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Aslam S, Abbas S, Nizamuddin S, Shehbaz M, Parveen A, Sultan F, Raza A. Clinical presentation and outcome of enteric fever in adult patients with cancer: a perspective from Pakistan. Access Microbiol 2024; 6:000719.v3. [PMID: 38868370 PMCID: PMC11165633 DOI: 10.1099/acmi.0.000719.v3] [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: 10/02/2023] [Accepted: 03/19/2024] [Indexed: 06/14/2024] Open
Abstract
Introduction. Enteric fever is a significant health concern in endemic countries. While extensive research has been conducted to understand its presentation and outcomes in non-cancer patients, limited data exist on its impact on cancer patients. This descriptive study aims to investigate the clinical presentation and outcome in cancer patients. Methodology. This retrospective observational study analysed 90 adult cancer patients from a single centre in Pakistan from January 2017 to December 2022. Inclusion criteria involved documented blood culture infections with Salmonella typhi or paratyphi A, B, or C. We examined clinical presentation, laboratory parameters, antimicrobial resistance, complications, and outcomes. Additionally, we explored the effects of chemotherapy, comorbidities, type of malignancy, and patient age on complications and mortality. Results. Salmonella typhi was the most prevalent organism (72.2 %), followed by Salmonella paratyphi A (22.2 %) and B (5.5 %). Variably-resistant isolates constituted 51.5 %, multi-drug resistant (MDR) isolates accounted for 20 %, extensively drug-resistant (XDR) for 14.4 % and ESBL-producers for 15.5 %, of all enteric fever infections. Enteric fever-associated complications were observed in 21.1 % of cases. Chemotherapy in the preceding month did not affect mortality, nor did age, gender, or malignancy type. However, comorbidities were statistically significant for mortality (p-value 0.03). A total of 8.8 % of patients required ICU care, and the all-cause 30 day mortality rate was 13.3 % Conclusion. Enteric fever remains prevalent in our geographical region. Unlike non-typhoidal Salmonella (NTS), enteric fever does not behave differently in an immunocompromised population, including cancer patients.
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Affiliation(s)
- Seemal Aslam
- Fellow Infectious Diseases, Department of Internal Medicine, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Salma Abbas
- Consultant Internal Medicine & Infectious Diseases, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Summiya Nizamuddin
- Consultant Medical Microbiologist, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Muhammad Shehbaz
- Fellow Infectious Diseases, Department of Internal Medicine, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Azra Parveen
- Consultant Internal Medicine & Infectious Diseases, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Faisal Sultan
- Consultant Internal Medicine & Infectious Diseases, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
| | - Aun Raza
- Consultant Internal Medicine & Infectious Diseases, Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, Pakistan
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Marks F, Im J, Park SE, Pak GD, Jeon HJ, Wandji Nana LR, Phoba MF, Mbuyi-Kalonji L, Mogeni OD, Yeshitela B, Panzner U, Cruz Espinoza LM, Beyene T, Owusu-Ansah M, Twumasi-Ankrah S, Yeshambaw M, Alemu A, Adewusi OJ, Adekanmbi O, Higginson E, Adepoju A, Agbi S, Cakpo EG, Ogunleye VO, Tunda GN, Ikhimiukor OO, Mbuyamba J, Toy T, Agyapong FO, Osei I, Amuasi J, Razafindrabe TJL, Raminosoa TM, Nyirenda G, Randriamampionona N, Seo HW, Seo H, Siribie M, Carey ME, Owusu M, Meyer CG, Rakotozandrindrainy N, Sarpong N, Razafindrakalia M, Razafimanantsoa R, Ouedraogo M, Kim YJ, Lee J, Zellweger RM, Kang SSY, Park JY, Crump JA, Hardy L, Jacobs J, Garrett DO, Andrews JR, Poudyal N, Kim DR, Clemens JD, Baker SG, Kim JH, Dougan G, Sugimoto JD, Van Puyvelde S, Kehinde A, Popoola OA, Mogasale V, Breiman RF, MacWright WR, Aseffa A, Tadesse BT, Haselbeck A, Adu-Sarkodie Y, Teferi M, Bassiahi AS, Okeke IN, Lunguya-Metila O, Owusu-Dabo E, Rakotozandrindrainy R. Incidence of typhoid fever in Burkina Faso, Democratic Republic of the Congo, Ethiopia, Ghana, Madagascar, and Nigeria (the Severe Typhoid in Africa programme): a population-based study. Lancet Glob Health 2024; 12:e599-e610. [PMID: 38485427 PMCID: PMC10951957 DOI: 10.1016/s2214-109x(24)00007-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/06/2023] [Accepted: 01/03/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Typhoid Fever remains a major cause of morbidity and mortality in low-income settings. The Severe Typhoid in Africa programme was designed to address regional gaps in typhoid burden data and identify populations eligible for interventions using novel typhoid conjugate vaccines. METHODS A hybrid design, hospital-based prospective surveillance with population-based health-care utilisation surveys, was implemented in six countries in sub-Saharan Africa. Patients presenting with fever (≥37·5°C axillary or ≥38·0°C tympanic) or reporting fever for three consecutive days within the previous 7 days were invited to participate. Typhoid fever was ascertained by culture of blood collected upon enrolment. Disease incidence at the population level was estimated using a Bayesian mixture model. FINDINGS 27 866 (33·8%) of 82 491 participants who met inclusion criteria were recruited. Blood cultures were performed for 27 544 (98·8%) of enrolled participants. Clinically significant organisms were detected in 2136 (7·7%) of these cultures, and 346 (16·2%) Salmonella enterica serovar Typhi were isolated. The overall adjusted incidence per 100 000 person-years of observation was highest in Kavuaya and Nkandu 1, Democratic Republic of the Congo (315, 95% credible interval 254-390). Overall, 46 (16·4%) of 280 tested isolates showed ciprofloxacin non-susceptibility. INTERPRETATION High disease incidence (ie, >100 per 100 000 person-years of observation) recorded in four countries, the prevalence of typhoid hospitalisations and complicated disease, and the threat of resistant typhoid strains strengthen the need for rapid dispatch and implementation of effective typhoid conjugate vaccines along with measures designed to improve clean water, sanitation, and hygiene practices. FUNDING The Bill & Melinda Gates Foundation.
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Affiliation(s)
- Florian Marks
- International Vaccine Institute, Seoul, South Korea; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK; Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany; Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar.
| | - Justin Im
- International Vaccine Institute, Seoul, South Korea
| | - Se Eun Park
- International Vaccine Institute, Seoul, South Korea; Yonsei University Graduate School of Public Health, Seoul, South Korea; Yonsei University Graduate School of Public Health, Seoul, South Korea
| | - Gi Deok Pak
- International Vaccine Institute, Seoul, South Korea
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, South Korea; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK; Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | | | - Marie-France Phoba
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Department of Medical Biology, Microbiology Service, University Teaching Hospital of Kinshasa, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Lisette Mbuyi-Kalonji
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Department of Medical Biology, Microbiology Service, University Teaching Hospital of Kinshasa, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Tigist Beyene
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Michael Owusu-Ansah
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Sampson Twumasi-Ankrah
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Department of Statistics and Actuarial Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Ashenafi Alemu
- Department of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Olukemi Adekanmbi
- Department of Medicine, University of Ibadan, Ibadan, Nigeria; Department of Community Medicine, University College Hospital, Ibadan, Nigeria
| | - Ellen Higginson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Akinlolu Adepoju
- Department of Paediatrics, University of Ibadan, Ibadan, Nigeria; Department of Community Medicine, University College Hospital, Ibadan, Nigeria
| | - Sarah Agbi
- Department of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Enoch G Cakpo
- Institut Supérieur des Sciences de la Population, Ouagadougou, Burkina Faso
| | - Veronica O Ogunleye
- Department of Community Medicine, University College Hospital, Ibadan, Nigeria
| | - Gaëlle Nkoji Tunda
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Faculty of Medicine, Congo Protestant University, Kinshasa, Democratic Republic of the Congo
| | - Odion O Ikhimiukor
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Jules Mbuyamba
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Department of Medical Biology, Microbiology Service, University Teaching Hospital of Kinshasa, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Trevor Toy
- International Vaccine Institute, Seoul, South Korea
| | - Francis Opoku Agyapong
- Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Isaac Osei
- Medical Research Council Unit, The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia; Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - John Amuasi
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Bernhard Nocht Institute of Tropical Medicine, Hamburg, Germany; Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | | | - Tiana Mirana Raminosoa
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | | | | | | | - Hyejin Seo
- International Vaccine Institute, Seoul, South Korea
| | | | - Megan E Carey
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK; International AIDS Vaccine Initiative, Chelsea & Westminster Hospital, London, UK
| | - Michael Owusu
- Department of Medical Diagnostics, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Centre for Health System Strengthening (CfHSS), Kumasi, Ghana; Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Christian G Meyer
- Institute of Tropical Medicine, Eberhard-Karls University Tübingen, Tübingen, Germany; Duy Tan University, Da Nang, Viet Nam
| | | | - Nimarko Sarpong
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | | | | | - Jooah Lee
- International Vaccine Institute, Seoul, South Korea; Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | | | | | - Ju Yeon Park
- International Vaccine Institute, Seoul, South Korea; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - John A Crump
- Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven Belgium
| | | | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - John D Clemens
- International Vaccine Institute, Seoul, South Korea; Jonathan and Karin Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Stephen G Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Jerome H Kim
- International Vaccine Institute, Seoul, South Korea; Department of Life Sciences, College of Natural Sciences, Seoul National University, Seoul, South Korea
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Jonathan D Sugimoto
- International Vaccine Institute, Seoul, South Korea; Epidemiologic Research and Information Center, Cooperative Studies Program, Office of Research and Development, United States Department of Veterans Affairs, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA USA
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK; Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerpen, Belgium
| | - Aderemi Kehinde
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oluwafemi A Popoola
- Department of Community Medicine, University College Hospital, Ibadan, Nigeria; Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | | | - Robert F Breiman
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA; Infectious Diseases and Oncology Research Institute, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Birkneh Tilahun Tadesse
- International Vaccine Institute, Seoul, South Korea; Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; Center for Innovative Drug Development and Therapeutic Trials for Africa, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Yaw Adu-Sarkodie
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana; Department of Clinical Microbiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Octavie Lunguya-Metila
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo; Department of Medical Biology, Microbiology Service, University Teaching Hospital of Kinshasa, University of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Ellis Owusu-Dabo
- School of Public Health, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Webster E, Palanco Lopez P, Kirchhelle C. Shifting targets: typhoid's transformation from an environmental to a vaccine-preventable disease, 1940-2019. THE LANCET. INFECTIOUS DISEASES 2024; 24:e232-e244. [PMID: 37995738 DOI: 10.1016/s1473-3099(23)00500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 11/25/2023]
Abstract
160 years after the discovery of its waterborne transmission and 120 years after the development of the first-generation of vaccines, typhoid fever remains a major health threat globally. In this Historical Review, we use WHO's Institutional Repository for Information Sharing to examine changes in typhoid control policy from January, 1940, to December, 2019. We used a mixed-methods approach in the analysis of infection control priorities, combining semi-inductive thematic coding with historical analysis to show major thematic shifts in typhoid control policy, away from water, sanitation, and hygiene (WASH)-based control towards vaccine-based interventions concurrent with declining attention to the disease. Documentary analysis shows that, although international planners never officially disavowed WASH and low-income countries persistently lobbied for WASH, vaccines emerged as a permanent stopgap while meaningful support of sustained WASH strengthening lost momentum-with serious, long-term ramifications for typhoid control.
