1
|
Laxminarayan R, Impalli I, Rangarajan R, Cohn J, Ramjeet K, Trainor BW, Strathdee S, Sumpradit N, Berman D, Wertheim H, Outterson K, Srikantiah P, Theuretzbacher U. Expanding antibiotic, vaccine, and diagnostics development and access to tackle antimicrobial resistance. Lancet 2024; 403:2534-2550. [PMID: 38797178 DOI: 10.1016/s0140-6736(24)00878-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 03/13/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024]
Abstract
The increasing number of bacterial infections globally that do not respond to any available antibiotics indicates a need to invest in-and ensure access to-new antibiotics, vaccines, and diagnostics. The traditional model of drug development, which depends on substantial revenues to motivate investment, is no longer economically viable without push and pull incentives. Moreover, drugs developed through these mechanisms are unlikely to be affordable for all patients in need, particularly in low-income and middle-income countries. New, publicly funded models based on public-private partnerships could support investment in antibiotics and novel alternatives, and lower patients' out-of-pocket costs, making drugs more accessible. Cost reductions can be achieved with public goods, such as clinical trial networks and platform-based quality assurance, manufacturing, and product development support. Preserving antibiotic effectiveness relies on accurate and timely diagnosis; however scaling up diagnostics faces technological, economic, and behavioural challenges. New technologies appeared during the COVID-19 pandemic, but there is a need for a deeper understanding of market, physician, and consumer behaviour to improve the use of diagnostics in patient management. Ensuring sustainable access to antibiotics also requires infection prevention. Vaccines offer the potential to prevent infections from drug-resistant pathogens, but funding for vaccine development has been scarce in this context. The High-Level Meeting of the UN General Assembly in 2024 offers an opportunity to rethink how research and development can be reoriented to serve disease management, prevention, patient access, and antibiotic stewardship.
Collapse
Affiliation(s)
- Ramanan Laxminarayan
- One Health Trust, Bengaluru, India; High Meadows Environmental Institute, Princeton University, Princeton, NJ, USA.
| | | | | | - Jennifer Cohn
- Global Antibiotic Research and Development Partnership, Geneva, Switzerland
| | | | | | - Steffanie Strathdee
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Nithima Sumpradit
- Food and Drug Administration, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Heiman Wertheim
- Department of Medical Microbiology and Radboudumc Center for Infectious Diseases, Radboudumc, Netherlands
| | | | | | | |
Collapse
|
2
|
Tolley A, Bansal A, Murerwa R, Howard Dicks J. Cost-effectiveness of point-of-care diagnostics for AMR: a systematic review. J Antimicrob Chemother 2024; 79:1248-1269. [PMID: 38498622 PMCID: PMC11144491 DOI: 10.1093/jac/dkae067] [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: 10/08/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major threat to global health. By 2050, it is forecast that AMR will cause 10 million deaths and cost 100 trillion USD annually. Point-of-care tests (POCTs) may represent a cost-effective approach to reduce AMR. OBJECTIVES We systematically reviewed which POCTs addressing AMR have undergone economic evaluation in primary and secondary healthcare globally, how these POCTs have been economically evaluated, and which are cost-effective in reducing antimicrobial prescribing or the burden of AMR. Clinical cost-effectiveness was additionally addressed. METHODS This systematic review, accordant with PRISMA guidelines, was pre-registered on PROSPERO (CRD42022315192). MEDLINE, PubMed, Embase, Cochrane Library, and Google Scholar were searched from 2000 to 2023 for relevant publications. Quality assessment was performed using the Consensus of Health Economic Criteria. RESULTS The search strategy identified 1421 studies, of which 20 met the inclusion criteria. The most common POCTs assessed were for respiratory infections (n = 10), STIs (n = 3), and febrile patients in low- and middle-income countries (n = 3). All studies assessed costs from a healthcare provider perspective; five additionally considered the societal cost of AMR.Eighteen studies identified POCT strategies that reduced antimicrobial prescribing. Of these, 10 identified POCTs that would be considered cost-effective at a willingness-to-pay (WTP) threshold of £33.80 per antibiotic prescription avoided. Most POCT strategies improved clinical outcomes (n = 14); the remainder were clinically neutral. CONCLUSIONS There is evidence that some POCTs are cost-effective in reducing antimicrobial prescribing, with potential concomitant clinical benefits. Such interventions-especially CRP POCTs in both high- and low-income settings-merit further, large-scale clinical evaluation.
Collapse
Affiliation(s)
- Abraham Tolley
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Akhil Bansal
- Faculty of Medicine and Health, University of Sydney, Sydney, Australia
- Department of Internal Medicine, St Vincent’s Hospital, Sydney, Australia
| | | | | |
Collapse
|
3
|
Salluh JIF, Póvoa P, Beane A, Kalil A, Sendagire C, Sweeney DA, Pilcher D, Polverino E, Tacconelli E, Estenssoro E, Frat JP, Ramirez J, Reyes LF, Roca O, Nseir S, Nobre V, Lisboa T, Martin-Loeches I. Challenges for a broad international implementation of the current severe community-acquired pneumonia guidelines. Intensive Care Med 2024; 50:526-538. [PMID: 38546855 DOI: 10.1007/s00134-024-07381-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/29/2024] [Indexed: 04/16/2024]
Abstract
Severe community-acquired pneumonia (sCAP) remains one of the leading causes of admission to the intensive care unit, thus consuming a large share of resources and is associated with high mortality rates worldwide. The evidence generated by clinical studies in the last decade was translated into recommendations according to the first published guidelines focusing on severe community-acquired pneumonia. Despite the advances proposed by the present guidelines, several challenges preclude the prompt implementation of these diagnostic and therapeutic measures. The present article discusses the challenges for the broad implementation of the sCAP guidelines and proposes solutions when applicable.
Collapse
Affiliation(s)
- Jorge I F Salluh
- D'Or Institute for Research and Education (IDOR), Rio de Janeiro, RJ, Brazil.
- Postgraduate Program of Internal Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, UFRJ, Brazil.
