUBMITTER: Trimarsanto H

PROVIDER: S-EPMC9789135 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

Trimarsanto Hidayat H Amato Roberto R Pearson Richard D RD Sutanto Edwin E Noviyanti Rintis R Trianty Leily L Marfurt Jutta J Pava Zuleima Z Echeverry Diego F DF Lopera-Mesa Tatiana M TM Montenegro Lidia M LM Tobón-Castaño Alberto A Grigg Matthew J MJ Barber Bridget B William Timothy T Anstey Nicholas M NM Getachew Sisay S Petros Beyene B Aseffa Abraham A Assefa Ashenafi A Rahim Awab G AG Chau Nguyen H NH Hien Tran T TT Alam Mohammad S MS Khan Wasif A WA Ley Benedikt B Thriemer Kamala K Wangchuck Sonam S Hamedi Yaghoob Y Adam Ishag I Liu Yaobao Y Gao Qi Q Sriprawat Kanlaya K Ferreira Marcelo U MU Laman Moses M Barry Alyssa A Mueller Ivo I Lacerda Marcus V G MVG Llanos-Cuentas Alejandro A Krudsood Srivicha S Lon Chanthap C Mohammed Rezika R Yilma Daniel D Pereira Dhelio B DB Espino Fe E J FEJ Chu Cindy S CS Vélez Iván D ID Namaik-Larp Chayadol C Villegas Maria F MF Green Justin A JA Koh Gavin G Rayner Julian C JC Drury Eleanor E Gonçalves Sónia S Simpson Victoria V Miotto Olivo O Miles Alistair A White Nicholas J NJ Nosten Francois F Kwiatkowski Dominic P DP Price Ric N RN Auburn Sarah S

Communications biology 20221223 1

Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with hi ...[more]

PMID: 36564617

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Project description:BackgroundCross-border malaria transmission is an important problem for national malaria control programmes. The epidemiology of cross-border malaria is further complicated in areas where Plasmodium falciparum and Plasmodium vivax are both endemic. By combining passive case detection data with entomological data, a transmission scenario on the northwestern Thai-Myanmar border where P. falciparum is likely driven by importation was described, whereas P. vivax is also locally transmitted. This study highlights the differences in the level of control required to eliminate P. falciparum and P. vivax from the same region.MethodsMalaria case data were collected from malaria clinics in Suan Oi village, Tak Province, Thailand between 2011 and 2014. Infections were diagnosed by light microscopy. Demographic data, including migrant status, were correlated with concomitantly collected entomology data from 1330 mosquito trap nights using logistic regression. Malaria infection in the captured mosquitoes was detected by ELISA.ResultsRecent migrants were almost four times more likely to be infected with P. falciparum compared with Thai patients (OR 3.84, p < 0.001) and cases were significantly associated with seasonal migration. However, P. falciparum infection was not associated with the Anopheles mosquito capture rates, suggesting predominantly imported infections. In contrast, recent migrants were equally likely to present with P. vivax as mid-term migrants. Both migrant groups were twice as likely to be infected with P. vivax in comparison to the resident Thai population (OR 1.96, p < 0.001 and OR 1.94, p < 0.001, respectively). Plasmodium vivax cases were strongly correlated with age and local capture rates of two major vector species Anopheles minimus and Anopheles maculatus (OR 1.23, p = 0.020 and OR 1.33, p = 0.046, respectively), suggesting that a high level of local transmission might be causing these infections.ConclusionsOn the Thai-Myanmar border, P. falciparum infections occur mostly in the recent migrant population with a seasonality reflecting that of agricultural activity, rather than that of the local mosquito population. This suggests that P. falciparum was mostly imported. In contrast, P. vivax cases were significantly associated with mosquito capture rates and less with migrant status, indicating local transmission. This highlights the different timelines and requirements for P. falciparum and P. vivax elimination in the same region and underlines the importance of multinational, cross-border malaria control.