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Affiliation(s)
- Emily Webster
- Department of Philosophy, Durham University, Durham, UK; Department of Philosophy, University of Johannesburg, Johannesburg, South Africa
| | | | - Claas Kirchhelle
- School of History, University College Dublin, Dublin, Ireland; Oxford Vaccine Group, University of Oxford, Oxford, UK.
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4
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Mylona E, Hefele L, Tran Vu Thieu N, Trinh Van T, Nguyen Ngoc Minh C, Tran Tuan A, Karkey A, Dongol S, Basnyat B, Voong Vinh P, Ho Ngoc Dan T, Russell P, Charles RC, Parry CM, Baker S. The Identification of Enteric Fever-Specific Antigens for Population-Based Serosurveillance. J Infect Dis 2024; 229:833-844. [PMID: 37403670 PMCID: PMC10938218 DOI: 10.1093/infdis/jiad242] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/21/2023] [Accepted: 07/04/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Enteric fever, caused by Salmonella enterica serovars Typhi and Paratyphi A, is a major public health problem in low- and middle-income countries. Moderate sensitivity and scalability of current methods likely underestimate enteric fever burden. Determining the serological responses to organism-specific antigens may improve incidence measures. METHODS Plasma samples were collected from blood culture-confirmed enteric fever patients, blood culture-negative febrile patients over the course of 3 months, and afebrile community controls. A panel of 17 Salmonella Typhi and Paratyphi A antigens was purified and used to determine antigen-specific antibody responses by indirect ELISAs. RESULTS The antigen-specific longitudinal antibody responses were comparable between enteric fever patients, patients with blood culture-negative febrile controls, and afebrile community controls for most antigens. However, we found that IgG responses against STY1479 (YncE), STY1886 (CdtB), STY1498 (HlyE), and the serovar-specific O2 and O9 antigens were greatly elevated over a 3-month follow up period in S. Typhi/S. Paratyphi A patients compared to controls, suggesting seroconversion. CONCLUSIONS We identified a set of antigens as good candidates to demonstrate enteric fever exposure. These targets can be used in combination to develop more sensitive and scalable approaches to enteric fever surveillance and generate invaluable epidemiological data for informing vaccine policies. CLINICAL TRIAL REGISTRATION ISRCTN63006567.
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Affiliation(s)
- Elli Mylona
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | - Lisa Hefele
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Grand Duchy of Luxembourg
| | - Nga Tran Vu Thieu
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tan Trinh Van
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Chau Nguyen Ngoc Minh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Anh Tran Tuan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Abhilasha Karkey
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Sabina Dongol
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Thanh Ho Ngoc Dan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paula Russell
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
| | | | - Christopher M Parry
- Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
- Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, United Kingdom
- IAVI Human Immunology Laboratory, Imperial College London, London, UK
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5
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Dodd R, Awuor AO, Garcia Bardales PF, Khanam F, Mategula D, Onwuchekwa U, Sarwar G, Yousafzai MT, Ahmed N, Atlas HE, Amirul Islam Bhuiyan M, Colston JM, Conteh B, Diawara M, Dilruba N, Elwood S, Fatima I, Feutz E, Galagan SR, Haque S, Taufiqul Islam M, Karim M, Keita B, Kosek MN, Kotloff KL, Lefu C, Mballow M, Ndalama M, Ndeketa L, Ogwel B, Okonji C, Paredes Olortegui M, Pavlinac PB, Pinedo Vasquez T, Platts-Mills JA, Qadri F, Qureshi S, Rogawski McQuade ET, Sultana S, Traore MO, Cunliffe NA, Jahangir Hossain M, Omore R, Qamar FN, Tapia MD, Peñataro Yori P, Zaman K, McGrath CJ. Population Enumeration and Household Utilization Survey Methods in the Enterics for Global Health (EFGH): Shigella Surveillance Study. Open Forum Infect Dis 2024; 11:S17-S24. [PMID: 38532956 PMCID: PMC10962723 DOI: 10.1093/ofid/ofae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Background Accurate estimation of diarrhea incidence from facility-based surveillance requires estimating the population at risk and accounting for case patients who do not seek care. The Enterics for Global Health (EFGH) Shigella surveillance study will characterize population denominators and healthcare-seeking behavior proportions to calculate incidence rates of Shigella diarrhea in children aged 6-35 months across 7 sites in Africa, Asia, and Latin America. Methods The Enterics for Global Health (EFGH) Shigella surveillance study will use a hybrid surveillance design, supplementing facility-based surveillance with population-based surveys to estimate population size and the proportion of children with diarrhea brought for care at EFGH health facilities. Continuous data collection over a 24 month period captures seasonality and ensures representative sampling of the population at risk during the period of facility-based enrollments. Study catchment areas are broken into randomized clusters, each sized to be feasibly enumerated by individual field teams. Conclusions The methods presented herein aim to minimize the challenges associated with hybrid surveillance, such as poor parity between survey area coverage and facility coverage, population fluctuations, seasonal variability, and adjustments to care-seeking behavior.
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Affiliation(s)
- Ryan Dodd
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Alex O Awuor
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | | | - Farhana Khanam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Donnie Mategula
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Health Systems and Policy, Kamuzu University of Health Sciences, School of Global Public Health, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Uma Onwuchekwa
- Centre Pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - Golam Sarwar
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Naveed Ahmed
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Hannah E Atlas
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Md Amirul Islam Bhuiyan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Josh M Colston
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Bakary Conteh
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Manan Diawara
- Centre Pour le Développement des Vaccins du Mali (CVD-Mali), Bamako, Mali
| | - Nasrin Dilruba
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sarah Elwood
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Irum Fatima
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Erika Feutz
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Sean R Galagan
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Shahinur Haque
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Taufiqul Islam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Mehrab Karim
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Belali Keita
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Margaret N Kosek
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Clement Lefu
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Mamadou Mballow
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Maureen Ndalama
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Latif Ndeketa
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Department of Health Systems and Policy, Kamuzu University of Health Sciences, School of Global Public Health, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Billy Ogwel
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Caleb Okonji
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | | | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | | | - James A Platts-Mills
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Firdausi Qadri
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Sonia Qureshi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | | | - Shazia Sultana
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | | | - Nigel A Cunliffe
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - M Jahangir Hossain
- Medical Research Council Unit The Gambia, London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Richard Omore
- Kenya Medical Research Institute, Center for Global Health Research (KEMRI-CGHR), Kisumu, Kenya
| | - Farah Naz Qamar
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Milagritos D Tapia
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Pablo Peñataro Yori
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - K Zaman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Christine J McGrath
- Department of Global Health, University of Washington, Seattle, Washington, USA
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6
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Sekwadi P, Smith AM, Maruma W, Mongologa G, Tsele G, Ngomane M, Tau N, Williams S, Disenyeng B, Sebiloane M, Johnston L, Erasmus L, Thomas J. A Prolonged Outbreak of Enteric Fever Associated With Illegal Miners in the City of Matlosana, South Africa, November 2020-September 2022. Open Forum Infect Dis 2024; 11:ofae118. [PMID: 38505295 PMCID: PMC10950048 DOI: 10.1093/ofid/ofae118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
Background In South Africa, the annual incidence of enteric fever averaged 0.1 per 100 000 persons between 2003 and 2018. During 2021 an increase in the number of enteric fever cases was observed. An outbreak investigation was conducted to determine the magnitude and source of the outbreak. Methods We performed a cross-sectional descriptive study. Data were collected through telephonic or face-to-face interviews with cases or proxies via a standardized case investigation form. Whole genome sequencing was performed on all Salmonella Typhi isolates. Drinking water samples were collected, tested, and analyzed. Descriptive analysis was performed with Microsoft Excel. Results Between January 2020 and September 2022, a cluster of 53 genetically highly related Salmonella Typhi isolates was identified from 5 provinces in South Africa. Isolates associated with the cluster showed ≤5 allelic differences, as determined following core genome multilocus sequence typing analysis. Most cases (60%, 32/53) were in the North West province. Males represented 68% (36/53). Of these, 72% (26/36) were aged 15 to 49 years, with a median age of 31 years. Where occupation was known within this age group, 78% (14/18) were illegal gold miners. Illegal miners reported illness onset while working underground. Five municipal tap water samples were tested and showed no evidence of fecal contamination. Conclusions This outbreak predominantly affected illegal gold miners, likely due to the consumption of contaminated groundwater while working in a gold mine shaft. In addition, this investigation highlights the value of whole genome sequencing to detect clusters and support epidemiologic investigation of enteric fever outbreaks.