| | - Pedro Póvoa
- NOVA Medical School, CHRC, New University of Lisbon, Lisbon, Portugal
- Research Unit of Clinical Epidemiology, Institute of Clinical Research, Odense University Hospital, University of Southern Denmark Centre for Clinical Epidemiology, Odense, Denmark
- Department of Intensive Care, Hospital de São Francisco Xavier, CHLO, Lisbon, Portugal
| | - Abi Beane
- Pandemic Science Hub and Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK
- NICS-MORU, Colombo, Sri Lanka
| | - Andre Kalil
- Division of Infectious Diseases, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Cornelius Sendagire
- Anesthesia and Critical Care, Makerere University College of Health Sciences, P.O. Box 7072, Kampala, Uganda
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of California, La Jolla, San Diego, CA, USA
| | - David Pilcher
- Department of Intensive Care, Alfred Health, Commercial Road3004, Prahran, VIC, Australia
- The Australian and New Zealand Intensive Care Society (ANZICS) Centre for Outcome and Resource Evaluation, Camberwell, Australia
| | - Eva Polverino
- Pneumology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, CIBERES, Barcelona, Spain
| | - Evelina Tacconelli
- Division of Infectious Diseases, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Elisa Estenssoro
- Hospital Interzonal de Agudos General San Martín, Servicio de Terapia Intensiva, Buenos Aires, Argentina
| | - Jean-Pierre Frat
- CHU de Poitiers, Médecine Intensive Réanimation, Poitiers, France
- INSERM, CIC-1402, IS-ALIVE, Faculté de Médecine Et de Pharmacie de Poitiers, Université de Poitiers, Poitiers, France
| | - Julio Ramirez
- Norton Infectious Diseases Institute, Norton Healthcare, Louisville, KY, USA
- University of Louisville, Louisville, KY, USA
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de La Sabana, Chia, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Oriol Roca
- Servei de Medicina Intensiva, Parc Taulí Hospital Universitari, Institut de Recerca Part Taulí - I3PT, Parc del Taulí 1, 08028, Sabadell, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Saad Nseir
- Centre de Réanimation, CHU de Lille, 59000, Lille, France
- Team Fungal Associated Invasive and Inflammatory Diseases, Lille Inflammation Research International Center, Université de Lille, INSERM U995, Lille, France
| | - Vandack Nobre
- Department of Internal Medicine, Medical School and University Hospital, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Thiago Lisboa
- Critical Care Department, Programa de Pós-Graduação em Ciencias Pneumologicas, Hospital de Clinicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ignacio Martin-Loeches
- Department of Intensive Care Medicine, Multidisciplinary Intensive Care Research Organization, St. James's University Hospital, Trinity Centre for Health Sciences, Dublin, Ireland
| |
Collapse
|
4
|
Vloemans D, Van Hileghem L, Ordutowski H, Dal Dosso F, Spasic D, Lammertyn J. Self-Powered Microfluidics for Point-of-Care Solutions: From Sampling to Detection of Proteins and Nucleic Acids. Methods Mol Biol 2024; 2804:3-50. [PMID: 38753138 DOI: 10.1007/978-1-0716-3850-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Self-powered microfluidics presents a revolutionary approach to address the challenges of healthcare in decentralized and point-of-care settings where limited access to resources and infrastructure prevails or rapid clinical decision-making is critical. These microfluidic systems exploit physical and chemical phenomena, such as capillary forces and surface tension, to manipulate tiny volumes of fluids without the need for external power sources, making them cost-effective and highly portable. Recent technological advancements have demonstrated the ability to preprogram complex multistep liquid operations within the microfluidic circuit of these standalone systems, which enabled the integration of sensitive detection and readout principles. This chapter first addresses how the accessibility to in vitro diagnostics can be improved by shifting toward decentralized approaches like remote microsampling and point-of-care testing. Next, the crucial role of self-powered microfluidic technologies to enable this patient-centric healthcare transition is emphasized using various state-of-the-art examples, with a primary focus on applications related to biofluid collection and the detection of either proteins or nucleic acids. This chapter concludes with a summary of the main findings and our vision of the future perspectives in the field of self-powered microfluidic technologies and their use for in vitro diagnostics applications.
Collapse
Affiliation(s)
- Dries Vloemans
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | | | - Henry Ordutowski
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | | | - Dragana Spasic
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Leuven, Belgium.
| |
Collapse
|
5
|
Holm M, MacWright WR, Poudyal N, Shaw A, Joh HS, Gallagher P, Kim JH, Shaikh A, Seo HJ, Kwon SY, Prifti K, Dolabella B, Taylor BEW, Yeats C, Aanensen DM, Stelling J, Marks F. Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA). Clin Infect Dis 2023; 77:S500-S506. [PMID: 38118015 PMCID: PMC10732560 DOI: 10.1093/cid/ciad567] [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: 07/14/2023] [Indexed: 12/22/2023] Open
Abstract
BACKGROUND In 2015, the UK government established the Fleming Fund with the aim to address critical gaps in surveillance of antimicrobial resistance (AMR) in low- and middle-income countries in Asia and Africa. Among a large portfolio of grants, the Capturing Data on Antimicrobial Resistance Patterns and Trends in Use in Regions of Asia (CAPTURA) project was awarded with the specific objective of expanding the volume of historical data on AMR, consumption (AMC), and use (AMU) in the human healthcare sector across 12 countries in South and Southeast Asia. METHODS Starting in early 2019, the CAPTURA consortium began working with local governments and >100 relevant data-holding facilities across the region to identify, assess for quality, prioritize, and subsequently retrieve data on AMR, AMC, and AMU. Relevant and shared data were collated and analyzed to provide local overviews for national stakeholders as well as regional context, wherever possible. RESULTS From the vast information resource generated on current surveillance capacity and data availability, the project has highlighted gaps and areas for quality improvement and supported comprehensive capacity-building activities to optimize local data-collection and -management practices. CONCLUSIONS The project has paved the way for expansion of surveillance networks to include both the academic and private sector in several countries and has actively engaged in discussions to promote data sharing at the local, national, and regional levels. This paper describes the overarching approach to, and emerging lessons from, the CAPTURA project, and how it contributes to other ongoing efforts to strengthen national AMR surveillance in the region and globally.
Collapse
Affiliation(s)
- Marianne Holm
- International Vaccine Institute, Seoul, Republic of Korea
| | | | - Nimesh Poudyal
- International Vaccine Institute, Seoul, Republic of Korea
| | - Alina Shaw
- Public Health Surveillance Group LLC, Princeton, New Jersey, USA
| | - Hea Sun Joh
- International Vaccine Institute, Seoul, Republic of Korea
| | | | - Jong-Hoon Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Affan Shaikh
- Public Health Surveillance Group LLC, Princeton, New Jersey, USA
| | - Hye Jin Seo
- International Vaccine Institute, Seoul, Republic of Korea
| | - Soo Young Kwon
- International Vaccine Institute, Seoul, Republic of Korea
| | - Kristi Prifti
- International Vaccine Institute, Seoul, Republic of Korea
| | - Brooke Dolabella
- Public Health Surveillance Group LLC, Princeton, New Jersey, USA
| | - Ben E W Taylor
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Oxford University, Oxford, United Kingdom
| | - Corin Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Oxford University, Oxford, United Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Oxford University, Oxford, United Kingdom
| | - John Stelling
- Brigham & Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| |
Collapse
|
6
|
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 GJ, 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.
Collapse
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
| |
Collapse
|
7
|
Wheeler NE, Price V, Cunningham-Oakes E, Tsang KK, Nunn JG, Midega JT, Anjum MF, Wade MJ, Feasey NA, Peacock SJ, Jauneikaite E, Baker KS. Innovations in genomic antimicrobial resistance surveillance. THE LANCET. MICROBE 2023; 4:e1063-e1070. [PMID: 37977163 DOI: 10.1016/s2666-5247(23)00285-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.
