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Lappan R, Chown SL, French M, Perlaza-Jiménez L, Macesic N, Davis M, Brown R, Cheng A, Clasen T, Conlan L, Goddard F, Henry R, Knight DR, Li F, Luby S, Lyras D, Ni G, Rice SA, Short F, Song J, Whittaker A, Leder K, Lithgow T, Greening C. Towards integrated cross-sectoral surveillance of pathogens and antimicrobial resistance: Needs, approaches, and considerations for linking surveillance to action. ENVIRONMENT INTERNATIONAL 2024; 192:109046. [PMID: 39378692 DOI: 10.1016/j.envint.2024.109046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 09/30/2024] [Accepted: 10/01/2024] [Indexed: 10/10/2024]
Abstract
Pathogenic and antimicrobial-resistant (AMR) microorganisms are continually transmitted between human, animal, and environmental reservoirs, contributing to the high burden of infectious disease and driving the growing global AMR crisis. The sheer diversity of pathogens, AMR mechanisms, and transmission pathways connecting these reservoirs create the need for comprehensive cross-sectoral surveillance to effectively monitor risks. Current approaches are often siloed by discipline and sector, focusing independently on parts of the whole. Here we advocate that integrated surveillance approaches, developed through transdisciplinary cross-sector collaboration, are key to addressing the dual crises of infectious diseases and AMR. We first review the areas of need, challenges, and benefits of cross-sectoral surveillance, then summarise and evaluate the major detection methods already available to achieve this (culture, quantitative PCR, and metagenomic sequencing). Finally, we outline how cross-sectoral surveillance initiatives can be fostered at multiple scales of action, and present key considerations for implementation and the development of effective systems to manage and integrate this information for the benefit of multiple sectors. While methods and technologies are increasingly available and affordable for comprehensive pathogen and AMR surveillance across different reservoirs, it is imperative that systems are strengthened to effectively manage and integrate this information.
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Affiliation(s)
- Rachael Lappan
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Securing Antarctica's Environmental Future, Monash University, Melbourne, Australia.
| | - Steven L Chown
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Securing Antarctica's Environmental Future, Monash University, Melbourne, Australia
| | - Matthew French
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Faculty of Art, Design and Architecture (MADA), Monash University, Melbourne, Australia
| | - Laura Perlaza-Jiménez
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Nenad Macesic
- Centre to Impact AMR, Monash University, Melbourne, Australia; Department of Infectious Diseases, Alfred Health, Melbourne, Australia; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| | - Mark Davis
- Centre to Impact AMR, Monash University, Melbourne, Australia; School of Social Sciences, Monash University, Melbourne, Australia
| | - Rebekah Brown
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Monash Sustainable Development Institute, Melbourne, Australia
| | - Allen Cheng
- Centre to Impact AMR, Monash University, Melbourne, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia; Infection Prevention and Healthcare Epidemiology Unit, Alfred Health, Melbourne, Australia
| | - Thomas Clasen
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Lindus Conlan
- Centre to Impact AMR, Monash University, Melbourne, Australia
| | - Frederick Goddard
- RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Rebekah Henry
- Centre to Impact AMR, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Department of Civil Engineering, Monash University, Melbourne, Australia
| | - Daniel R Knight
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, WA, Australia; School of Biomedical Sciences, The University of Western Australia, WA, Australia
| | - Fuyi Li
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection and Cancer Programs, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Stephen Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Dena Lyras
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Gaofeng Ni
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Scott A Rice
- Microbiomes for One Systems Health, CSIRO Agriculture and Food, Canberra, Australia
| | - Francesca Short
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Jiangning Song
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection and Cancer Programs, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Andrea Whittaker
- Centre to Impact AMR, Monash University, Melbourne, Australia; School of Social Sciences, Monash University, Melbourne, Australia
| | - Karin Leder
- Centre to Impact AMR, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia
| | - Chris Greening
- Centre to Impact AMR, Monash University, Melbourne, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Australia; RISE: Revitalising Informal Settlements and their Environments, Melbourne, Australia; Securing Antarctica's Environmental Future, Monash University, Melbourne, Australia.