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Affiliation(s)
- Phuti Sekwadi
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Anthony Marius Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - Wellington Maruma
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Julius Global Health, Julius Center for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Gift Mongologa
- Health Programmes Directorate, North West Provincial Department of Health, Mahikeng, South Africa
| | - Grace Tsele
- Health Programmes Directorate, North West Provincial Department of Health, Mahikeng, South Africa
| | - Mimmy Ngomane
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Nomsa Tau
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Shannon Williams
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Bolele Disenyeng
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mahlaku Sebiloane
- South African Field Epidemiology Training Program, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Leigh Johnston
- South African Field Epidemiology Training Program, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Linda Erasmus
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Juno Thomas
- Centre for Enteric Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
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7
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Patel PD, Liang Y, Meiring JE, Chasweka N, Patel P, Misiri T, Mwakiseghile F, Wachepa R, Banda HC, Shumba F, Kawalazira G, Dube Q, Nampota-Nkomba N, Nyirenda OM, Girmay T, Datta S, Jamka LP, Tracy JK, Laurens MB, Heyderman RS, Neuzil KM, Gordon MA. Efficacy of typhoid conjugate vaccine: final analysis of a 4-year, phase 3, randomised controlled trial in Malawian children. Lancet 2024; 403:459-468. [PMID: 38281499 PMCID: PMC10850983 DOI: 10.1016/s0140-6736(23)02031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/18/2023] [Accepted: 09/18/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND Randomised controlled trials of typhoid conjugate vaccines among children in Africa and Asia have shown high short-term efficacy. Data on the durability of protection beyond 2 years are sparse. We present the final analysis of a randomised controlled trial in Malawi, encompassing more than 4 years of follow-up, with the aim of investigating vaccine efficacy over time and by age group. METHODS In this phase 3, double-blind, randomised controlled efficacy trial in Blantyre, Malawi, healthy children aged 9 months to 12 years were randomly assigned (1:1) by an unmasked statistician to receive a single dose of Vi polysaccharide conjugated to tetanus toxoid vaccine (Vi-TT) or meningococcal capsular group A conjugate (MenA) vaccine. Children had to have no previous history of typhoid vaccination and reside in the study areas for inclusion and were recruited from government schools and health centres. Participants, their parents or guardians, and the study team were masked to vaccine allocation. Nurses administering vaccines were unmasked. We did surveillance for febrile illness from vaccination until follow-up completion. The primary outcome was first occurrence of blood culture-confirmed typhoid fever. Eligible children who were randomly assigned and vaccinated were included in the intention-to-treat analyses. This trial is registered at ClinicalTrials.gov, NCT03299426. FINDINGS Between Feb 21, 2018, and Sept 27, 2018, 28 130 children were vaccinated; 14 069 were assigned to receive Vi-TT and 14 061 to receive MenA. After a median follow-up of 4·3 years (IQR 4·2-4·5), 24 (39·7 cases per 100 000 person-years) children in the Vi-TT group and 110 (182·7 cases per 100 000 person-years) children in the MenA group were diagnosed with a first episode of blood culture-confirmed typhoid fever. In the intention-to-treat population, efficacy of Vi-TT was 78·3% (95% CI 66·3-86·1), and 163 (129-222) children needed to be vaccinated to prevent one case. Efficacies by age group were 70·6% (6·4-93·0) for children aged 9 months to 2 years; 79·6% (45·8-93·9) for children aged 2-4 years; and 79·3% (63·5-89·0) for children aged 5-12 years. INTERPRETATION A single dose of Vi-TT is durably efficacious for at least 4 years among children aged 9 months to 12 years and shows efficacy in all age groups, including children younger than 2 years. These results support current WHO recommendations in typhoid-endemic areas for mass campaigns among children aged 9 months to 15 years, followed by routine introduction in the first 2 years of life. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Priyanka D Patel
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Yuanyuan Liang
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - James E Meiring
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Nedson Chasweka
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Pratiksha Patel
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Theresa Misiri
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Felistas Mwakiseghile
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Richard Wachepa
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Happy C Banda
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Florence Shumba
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Gift Kawalazira
- District Health Office, Blantyre District Council, Blantyre, Malawi
| | | | | | - Osward M Nyirenda
- Blantyre Malaria Project, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Tsion Girmay
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shrimati Datta
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Leslie P Jamka
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - J Kathleen Tracy
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Kathleen M Neuzil
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Melita A Gordon
- Malawi-Liverpool-Wellcome Program, Kamuzu University of Health Sciences, Blantyre, Malawi
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8
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Kim JH, Choi J, Kim C, Pak GD, Parajulee P, Haselbeck A, Park SE, Mogasale V, Jeon HJ, Browne AJ, Owusu-Dabo E, Rakotozandrindrainy R, Bassiahi AS, Teferi M, Lunguya-Metila O, Dolecek C, Pitzer VE, Crump JA, Hay SI, Marks F. Mapping the incidence rate of typhoid fever in sub-Saharan Africa. PLoS Negl Trop Dis 2024; 18:e0011902. [PMID: 38408128 DOI: 10.1371/journal.pntd.0011902] [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: 04/26/2023] [Revised: 03/26/2024] [Accepted: 01/04/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND With more than 1.2 million illnesses and 29,000 deaths in sub-Saharan Africa in 2017, typhoid fever continues to be a major public health problem. Effective control of the disease would benefit from an understanding of the subnational geospatial distribution of the disease incidence. METHOD We collated records of the incidence rate of typhoid fever confirmed by culture of blood in Africa from 2000 to 2022. We estimated the typhoid incidence rate for sub-Saharan Africa on 20 km × 20 km grids by exploring the association with geospatial covariates representing access to improved water and sanitation, health conditions of the population, and environmental conditions. RESULTS We identified six published articles and one pre-print representing incidence rate estimates in 22 sites in 2000-2022. Estimated incidence rates showed geospatial variation at sub-national, national, and regional levels. The incidence rate was high in Western and Eastern African subregions followed by Southern and Middle African subregions. By age, the incidence rate was highest among 5-14 yo followed by 2-4 yo, > 14 yo, and 0-1 yo. When aggregated across all age classes and grids that comprise each country, predicted incidence rates ranged from 43.7 (95% confidence interval: 0.6 to 591.2) in Zimbabwe to 2,957.8 (95% CI: 20.8 to 4,245.2) in South Sudan per 100,000 person-years. Sub-national heterogeneity was evident with the coefficient of variation at the 20 km × 20 km grid-level ranging from 0.7 to 3.3 and was generally lower in high-incidence countries and widely varying in low-incidence countries. CONCLUSION Our study provides estimates of 20 km × 20 km incidence rate of typhoid fever across sub-Saharan Africa based on data collected from 2000 through 2020. Increased understanding of the subnational geospatial variation of typhoid fever in Africa may inform more effective intervention programs by better targeting resources to heterogeneously disturbed disease risk.
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Affiliation(s)
- Jong-Hoon Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Jungsoon Choi
- Department of Mathematics, Hanyang University, Seoul, Republic of Korea
| | - Chaelin Kim
- International Vaccine Institute, Seoul, Republic of Korea
| | - Gi Deok Pak
- International Vaccine Institute, Seoul, Republic of Korea
| | | | | | - Se Eun Park
- International Vaccine Institute, Seoul, Republic of Korea
- Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | | | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, Republic of Korea
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Annie J Browne
- Malaria Atlas Project, Telethon Kids Institute, Perth, Australia
| | - Ellis Owusu-Dabo
- Malaria Atlas Project, Telethon Kids Institute, Perth, Australia
| | - Raphaël Rakotozandrindrainy
- School of Public Health, Kwame Nkrumah University of Science and Technology, Laing Building Complex J.W. Acheampong CI, Kumasi, Ghana
| | | | - Mekonnen Teferi
- Armauer Hansen Research Institute, ALERT Compound Zenebework, Addis Ababa, Ethiopia
| | - Octavie Lunguya-Metila
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of Congo
- Department of Medical Biology, Microbiology Service, University Teaching Hospital, Ave De L'hopital, Kinshasa, Democratic Republic of the Congo
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, New Haven, Connecticut, United States of America
| | - John A Crump
- Centre for International Health, Division of Health Sciences, University of Otago, Dunedin, New Zealand
| | - Simon I Hay
- Institute for Health Metrics and Evaluation (IHME), University of Washington, Seattle, Washington, United States of America
- Department of Health Metrics Sciences, University of Washington, Seattle, Washington, United States of America
| | - 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 Biomedical Campus, Cambridge, United Kingdom
- School of Public Health, Kwame Nkrumah University of Science and Technology, Laing Building Complex J.W. Acheampong CI, Kumasi, Ghana
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
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9
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Martin LB, Khanam F, Qadri F, Khalil I, Sikorski MJ, Baker S. Vaccine value profile for Salmonella enterica serovar Paratyphi A. Vaccine 2023; 41 Suppl 2:S114-S133. [PMID: 37951691 DOI: 10.1016/j.vaccine.2023.01.054] [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: 10/02/2022] [Revised: 12/27/2022] [Accepted: 01/23/2023] [Indexed: 11/14/2023]
Abstract
In Asia, there are an estimated 12 million annual cases of enteric fever, a potentially fatal systemic bacterial infection caused by Salmonella enterica serovars Typhi (STy) and Paratyphi A (SPA). The recent availability of typhoid conjugate vaccines (TCV), an increasing incidence of disease caused by SPA and growing antimicrobial resistance (AMR) across the genus Salmonella makes a bivalent STy/SPA vaccine a useful public health proposition. The uptake of a stand-alone paratyphoid vaccine is likely low thus, there is a pipeline of bivalent STy/SPA candidate vaccines. Several candidates are close to entering clinical trials, which if successful should facilitate a more comprehensive approach for enteric fever control. Additionally, the World Health Organization (WHO) has made advancing the development of vaccines that protect young children and working aged adults against both agents of enteric fever a priority objective. This "Vaccine Value Profile" (VVP) addresses information related predominantly to invasive disease caused by SPA prevalent in Asia. Information is included on stand-alone SPA candidate vaccines and candidate vaccines targeting SPA combined with STy. Out of scope for the first version of this VVP is a wider discussion on the development of a universal Salmonella combination candidate vaccine, addressing both enteric fever and invasive non-typhoidal Salmonella disease, for use globally. This VVP is a detailed, high-level assessment of existing, publicly available information to inform and contextualize the public health, economic, and societal potential of pipeline vaccines and vaccine-like products for SPA. Future versions of this VVP will be updated to reflect ongoing activities such as vaccine development strategies and "Full Vaccine Value Assessment" that will inform the value proposition of an SPA vaccine. This VVP was developed by an expert working group from academia, non-profit organizations, public-private partnerships, and multi-lateral organizations as well as in collaboration with stakeholders from the WHO South-East Asian Region. All contributors have extensive expertise on various elements of the VVP for SPA and collectively aimed to identify current research and knowledge gaps.