Collapse
Affiliation(s)
- Nicole E Wheeler
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, Edgbaston, UK
| | - Vivien Price
- Department of Clinical Infection, Immunology and Microbiology, Liverpool Centre for Global Health Research, University of Liverpool, Liverpool, UK
| | - Edward Cunningham-Oakes
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Kara K Tsang
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Muna F Anjum
- Department of Bacteriology, Animal and Plant Health Agency, Surrey, UK
| | - Matthew J Wade
- Data Analytics and Surveillance Group, UK Health Security Agency, London, UK; School of Engineering, Newcastle University, Newcastle-upon-Tyne, UK
| | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| | | | - Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Kate S Baker
- Centre for Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| |
Collapse
|
8
|
Jauneikaite E, Baker KS, Nunn JG, Midega JT, Hsu LY, Singh SR, Halpin AL, Hopkins KL, Price JR, Srikantiah P, Egyir B, Okeke IN, Holt KE, Peacock SJ, Feasey NA. Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities. THE LANCET. MICROBE 2023; 4:e1040-e1046. [PMID: 37977161 DOI: 10.1016/s2666-5247(23)00282-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/16/2023] [Accepted: 08/22/2023] [Indexed: 11/19/2023]
Abstract
Integration of genomic technologies into routine antimicrobial resistance (AMR) surveillance in health-care facilities has the potential to generate rapid, actionable information for patient management and inform infection prevention and control measures in near real time. However, substantial challenges limit the implementation of genomics for AMR surveillance in clinical settings. Through a workshop series and online consultation, international experts from across the AMR and pathogen genomics fields convened to review the evidence base underpinning the use of genomics for AMR surveillance in a range of settings. Here, we summarise the identified challenges and potential benefits of genomic AMR surveillance in health-care settings, and outline the recommendations of the working group to realise this potential. These recommendations include the definition of viable and cost-effective use cases for genomic AMR surveillance, strengthening training competencies (particularly in bioinformatics), and building capacity at local, national, and regional levels using hub and spoke models.
Collapse
Affiliation(s)
- Elita Jauneikaite
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK; NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, Hammersmith Hospital, London, UK
| | - Kate S Baker
- Department of Clinical Infection, Microbiology, and Immunology, University of Liverpool, Liverpool, UK; Department of Genetics, University of Cambridge, Cambridge, UK.
| | - Jamie G Nunn
- Infectious Disease Challenge Area, Wellcome Trust, London, UK
| | | | - Li Yang Hsu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Shweta R Singh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, US Centers for Disease Control And Prevention, Atlanta, GA, USA
| | - Katie L Hopkins
- HCAI, Fungal, AMR, AMU, and Sepsis Division and Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, UK Health Security Agency, London, UK
| | - James R Price
- Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Padmini Srikantiah
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Beverly Egyir
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon-Accra, Ghana
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | | | - Nicholas A Feasey
- Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, UK; Malawi Liverpool Wellcome Research Programme, Chichiri, Blantyre, Malawi
| |
Collapse
|
9
|
Hernández-Neuta I, Magoulopoulou A, Pineiro F, Lisby JG, Gulberg M, Nilsson M. Highly multiplexed targeted sequencing strategy for infectious disease surveillance. BMC Biotechnol 2023; 23:31. [PMID: 37612665 PMCID: PMC10463907 DOI: 10.1186/s12896-023-00804-7] [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: 03/13/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs). RESULTS Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis. CONCLUSIONS Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings.
Collapse
Affiliation(s)
- Iván Hernández-Neuta
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden
| | - Anastasia Magoulopoulou
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden
| | - Flor Pineiro
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden
| | - Jan Gorm Lisby
- Department of Clinical Microbiology, Amager and Hvidovre Hospital, University of Copenhagen, Kettegaard Alle 30, Hvidovre, 2650, Denmark
| | - Mats Gulberg
- Q-linea AB, Dag Hammarskjölds Väg 52A, Uppsala, 752 37, Sweden
| | - Mats Nilsson
- Department of Biochemistry and Biophysics, Faculty of Science, Stockholm University, Svante Arrhenius väg 16C, Stockholm, 104 05, Sweden.
- Science for Life Laboratory (SciLifeLab), Tomtebodavägen 23, 171 65, Solna, Sweden.
| |
Collapse
|
10
|
Baker M, Zhang X, Maciel-Guerra A, Dong Y, Wang W, Hu Y, Renney D, Hu Y, Liu L, Li H, Tong Z, Zhang M, Geng Y, Zhao L, Hao Z, Senin N, Chen J, Peng Z, Li F, Dottorini T. Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China. NATURE FOOD 2023; 4:707-720. [PMID: 37563495 PMCID: PMC10444626 DOI: 10.1038/s43016-023-00814-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.
Collapse
Affiliation(s)
- Michelle Baker
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Xibin Zhang
- Shandong New Hope Liuhe Group Co. Ltd and Qingdao Key Laboratory of Animal Feed Safety, Qingdao, People's Republic of China
| | | | - Yinping Dong
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Wei Wang
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Yujie Hu
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - David Renney
- Nimrod Veterinary Products Ltd., Moreton-in-Marsh, UK
| | - Yue Hu
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK
| | - Longhai Liu
- Shandong Kaijia Food Co., Weifang, People's Republic of China
| | - Hui Li
- Luoyang Center for Disease Control and Prevention, Luoyang City, People's Republic of China
| | - Zhiqin Tong
- Luoyang Center for Disease Control and Prevention, Luoyang City, People's Republic of China
| | - Meimei Zhang
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, People's Republic of China
| | - Yingzhi Geng
- Liaoning Provincial Center for Disease Control and Prevention, Shenyang City, People's Republic of China
| | - Li Zhao
- Agricultural Biopharmaceutical Laboratory, College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao City, People's Republic of China
| | - Zhihui Hao
- Chinese Veterinary Medicine Innovation Center, College of Veterinary Medicine, China Agricultural University, Beijing City, People's Republic of China
| | - Nicola Senin
- Department of Engineering, University of Perugia, Perugia, Italy
| | - Junshi Chen
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China
| | - Zixin Peng
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| | - Fengqin Li
- NHC Key Laboratory of Food Safety Risk Assessment, China National Center for Food Safety Risk Assessment, Beijing, People's Republic of China.
| | - Tania Dottorini
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, UK.
- Centre for Smart Food Research, Nottingham Ningbo China Beacons of Excellence Research and Innovation Institute, University of Nottingham Ningbo China, Ningbo, People's Republic of China.
| |
Collapse
|
11
|
Carey ME, Dyson ZA, Argimón S, Cerdeira L, Yeats C, Aanensen D, Mboowa G, Baker S, Tessema SK, Smith AM, Okeke IN, Holt KE. Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open Forum Infect Dis 2023; 10:S38-S46. [PMID: 37274533 PMCID: PMC10236510 DOI: 10.1093/ofid/ofad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Megan E Carey
- Correspondence: Megan E. Carey, PhD, MSPH, Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK ()
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Louise Cerdeira
- Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Corin Yeats
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gerald Mboowa
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- IAVI, Chelsea & Westminster Hospital, London, United Kingdom
| | - Sofonias K Tessema
- Africa Centres for Disease Control and Prevention, Addis Ababa, Ethiopia
| | - Anthony M Smith
- Division of the National Health Laboratory Service, Centre for Enteric Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia
| |
Collapse
|
12
|
Conrad S, Gant Kanegusuku A, Conklin SE. Taking a step back from testing: Preanalytical considerations in molecular infectious disease diagnostics. Clin Biochem 2023; 115:22-32. [PMID: 36495954 PMCID: PMC9729171 DOI: 10.1016/j.clinbiochem.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Recent studies evaluating the preanalytical factors that impact the outcome of nucleic-acid based methods for the confirmation of SARS-CoV-2 have illuminated the importance of identifying variables that promoted accurate testing, while using scarce resources efficiently. The majority of laboratory errors occur in the preanalytical phase. While there are many resources identifying and describing mechanisms for main laboratory testing on automated platforms, there are fewer comprehensive resources for understanding important preanalytical and environmental factors that affect accurate molecular diagnostic testing of infectious diseases. This review identifies evidence-based factors that have been documented to impact the outcome of nucleic acid-based molecular techniques for the diagnosis of infectious diseases.