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Saha S, Hooda Y, Malavige GN, Nisar MI. Overcoming colonialism in pathogen genomics. Lancet Digit Health 2024; 6:e520-e525. [PMID: 38906617 DOI: 10.1016/s2589-7500(24)00091-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 03/15/2024] [Accepted: 04/25/2024] [Indexed: 06/23/2024]
Abstract
Historical legacies of colonialism affect the distribution and control of scientific knowledge today, including within the pathogen genomics field, which remains dominated by high-income countries (HICs). We discuss the imperatives for decolonising pathogen genomics, including the need for more equitable representation, collaboration, and capacity-strengthening, and the shared responsibilities that both low-income and middle-income countries (LMICs) and HICs have in this endeavour. By highlighting examples from LMICs, we illuminate the pathways and challenges that researchers in LMICs face in the bid to gain autonomy in this crucial domain. Recognising the inherent value of local expertise and resources, we argue for a more inclusive, globally collaborative approach to pathogen genomics. Such an approach not only fosters scientific growth and innovation, but also strengthens global health security by equipping all nations with the tools needed to respond to health crises.
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Affiliation(s)
- Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh.
| | - Yogesh Hooda
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Gathsaurie Neelika Malavige
- Allergy lmmunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Muhammad Imran Nisar
- Department of Paediatrics and Child Health, Faculty of Health Sciences, Medical College, The Aga Khan University, Karachi, Pakistan; CITRIC Centre for Bioinformatics and Computational Biology, The Aga Khan University, Karachi, Pakistan
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3
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Opperman CJ, Singh S, Goosen W, Cox H, Warren R, Esmail A. Incorporating direct molecular diagnostics in management algorithms for nontuberculous mycobacteria: Is it high time? IJID REGIONS 2024; 10:140-145. [PMID: 38304760 PMCID: PMC10831244 DOI: 10.1016/j.ijregi.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
Nontuberculous mycobacteria (NTM) are a group of acid-fast mycobacteria other than Mycobacterium tuberculosis complex (MTBC) that cause pulmonary disease that is similar to the disease caused by MTBC. International guidelines for the diagnosis of pulmonary NTM disease are rigid and have remained unchanged for nearly 2 decades. In this opinion piece, we provide a new perspective on the traditional criteria by suggesting a diagnostic algorithm that incorporates direct molecular identification of NTM performed on raw sputum specimens (using Sanger or targeted deep sequencing approaches, among others) paired with traditional culture methods. Our approach ensures a more rapid diagnosis of pulmonary NTM disease, thus, facilitating timeous clinical diagnosis, and prompt treatment initiation, where indicated, and leverages recent advances in novel molecular techniques into routine NTM identification practice.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB Laboratory, Cape Town, South Africa
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Sarishna Singh
- National Health Laboratory Service, Green Point TB Laboratory, Cape Town, South Africa
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Wynand Goosen
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Helen Cox
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research, University of Cape Town, Cape Town, South Africa
| | - Rob Warren
- SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Aliasgar Esmail
- UCT Lung Institute, Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine, University of Cape Town, & Groote Schuur Hospital
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4
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Yerlikaya S, Broger T, Isaacs C, Bell D, Holtgrewe L, Gupta-Wright A, Nahid P, Cattamanchi A, Denkinger CM. Blazing the trail for innovative tuberculosis diagnostics. Infection 2024; 52:29-42. [PMID: 38032537 PMCID: PMC10811035 DOI: 10.1007/s15010-023-02135-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
The COVID-19 pandemic brought diagnostics into the spotlight in an unprecedented way not only for case management but also for population health, surveillance, and monitoring. The industry saw notable levels of investment and accelerated research which sparked a wave of innovation. Simple non-invasive sampling methods such as nasal swabs have become widely used in settings ranging from tertiary hospitals to the community. Self-testing has also been adopted as standard practice using not only conventional lateral flow tests but novel and affordable point-of-care molecular diagnostics. The use of new technologies, including artificial intelligence-based diagnostics, have rapidly expanded in the clinical setting. The capacity for next-generation sequencing and acceptance of digital health has significantly increased. However, 4 years after the pandemic started, the market for SARS-CoV-2 tests is saturated, and developers may benefit from leveraging their innovations for other diseases; tuberculosis (TB) is a worthwhile portfolio expansion for diagnostics developers given the extremely high disease burden, supportive environment from not-for-profit initiatives and governments, and the urgent need to overcome the long-standing dearth of innovation in the TB diagnostics field. In exchange, the current challenges in TB detection may be resolved by adopting enhanced swab-based molecular methods, instrument-based, higher sensitivity antigen detection technologies, and/or artificial intelligence-based digital health technologies developed for COVID-19. The aim of this article is to review how such innovative approaches for COVID-19 diagnosis can be applied to TB to have a comparable impact.