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Affiliation(s)
- Laura B Martin
- Independent Consultant (current affiliation US Pharmacopeia Convention), USA.
| | - Farhana Khanam
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | | | | | - Stephen Baker
- University of Cambridge School of Clinical Medicine, UK.
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Feng Y, Pan H, Zheng B, Li F, Teng L, Jiang Z, Feng M, Zhou X, Peng X, Xu X, Wang H, Wu B, Xiao Y, Baker S, Zhao G, Yue M. An integrated nationwide genomics study reveals transmission modes of typhoid fever in China. mBio 2023; 14:e0133323. [PMID: 37800953 PMCID: PMC10653838 DOI: 10.1128/mbio.01333-23] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/16/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi, resulting in a significant disease burden across developing countries. Historically, China was very much close to the global epicenter of typhoid, but the role of typhoid transmission within China and among epicenter remains overlooked in previous investigations. By using newly produced genomics on a national scale, we clarify the complex local and global transmission history of such a notorious disease agent in China spanning the most recent five decades, which largely undermines the global public health network.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Hang Pan
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fang Li
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Lin Teng
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Zhijie Jiang
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Mengyao Feng
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Xiao Zhou
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Xianqi Peng
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Xuebin Xu
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Haoqiu Wang
- Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Beibei Wu
- Zhejiang Province Center for Disease Control and Prevention, Hangzhou, China
- School of Public Health and Managemet, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Guoping Zhao
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Min Yue
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
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11
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Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
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Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
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12
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da Silva KE, Date K, Hirani N, LeBoa C, Jayaprasad N, Borhade P, Warren J, Shimpi R, Hoffman SA, Mikoleit M, Bhatnagar P, Cao Y, Haldar P, Harvey P, Zhang C, Daruwalla S, Dharmapalan D, Gavhane J, Joshi S, Rai R, Rathod V, Shetty K, Warrier DS, Yadav S, Chakraborty D, Bahl S, Katkar A, Kunwar A, Yewale V, Dutta S, Luby SP, Andrews JR. Population structure and antimicrobial resistance patterns of Salmonella Typhi and Paratyphi A amid a phased municipal vaccination campaign in Navi Mumbai, India. mBio 2023; 14:e0117923. [PMID: 37504577 PMCID: PMC10470601 DOI: 10.1128/mbio.01179-23] [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: 05/15/2023] [Accepted: 06/22/2023] [Indexed: 07/29/2023] Open
Abstract
We performed whole-genome sequencing of 174 Salmonella Typhi and 54 Salmonella Paratyphi A isolates collected through prospective surveillance in the context of a phased typhoid conjugate vaccine introduction in Navi Mumbai, India. We investigate the temporal and geographical patterns of emergence and spread of antimicrobial resistance. We evaluated the relationship between the spatial distance between households and genetic clustering of isolates. Most isolates were non-susceptible to fluoroquinolones, with nearly 20% containing ≥3 quinolone resistance-determining region mutations. Two H58 isolates carried an IncX3 plasmid containing blaSHV-12, associated with ceftriaxone resistance, suggesting that the ceftriaxone-resistant isolates from India independently evolved on multiple occasions. Among S. Typhi, we identified two main clades circulating (2.2 and 4.3.1 [H58]); 2.2 isolates were closely related following a single introduction around 2007, whereas H58 isolates had been introduced multiple times to the city. Increasing geographic distance between isolates was strongly associated with genetic clustering (odds ratio [OR] = 0.72 per km; 95% credible interval [CrI]: 0.66-0.79). This effect was seen for distances up to 5 km (OR = 0.65 per km; 95% CrI: 0.59-0.73) but not seen for distances beyond 5 km (OR = 1.02 per km; 95% CrI: 0.83-1.26). There was a non-significant reduction in odds of clustering for pairs of isolates in vaccination communities compared with non-vaccination communities or mixed pairs compared with non-vaccination communities. Our findings indicate that S. Typhi was repeatedly introduced into Navi Mumbai and then spread locally, with strong evidence of spatial genetic clustering. In addition to vaccination, local interventions to improve water and sanitation will be critical to interrupt transmission. IMPORTANCE Enteric fever remains a major public health concern in many low- and middle-income countries, as antimicrobial resistance (AMR) continues to emerge. Geographical patterns of typhoidal Salmonella spread, critical to monitoring AMR and planning interventions, are poorly understood. We performed whole-genome sequencing of S. Typhi and S. Paratyphi A isolates collected in Navi Mumbai, India before and after a typhoid conjugate vaccine introduction. From timed phylogenies, we found two dominant circulating lineages of S. Typhi in Navi Mumbai-lineage 2.2, which expanded following a single introduction a decade prior, and 4.3.1 (H58), which had been introduced repeatedly from other parts of India, frequently containing "triple mutations" conferring high-level ciprofloxacin resistance. Using Bayesian hierarchical statistical models, we found that spatial distance between cases was strongly associated with genetic clustering at a fine scale (<5 km). Together, these findings suggest that antimicrobial-resistant S. Typhi frequently flows between cities and then spreads highly locally, which may inform surveillance and prevention strategies.
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Affiliation(s)
- Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Kashmira Date
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nilma Hirani
- Grant Government Medical College & Sir J J Hospital, Mumbai, Maharashtra, India
| | - Christopher LeBoa
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California, USA
| | - Niniya Jayaprasad
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Priyanka Borhade
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Joshua Warren
- Yale School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Rahul Shimpi
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Seth A. Hoffman
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew Mikoleit
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pankaj Bhatnagar
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Yanjia Cao
- Department of Geography, The University of Hong Kong, Hong Kong
| | - Pradeep Haldar
- Ministry of Health & Family Welfare, Government of India, New Delhi, India
| | - Pauline Harvey
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Chenhua Zhang
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Savita Daruwalla
- Department of Pediatrics, NMMC General Hospital, Navi Mumbai, India
| | | | - Jeetendra Gavhane
- Department of Pediatrics, MGM New Bombay Hospital, MGM Medical College, Navi Mumbai, India
| | - Shrikrishna Joshi
- Dr. Joshi’s Central Clinical Microbiology Laboratory, Navi Mumbai, India
| | - Rajesh Rai
- Department of Pediatrics & Neonatology, Dr. D.Y. Patil Medical College and Hospital, Navi Mumbai, India
| | - Varsha Rathod
- Rajmata Jijau Hospital, Airoli (NMMC), Navi Mumbai, India
| | - Keertana Shetty
- Department of Microbiology, Dr. D.Y. Patil Medical College and Hospital, Navi Mumbai, India
| | | | - Shalini Yadav
- Department of Microbiology, MGM New Bombay Hospital, Navi Mumbai, India
| | - Debjit Chakraborty
- National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research, Kolkata, India
| | - Sunil Bahl
- World Health Organization South-East Asia Regional Office, New Delhi, India
| | - Arun Katkar
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Abhishek Kunwar
- World Health Organization-Country Office for India, National Public Health Surveillance Project, New Delhi, India
| | - Vijay Yewale
- Dr. Yewale Multispecialty Hospital for Children, Navi Mumbai, India
| | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Indian Council of Medical Research, Kolkata, India
| | - Stephen P. Luby
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Jason R. Andrews
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
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13
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Saha T, Arisoyin AE, Bollu B, Ashok T, Babu A, Issani A, Jhaveri S, Avanthika C. Enteric Fever: Diagnostic Challenges and the Importance of Early Intervention. Cureus 2023; 15:e41831. [PMID: 37575696 PMCID: PMC10423039 DOI: 10.7759/cureus.41831] [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] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Enteric fever is a systemic infection caused by highly virulent Salmonella enterica serovars: Typhi and Paratyphi. Diagnosis of enteric fever is challenging due to a wide variety of clinical features which overlap with other febrile illnesses. The current diagnostic methods are limited because of the suboptimal sensitivity of conventional tests like blood culture in detecting organisms and the invasive nature of bone marrow culture. It emphasizes the need to develop improved and more reliable diagnostic modalities. The rising rates of multidrug-resistant Salmonella strains call for an accurate understanding of the current management of the disease. Proper public health measures and large-scale immunization programs will help reduce the burden of the disease. A comprehensive surveillance system can help detect the chronic carrier state and is crucial in understanding antibiotic susceptibility patterns. We conducted an all-language literature search on Medline, Cochrane, Embase, and Google Scholar till May 2022. The following search words and medical subject headings (MeSH) were used: "enteric fever," "Salmonella Typhi," "multidrug-resistant Salmonella," chronic carrier state," "Salmonella detection, "and "typhoid vaccine." We reviewed the literature on clinical features, pathophysiology, new diagnostic tests, and interventions to prevent the disease. This article explores enteric fever and its various clinical features and addresses the emerging threat of multidrug resistance. It focuses on novel methods for diagnosis and prevention strategies, including vaccines and the use of surveillance systems employed across different parts of the world.
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Affiliation(s)
- Tias Saha
- Internal Medicine, Samorita General Hospital, Faridpur, BGD
- Internal Medicine, Diabetic Association Medical College, Faridpur, BGD
| | | | - Bhaswanth Bollu
- Emergency Medicine, All India Institute of Medical Sciences, New Delhi, IND
| | - Tejaswini Ashok
- Internal Medicine, Jagadguru Sri Shivarathreeshwara Medical College, Mysore, IND
| | - Athira Babu
- Pediatrics, Saudi German Hospital, Dubai, ARE
| | - Ali Issani
- Emergency Medicine, Aga Khan University, Karachi, PAK
| | - Sharan Jhaveri
- Internal Medicine, Nathiba Hargovandas Lakhmichand Municipal Medical College, Ahmedabad, IND
| | - Chaithanya Avanthika
- Pediatrics, Icahn School of Medicine at Mount Sinai, Elmhurst Hospital Center, New York, USA
- Medicine and Surgery, Karnataka Institute of Medical Sciences, Hubli, IND
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14
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Aiemjoy K, Seidman JC, Charles RC, Andrews JR. Seroepidemiology for Enteric Fever: Emerging Approaches and Opportunities. Open Forum Infect Dis 2023; 10:S21-S25. [PMID: 37274530 PMCID: PMC10236506 DOI: 10.1093/ofid/ofad021] [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
Safe and effective typhoid conjugate vaccines (TCVs) are available, but many countries lack the high-resolution data needed to prioritize TCV introduction to the highest-risk communities. Here we discuss seroepidemiology-an approach using antibody response data to characterize infection burden-as a potential tool to fill this data gap. Serologic tests for typhoid have existed for over a hundred years, but only recently were antigens identified that were sensitive and specific enough to use as epidemiologic markers. These antigens, coupled with new methodological developments, permit estimating seroincidence-the rate at which new infections occur in a population-from cross-sectional serosurveys. These new tools open up many possible applications for enteric fever seroepidemiology, including generating high-resolution surveillance data, monitoring vaccine impact, and integrating with other serosurveillance initiatives. Challenges remain, including distinguishing Salmonella Typhi from Salmonella Paratyphi infections and accounting for reinfections. Enteric fever seroepidemiology can be conducted at a fraction of the cost, time, and sample size of surveillance blood culture studies and may enable more efficient and scalable surveillance for this important infectious disease.