Collapse
Affiliation(s)
- Stephanie Conrad
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA
| | | | - Steven E Conklin
- Department of Pathology and Laboratory Medicine, Tufts Medical Center, Boston, MA, USA; Department of Anatomic & Clinical Pathology, Tufts University School of Medicine, Boston, MA, USA.
| |
Collapse
|
13
|
Nguyen QH, Ming DK, Luu AP, Chanh HQ, Tam DTH, Truong NT, Huy VX, Hernandez B, Van Nuil JI, Paton C, Georgiou P, Nguyen NM, Holmes A, Tho PV, Yacoub S. Mapping patient pathways and understanding clinical decision-making in dengue management to inform the development of digital health tools. BMC Med Inform Decis Mak 2023; 23:24. [PMID: 36732718 PMCID: PMC9893980 DOI: 10.1186/s12911-023-02116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Dengue is a common viral illness and severe disease results in life-threatening complications. Healthcare services in low- and middle-income countries treat the majority of dengue cases worldwide. However, the clinical decision-making processes which result in effective treatment are poorly characterised within this setting. In order to improve clinical care through interventions relating to digital clinical decision-support systems (CDSS), we set out to establish a framework for clinical decision-making in dengue management to inform implementation. METHODS We utilised process mapping and task analysis methods to characterise existing dengue management at the Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam. This is a tertiary referral hospital which manages approximately 30,000 patients with dengue each year, accepting referrals from Ho Chi Minh city and the surrounding catchment area. Initial findings were expanded through semi-structured interviews with clinicians in order to understand clinical reasoning and cognitive factors in detail. A grounded theory was used for coding and emergent themes were developed through iterative discussions with clinician-researchers. RESULTS Key clinical decision-making points were identified: (i) at the initial patient evaluation for dengue diagnosis to decide on hospital admission and the provision of fluid/blood product therapy, (ii) in those patients who develop severe disease or other complications, (iii) at the point of recurrent shock in balancing the need for fluid therapy with complications of volume overload. From interviews the following themes were identified: prioritising clinical diagnosis and evaluation over existing diagnostics, the role of dengue guidelines published by the Ministry of Health, the impact of seasonality and caseload on decision-making strategies, and the potential role of digital decision-support and disease scoring tools. CONCLUSIONS The study highlights the contemporary priorities in delivering clinical care to patients with dengue in an endemic setting. Key decision-making processes and the sources of information that were of the greatest utility were identified. These findings serve as a foundation for future clinical interventions and improvements in healthcare. Understanding the decision-making process in greater detail also allows for development and implementation of CDSS which are suited to the local context.
Collapse
Affiliation(s)
- Quang Huy Nguyen
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Damien K. Ming
- grid.7445.20000 0001 2113 8111Centre for Antimicrobial Optimisation (CAMO), Imperial College London, London, UK
| | - An Phuoc Luu
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ho Quang Chanh
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Dong Thi Hoai Tam
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thanh Truong
- grid.414273.70000 0004 0469 2382Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Vo Xuan Huy
- grid.414273.70000 0004 0469 2382Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Bernard Hernandez
- grid.7445.20000 0001 2113 8111Centre for BioInspired Technology, Imperial College London, London, UK
| | - Jennifer Ilo Van Nuil
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Chris Paton
- grid.29980.3a0000 0004 1936 7830Department of Information Science, University of Otago, Dunedin, New Zealand ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Pantelis Georgiou
- grid.7445.20000 0001 2113 8111Centre for BioInspired Technology, Imperial College London, London, UK
| | - Nguyet Minh Nguyen
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Alison Holmes
- grid.7445.20000 0001 2113 8111Centre for Antimicrobial Optimisation (CAMO), Imperial College London, London, UK
| | - Phan Vinh Tho
- grid.414273.70000 0004 0469 2382Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Sophie Yacoub
- grid.412433.30000 0004 0429 6814Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | |
Collapse
|
14
|
Birgand G, Ahmad R, Bulabula ANH, Singh S, Bearman G, Sánchez EC, Holmes A. Innovation for infection prevention and control-revisiting Pasteur's vision. Lancet 2022; 400:2250-2260. [PMID: 36528378 PMCID: PMC9754656 DOI: 10.1016/s0140-6736(22)02459-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Louis Pasteur has long been heralded as one of the fathers of microbiology and immunology. Less known is Pasteur's vision on infection prevention and control (IPC) that drove current infection control, public health, and much of modern medicine and surgery. In this Review, we revisited Pasteur's pioneering works to assess progress and challenges in the process and technological innovation of IPC. We focused on Pasteur's far-sighted conceptualisation of the hospital as a reservoir of microorganisms and amplifier of transmission, aseptic technique in surgery, public health education, interdisciplinary working, and the protection of health services and patients. Examples from across the globe help inform future thinking for IPC innovation, adoption, scale up and sustained use.
Collapse
Affiliation(s)
- Gabriel Birgand
- Centre d'appui pour la Prévention des Infections Associées aux Soins, Nantes, France; National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK
| | - Raheelah Ahmad
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK; School of Health and Psychological Sciences, City University of London, London, UK; Institute of Business and Health Management, Dow University of Health Sciences, Karachi, Pakistan
| | | | - Sanjeev Singh
- Department of Medicine, Amrita Institute of Medical Sciences, Amrita University, Kerala, India
| | - Gonzalo Bearman
- Division of Infectious Diseases, Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Enrique Castro Sánchez
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK; College of Nursing, Midwifery and Healthcare, Richard Wells Centre, University of West London, London, UK
| | - Alison Holmes
- National Institute for Health and Care Research Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London, London, UK; Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.
