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

被引：9

作者：

Trimarsanto, Hidayat ^{[1
,2
,3
]}

Amato, Roberto ^{[4
]}

Pearson, Richard D. ^{[4
]}

Sutanto, Edwin ^{[3
,5
]}

Noviyanti, Rintis ^{[3
]}

Trianty, Leily ^{[3
]}

Marfurt, Jutta ^{[1
,2
]}

Pava, Zuleima ^{[1
,2
]}

Echeverry, Diego F. ^{[6
,7
,8
]}

Lopera-Mesa, Tatiana M. ^{[9
]}

Montenegro, Lidia M. ^{[9
]}

Tobon-Castano, Alberto ^{[9
]}

Grigg, Matthew J. ^{[1
,2
,10
]}

Barber, Bridget ^{[1
,2
,10
]}

William, Timothy ^{[10
,11
]}

Anstey, Nicholas M. ^{[1
,2
]}

Getachew, Sisay ^{[12
,13
]}

Petros, Beyene ^{[12
]}

Aseffa, Abraham ^{[13
]}

Assefa, Ashenafi ^{[14
]}

Rahim, Awab G. ^{[15
,16
]}

Chau, Nguyen H. ^{[17
]}

Hien, Tran T. ^{[17
]}

Alam, Mohammad S. ^{[18
]}

Khan, Wasif A. ^{[18
]}

Ley, Benedikt ^{[1
,2
]}

Thriemer, Kamala ^{[1
,2
]}

Wangchuck, Sonam ^{[19
]}

Hamedi, Yaghoob ^{[20
]}

Adam, Ishag ^{[21
]}

Liu, Yaobao ^{[22
,23
]}

Gao, Qi ^{[22
]}

Sriprawat, Kanlaya ^{[24
]}

Ferreira, Marcelo U. ^{[25
,26
]}

Laman, Moses ^{[27
]}

Barry, Alyssa ^{[28
,29
,30
]}

Mueller, Ivo ^{[29
,31
]}

Lacerda, Marcus V. G. ^{[32
,33
]}

Llanos-Cuentas, Alejandro ^{[34
]}

Krudsood, Srivicha ^{[35
]}

Lon, Chanthap ^{[36
]}

Mohammed, Rezika ^{[37
]}

Yilma, Daniel ^{[38
]}

Pereira, Dhelio B. ^{[39
]}

Espino, Fe E. J. ^{[40
]}

Chu, Cindy S. ^{[15
,24
]}

Velez, Ivan D. ^{[9
]}

Namaik-larp, Chayadol ^{[41
]}

Villegas, Maria F. ^{[42
]}

Green, Justin A. ^{[43
]}

机构：

[1] Menzies Sch Hlth Res, Global & Trop Hlth Div, Darwin, NT, Australia

[2] Charles Darwin Univ, Darwin, NT, Australia

[3] Eijkman Inst Mol Biol, Jakarta, Indonesia

[4] Wellcome Sanger Inst, Wellcome Genome Campus, Cambridge, England

[5] Exeins Hlth Initiat, Jakarta, Indonesia

[6] Int Training & Med Res Ctr CIDEIM, Cali, Colombia

[7] Univ Valle, Dept Microbiol, Cali, Colombia

[8] Univ Icesi, Cali, Colombia

[9] Univ Antioquia, Malaria Grp, Medellin, Colombia

[10] Infect Dis Soc Sabah Menzies Sch Hlth Res Clin Re, Kota Kinabalu, Sabah, Malaysia

[11] Queen Elizabeth Hosp, Clin Res Ctr, Kota Kinabalu, Sabah, Malaysia

[12] Addis Ababa Univ, Coll Nat Sci, Addis Ababa, Ethiopia

[13] Armauer Hansen Res Inst, Addis Ababa, Ethiopia

[14] Ethiopian Publ Hlth Inst, Addis Ababa, Ethiopia

[15] Mahidol Univ, Mahidol Oxford Trop Med Res Unit, Bangkok, Thailand

[16] Nangarhar Univ, Nangarhar Med Fac, Minist Higher Educ, Jalalabad, Afghanistan

[17] Oxford Univ Clin Res Unit, Hosp Trop Dis, Ho Chi Minh City, Vietnam

[18] Int Ctr Diarrheal Dis Res, Infect Dis Div, Dhaka, Bangladesh

[19] Minist Hlth, Dept Publ Hlth, Royal Ctr Dis Control, Thimphu, Bhutan

[20] Hormozgan Univ Med Sci, Infect & Trop Dis Res Ctr, Bandar Abbas, Hormozgan Provi, Iran

[21] Univ Khartoum, Fac Med, Khartoum, Sudan

[22] Jiangsu Inst Parasit Dis, Natl Hlth Commiss Key Lab Parasit Dis Control & P, Jiangsu Prov Key Lab Parasite & Vector Control Te, Wuxi, Jiangsu, Peoples R China

[23] Nanjing Med Univ, Sch Publ Hlth, Nanjing, Peoples R China

[24] Mahidol Univ, Fac Trop Med, Shoklo Malaria Res Unit, Mae Sot, Thailand

[25] Univ Sao Paulo, Inst Biomed Sci, Dept Parasitol, Sao Paulo, Brazil

[26] NOVA Univ Lisbon, Inst Hyg & Trop Med, Global Hlth & Trop Med, Lisbon, Portugal

[27] Papua New Guinea Inst Med Res, Madang, Papua N Guinea

[28] Deakin Univ, Geelong, Vic, Australia

[29] Walter & Eliza Hall Inst Med Res, Populat Hlth & Immun Div, Parkville, Vic, Australia

[30] Univ Melbourne, Dept Med Biol, Melbourne, Vic, Australia

[31] Inst Pasteur, Dept Parasites & Insect Vectors, Paris, France

[32] Fundacao Med Trop, Manaus, Amazonas, Brazil

[33] Fundacao Oswaldo Cruz, Rio De Janeiro, Brazil

[34] Univ Peruana Cayetano Heredia, Lima, Peru

[35] Mahidol Univ, Bangkok, Thailand

[36] Armed Forces Res Inst Med Sci, Bangkok, Thailand

[37] Univ Gondar, Gondar, Ethiopia

[38] Jimma Univ, Jimma, Ethiopia

[39] Ctr Pesquisa Med Trop, Porto Velho, Brazil

[40] Res Inst Trop Med, Manila, Philippines

[41] Umphang Hosp, Tak, Thailand

[42] Ctr Invest Clin, Cali, Colombia

[43] GlaxoSmithKline, Brentford, England

[44] Univ Cambridge, Sch Clin Med, Cambridge Inst Med Res, Cambridge, England

[45] Univ Oxford, Ctr Trop Med & Global Hlth, Nuffield Dept Med, Oxford, England

来源：

COMMUNICATIONS BIOLOGY | 2022年 / 5卷 / 01期

基金：

英国医学研究理事会; 英国惠康基金; 澳大利亚国家健康与医学研究理事会;

关键词：

GENOMIC ANALYSIS; CHLOROQUINE; INFECTIONS; FALCIPARUM;

D O I：

10.1038/s42003-022-04352-2

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：10

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