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Affiliation(s)
- Kristen Aiemjoy
- Correspondence: Kristen Aiemjoy, PhD, MSc, Department of Public Health Sciences, University of California, Davis School of Medicine, One Shields Ave, Medical Sciences 1C, Davis, CA 95616 (); Jason Andrews, MD, SM, DTM&H, Stanford University School of Medicine, 300 Pasteur Dr, Rm S101D, MC 5107, Stanford, CA 94305 ()
| | | | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jason R Andrews
- Correspondence: Kristen Aiemjoy, PhD, MSc, Department of Public Health Sciences, University of California, Davis School of Medicine, One Shields Ave, Medical Sciences 1C, Davis, CA 95616 (); Jason Andrews, MD, SM, DTM&H, Stanford University School of Medicine, 300 Pasteur Dr, Rm S101D, MC 5107, Stanford, CA 94305 ()
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15
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Chen J, Long JE, Vannice K, Shewchuk T, Kumar S, Duncan Steele A, Zaidi AKM. Taking on Typhoid: Eliminating Typhoid Fever as a Global Health Problem. Open Forum Infect Dis 2023; 10:S74-S81. [PMID: 37274535 PMCID: PMC10236514 DOI: 10.1093/ofid/ofad055] [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
Typhoid fever is a significant global health problem that impacts people living in areas without access to clean water and sanitation. However, collaborative international partnerships and new research have improved both knowledge of the burden in countries with endemic disease and the tools for improved surveillance, including environmental surveillance. Two typhoid conjugate vaccines (TCVs) have achieved World Health Organization prequalification, with several more in the development pipeline. Despite hurdles posed by the coronavirus disease 2019 pandemic, multiple TCV efficacy trials have been conducted in high-burden countries, and data indicate that TCVs provide a high degree of protection from typhoid fever, are safe to use in young children, provide lasting protection, and have the potential to combat typhoid antimicrobial resistance. Now is the time to double down on typhoid control and elimination by sustaining progress made through water, sanitation, and hygiene improvements and accelerating TCV introduction in high-burden locations.
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Affiliation(s)
- Jessie Chen
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Jessica E Long
- Correspondence: Jessica Long, PhD MPH, 500 5th Ave N, Seattle, WA 98109 ()
| | - Kirsten Vannice
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Tanya Shewchuk
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Supriya Kumar
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - A Duncan Steele
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Anita K M Zaidi
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, Washington, USA
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16
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Jacob JJ, Pragasam AK, Vasudevan K, Velmurugan A, Priya Teekaraman M, Priya Thirumoorthy T, Ray P, Gupta M, Kapil A, Bai SP, Nagaraj S, Saigal K, Chandola TR, Thomas M, Bavdekar A, Ebenezer SE, Shastri J, De A, Dutta S, Alexander AP, Koshy RM, Jinka DR, Singh A, Srivastava SK, Anandan S, Dougan G, John J, Kang G, Veeraraghavan B, Mutreja A. Genomic analysis unveils genome degradation events and gene flux in the emergence and persistence of S. Paratyphi A lineages. PLoS Pathog 2023; 19:e1010650. [PMID: 37115804 PMCID: PMC10171690 DOI: 10.1371/journal.ppat.1010650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/10/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Paratyphoid fever caused by S. Paratyphi A is endemic in parts of South Asia and Southeast Asia. The proportion of enteric fever cases caused by S. Paratyphi A has substantially increased, yet only limited data is available on the population structure and genetic diversity of this serovar. We examined the phylogenetic distribution and evolutionary trajectory of S. Paratyphi A isolates collected as part of the Indian enteric fever surveillance study "Surveillance of Enteric Fever in India (SEFI)." In the study period (2017-2020), S. Paratyphi A comprised 17.6% (441/2503) of total enteric fever cases in India, with the isolates highly susceptible to all the major antibiotics used for treatment except fluoroquinolones. Phylogenetic analysis clustered the global S. Paratyphi A collection into seven lineages (A-G), and the present study isolates were distributed in lineages A, C and F. Our analysis highlights that the genome degradation events and gene acquisitions or losses are key molecular events in the evolution of new S. Paratyphi A lineages/sub-lineages. A total of 10 hypothetically disrupted coding sequences (HDCS) or pseudogenes-forming mutations possibly associated with the emergence of lineages were identified. The pan-genome analysis identified the insertion of P2/PSP3 phage and acquisition of IncX1 plasmid during the selection in 2.3.2/2.3.3 and 1.2.2 genotypes, respectively. We have identified six characteristic missense mutations associated with lipopolysaccharide (LPS) biosynthesis genes of S. Paratyphi A, however, these mutations confer only a low structural impact and possibly have minimal impact on vaccine effectiveness. Since S. Paratyphi A is human-restricted, high levels of genetic drift are not expected unless these bacteria transmit to naive hosts. However, public-health investigation and monitoring by means of genomic surveillance would be constantly needed to avoid S. Paratyphi A serovar becoming a public health threat similar to the S. Typhi of today.
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Affiliation(s)
| | | | - Karthick Vasudevan
- Christian Medical College, Vellore, India
- REVA University, Bangalore, India
| | | | | | | | - Pallab Ray
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Madhu Gupta
- Post Graduate Institute of Medical & Educational Research, Chandigarh, India
| | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi, India
| | | | | | | | | | | | | | | | - Jayanthi Shastri
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | - Anuradha De
- Topiwala National Medical College & BYL Nair Charitable Hospital, Mumbai, India
| | - Shantha Dutta
- ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | | | | | | | | | | | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jacob John
- Christian Medical College, Vellore, India
| | | | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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17
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Mahmoud A, Oluyemisi A, Uwishema O, Sun J, Jobran AW, David S, Wireko AA, Adanur I, Dost B, Onyeaka H. Recent advances in the diagnosis and management of typhoid fever in Africa: A review. Int J Health Plann Manage 2023; 38:317-329. [PMID: 36457176 DOI: 10.1002/hpm.3599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/03/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022] Open
Abstract
Typhoid fever, a classical disease of enteric origin caused by Salmonella species of bacteria, is among the most important diseases threatening public health in Africa. The African continent is a marker for both low resources within the healthcare system and poor disease control policy formulations in managing endemic infectious diseases. Since the colonial era, the Widal serological test has been used to confirm typhoid fever in Africa, however recent studies recommend blood culture, and when blood culture cannot be obtained, clinical findings, laboratory Widal test confirmation, and ruling out other febrile illnesses as confirmatory pathway to diagnose typhoid fever in Africa. Managing typhoid fever relies on antimicrobials. In 1980s chloramphenicol was the medication of choice. Years later, amoxicillin and co-trimoxazole were adopted. However, the instantaneous rise of resistant strains of Salmonella enterica confers an important challenge to treat the burdensome enteric fever. The current treatment algorithm of typhoid fever in Africa relies significantly on the use of fluoroquinolones, macrolides, and cephalosporins. Developed nations have successfully addressed and controlled typhoid fever via improvement in accessing safe water and food, better sanitary and hygienic behaviours, and vaccines development. Nevertheless, there is significant evidence to infer improvement in the diagnosis management of typhoid fever over the last few decades, and efforts are underway to control the disease spread in Africa. This review aims to provide an overview of the latest developments in typhoid fever diagnosis and management in Africa and provide key recommendations for a coordinated approach to mitigate typhoid in the continent.
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Affiliation(s)
- Ashraf Mahmoud
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, Kilimanjaro Christian Medical University College KCMUCo, Moshi, Tanzania
| | - Adekunbi Oluyemisi
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,School of Public and Allied Health, Babcock University, Ilishan-Remo, Ogun State, Nigeria
| | - Olivier Uwishema
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Clinton Global Initiative University, New York, New York, USA.,Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Jeffrey Sun
- Clinton Global Initiative University, New York, New York, USA.,Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Afnan Waleed Jobran
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, Al-Quds University, Hebron, Palestine
| | - Success David
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka, Nigeria
| | - Andrew Awuah Wireko
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, Sumy State University, Sumy, Ukraine
| | - Irem Adanur
- Oli Health Magazine Organization, Research and Education, Kigali, Rwanda.,Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Burhan Dost
- Department of Anesthesiology, School of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Helen Onyeaka
- School of Chemical Engineering, University of Birmingham, Birmingham, UK
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18
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Uzzell CB, Troman CM, Rigby J, Raghava Mohan V, John J, Abraham D, Srinivasan R, Nair S, Meschke JS, Elviss N, Kang G, Feasey NA, Grassly NC. Environmental surveillance for Salmonella Typhi as a tool to estimate the incidence of typhoid fever in low-income populations. Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.17687.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Background: The World Health Organisation recommends prioritised use of recently prequalified typhoid conjugate vaccines in countries with the highest incidence of typhoid fever. However, representative typhoid surveillance data are lacking in many low-income countries because of the costs and challenges of diagnostic clinical microbiology. Environmental surveillance (ES) of Salmonella Typhi in sewage and wastewater using molecular methods may offer a low-cost alternative, but its performance in comparison with clinical surveillance has not been assessed. Methods: We developed a harmonised protocol for typhoid ES and its implementation in communities in India and Malawi where it will be compared with findings from hospital-based surveillance for typhoid fever. The protocol includes methods for ES site selection based on geospatial analysis, grab and trap sample collection at sewage and wastewater sites, and laboratory methods for sample processing, concentration and quantitative polymerase chain reaction (PCR) to detect Salmonella Typhi. The optimal locations for ES sites based on digital elevation models and mapping of sewage and river networks are described for each community and their suitability confirmed through field investigation. We will compare the prevalence and abundance of Salmonella Typhi in ES samples collected each month over a 12-month period to the incidence of blood culture confirmed typhoid cases recorded at referral hospitals serving the study areas. Conclusions: If environmental detection of Salmonella Typhi correlates with the incidence of typhoid fever estimated through clinical surveillance, typhoid ES may be a powerful and low-cost tool to estimate the local burden of typhoid fever and support the introduction of typhoid conjugate vaccines. Typhoid ES could also allow the impact of vaccination to be assessed and rapidly identify circulation of drug resistant strains.