| |
Collapse
|
15
|
Hasbun R. Progress and Challenges in Bacterial Meningitis: A Review. JAMA 2022; 328:2147-2154. [PMID: 36472590 DOI: 10.1001/jama.2022.20521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE Bacterial meningitis is a worldwide health problem, with incidence rates ranging from approximately 0.9 per 100 000 individuals per year in high-income countries to 80 per 100 000 individuals per year in low-income countries. In low-income countries, bacterial meningitis has a mortality rate of up to 54%. Up to 24% of those who survive develop chronic neurological sequelae, such as hearing loss or focal neurological deficits. OBSERVATIONS Streptococcus pneumoniae causes about 72% and Neisseria meningitidis causes about 11% of cases of bacterial meningitis in people older than 16 years. Escherichia coli and Streptococcus agalactiae cause about 35% of cases of early-onset neonatal meningitis. In adults, risk factors for bacterial meningitis include older age and immunosuppressive conditions. The most common symptoms are headache (84%), fever (74%), stiff neck (74%), altered mental status (median [IQR] Glasgow Coma Scale score of 11 [9-14] on a scale ranging from 3-15), and nausea (62%). Brain imaging should be performed before lumbar puncture if patients present with altered mental status, focal neurological deficits, papilledema, or history of immunocompromising conditions or central nervous system disease. Bacterial meningitis should be suspected if any of the following are present on admission: serum leukocytes greater than 10.0 ×109/L, cerebrospinal fluid (CSF) leukocytes greater than 2000/μL, CSF granulocytes greater than 1180/μL, CSF protein greater than 2.2 g/L, CSF glucose less than 34.23 mg/dL, or fever. A positive Gram stain result for bacteria is diagnostic, but the sensitivity of a positive Gram stain result for bacterial meningitis ranges from 50% to 90%. In countries in which the prevalence of ceftriaxone-resistant Streptococcus pneumoniae exceeds 1%, vancomycin and ceftriaxone are the empirical antibiotics of choice, with the addition of ampicillin in neonates, older patients, and immunocompromised patients. Adjunctive dexamethasone should be used in patients with bacterial meningitis but stopped if Listeria monocytogenes is confirmed. CONCLUSIONS AND RELEVANCE Bacterial meningitis affects approximately 0.9 per 100 000 individuals to 80 per 100 000 individuals per year and has a mortality rate as high as 54%. First-line therapy is prompt empirical intravenous antibiotic therapy and adjunctive dexamethasone.
Collapse
Affiliation(s)
- Rodrigo Hasbun
- Section of Infectious Diseases, UT Health McGovern Medical School, Houston, Texas
| |
Collapse
|
16
|
Nkinda L, Mwakawanga DL, Kibwana UO, Mikomangwa WP, Myemba DT, Sirili N, Mwakalukwa R, Kilonzi M, Sambayi G, Maganda BA, Njiro BJ, Ndumwa HP, Mutagonda R, Marealle AI, Felix FF, Mlyuka HJ, Makuka G, Kubigwa SW, Kunambi PP, Mfaume R, Nshau AB, Bwire GM, Scherpbier R, Nyankesha E. Implementation of antibiotic stewardship programmes in paediatric patients in regional referral hospitals in Tanzania: experience from prescribers and dispensers. JAC Antimicrob Resist 2022; 4:dlac118. [PMID: 36439992 PMCID: PMC9683393 DOI: 10.1093/jacamr/dlac118] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/31/2022] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND In 2017, Tanzania launched the National Action Plan for Antimicrobial Resistance (NAPAR), 2017-2022 and implementation of antibiotic stewardship programmes (ASPs) was one of the agendas. Since the launch of the National Action Plan, no study has been done to assess its implementation. OBJECTIVES To explore the experiences of prescribers and dispensers on implementing ASPs among paediatric patients attending Regional Referral Hospitals (RRHs) in Tanzania. METHODS An exploratory qualitative study was conducted among key informants, in 14 RRHs in Tanzania between July and August 2020. A total of 28 key informants, 14 dispensers in charge of pharmacies and 14 medical doctors in charge of paediatric departments (prescribers), were interviewed. A hybrid thematic analysis was conducted on the gathered information. RESULTS Most of the study participants were not conversant with the term 'antibiotic stewardship'. Some had heard about the programmes but were not aware of the activities involved in the programme. Those who were knowledgeable on ASPs mentioned the lack of existence of such programmes in their settings. They further added that absence or limited knowledge of the stewardship concepts may have influenced the current poor practices. Barriers to the implementation of ASPs mentioned were lack of laboratory facilities to support culture and susceptibility tests, lack of materials and reagents, management pressure to prevent loss or to generate income, patients' influence and limited training opportunities. CONCLUSIONS Despite launching the NAPAR in 2017, we found limited implementation of ASPs in the management of paediatric patients. This study highlighted some barriers and identified possible intervention points.
Collapse
Affiliation(s)
- Lilian Nkinda
- School of Medicine, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | - Dorkasi L Mwakawanga
- School of Nursing, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | - Upendo O Kibwana
- School of Medicine, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | - Wigilya P Mikomangwa
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - David T Myemba
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Nathanael Sirili
- School of Public Health and Social Sciences, Muhimbili University of Health and Allied Sciences, PO Box 65015, Dar es Salaam, Tanzania
| | - Rodgers Mwakalukwa
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Manase Kilonzi
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Godfrey Sambayi
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Betty A Maganda
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Belinda J Njiro
- School of Medicine, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | - Harrieth P Ndumwa
- School of Medicine, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | - Ritah Mutagonda
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Alphonce I Marealle
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Fatuma F Felix
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Hamu J Mlyuka
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Gerald Makuka
- School of Medicine, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | | | - Peter P Kunambi
- School of Medicine, Muhimbili University of Health and Allied Sciences, PO Box 65001, Dar es Salaam, Tanzania
| | - Rashid Mfaume
- Regional Administrative Secretary, Dar es Salaam Region, PO Box 5429, Dar es Salaam, Tanzania
| | - Arapha Bashir Nshau
- Pharmacy Council, Ministry of Health, Community Development, Gender, Elderly and Children, PO Box 31818, Dar es Salaam, Tanzania
| | - George M Bwire
- School of Pharmacy, Muhimbili University of Health and Allied Sciences, PO Box 65013, Dar es Salaam, Tanzania
| | - Robert Scherpbier
- United Nations Children’s Fund, Bâtiment BIT, 4 Route des Morillons, CH-1211 Geneva 22, Switzerland
| | - Elevanie Nyankesha
- United Nations Children’s Fund, 3 United Nations Plaza, New York, NY 10017, USA
| |
Collapse
|
17
|
Validation of Three MicroScan® Antimicrobial Susceptibility Testing Plates Designed for Low-Resource Settings. Diagnostics (Basel) 2022; 12:diagnostics12092106. [PMID: 36140507 PMCID: PMC9497938 DOI: 10.3390/diagnostics12092106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/17/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022] Open
Abstract
Easy and robust antimicrobial susceptibility testing (AST) methods are essential in clinical bacteriology laboratories (CBL) in low-resource settings (LRS). We evaluated the Beckman Coulter MicroScan lyophilized broth microdilution panel designed to support Médecins Sans Frontières (MSF) CBL activity in difficult settings, in particular with the Mini-Lab. We evaluated the custom-designed MSF MicroScan Gram-pos microplate (MICPOS1) for Staphylococcus and Enterococcus species, MSF MicroScan Gram-neg microplate (MICNEG1) for Gram-negative bacilli, and MSF MicroScan Fastidious microplate (MICFAST1) for Streptococci and Haemophilus species using 387 isolates from routine CBLs from LRS against the reference methods. Results showed that, for all selected antibiotics on the three panels, the proportion of the category agreement was above 90% and the proportion of major and very major errors was below 3%, as per ISO standards. The use of the Prompt inoculation system was found to increase the MIC and the major error rate for some antibiotics when testing Staphylococci. The readability of the manufacturer’s user manual was considered challenging for low-skilled staff. The inoculations and readings of the panels were estimated as easy to use. In conclusion, the three MSF MicroScan MIC panels performed well against clinical isolates from LRS and provided a convenient, robust, and standardized AST method for use in CBL in LRS.
