Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseas...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-07-01
|
| Series: | Frontiers in Cellular and Infection Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fcimb.2022.757844/full |
| _version_ | 1811225748600520704 |
|---|---|
| author | Beatus M. Lyimo Beatus M. Lyimo Zachary R. Popkin-Hall David J. Giesbrecht Celine I. Mandara Rashid A. Madebe Catherine Bakari Dativa Pereus Misago D. Seth Ramadhan M. Ngamba Ruth B. Mbwambo Bronwyn MacInnis Bronwyn MacInnis Daniel Mbwambo Issa Garimo Frank Chacky Sijenunu Aaron Abdallah Lusasi Fabrizio Molteni Ritha Njau Jane A. Cunningham Samwel Lazaro Ally Mohamed Jonathan J. Juliano Jeffrey A. Bailey Deus S. Ishengoma Deus S. Ishengoma Deus S. Ishengoma |
| author_facet | Beatus M. Lyimo Beatus M. Lyimo Zachary R. Popkin-Hall David J. Giesbrecht Celine I. Mandara Rashid A. Madebe Catherine Bakari Dativa Pereus Misago D. Seth Ramadhan M. Ngamba Ruth B. Mbwambo Bronwyn MacInnis Bronwyn MacInnis Daniel Mbwambo Issa Garimo Frank Chacky Sijenunu Aaron Abdallah Lusasi Fabrizio Molteni Ritha Njau Jane A. Cunningham Samwel Lazaro Ally Mohamed Jonathan J. Juliano Jeffrey A. Bailey Deus S. Ishengoma Deus S. Ishengoma Deus S. Ishengoma |
| author_sort | Beatus M. Lyimo |
| collection | DOAJ |
| description | Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent. |
| first_indexed | 2024-04-12T09:12:39Z |
| format | Article |
| id | doaj.art-70348c047f974cd98909f7207a091fdc |
| institution | Directory Open Access Journal |
| issn | 2235-2988 |
| language | English |
| last_indexed | 2024-04-12T09:12:39Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cellular and Infection Microbiology |
| spelling | doaj.art-70348c047f974cd98909f7207a091fdc2022-12-22T03:38:56ZengFrontiers Media S.A.Frontiers in Cellular and Infection Microbiology2235-29882022-07-011210.3389/fcimb.2022.757844757844Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in AfricaBeatus M. Lyimo0Beatus M. Lyimo1Zachary R. Popkin-Hall2David J. Giesbrecht3Celine I. Mandara4Rashid A. Madebe5Catherine Bakari6Dativa Pereus7Misago D. Seth8Ramadhan M. Ngamba9Ruth B. Mbwambo10Bronwyn MacInnis11Bronwyn MacInnis12Daniel Mbwambo13Issa Garimo14Frank Chacky15Sijenunu Aaron16Abdallah Lusasi17Fabrizio Molteni18Ritha Njau19Jane A. Cunningham20Samwel Lazaro21Ally Mohamed22Jonathan J. Juliano23Jeffrey A. Bailey24Deus S. Ishengoma25Deus S. Ishengoma26Deus S. Ishengoma27National Institute for Medical Research, Dar es Salaam, TanzaniaSchool of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, TanzaniaSchool of Medicine, University of North Carolina, Chapel Hill, NC, United StatesPathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United StatesNational Institute for Medical Research, Dar es Salaam, TanzaniaNational Institute for Medical Research, Dar es Salaam, TanzaniaNational Institute for Medical Research, Dar es Salaam, TanzaniaNational Institute for Medical Research, Dar es Salaam, TanzaniaNational Institute for Medical Research, Dar es Salaam, TanzaniaNational Institute for Medical Research, Dar es Salaam, TanzaniaNational Institute for Medical Research, Dar es Salaam, TanzaniaImmunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United StatesInfectious Disease and Microbiome Program, Broad Institute, Boston, MA, United StatesNational Malaria Control Programme, Dodoma, TanzaniaNational Malaria Control Programme, Dodoma, TanzaniaNational Malaria Control Programme, Dodoma, TanzaniaNational Malaria Control Programme, Dodoma, TanzaniaNational Malaria Control Programme, Dodoma, TanzaniaSwiss Tropical Public Health Institute, Dar es Salaam, TanzaniaWorld Health Organization, Country Office, Dar es Salaam, Tanzania0Global Malaria Programme, World Health Organization, Headquarters, Geneva, SwitzerlandNational Malaria Control Programme, Dodoma, TanzaniaNational Malaria Control Programme, Dodoma, TanzaniaSchool of Medicine, University of North Carolina, Chapel Hill, NC, United StatesPathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United StatesNational Institute for Medical Research, Dar es Salaam, TanzaniaImmunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States1Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, AustraliaRecent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.https://www.frontiersin.org/articles/10.3389/fcimb.2022.757844/fullnext generation sequencingCRISPR-Cas systemspathogen genomicsmalaria diagnosismalaria molecular surveillanceAfrica |
| spellingShingle | Beatus M. Lyimo Beatus M. Lyimo Zachary R. Popkin-Hall David J. Giesbrecht Celine I. Mandara Rashid A. Madebe Catherine Bakari Dativa Pereus Misago D. Seth Ramadhan M. Ngamba Ruth B. Mbwambo Bronwyn MacInnis Bronwyn MacInnis Daniel Mbwambo Issa Garimo Frank Chacky Sijenunu Aaron Abdallah Lusasi Fabrizio Molteni Ritha Njau Jane A. Cunningham Samwel Lazaro Ally Mohamed Jonathan J. Juliano Jeffrey A. Bailey Deus S. Ishengoma Deus S. Ishengoma Deus S. Ishengoma Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa Frontiers in Cellular and Infection Microbiology next generation sequencing CRISPR-Cas systems pathogen genomics malaria diagnosis malaria molecular surveillance Africa |
| title | Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa |
| title_full | Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa |
| title_fullStr | Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa |
| title_full_unstemmed | Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa |
| title_short | Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa |
| title_sort | potential opportunities and challenges of deploying next generation sequencing and crispr cas systems to support diagnostics and surveillance towards malaria control and elimination in africa |
| topic | next generation sequencing CRISPR-Cas systems pathogen genomics malaria diagnosis malaria molecular surveillance Africa |
| url | https://www.frontiersin.org/articles/10.3389/fcimb.2022.757844/full |
| work_keys_str_mv | AT beatusmlyimo potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT beatusmlyimo potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT zacharyrpopkinhall potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT davidjgiesbrecht potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT celineimandara potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT rashidamadebe potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT catherinebakari potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT dativapereus potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT misagodseth potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT ramadhanmngamba potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT ruthbmbwambo potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT bronwynmacinnis potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT bronwynmacinnis potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT danielmbwambo potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT issagarimo potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT frankchacky potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT sijenunuaaron potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT abdallahlusasi potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT fabriziomolteni potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT rithanjau potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT janeacunningham potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT samwellazaro potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT allymohamed potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT jonathanjjuliano potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT jeffreyabailey potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT deussishengoma potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT deussishengoma potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica AT deussishengoma potentialopportunitiesandchallengesofdeployingnextgenerationsequencingandcrisprcassystemstosupportdiagnosticsandsurveillancetowardsmalariacontrolandeliminationinafrica |