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Abstract
PURPOSE OF REVIEW Momentum for achieving widespread control of typhoid fever has been growing over the past decade. Typhoid conjugate vaccines represent a potentially effective tool to reduce the burden of disease in the foreseeable future and new data have recently emerged to better frame their use-case. RECENT FINDINGS We describe how antibiotic resistance continues to pose a major challenge in the treatment of typhoid fever, as exemplified by the emergence of azithromycin resistance and the spread of Salmonella Typhi strains resistant to third-generation cephalosporins. We review efficacy and effectiveness data for TCVs, which have been shown to have high-level efficacy (≥80%) against typhoid fever in diverse field settings. Data from randomized controlled trials and observational studies of TCVs are reviewed herein. Finally, we review data from multicountry blood culture surveillance studies that have provided granular insights into typhoid fever epidemiology. These data are becoming increasingly important as countries decide how best to introduce TCVs into routine immunization schedules and determine the optimal delivery strategy. SUMMARY Continued advocacy is needed to address the ongoing challenge of typhoid fever to improve child health and tackle the rising challenge of antimicrobial resistance.
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Clinical profiles and antimicrobial resistance patterns of invasive Salmonella infections in children in China. Eur J Clin Microbiol Infect Dis 2022; 41:1215-1225. [PMID: 36040531 PMCID: PMC9489584 DOI: 10.1007/s10096-022-04476-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/18/2022] [Indexed: 11/06/2022]
Abstract
Invasive Salmonella infections result in a significant burden of disease including morbidity, mortality, and financial cost in many countries. Besides typhoid fever, the clinical impact of non-typhoid Salmonella infections is increasingly recognized with the improvement of laboratory detection capacity and techniques. A retrospective multicenter study was conducted to analyze the clinical profiles and antimicrobial resistance patterns of invasive Salmonella infections in hospitalized children in China during 2016–2018. A total of 130 children with invasive Salmonella infections were included with the median age of 12 months (range: 1–144 months). Seventy-nine percent of cases occurred between May and October. Pneumonia was the most common comorbidity in 33 (25.4%) patients. Meningitis and septic arthritis caused by nontyphoidal Salmonella (NTS) infections occurred in 12 (9.2%) patients and 5 (3.8%) patients. Patients < 12 months (OR: 16.04) and with septic shock (OR: 23.4), vomit (OR: 13.33), convulsion (OR: 15.86), C-reactive protein (CRP) ≥ 40 g/L (OR: 5.56), and a higher level of procalcitonin (PCT) (OR: 1.05) on admission were statistically associated to an increased risk of developing meningitis. Compared to 114 patients with NTS infections, 16 patients with typhoid fever presented with higher levels of CRP and PCT (P < 0.05). The rates of resistance to ampicillin, sulfamethoxazole/trimethoprim, ciprofloxacin, and ceftriaxone among Salmonella Typhi and NTS isolates were 50% vs 57.3%, 9.1% vs 24.8%, 0% vs 11.2%, and 0% vs 9.9%, respectively. NTS has been the major cause of invasive Salmonella infections in Chinese children and can result in severe diseases. Antimicrobial resistance among NTS was more common.
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21
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da Silva KE, Tanmoy AM, Pragasam AK, Iqbal J, Sajib MSI, Mutreja A, Veeraraghavan B, Tamrakar D, Qamar FN, Dougan G, Bogoch I, Seidman JC, Shakya J, Vaidya K, Carey ME, Shrestha R, Irfan S, Baker S, Luby SP, Cao Y, Dyson ZA, Garrett DO, John J, Kang G, Hooda Y, Saha SK, Saha S, Andrews JR. The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study. THE LANCET MICROBE 2022; 3:e567-e577. [PMID: 35750070 PMCID: PMC9329132 DOI: 10.1016/s2666-5247(22)00093-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background The emergence of increasingly antimicrobial-resistant Salmonella enterica serovar Typhi (S Typhi) threatens to undermine effective treatment and control. Understanding where antimicrobial resistance in S Typhi is emerging and spreading is crucial towards formulating effective control strategies. Methods In this genomic epidemiology study, we sequenced the genomes of 3489 S Typhi strains isolated from prospective enteric fever surveillance studies in Nepal, Bangladesh, Pakistan, and India (between 2014 and 2019), and combined these with a global collection of 4169 S Typhi genome sequences isolated between 1905 and 2018 to investigate the temporal and geographical patterns of emergence and spread of antimicrobial-resistant S Typhi. We performed non-parametric phylodynamic analyses to characterise changes in the effective population size of fluoroquinolone-resistant, extensively drug-resistant (XDR), and azithromycin-resistant S Typhi over time. We inferred timed phylogenies for the major S Typhi sublineages and used ancestral state reconstruction methods to estimate the frequency and timing of international and intercontinental transfers. Findings Our analysis revealed a declining trend of multidrug resistant typhoid in south Asia, except for Pakistan, where XDR S Typhi emerged in 2016 and rapidly replaced less-resistant strains. Mutations in the quinolone-resistance determining region (QRDR) of S Typhi have independently arisen and propagated on at least 94 occasions, nearly all occurring in south Asia. Strains with multiple QRDR mutations, including triple mutants with high-level fluoroquinolone resistance, have been increasing in frequency and displacing strains with fewer mutations. Strains containing acrB mutations, conferring azithromycin resistance, emerged in Bangladesh around 2013 and effective population size of these strains has been steadily increasing. We found evidence of frequent international (n=138) and intercontinental transfers (n=59) of antimicrobial-resistant S Typhi, followed by local expansion and replacement of drug-susceptible clades. Interpretation Independent acquisition of plasmids and homoplastic mutations conferring antimicrobial resistance have occurred repeatedly in multiple lineages of S Typhi, predominantly arising in south Asia before spreading to other regions. Funding Bill & Melinda Gates Foundation.
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22
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Garrett DO, Longley AT, Aiemjoy K, Yousafzai MT, Hemlock C, Yu AT, Vaidya K, Tamrakar D, Saha S, Bogoch II, Date K, Saha S, Islam MS, Sayeed KMI, Bern C, Shakoor S, Dehraj IF, Mehmood J, Sajib MSI, Islam M, Thobani RS, Hotwani A, Rahman N, Irfan S, Naga SR, Memon AM, Pradhan S, Iqbal K, Shrestha R, Rahman H, Hasan MM, Qazi SH, Kazi AM, Saddal NS, Jamal R, Hunzai MJ, Hossain T, Marks F, Carter AS, Seidman JC, Qamar FN, Saha SK, Andrews JR, Luby SP. Incidence of typhoid and paratyphoid fever in Bangladesh, Nepal, and Pakistan: results of the Surveillance for Enteric Fever in Asia Project. Lancet Glob Health 2022; 10:e978-e988. [PMID: 35714648 PMCID: PMC9210262 DOI: 10.1016/s2214-109x(22)00119-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 02/28/2022] [Accepted: 03/11/2022] [Indexed: 01/03/2023]
Abstract
BACKGROUND Precise enteric fever disease burden data are needed to inform prevention and control measures, including the use of newly available typhoid vaccines. We established the Surveillance for Enteric Fever in Asia Project (SEAP) to inform these strategies. METHODS From September, 2016, to September, 2019, we conducted prospective clinical surveillance for Salmonella enterica serotype Typhi (S Typhi) and Paratyphi (S Paratyphi) A, B, and C at health facilities in predetermined catchment areas in Dhaka, Bangladesh; Kathmandu and Kavrepalanchok, Nepal; and Karachi, Pakistan. Patients eligible for inclusion were outpatients with 3 or more consecutive days of fever in the last 7 days; inpatients with suspected or confirmed enteric fever; patients with blood culture-confirmed enteric fever from the hospital laboratories not captured by inpatient or outpatient enrolment and cases from the laboratory network; and patients with non-traumatic ileal perforation under surgical care. We used a hybrid surveillance model, pairing facility-based blood culture surveillance with community surveys of health-care use. Blood cultures were performed for enrolled patients. We calculated overall and age-specific typhoid and paratyphoid incidence estimates for each study site. Adjusted estimates accounted for the sensitivity of blood culture, the proportion of eligible individuals who consented and provided blood, the probability of care-seeking at a study facility, and the influence of wealth and education on care-seeking. We additionally calculated incidence of hospitalisation due to typhoid and paratyphoid. FINDINGS A total of 34 747 patients were enrolled across 23 facilitates (six tertiary hospitals, surgical wards of two additional hospitals, and 15 laboratory network sites) during the study period. Of the 34 303 blood cultures performed on enrolled patients, 8705 (26%) were positive for typhoidal Salmonella. Adjusted incidence rates of enteric fever considered patients in the six tertiary hospitals. Adjusted incidence of S Typhi, expressed per 100 000 person-years, was 913 (95% CI 765-1095) in Dhaka. In Nepal, the adjusted typhoid incidence rates were 330 (230-480) in Kathmandu and 268 (202-362) in Kavrepalanchok. In Pakistan, the adjusted incidence rates per hospital site were 176 (144-216) and 103 (85-126). The adjusted incidence rates of paratyphoid (of which all included cases were due to S Paratyphi A) were 128 (107-154) in Bangladesh, 46 (34-62) and 81 (56-118) in the Nepal sites, and 23 (19-29) and 1 (1-1) in the Pakistan sites. Adjusted incidence of hospitalisation was high across sites, and overall, 2804 (32%) of 8705 patients with blood culture-confirmed enteric fever were hospitalised. INTERPRETATION Across diverse communities in three south Asian countries, adjusted incidence exceeded the threshold for "high burden" of enteric fever (100 per 100 000 person-years). Incidence was highest among children, although age patterns differed across sites. The substantial disease burden identified highlights the need for control measures, including improvements to water and sanitation infrastructure and the implementation of typhoid vaccines. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Denise O Garrett
- Applied Epidemiology, Sabin Vaccine Institute, Washington, DC, USA.