Collapse
|
18
|
Okeke IN, Aboderin AO, Egwuenu A, Underwood A, Afolayan AO, Kekre M, Oaikhena AO, Odih EE, Omotayo HT, Dada-Adegbola H, Ogunleye VO, Ikhimiukor OO, Aanensen DM, Ihekweazu C. Establishing a national reference laboratory for antimicrobial resistance using a whole-genome sequencing framework: Nigeria's experience. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35980376 DOI: 10.1099/mic.0.001208] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Whole-genome sequencing (WGS) is finding important applications in the surveillance of antimicrobial resistance (AMR), providing the most granular data and broadening the scope of niches and locations that can be surveilled. A common but often overlooked application of WGS is to replace or augment reference laboratory services for AMR surveillance. WGS has supplanted traditional strain subtyping in many comprehensive reference laboratories and is now the gold standard for rapidly ruling isolates into or out of suspected outbreak clusters. These and other properties give WGS the potential to serve in AMR reference functioning where a reference laboratory did not hitherto exist. In this perspective, we describe how we have employed a WGS approach, and an academic-public health system collaboration, to provide AMR reference laboratory services in Nigeria, as a model for leapfrogging to national AMR surveillance.
Collapse
Affiliation(s)
- Iruka N Okeke
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | | | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK
| | - Ayorinde O Afolayan
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Anderson O Oaikhena
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Hamzat T Omotayo
- World Health Organization, Nigeria Country Office, Abuja, Nigeria
| | - Hannah Dada-Adegbola
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Veronica O Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Oyo State, Nigeria
| | - Odion O Ikhimiukor
- Global Health Research Unit for the Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Old Road Campus, Oxford, UK.,Wellcome Genome Campus, Hinxton, UK
| | | |
Collapse
|
19
|
Keddy KH, Saha S, Kariuki S, Kalule JB, Qamar FN, Haq Z, Okeke IN. Using big data and mobile health to manage diarrhoeal disease in children in low-income and middle-income countries: societal barriers and ethical implications. THE LANCET INFECTIOUS DISEASES 2022; 22:e130-e142. [DOI: 10.1016/s1473-3099(21)00585-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 12/28/2022]
|
20
|
Qaqish B, Sallam M, Al-Khateeb M, Reisdorf E, Mahafzah A. Assessment of COVID-19 Molecular Testing Capacity in Jordan: A Cross-Sectional Study at the Country Level. Diagnostics (Basel) 2022; 12:diagnostics12040909. [PMID: 35453957 PMCID: PMC9024853 DOI: 10.3390/diagnostics12040909] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) pandemic control measures rely on the accurate and timely diagnosis of infected individuals. Real-time polymerase chain reaction (qPCR) remains the gold-standard method for laboratory diagnosis of the disease. Delayed diagnosis due to challenges that face laboratories performing COVID-19 testing can hinder public health control measures. Such challenges may be related to shortages in staff, equipment or materials, improper inventory management, flawed workflow, or long turnaround time (TAT). The aim of the current study was to assess the overall COVID-19 molecular testing capacity in Jordan as of April 2021. In addition, the study’s objectives included the identification of potential defects that could comprise the utility of the COVID-19 molecular testing capacity in the country. All laboratories certified by the Ministry of Health (MoH) in Jordan to conduct molecular testing for SARS-CoV-2 were invited to participate in this study. Data were obtained from the participating laboratories (those which agreed to participate) by either telephone interviews or a self-reported written questionnaire with items assessing the key aspects of COVID-19 molecular testing. The full molecular testing capacity in each laboratory was self-reported considering 24 working hours. The total number of participating laboratories was 51 out of 77 (66.2%), with the majority being affiliated with MoH (n = 17) and private laboratories (n = 20). The total molecular COVID-19 testing capacity among the participating laboratories was estimated at 574,441 tests per week, while the actual highest number of tests performed over a single week was 310,047 (54.0%, reported in March 2021). Laboratories affiliated with the MoH were operating at a level closer to their maximum capacity (87.2% of their estimated full capacity for COVID-19 testing) compared to private hospital laboratories (41.3%, p = 0.004), private laboratories (20.8%, p < 0.001), and academic/research laboratories (14.7%, p < 0.001, ANOVA). The national average daily COVID-19 molecular testing was 349.2 tests per 100,000 people in April 2021. The average TAT over the first week of April 2021 for COVID-19 testing was 932 min among the participating laboratories, with the longest TAT among MoH laboratories (mean: 1959 min) compared to private laboratories (mean: 333 min, p < 0.001). Molecular COVID-19 testing potential in Jordan has not been fully utilized, particularly for private laboratories and those belonging to academic/research centers. Supply-chain challenges and shortages in staff were identified as potential obstacles hindering the exploitation of full molecular testing capacity for COVID-19 in the country.
Collapse
Affiliation(s)
- Bara’a Qaqish
- Abt Associates, United States Agency for International Development (USAID) Funded Local Health System Sustainability Project (LHSS), Amman 11822, Jordan;
| | - Malik Sallam
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Department of Translational Medicine, Faculty of Medicine, Lund University, 22184 Malmo, Sweden
- Correspondence: (M.S.); (A.M.)
| | | | - Erik Reisdorf
- Infectious Disease Detection and Surveillance (IDDS), Rockville, MD 20894, USA;
| | - Azmi Mahafzah
- Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan
- Department of Clinical Laboratories and Forensic Medicine, Jordan University Hospital, Amman 11942, Jordan
- Correspondence: (M.S.); (A.M.)
| |
Collapse
|
21
|
Waddington C, Carey ME, Boinett CJ, Higginson E, Veeraraghavan B, Baker S. Exploiting genomics to mitigate the public health impact of antimicrobial resistance. Genome Med 2022; 14:15. [PMID: 35172877 PMCID: PMC8849018 DOI: 10.1186/s13073-022-01020-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/04/2022] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major global public health threat, which has been largely driven by the excessive use of antimicrobials. Control measures are urgently needed to slow the trajectory of AMR but are hampered by an incomplete understanding of the interplay between pathogens, AMR encoding genes, and mobile genetic elements at a microbial level. These factors, combined with the human, animal, and environmental interactions that underlie AMR dissemination at a population level, make for a highly complex landscape. Whole-genome sequencing (WGS) and, more recently, metagenomic analyses have greatly enhanced our understanding of these processes, and these approaches are informing mitigation strategies for how we better understand and control AMR. This review explores how WGS techniques have advanced global, national, and local AMR surveillance, and how this improved understanding is being applied to inform solutions, such as novel diagnostic methods that allow antimicrobial use to be optimised and vaccination strategies for better controlling AMR. We highlight some future opportunities for AMR control informed by genomic sequencing, along with the remaining challenges that must be overcome to fully realise the potential of WGS approaches for international AMR control.
