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Advancing One Health genomics in Africa: opportunities and challenges for outbreak and antimicrobial resistance control.

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Τίτλος: Advancing One Health genomics in Africa: opportunities and challenges for outbreak and antimicrobial resistance control.
Συγγραφείς: Derar DI; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt., Hany F; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt., Eltaher H; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt., Mahmoud S; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt., Sedarous Y; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt., Ruan Z; Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China., Alkhaldi M; The Global Health Network-The Middle East and North Africa Network (TGHN-MENA), Dubai, United Arab Emirates.; School of Health Sciences and Psychology, Department of Public Health, Canadian University Dubai, Dubai, United Arab Emirates.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; School of Physical and Occupational Therapy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada., Elhadidy M; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.; The Global Health Network-The Middle East and North Africa Network (TGHN-MENA), Dubai, United Arab Emirates.; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
Πηγή: Clinical microbiology reviews [Clin Microbiol Rev] 2026 Sep 10; Vol. 39 (3), pp. e0038725. Date of Electronic Publication: 2026 Jun 09.
Τύπος έκδοσης: Journal Article; Review
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: American Society for Microbiology Country of Publication: United States NLM ID: 8807282 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-6618 (Electronic) Linking ISSN: 08938512 NLM ISO Abbreviation: Clin Microbiol Rev Subsets: MEDLINE
Imprint Name(s): Original Publication: [Washington, DC] : American Society for Microbiology, [c1988-
Ιατρικοί όροι (MeSH): Genomics*/methods , Disease Outbreaks*/prevention & control , One Health* , Drug Resistance, Bacterial*, Africa/epidemiology ; Humans ; Animals ; Public Health Infrastructure
Περίληψη: SUMMARYAfrica's ongoing struggles with emerging epidemics and antimicrobial resistance (AMR) underscore the urgency of integrating pathogen genomics and surveillance systems into the continent's One Health strategy, particularly given the existing limitations in preparedness and technological resources. This review brings together current evidence on the growth of sequencing infrastructure, the development of regional genomic hubs, and the establishment of governance frameworks, while identifying critical challenges in data integration, bioinformatics capacity, and sustainable financing. Special focus is placed on the lack of African-based genomic data, with our analysis showing that only 1.82% of the global total is available. Case studies illustrate the immense potential and importance of pathogen genomics, giving policymakers a tangible sense of its impact. These examples demonstrate how genomic technologies integrated with artificial intelligence (AI) are transforming outbreak response, AMR surveillance, and stewardship programs by enabling early detection of zoonotic threats, mapping transmission pathways, and guiding vaccine development. However, to fully realize this scientific intel, it is essential to embed One Health pathogen surveillance within strong policy and system frameworks to ensure the translation of technical progress into lasting institutional capacity and sustainable impact. Long-term implementation depends on coordinated investment and advocacy across four interdependent pillars: data architecture, governance and sovereignty, human capital, and technical capacity.
Competing Interests: The authors declare no conflict of interest.
Contributed Indexing: Keywords: AI-driven tools; Africa; One Health; antimicrobial resistance; outbreak preparedness; pathogen genomics; policy frameworks; surveillance systems
Entry Date(s): Date Created: 20260609 Date Completed: 20260910 Latest Revision: 20260912
Update Code: 20260912
PubMed Central ID: PMC13560690
DOI: 10.1128/cmr.00387-25
PMID: 42262139
Βάση Δεδομένων: MEDLINE
FullText Text:
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PubType: Academic Journal
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  Data: Advancing One Health genomics in Africa: opportunities and challenges for outbreak and antimicrobial resistance control.
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  Data: <searchLink fieldCode="AU" term="%22Derar+DI%22">Derar DI</searchLink>; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.<br /><searchLink fieldCode="AU" term="%22Hany+F%22">Hany F</searchLink>; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.<br /><searchLink fieldCode="AU" term="%22Eltaher+H%22">Eltaher H</searchLink>; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.<br /><searchLink fieldCode="AU" term="%22Mahmoud+S%22">Mahmoud S</searchLink>; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.<br /><searchLink fieldCode="AU" term="%22Sedarous+Y%22">Sedarous Y</searchLink>; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.<br /><searchLink fieldCode="AU" term="%22Ruan+Z%22">Ruan Z</searchLink>; Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.; Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, China.<br /><searchLink fieldCode="AU" term="%22Alkhaldi+M%22">Alkhaldi M</searchLink>; The Global Health Network-The Middle East and North Africa Network (TGHN-MENA), Dubai, United Arab Emirates.; School of Health Sciences and Psychology, Department of Public Health, Canadian University Dubai, Dubai, United Arab Emirates.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.; School of Physical and Occupational Therapy, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada.<br /><searchLink fieldCode="AU" term="%22Elhadidy+M%22">Elhadidy M</searchLink>; Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza, Egypt.; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, Giza, Egypt.; The Global Health Network-The Middle East and North Africa Network (TGHN-MENA), Dubai, United Arab Emirates.; Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.