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Affiliation(s)
- Seda Yerlikaya
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany.
| | - Tobias Broger
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | | | - David Bell
- Independent Consultant, Lake Jackson, TX, USA
| | - Lydia Holtgrewe
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
| | - Ankur Gupta-Wright
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- Institute for Global Health, University College London, London, UK
| | - Payam Nahid
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, CA, USA
| | - Adithya Cattamanchi
- UCSF Center for Tuberculosis, University of California San Francisco, San Francisco, CA, USA
- Division of Pulmonary Diseases and Critical Care Medicine, University of California Irvine, Irvine, CA, USA
| | - Claudia M Denkinger
- Division of Infectious Diseases and Tropical Medicine, Heidelberg University Hospital and Faculty of Medicine, Heidelberg University, Heidelberg, Germany
- German Centre for Infection Research, Partner Site Heidelberg University Hospital, Heidelberg, Germany
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Adams AM, Arrazola J, Daly ER, Tompkins M. Threat Agnostic Epidemiology and Surveillance in US Public Health Agencies: Future Potential and Needs. Health Secur 2024; 22:25-30. [PMID: 38079238 DOI: 10.1089/hs.2023.0071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Affiliation(s)
- Andrew M Adams
- Andrew M. Adams, MPH, is a Senior Program Analyst, Preparedness and Response; the Council of State and Territorial Epidemiologists, Atlanta, GA
| | - Jessica Arrazola
- Jessica Arrazola, DrPH, MPH, MCHES, is Director of Educational Strategy; the Council of State and Territorial Epidemiologists, Atlanta, GA
| | - Elizabeth R Daly
- Elizabeth R. Daly, DrPH, MPH, is Director of Infectious Disease Programs; the Council of State and Territorial Epidemiologists, Atlanta, GA
| | - Megan Tompkins
- Megan Tompkins, MPH, is Data Modernization Implementation Lead; the Council of State and Territorial Epidemiologists, Atlanta, GA
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Pronyk PM, de Alwis R, Rockett R, Basile K, Boucher YF, Pang V, Sessions O, Getchell M, Golubchik T, Lam C, Lin R, Mak TM, Marais B, Twee-Hee Ong R, Clapham HE, Wang L, Cahyorini Y, Polotan FGM, Rukminiati Y, Sim E, Suster C, Smith GJD, Sintchenko V. Advancing pathogen genomics in resource-limited settings. CELL GENOMICS 2023; 3:100443. [PMID: 38116115 PMCID: PMC10726422 DOI: 10.1016/j.xgen.2023.100443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Genomic sequencing has emerged as a powerful tool to enhance early pathogen detection and characterization with implications for public health and clinical decision making. Although widely available in developed countries, the application of pathogen genomics among low-resource, high-disease burden settings remains at an early stage. In these contexts, tailored approaches for integrating pathogen genomics within infectious disease control programs will be essential to optimize cost efficiency and public health impact. We propose a framework for embedding pathogen genomics within national surveillance plans across a spectrum of surveillance and laboratory capacities. We adopt a public health approach to genomics and examine its application to high-priority diseases relevant in resource-limited settings. For each grouping, we assess the value proposition for genomics to inform public health and clinical decision-making, alongside its contribution toward research and development of novel diagnostics, therapeutics, and vaccines.
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Affiliation(s)
- Paul Michael Pronyk
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore.
| | - Ruklanthi de Alwis
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore; Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Rebecca Rockett
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Yann Felix Boucher
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore; Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore 117549, Singapore; Singapore Centre for Environmental Life Sciences Engineering, National University of Singapore, Singapore 117549, Singapore; Nanyang Technological University, Singapore 639798, Singapore
| | - Vincent Pang
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore
| | - October Sessions
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Marya Getchell
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Tanya Golubchik
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia; Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Connie Lam
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Raymond Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore 308442, Singapore
| | - Tze-Minn Mak
- Bioinformatics Institute, Agency for Science, Technology and Research, Singapore 138671, Singapore
| | - Ben Marais
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Hannah Eleanor Clapham
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore 117549, Singapore
| | - Linfa Wang
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore; Programme for Research in Epidemic Preparedness and Response (PREPARE), Ministry of Health, Singapore 169854, Singapore
| | - Yorin Cahyorini
- Center for Health Resilience and Resource Policy, Ministry of Health, Jakarta 12950, Indonesia
| | - Francisco Gerardo M Polotan
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, Muntinlupa 1781, Metro Manila, Philippines
| | - Yuni Rukminiati
- Center for Health Resilience and Resource Policy, Ministry of Health, Jakarta 12950, Indonesia
| | - Eby Sim
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Carl Suster
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Gavin J D Smith
- Emerging Infectious Diseases Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Vitali Sintchenko
- Sydney Infectious Diseases Institute, The University of Sydney, Camperdown, NSW 2006, Australia; Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia; Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
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Marais G, Valley-Omar Z, Marais S, McMullen K, Bateman K, der Westhuizen DV, Maseko M, Hardie D, Brink A. Clinical metagenomics in a resource-limited setting. J Infect 2023; 87:604-606. [PMID: 37852478 DOI: 10.1016/j.jinf.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/11/2023] [Accepted: 10/13/2023] [Indexed: 10/20/2023]
Affiliation(s)
- Gert Marais
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa; Groote Schuur Hospital National Health Laboratory Service Laboratory, Cape Town, Western Cape, South Africa.