Project description:BackgroundChina has reached important milestones in the elimination of malaria. However, the numbers of imported recurrent cases of Plasmodium vivax and P. ovale are gradually increasing, which increases the risk of malaria re-establishment in locations where Anopheles mosquitoes exist. The aim of this study is to characterize the epidemiological profiles of imported recurrent P. vivax and P. ovale cases, quantifying the recurrence burden and guiding the development of appropriate public health intervention strategies.MethodsIndividual-level data of imported recurrent P. vivax and P. ovale cases were collected from 2013 to 2020 in China via the Parasitic Diseases Information Reporting Management System. Demographic characteristics, temporal and spatial distributions, and the interval from previous infection to recurrence were analyzed by SAS, ArcGIS and GraphPad Prism software, respectively, to explore the epidemiological profiles of imported recurrent cases.ResultsA total of 307 imported recurrent cases, including 179 P. vivax and 128 P. ovale cases, were recorded. The majority of cases occurred in males (P. vivax 91.1%, P. ovale 93.8%) and migrant workers (P. vivax 43.2%, P. ovale 44.7%). Individuals aged 30-39 years had the highest P. vivax and P. ovale recurrent infection rates, respectively. The number of imported recurrent cases of infection by these two malaria species increased from 2013 to 2018, and P. vivax infection showed well-defined seasonality, with two peaks in February and June, respectively. More than 90% of patients with recurrent cases did not receive radical treatment for previous infection. Most imported recurrent P. vivax cases were reported in Yunnan Province and were imported from Myanmar, Ethiopia, and Pakistan, while most recurrent P. ovale cases were reported in southern China and primarily imported from Cameroon, Ghana, and Nigeria. The intervals from previous malaria infection to recurrence among different continents were significantly different (P = 0.0016) for P. vivax malaria but not for P. ovale malaria (P = 0.2373).ConclusionsThe large number of imported recurrent cases has been a major challenge in the prevention of malaria re-establishment in China. This study provides evidence to guide the development of appropriate public health intervention strategies for imported recurrent P. vivax and P. ovale cases.

Project description:BackgroundThis study aimed at exploring the epidemiological pattern of imported malaria in China before malaria elimination in 2021, to provide evidence-based data for preventing malaria re-establishment in China.MethodsNine-year surveillance data on imported malaria in four provincial-level administrative divisions (PLADs) (Anhui, Chongqing, Guangxi, and Zhejiang) between 2011 and 2019 were thoroughly collected and analyzed.ResultsA quite stable trend in imported malaria cases between 2011 and 2019 was observed. In total, 6,064 imported patients were included. Plasmodium falciparum was the most frequently reported species (4,575, 75.6%). Cases of malaria were most frequently imported from Western Africa (54.4%). We identified an increasing trend in P. ovale and a persistence of P. vivax infections among the cases of malaria imported from Western Africa. Most patients (97.5%) were 20-50 years old. Among imported malaria infections, the main purposes for traveling abroad were labor export (4,914/6,064, 81.0%) and business trips (649, 10.7%). Most patients (2,008/6,064, 33.1%) first visited county-level medical institutions when they sought medical help in China. More patients were diagnosed within 3 days after visiting Centers for Disease Control and Prevention (CDCs) or entry-exit quarantine facilities (EQFs) (1,147/1609, 71.3%) than after visiting medical institutions (2,182/3993, 54.6%).ConclusionImported malaria still poses a threat to the malaria-free status of China. County-level institutions are the primary targets in China to improve the sensitivity of the surveillance system and prevent the re-establishment of malaria. Health education should focus on exported labors, especially to Western and Central Africa. Increasing trend in P. ovale and persistence of P. vivax infections indicated their underestimations in Western Africa. Efficient diagnostic tools and sensitive monitoring systems are required to identify Plasmodium species in Africa.

Dataset Information

A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

Publications

A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

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