Collapse
Affiliation(s)
- Claire Waddington
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Balaji Veeraraghavan
- Department of Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK. .,Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK.
| |
Collapse
|
22
|
Rawson TM, Peiffer-Smadja N, Holmes A. Artificial Intelligence in Infectious Diseases. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
23
|
Datar R, Orenga S, Pogorelcnik R, Rochas O, Simner PJ, van Belkum A. Recent Advances in Rapid Antimicrobial Susceptibility Testing. Clin Chem 2021; 68:91-98. [DOI: 10.1093/clinchem/hvab207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/17/2021] [Indexed: 12/30/2022]
Abstract
Abstract
Background
Antimicrobial susceptibility testing (AST) is classically performed using growth-based techniques that essentially require viable bacterial matter to become visible to the naked eye or a sophisticated densitometer.
Content
Technologies based on the measurement of bacterial density in suspension have evolved marginally in accuracy and rapidity over the 20th century, but assays expanded for new combinations of bacteria and antimicrobials have been automated, and made amenable to high-throughput turn-around. Over the past 25 years, elevated AST rapidity has been provided by nucleic acid-mediated amplification technologies, proteomic and other “omic” methodologies, and the use of next-generation sequencing. In rare cases, AST at the level of single-cell visualization was developed. This has not yet led to major changes in routine high-throughput clinical microbiological detection of antimicrobial resistance.
Summary
We here present a review of the new generation of methods and describe what is still urgently needed for their implementation in day-to-day management of the treatment of infectious diseases.
Collapse
Affiliation(s)
- Rucha Datar
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | - Sylvain Orenga
- bioMérieux, Microbiology Research, La Balme Les Grottes, France
| | | | - Olivier Rochas
- bioMérieux, Corporate Business Development, Marcy l'Etoile, France
| | - Patricia J Simner
- Department of Pathology, Bacteriology, Division of Medical Microbiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alex van Belkum
- bioMérieux, Open Innovation and Partnerships, La Balme Les Grottes, France
| |
Collapse
|
24
|
Cubas-Atienzar AI, Williams CT, Karkey A, Dongol S, Sulochana M, Rajendra S, Hobbs G, Evans K, Musicha P, Feasey N, Cuevas LE, Adams ER, Edwards T. A novel air-dried multiplex high-resolution melt assay for the detection of extended-spectrum β-lactamase and carbapenemase genes. J Glob Antimicrob Resist 2021; 27:123-131. [PMID: 34482019 PMCID: PMC8692233 DOI: 10.1016/j.jgar.2021.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES This study aimed to develop and evaluate a novel air-dried high-resolution melt (HRM) assay to detect eight major extended-spectrum β-lactamase (ESBL) (blaSHV and blaCTX-M groups 1 and 9) and carbapenemase (blaNDM, blaIMP, blaKPC, blaVIM and blaOXA-48-like) genes that confer resistance to cephalosporins and carbapenems. METHODS The assay was evaluated using 439 DNA samples extracted from bacterial isolates from Nepal, Malawi and the UK and 390 clinical isolates from Nepal with known antimicrobial susceptibility. Assay reproducibility was evaluated across five different real-time quantitative PCR (qPCR) instruments [Rotor-Gene® Q, QuantStudioTM 5, CFX96, LightCycler® 480 and Magnetic Induction Cycler (Mic)]. Assay stability was also assessed under different storage temperatures (6.2 ± 0.9°C, 20.4 ± 0.7°C and 29.7 ± 1.4°C) at six time points over 8 months. RESULTS The sensitivity and specificity (with 95% confidence intervals) for detecting ESBL and carbapenemase genes was 94.7% (92.5-96.5%) and 99.2% (98.8-99.5%) compared with the reference gel-based PCR and sequencing and 98.3% (97.0-99.3%) and 98.5% (98.0-98.9%) compared with the original HRM wet PCR mix format. Overall agreement was 91.1% (90.0-92.9%) when predicting phenotypic resistance to cefotaxime and meropenem among Enterobacteriaceae isolates. We observed almost perfect inter-machine reproducibility of the air-dried HRM assay, and no loss of sensitivity occurred under all storage conditions and time points. CONCLUSION We present a ready-to-use air-dried HRM PCR assay that offers an easy, thermostable, fast and accurate tool for the detection of ESBL and carbapenemase genes in DNA samples to improve antimicrobial resistance detection.
Collapse
Affiliation(s)
- Ana I Cubas-Atienzar
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Abhilasha Karkey
- Oxford Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Sabina Dongol
- Oxford Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Manandhar Sulochana
- Oxford Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Shrestha Rajendra
- Oxford Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Glyn Hobbs
- Liverpool John Moores University, Liverpool, UK
| | - Katie Evans
- Liverpool John Moores University, Liverpool, UK
| | | | - Nicholas Feasey
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Luis E Cuevas
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Emily R Adams
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Thomas Edwards
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK.
| |
Collapse
|
25
|
Harste HJ, Kiff G, Okeke IN, Adebiyi AO, Ravikumar KL, Nagaraj G, Ajiboye JJ, Osma Castro ECD, Herrera E, Aanensen DM. Good Financial Grant Practice: A Tool for Developing and Demonstrating Institutional Financial and Grant Management Capacity in Global Health. Clin Infect Dis 2021; 73:S275-S282. [PMID: 34850833 PMCID: PMC8634540 DOI: 10.1093/cid/ciab768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The administration and governance of grant funding across global health organizations presents enormous challenges. Meeting these challenges is crucial to ensuring that funds are used in the most effective way to improve health outcomes, in line with the United Nations' Sustainable Development Goal 3, "Ensure healthy lives and promote well-being for all at all ages." The Good Financial Grant Practice (GFGP) Standard (ARS 1651) is the world's first and, currently, only international standard for the financial governance and management of grant funding. Through consensus building and global harmonization between both low- and middle-income and high-income country players, the GFGP Standard has achieved a leveling impact: GFGP applies equally to, and can be implemented by, all types of organization, regardless of location, size, or whether they predominantly give or receive funding. GFGP can be used as a tool for addressing some of the challenges of the current funding model. Here, we describe our experiences and lessons learned from implementing GFGP across 4 diverse research institutions in India, Nigeria, Colombia, and the Philippines as part of our National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance.
