Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization

被引：3

作者：

Carey, Megan E. ^{[1
,2
,3
]}

Dyson, Zoe A. ^{[3
,4
,5
]}

Argimon, Silvia ^{[6
]}

Cerdeira, Louise ^{[7
]}

Yeats, Corin ^{[6
]}

Aanensen, David ^{[6
]}

Mboowa, Gerald

Baker, Stephen ^{[1
,2
]}

Tessema, Sofonias K. ^{[8
]}

Smith, Anthony M. ^{[9
]}

Okeke, Iruka N. ^{[10
]}

Holt, Kathryn E. ^{[3
]}

机构：

[1] Univ Cambridge, Cambridge Inst Therapeut Immunol & Infect Dis, Dept Med, Cambridge, England

[2] Chelsea & Westminster Hosp, IAVI, London, England

[3] London Sch Hyg & Trop Med, Fac Infect & Trop Dis, Dept Infect Biol, London, England

[4] Monash Univ, Cent Clin Sch, Dept Infect Dis, Melbourne, Australia

[5] Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton, England

[6] Univ Oxford, Big Data Inst, Ctr Genom Pathogen Surveillance, Nuffield Dept Med, Oxford, England

[7] Univ Liverpool Liverpool Sch Trop Med, Dept Vector Biol, Liverpool, England

[8] Africa Ctr Dis Control & Prevent, Addis Ababa, Ethiopia

[9] Natl Inst Communicable Dis, Ctr Enter Dis, Div Natl Hlth Lab Serv, Johannesburg, South Africa

[10] Univ Ibadan, Fac Pharm, Dept Pharmaceut Microbiol, Ibadan, Nigeria

来源：

OPEN FORUM INFECTIOUS DISEASES | 2023年 / 10卷

基金：

英国惠康基金;

关键词：

analytic tools; data visualisation; genomics; Salmonella Typhi; typhoid fever; AFRICA;

D O I：

10.1093/ofid/ofad044

中图分类号：

R392 [医学免疫学]; Q939.91 [免疫学];

学科分类号：

100102 ;

摘要：

We describe freely available platforms that support the generation, analysis, and visualization of Salmonella Typhi genomic data, highlight opportunities to access training and tools, and outline remaining challenges. The global response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic demonstrated the value of timely and open sharing of genomic data with standardized metadata to facilitate monitoring of the emergence and spread of new variants. Here, we make the case for the value of Salmonella Typhi (S. Typhi) genomic data and demonstrate the utility of freely available platforms and services that support the generation, analysis, and visualization of S. Typhi genomic data on the African continent and more broadly by introducing the Africa Centres for Disease Control and Prevention's Pathogen Genomics Initiative, SEQAFRICA, Typhi Pathogenwatch, TyphiNET, and the Global Typhoid Genomics Consortium.

引用

页码：S38 / S46

页数：9

共 20 条

[1]

Africa Centres for Disease Control and Prevention, 2022, I PATH GEN IPG

[2] A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch [J].

Argimon, Silvia ;

Yeats, Corin A. ;

Goater, Richard J. ;

Abudahab, Khalil ;

Taylor, Benjamin ;

Underwood, Anthony ;

Sanchez-Buso, Leonor ;

Wong, Vanessa K. ;

Dyson, Zoe A. ;

Nair, Satheesh ;

Park, Se Eun ;

Marks, Florian ;

Page, Andrew J. ;

Keane, Jacqueline A. ;

Baker, Stephen ;

Holt, Kathryn E. ;

Dougan, Gordon ;

Aanensen, David M. .

NATURE COMMUNICATIONS, 2021, 12 (01)

[3] SARS-CoV-2 genomics as a springboard for future disease mitigation in LMICs [J].

Belman, Sophie ;

Saha, Senjuti ;

Beale, Mathew A. .

NATURE REVIEWS MICROBIOLOGY, 2022, 20 (01) :3-3

[4]

Cerdeira Louise, 2023, Zenodo, DOI 10.5281/ZENODO.5338903

[5]

Dyson ZA., 2021, J INFECT DIS, V224, P775

[6]

Dyson Zoe Anne, 2021, Zenodo

[7] Genomic characterization of invasive typhoidal and non-typhoidal Salmonella in southwestern Nigeria [J].

Ikhimiukor, Odion O. ;

Oaikhena, Anderson O. ;

Afolayan, Ayorinde O. ;

Fadeyi, Abayomi ;

Kehinde, Aderemi ;

Ogunleye, Veronica O. ;

Aboderin, Aaron O. ;

Oduyebo, Oyinlola O. ;

Elikwu, Charles J. ;

Odih, Erkison Ewomazino ;

Komolafe, Ifeoluwa ;

Argimon, Silvia ;

Egwuenu, Abiodun ;

Adebiyi, Ini ;

Sadare, Oluwadamilola A. ;

Okwor, Tochi ;

Kekre, Mihir ;

Underwood, Anthony ;

Ihekweazu, Chikwe ;

Aanensen, David M. ;

Okeke, Iruka N. .

PLOS NEGLECTED TROPICAL DISEASES, 2022, 16 (08)

[8] A bottom-up view of antimicrobial resistance transmission in developing countries [J].

Ikhimiukor, Odion O. ;

Odih, Erkison Ewomazino ;

Donado-Godoy, Pilar ;

Okeke, Iruka N. .

NATURE MICROBIOLOGY, 2022, 7 (06) :757-765

[9] Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers [J].

Ingle, Danielle J. ;

Nair, Satheesh ;

Hartman, Hassan ;

Ashton, Philip M. ;

Dyson, Zoe A. ;

Day, Martin ;

Freedman, Joanne ;

Chattaway, Marie A. ;

Holt, Kathryn E. ;

Dallman, Timothy J. .

PLOS NEGLECTED TROPICAL DISEASES, 2019, 13 (09)

[10] Genomic-informed pathogen surveillance in Africa: opportunities and challenges [J].

Inzaule, Seth C. ;

Tessema, Sofonias K. ;

Kebede, Yenew ;

Ouma, Ahmed E. Ogwell ;

Nkengasong, John N. .

LANCET INFECTIOUS DISEASES, 2021, 21 (09) :E281-E289

← 1 2 →