| | - Ashley T Longley
- National Foundation for the Centers for Disease Control and Prevention, Atlanta, GA, USA; Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kristen Aiemjoy
- Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Mohammad T Yousafzai
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Caitlin Hemlock
- Applied Epidemiology, Sabin Vaccine Institute, Washington, DC, USA
| | - Alexander T Yu
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Krista Vaidya
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Dipesh Tamrakar
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | - Shampa Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | - Isaac I Bogoch
- Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Kashmira Date
- Global Immunization Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Senjuti Saha
- Child Health Research Foundation, Dhaka, Bangladesh
| | | | | | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sadia Shakoor
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan; Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Irum F Dehraj
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Junaid Mehmood
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | | | - Rozina S Thobani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeb Rahman
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Seema Irfan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Shiva R Naga
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | | | - Sailesh Pradhan
- Kathmandu Medical College Teaching Hospital, Kathmandu, Nepal
| | | | - Rajeev Shrestha
- Dhulikhel Hospital, Kathmandu University Hospital, Kavrepalanchok, Nepal
| | | | | | - Saqib H Qazi
- Department of Surgery, Aga Khan University, Karachi, Pakistan
| | - Abdul M Kazi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Raza Jamal
- National Institute of Child Health, Karachi, Pakistan
| | - Mohammed J Hunzai
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Tanvir Hossain
- Maternal and Child Health Division, icddr,b, Dhaka, Bangladesh
| | - Florian Marks
- International Vaccine Institute, Seoul, South Korea; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge, UK; University of Antananarivo, Antananarivo, Madagascar; Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
| | - Alice S Carter
- Applied Epidemiology, Sabin Vaccine Institute, Washington, DC, USA
| | | | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Samir K Saha
- Child Health Research Foundation, Dhaka, Bangladesh; Bangladesh Institute of Child Health, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
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Dieye Y, Hull DM, Wane AA, Harden L, Fall C, Sambe-Ba B, Seck A, Fedorka-Cray PJ, Thakur S. Genomics of human and chicken Salmonella isolates in Senegal: Broilers as a source of antimicrobial resistance and potentially invasive nontyphoidal salmonellosis infections. PLoS One 2022; 17:e0266025. [PMID: 35325007 PMCID: PMC8947133 DOI: 10.1371/journal.pone.0266025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 03/11/2022] [Indexed: 11/19/2022] Open
Abstract
Salmonella enterica is the most common foodborne pathogen worldwide. It causes two types of diseases, a self-limiting gastroenteritis and an invasive, more threatening, infection. Salmonella gastroenteritis is caused by several serotypes and is common worldwide. In contrast, invasive salmonellosis is rare in high-income countries (HIC) while frequent in low- and middle-income countries (LMIC), especially in sub-Saharan Africa (sSA). Invasive Nontyphoidal Salmonella (iNTS), corresponding to serotypes other than Typhi and Paratyphi, have emerged in sSA and pose a significant risk to public health. We conducted a whole-genome sequence (WGS) analysis of 72 strains of Salmonella isolated from diarrheic human patients and chicken meat sold in multipurpose markets in Dakar, Senegal. Antimicrobial susceptibility testing combined with WGS data analysis revealed frequent resistance to fluoroquinolones and the sulfamethoxazole-trimethoprim combination that are among the most used treatments for invasive Salmonella. In contrast, resistance to the historical first-line drugs chloramphenicol and ampicillin, and to cephalosporins was rare. Antimicrobial resistance (AMR) was lower in clinical isolates compared to chicken strains pointing to the concern posed by the excessive use of antimicrobials in farming. Phylogenetic analysis suggested possible transmission of the emerging multidrug resistant (MDR) Kentucky ST198 and serotype Schwarzengrund from chicken to human. These results stress the need for active surveillance of Salmonella and AMR in order to address invasive salmonellosis caused by nontyphoidal Salmonella strains and other important bacterial diseases in sSA.
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Affiliation(s)
- Yakhya Dieye
- Pole of Microbiology, Institut Pasteur, Dakar, Sénégal
- Département Génie Chimique et Biologie Appliquée, École Supérieure Polytechnique, Université Cheikh Anta Diop, Dakar, Sénégal
- * E-mail:
| | - Dawn M. Hull
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Lyndy Harden
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Cheikh Fall
- Pole of Microbiology, Institut Pasteur, Dakar, Sénégal
| | | | | | - Paula J. Fedorka-Cray
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, United States of America
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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]
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25
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Sinha B, Rongsen-Chandola T, Goyal N, Arya A, Kumar CM, Chakravarty A, Aslam M, More D. Incidence of Enteric Fever in a Pediatric Cohort in North India: Comparison with Estimates from 20 Years Earlier. J Infect Dis 2021; 224:S558-S567. [PMID: 35238363 PMCID: PMC8892529 DOI: 10.1093/infdis/jiab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND An earlier cohort in 1995-1996 showed a very high burden of typhoid in Delhi. Our aim was to estimate the current overall and age-specific incidence of culture-confirmed enteric fever among children aged 6 months to 15 years in Delhi. METHODS We enrolled a cohort of 6000 children aged 6 months to <14 years in South Delhi and followed them up weekly for 24 months or until 15 completed years of child age, whichever was earlier. Blood culture to confirm enteric fever was done in children with ≥3 consecutive days of fever. RESULTS We recorded a total of 14 650 episodes of fever in the 11 510 person-years (PY) of follow-up. A total of 81 fever episodes were positive for enteric fever. The incidence (95% confidence interval) of all enteric fever was 703.7 (560.5-874.7) per 100 000 PY. The incidences of typhoid and paratyphoid fevers were 608.1 (95% confidence interval, 481.1-768.7) and 111.7 (59.5-191.1) per 100 000 PY, respectively, highest among children aged 10-15 years. CONCLUSIONS Despite a 35% reduction in incidence compared with the 1995-1996 cohort, our study suggested a substantial burden of enteric fever in the population. Continued efforts to improve water, sanitation, and hygiene parameters along with implementation of novel vaccination strategies and disease surveillance can help achieve the goal of disease elimination.
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Affiliation(s)
- Bireshwar Sinha
- Centre for Health Research and Development, Society for Applied Studies, New Delhi, India
| | | | - Nidhi Goyal
- Centre for Health Research and Development, Society for Applied Studies, New Delhi, India
| | - Alok Arya
- Centre for Health Research and Development, Society for Applied Studies, New Delhi, India
| | - Chandra Mohan Kumar
- Department of Pediatrics, Hakeem Abdul Hameed Centenary Hospital, Hamdard Institute of Medical Sciences & Research, New Delhi, India
| | - Aparna Chakravarty
- Department of Pediatrics, Hakeem Abdul Hameed Centenary Hospital, Hamdard Institute of Medical Sciences & Research, New Delhi, India
| | - Mohammed Aslam
- Centre for Health Research and Development, Society for Applied Studies, New Delhi, India
| | - Deepak More
- Clinical and Research Laboratories, Society for Applied Studies, New Delhi, India
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Kumar D, Sharma A, Rana SK, Prinja S, Ramanujam K, Karthikeyan AS, Raju R, Njarekkattuvalappil SK, Premkumar PS, Chauhan AS, Mohan VR, Ebenezer SE, Thomas MS, Gupta M, Singh A, Jinka DR, Thankaraj S, Koshy RM, Dhas Sankhro C, Kapil A, Shastri J, Saigal K, Perumal SPB, Nagaraj S, Anandan S, Thomas M, Ray P, John J, Kang G. Cost of Illness Due to Severe Enteric Fever in India. J Infect Dis 2021; 224:S540-S547. [PMID: 35238366 PMCID: PMC8892542 DOI: 10.1093/infdis/jiab282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Lack of robust data on economic burden due to enteric fever in India has made decision making on typhoid vaccination a challenge. Surveillance for Enteric Fever network was established to address gaps in typhoid disease and economic burden.
Methods
Patients hospitalized with blood culture-confirmed enteric fever and nontraumatic ileal perforation were identified at 14 hospitals. These sites represent urban referral hospitals (tier 3) and smaller hospitals in urban slums, remote rural, and tribal settings (tier 2). Cost of illness and productivity loss data from onset to 28 days after discharge from hospital were collected using a structured questionnaire. The direct and indirect costs of an illness episode were analyzed by type of setting.
Results
In total, 274 patients from tier 2 surveillance, 891 patients from tier 3 surveillance, and 110 ileal perforation patients provided the cost of illness data. The mean direct cost of severe enteric fever was US$119.1 (95% confidence interval [CI], US$85.8–152.4) in tier 2 and US$405.7 (95% CI, 366.9–444.4) in tier 3; 16.9% of patients in tier 3 experienced catastrophic expenditure.
Conclusions
The cost of treating enteric fever is considerable and likely to increase with emerging antimicrobial resistance. Equitable preventive strategies are urgently needed.