| | - Ziyaad Valley-Omar
- Groote Schuur Hospital National Health Laboratory Service Laboratory, Cape Town, Western Cape, South Africa; Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Suzaan Marais
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, Western Cape, South Africa; Neuroscience Institute, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kate McMullen
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kathleen Bateman
- Division of Neurology, Department of Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Diederick van der Westhuizen
- Groote Schuur Hospital National Health Laboratory Service Laboratory, Cape Town, Western Cape, South Africa; Division of Chemical Pathology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Moepeng Maseko
- Groote Schuur Hospital National Health Laboratory Service Laboratory, Cape Town, Western Cape, South Africa; Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Diana Hardie
- Groote Schuur Hospital National Health Laboratory Service Laboratory, Cape Town, Western Cape, South Africa; Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa; Groote Schuur Hospital National Health Laboratory Service Laboratory, Cape Town, Western Cape, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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8
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Nooh F, Chernet A, Reither K, Okuma J, Brattig NW, Utzinger J, Probst-Hensch N, Paris DH, Dreyfus A. Prevalence of fever of unidentified aetiology in East African adolescents and adults: a systematic review and meta-analysis. Infect Dis Poverty 2023; 12:55. [PMID: 37231500 DOI: 10.1186/s40249-023-01105-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Primary health care settings and hospitals of low- and middle-income countries have few accessible diagnostic tools and limited laboratory and human resources capacity to identify multiple pathogens with high accuracy. In addition, there is a paucity of information on fever and its underlying aetiology in the adolescent and adult population in East Africa. The purpose of this study was to estimate the pooled prevalence of fever of unidentified aetiology among adolescent and adult febrile patients seeking health care in East Africa. METHODS We pursued a systematic review using readily available electronic databases (i.e. PubMed, Cumulative Index to Nursing & Allied Health Literature, Scopus, Cochrane Library and Web of Science) without language restriction from inception date of the respective databases to October 31, 2022. We adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Identified studies were screened for relevance. Further analyses based on pre-set eligibility criteria were carried out for final inclusion. Two reviewers independently screened and extracted data. Risk of study bias was assessed. Meta-analysis of the prevalence of fever of unidentified aetiology was performed. RESULTS We identified 14,029 articles of which 25 were eligible for inclusion, reporting data from 8538 participants. The pooled prevalence of febrile cases with unidentified aetiology was 64% [95% confidence interval (CI): 51-77%, I2 = 99.6%] among febrile adolescents and adults in East Africa. For the proportion of patients with identified aetiology, the studies documented bacterial pathogens (human bloodstream infections), bacterial zoonotic pathogens and arboviruses as the main non-malarial causative agents in East Africa. CONCLUSIONS Our study provides evidence that almost two-thirds of adolescent and adult febrile patients attending health care facilities in East Africa might receive inappropriate treatments due to unidentified potential life-threatening fever aetiology. Hence, we call for a comprehensive fever syndromic surveillance to broaden a consequential differential diagnosis of syndromic fever and to considerably improve the course of patients' disease and treatment outcomes.
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Affiliation(s)
- Faisal Nooh
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
- College of Medicine and Health Sciences, Jigjiga University, Jigjiga, Ethiopia.
- College of Medicine and Health Sciences, University of Hargeisa, Hargeisa, Somaliland.
| | - Afona Chernet
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - James Okuma
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Norbert W Brattig
- Department Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniel H Paris
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Anou Dreyfus
- Swiss Tropical and Public Health Institute, Kreuzstrasse 2, 4123, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Section of Epidemiology, University of Zürich, Zurich, Switzerland
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