Collapse
Affiliation(s)
- Harry J Harste
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom; Wellcome Genome Campus, Hinxton, United Kingdom
| | - Genevieve Kiff
- Oxford University Clinical Research Unit, Hanoi, Vietnam; African Academy of Sciences, Nairobi, Kenya
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Akindele O Adebiyi
- College Research and Innovation Management, College of Medicine, University of Ibadan, Nigeria
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Jolaade J Ajiboye
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Erik C D Osma Castro
- AGROSAVIA (Corporación Colombiana de Investigación Agropecuaria), Bogotá, Colombia
| | - Elmer Herrera
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute of Tropical Medicine, Manila, Philippines
| | - David M Aanensen
- Oxford Big Data Institute, University of Oxford, Oxford, United Kingdom; Wellcome Genome Campus, Hinxton, United Kingdom
| |
Collapse
|
26
|
Lim C, Ashley EA, Hamers RL, Turner P, Kesteman T, Akech S, Corso A, Mayxay M, Okeke IN, Limmathurotsakul D, van Doorn HR. Surveillance strategies using routine microbiology for antimicrobial resistance in low- and middle-income countries. Clin Microbiol Infect 2021; 27:1391-1399. [PMID: 34111583 PMCID: PMC7613529 DOI: 10.1016/j.cmi.2021.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 04/27/2021] [Accepted: 05/25/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND Routine microbiology results are a valuable source of antimicrobial resistance (AMR) surveillance data in low- and middle-income countries (LMICs) as well as in high-income countries. Different approaches and strategies are used to generate AMR surveillance data. OBJECTIVES We aimed to review strategies for AMR surveillance using routine microbiology results in LMICs and to highlight areas that need support to generate high-quality AMR data. SOURCES We searched PubMed for papers that used routine microbiology to describe the epidemiology of AMR and drug-resistant infections in LMICs. We also included papers that, from our perspective, were critical in highlighting the biases and challenges or employed specific strategies to overcome these in reporting AMR surveillance in LMICs. CONTENT Topics covered included strategies of identifying AMR cases (including case-finding based on isolates from routine diagnostic specimens and case-based surveillance of clinical syndromes), of collecting data (including cohort, point-prevalence survey, and case-control), of sampling AMR cases (including lot quality assurance surveys), and of processing and analysing data for AMR surveillance in LMICs. IMPLICATIONS The various AMR surveillance strategies warrant a thorough understanding of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data across time and space. For instance, surveillance using case-finding based on results from clinical diagnostic specimens is relatively easy to implement and sustain in LMIC settings, but the estimates of incidence and proportion of AMR is at risk of biases due to underuse of microbiology. Case-based surveillance of clinical syndromes generates informative statistics that can be translated to clinical practices but needs financial and technical support as well as locally tailored trainings to sustain. Innovative AMR surveillance strategies that can easily be implemented and sustained with minimal costs will be useful for improving AMR data availability and quality in LMICs.
Collapse
Affiliation(s)
- Cherry Lim
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Elizabeth A Ashley
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Laos
| | - Raph L Hamers
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Cambodia Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Thomas Kesteman
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Viet Nam
| | - Samuel Akech
- KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya
| | - Alejandra Corso
- National/Regional Reference Laboratory for Antimicrobial Resistance (NRL), Servicio Antimicrobianos, Instituto Nacional de Enfermedades Infecciosas ANLIS Dr. Carlos G. Malbrán, Buenos Aires, Argentina
| | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital Wellcome Trust Research Unit, Vientiane, Laos; Institute of Research and Education Development (IRED), University of Health Sciences, Vientiane, Laos
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Direk Limmathurotsakul
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - H Rogier van Doorn
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Oxford University Clinical Research Unit, National Hospital for Tropical Diseases, Hanoi, Viet Nam.
| |
Collapse
|
27
|
Okeke IN, Ihekweazu C. The importance of molecular diagnostics for infectious diseases in low-resource settings. Nat Rev Microbiol 2021; 19:547-548. [PMID: 34183821 PMCID: PMC8237771 DOI: 10.1038/s41579-021-00598-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 02/03/2023]
Abstract
In settings with limited resources and a wide range of possible etiologies, molecular technologies offer an effective solution for infectious disease diagnostics, because they are agile, fast and flexible. Health systems that routinely use molecular diagnostics will achieve economies of scale, maximize limited expertize and rapidly respond to new threats.
Collapse
Affiliation(s)
- Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Oyo State, Nigeria.
| | | |
Collapse
|
28
|
Sharma M, Gangakhedkar RR, Bhattacharya S, Walia K. Understanding complexities in the uptake of indigenously developed rapid point-of-care diagnostics for containment of antimicrobial resistance in India. BMJ Glob Health 2021; 6:e006628. [PMID: 34580070 PMCID: PMC8477250 DOI: 10.1136/bmjgh-2021-006628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022] Open
Abstract
A good point-of-care diagnostic test holds a promise to reduce inappropriate use of antibiotics by enabling early detection of the pathogen and facilitating rapid testing of antimicrobial susceptibility. India has taken many initiatives in the recent past to augment the development and deployment of diagnostics in Indian health care system. Funding opportunities to promote innovation in diagnostics development were started in early 2000s through various ministries and departments. India released National Essential Diagnostics List which enlists essential tests and there is now Free Diagnostics Service Initiative of Government of India under National Health Mission that mandates to provide all essential tests free of cost. We wanted to understand how these initiatives have impacted the diagnostics that could be of use in containment of antimicrobial resistance (AMR) and whether there is a smooth process for bringing indigenously developed products relevant to AMR into the healthcare system. We conducted a longitudinal survey (January 2019 and January 2021) to understand the availability of market ready indigenous rapid diagnostics for AMR in the country and their progress towards introduction in the private market or uptake in healthcare system. We found that many innovators and developers are working towards development of rapid tests that can be useful in the containment of AMR in India. While there are many promising diagnostics on the horizon, the pathway for uptake of indigenously developed diagnostics in healthcare system remains disjointed and needs to be harmonised for the investments made towards development to translate as tangible gains. Since most of these efforts are government funded, it is incumbent upon the government to also provide a seamless pathway to make these diagnostics available in health care system. In absence of this guidance, most of these diagnostics will sit with the innovators/developers and will never be used for the purpose they were intended to serve.
Collapse
Affiliation(s)
- Monica Sharma
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Raman R Gangakhedkar
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| | - Sanjay Bhattacharya
- Department of Microbiology, Tata Medical Center, Kolkata, West Bengal, India
| | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
| |
Collapse
|
29
|
Wertheim HFL, Huong VTL, Kuijper EJ. Clinical microbiology laboratories in low-resource settings, it is not only about equipment and reagents, but also good governance for sustainability. Clin Microbiol Infect 2021; 27:1389-1390. [PMID: 34332110 DOI: 10.1016/j.cmi.2021.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/17/2021] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Heiman F L Wertheim
- Department of Medical Microbiology, Radboud UMC and Center for Infectious Diseases, Radboud UMC, Nijmegen, the Netherlands.
| | - Vu Thi Lan Huong
- Oxford University Clinical Research Unit, Dong Da, Hanoi, Viet Nam
| | - Ed J Kuijper
- Department of Medical Microbiology and Experimental Bacteriology, Leiden University Medical Center and RIVM, Leiden, the Netherlands
| |
Collapse
|
30
|
Artificial Intelligence in Infectious Diseases. Artif Intell Med 2021. [DOI: 10.1007/978-3-030-58080-3_103-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|