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  Data: <searchLink fieldCode="JN" term="%228807282%22">Clinical microbiology reviews</searchLink> [Clin Microbiol Rev] 2026 Sep 10; Vol. 39 (3), pp. e0038725. <i>Date of Electronic Publication: </i>2026 Jun 09.
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  Data: Journal Article; Review
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  Data: <i>Publisher: </i><searchLink fieldCode="PB" term="%22American+Society+for+Microbiology%22">American Society for Microbiology </searchLink><i>Country of Publication: </i>United States <i>NLM ID: </i>8807282 <i>Publication Model: </i>Print-Electronic <i>Cited Medium: </i>Internet <i>ISSN: </i>1098-6618 (Electronic) <i>Linking ISSN: </i><searchLink fieldCode="IS" term="%2208938512%22">08938512 </searchLink><i>NLM ISO Abbreviation: </i>Clin Microbiol Rev <i>Subsets: </i>MEDLINE
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  Data: <i>Original Publication</i>: [Washington, DC] : American Society for Microbiology, [c1988-
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  Data: <searchLink fieldCode="MM" term="%22Genomics%22">Genomics*</searchLink>/<searchLink fieldCode="MM" term="%22Genomics+methods%22">methods</searchLink> <br /><searchLink fieldCode="MM" term="%22Disease+Outbreaks%22">Disease Outbreaks*</searchLink>/<searchLink fieldCode="MM" term="%22Disease+Outbreaks+prevention+%26+control%22">prevention & control</searchLink> <br /><searchLink fieldCode="MM" term="%22One+Health%22">One Health*</searchLink> <br /><searchLink fieldCode="MM" term="%22Drug+Resistance%2C+Bacterial%22">Drug Resistance, Bacterial*</searchLink><br /><searchLink fieldCode="MH" term="%22Africa%22">Africa</searchLink>/<searchLink fieldCode="MH" term="%22Africa+epidemiology%22">epidemiology</searchLink> ; <searchLink fieldCode="MH" term="%22Humans%22">Humans</searchLink> ; <searchLink fieldCode="MH" term="%22Animals%22">Animals</searchLink> ; <searchLink fieldCode="MH" term="%22Public+Health+Infrastructure%22">Public Health Infrastructure</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: SUMMARYAfrica's ongoing struggles with emerging epidemics and antimicrobial resistance (AMR) underscore the urgency of integrating pathogen genomics and surveillance systems into the continent's One Health strategy, particularly given the existing limitations in preparedness and technological resources. This review brings together current evidence on the growth of sequencing infrastructure, the development of regional genomic hubs, and the establishment of governance frameworks, while identifying critical challenges in data integration, bioinformatics capacity, and sustainable financing. Special focus is placed on the lack of African-based genomic data, with our analysis showing that only 1.82% of the global total is available. Case studies illustrate the immense potential and importance of pathogen genomics, giving policymakers a tangible sense of its impact. These examples demonstrate how genomic technologies integrated with artificial intelligence (AI) are transforming outbreak response, AMR surveillance, and stewardship programs by enabling early detection of zoonotic threats, mapping transmission pathways, and guiding vaccine development. However, to fully realize this scientific intel, it is essential to embed One Health pathogen surveillance within strong policy and system frameworks to ensure the translation of technical progress into lasting institutional capacity and sustainable impact. Long-term implementation depends on coordinated investment and advocacy across four interdependent pillars: data architecture, governance and sovereignty, human capital, and technical capacity.
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  Data: The authors declare no conflict of interest.
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  Data: <i>Keywords: </i>AI-driven tools; Africa; One Health; antimicrobial resistance; outbreak preparedness; pathogen genomics; policy frameworks; surveillance systems
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