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Affiliation(s)
| | - Atul Sharma
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Saroj Kumar Rana
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Shankar Prinja
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | | | | | | | | | | | | | | | | | | | - Madhu Gupta
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Ashita Singh
- Chinchpada Christian Hospital, Maharashtra,India
| | | | - Shajin Thankaraj
- Makunda Christian Leprosy and General Hospital, Bazaricherra, Assam,India
| | - Roshine Mary Koshy
- Makunda Christian Leprosy and General Hospital, Bazaricherra, Assam,India
| | | | - Arti Kapil
- All India Institute of Medical Sciences, New Delhi,India
| | - Jayanthi Shastri
- Topiwala National Medical College and BYL Nair Charitable Hospital, Mumbai,India
| | | | | | | | | | - Maria Thomas
- Christian Medical College and Hospital, Ludhiana,India
| | - Pallab Ray
- Postgraduate Institute of Medical Education and Research, Chandigarh,India
| | - Jacob John
- Christian Medical College, Vellore,India
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Giri S, Mohan VR, Srinivasan M, Kumar N, Kumar V, Dhanapal P, Venkatesan J, Gunasekaran A, Abraham D, John J, Kang G. Case-Control Study of Household and Environmental Transmission of Typhoid Fever in India. J Infect Dis 2021; 224:S584-S592. [PMID: 35238355 PMCID: PMC8892545 DOI: 10.1093/infdis/jiab378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background Typhoid fever causes substantial morbidity and mortality in low- and middle-income countries. We conducted a case-control study in Vellore, southern India, to understand risk factors for transmission of typhoid. Methods From April 2018 to October 2019, households of blood culture-confirmed typhoid cases that occurred within a fever surveillance cohort aged 6 months–15 years, and controls matched for age, sex, geographic location, and socioeconomic status, were recruited. Information on risk factors was obtained using standard questionnaires. Household and environmental samples were collected for detection of Salmonella Typhi using real-time polymerase chain reaction. Multivariable analysis was used to evaluate associations between risk factors and typhoid. Results One hundred pairs of cases and controls were recruited. On multivariable regression analysis, mothers eating food from street vendors during the previous week (odds ratio [OR] = 2.04; 95% confidence interval [CI], 1.03–4.12; P = .04) was independently associated with typhoid, whereas treatment of household drinking water (OR = 0.45; 95% CI, 0.25–0.80; P = .007) was protective. There was no significant difference in S Typhi detection between the environmental samples from case and control households. Conclusions Street-vended food is a risk factor for typhoid in densely populated urban communities of Vellore. Improved sanitation facilities and awareness about point-of-use water treatment are likely to contribute to typhoid control.
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Affiliation(s)
- Sidhartha Giri
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | | | - Nirmal Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Vinoth Kumar
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Pavithra Dhanapal
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | | | - Annai Gunasekaran
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Dilip Abraham
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
| | - Jacob John
- Department of Community Health, Christian Medical College, Vellore, India
| | - Gagandeep Kang
- Division of Gastrointestinal Sciences, Christian Medical College, Vellore, India
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Kumar S, Ghosh RS, Iyer H, Ray A, Vannice K, MacLennan C, Shewchuk T, Steele D. Typhoid in India: An Age-old Problem With an Existing Solution. J Infect Dis 2021; 224:S469-S474. [PMID: 35238361 PMCID: PMC8892544 DOI: 10.1093/infdis/jiab441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Enteric fever continues to impact millions of people who lack adequate access to clean water and sanitation. The typhoid and paratyphoid fever burden in South Asia is broadly acknowledged, but current estimates of incidence, severity, and cost of illness from India are lacking. This supplement addresses this gap in our knowledge, presenting findings from two years of surveillance, conducted at multiple sites between October 2017 and February 2020, in the Surveillance for Enteric Fever in India (SEFI) network. Results provide contemporaneous evidence of high disease burden and cost of illness—the latter borne largely by patients in the absence of universal healthcare coverage in India. Against a backdrop of immediate priorities in the COVID-19 pandemic, these data are a reminder that typhoid, though often forgotten, remains a public health problem in India. Typhoid conjugate vaccines, produced by multiple Indian manufacturers, and recommended for use in high burden settings, ensure that the tools to tackle typhoid are an immediately available solution to this public health problem.
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Affiliation(s)
- Supriya Kumar
- Enteric and Diarrheal Diseases, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Raj Shankar Ghosh
- India Country Office, Bill & Melinda Gates Foundation, New Delhi, India
| | - Harish Iyer
- India Country Office, Bill & Melinda Gates Foundation, New Delhi, India
| | - Arindam Ray
- India Country Office, Bill & Melinda Gates Foundation, New Delhi, India
| | - Kirsten Vannice
- Enteric and Diarrheal Diseases, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Calman MacLennan
- Enteric and Diarrheal Diseases, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Tanya Shewchuk
- Global Delivery Program, Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | - Duncan Steele
- Enteric and Diarrheal Diseases, Bill & Melinda Gates Foundation, Seattle, Washington, USA
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29
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Phillips MT, Meiring JE, Voysey M, Warren JL, Baker S, Basnyat B, Clemens JD, Dolecek C, Dunstan SJ, Dougan G, Gordon MA, Thindwa D, Heyderman RS, Holt KE, Qadri F, Pollard AJ, Pitzer VE. A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data. Stat Med 2021; 40:5853-5870. [PMID: 34428309 PMCID: PMC9291985 DOI: 10.1002/sim.9159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/23/2021] [Accepted: 07/27/2021] [Indexed: 12/04/2022]
Abstract
Decisions about typhoid fever prevention and control are based on estimates of typhoid incidence and their uncertainty. Lack of specific clinical diagnostic criteria, poorly sensitive diagnostic tests, and scarcity of accurate and complete datasets contribute to difficulties in calculating age‐specific population‐level typhoid incidence. Using data from the Strategic Typhoid Alliance across Africa and Asia program, we integrated demographic censuses, healthcare utilization surveys, facility‐based surveillance, and serological surveillance from Malawi, Nepal, and Bangladesh to account for under‐detection of cases. We developed a Bayesian approach that adjusts the count of reported blood‐culture‐positive cases for blood culture detection, blood culture collection, and healthcare seeking—and how these factors vary by age—while combining information from prior published studies. We validated the model using simulated data. The ratio of observed to adjusted incidence rates was 7.7 (95% credible interval [CrI]: 6.0‐12.4) in Malawi, 14.4 (95% CrI: 9.3‐24.9) in Nepal, and 7.0 (95% CrI: 5.6‐9.2) in Bangladesh. The probability of blood culture collection led to the largest adjustment in Malawi, while the probability of seeking healthcare contributed the most in Nepal and Bangladesh; adjustment factors varied by age. Adjusted incidence rates were within or below the seroincidence rate limits of typhoid infection. Estimates of blood‐culture‐confirmed typhoid fever without these adjustments results in considerable underestimation of the true incidence of typhoid fever. Our approach allows each phase of the reporting process to be synthesized to estimate the adjusted incidence of typhoid fever while correctly characterizing uncertainty, which can inform decision‐making for typhoid prevention and control.
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Affiliation(s)
- Maile T Phillips
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - James E Meiring
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK.,Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Merryn Voysey
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Buddha Basnyat
- Oxford University Clinical Research Unit, Patan Academy of Health Sciences, Kathmandu, Nepal
| | - John D Clemens
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Mahidol Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Melita A Gordon
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.,Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Deus Thindwa
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Robert S Heyderman
- Malawi Liverpool Wellcome Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.,NIHR Global Health Research Unit on Mucosal Pathogens, Division of Infection and Immunity, University College London, London, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia.,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London
| | - Firdausi Qadri
- International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,National Institute for Health Research Oxford Biomedical Research Centre, Oxford, UK
| | - Virginia E Pitzer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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30
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Guevara PD, Maes M, Thanh DP, Duarte C, Rodriguez EC, Montaño LA, Dan THN, Nguyen TNT, Carey ME, Campos J, Chinen I, Perez E, Baker S. A genomic snapshot of Salmonella enterica serovar Typhi in Colombia. PLoS Negl Trop Dis 2021; 15:e0009755. [PMID: 34529660 PMCID: PMC8478212 DOI: 10.1371/journal.pntd.0009755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/28/2021] [Accepted: 08/24/2021] [Indexed: 11/23/2022] Open
Abstract
Little is known about the genetic diversity of Salmonella enterica serovar Typhi (S. Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized blood culture surveillance across Latin American makes estimating the true disease burden problematic. The Colombian National Health Service established a surveillance system for tracking bacterial pathogens, including S. Typhi, in 2006. Here, we characterized 77 representative Colombian S. Typhi isolates collected between 1997 and 2018 using pulse field gel electrophoresis (PFGE; the accepted genotyping method in Latin America) and whole genome sequencing (WGS). We found that the main S. Typhi clades circulating in Colombia were clades 2.5 and 3.5. Notably, the sequenced S. Typhi isolates from Colombia were closely related in a global phylogeny. Consequently, these data suggest that these are endemic clades circulating in Colombia. We found that AMR in S. Typhi in Colombia was uncommon, with a small subset of organisms exhibiting mutations associated with reduced susceptibility to fluoroquinolones. This is the first time that S. Typhi isolated from Colombia have been characterized by WGS, and after comparing these data with those generated using PFGE, we conclude that PFGE is unsuitable for tracking S. Typhi clones and mapping transmission. The genetic diversity of pathogens such as S. Typhi is limited in Latin America and should be targeted for future surveillance studies incorporating WGS.
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Affiliation(s)
| | - Mailis Maes
- University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Level 5 Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Carolina Duarte
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | | | | | - Thanh Ho Ngoc Dan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Megan E. Carey
- University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Level 5 Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
| | - Josefina Campos
- Red Pulsenet Latinoamérica y el Caribe, INEI-ANLIS “Dr Carlos Malbran, Buenos Aires, Argentina
| | - Isabel Chinen
- Red Pulsenet Latinoamérica y el Caribe, INEI-ANLIS “Dr Carlos Malbran, Buenos Aires, Argentina
| | - Enrique Perez
- Health Emergencies Department, Pan American Health Organization/World Health Organization, PAHO/WHO, Washington DC, United States of America
| | - Stephen Baker
- University of Cambridge School of Clinical Medicine Department of Medicine, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Level 5 Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, United Kingdom
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31
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Gauld JS, Olgemoeller F, Heinz E, Nkhata R, Bilima S, Wailan AM, Kennedy N, Mallewa J, Gordon MA, Read JM, Heyderman RS, Thomson NR, Diggle PJ, Feasey NA. Spatial and Genomic Data to Characterize Endemic Typhoid Transmission. Clin Infect Dis 2021; 74:1993-2000. [PMID: 34463736 PMCID: PMC9187325 DOI: 10.1093/cid/ciab745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Diverse environmental exposures and risk factors have been implicated in the transmission of Salmonella Typhi, but the dominant transmission pathways through the environment to susceptible humans remain unknown. Here, we use spatial, bacterial genomic, and hydrological data to refine our view of typhoid transmission in an endemic setting. METHODS A total of 546 patients presenting to Queen Elizabeth Central Hospital in Blantyre, Malawi, with blood culture-confirmed typhoid fever between April 2015 and January 2017 were recruited to a cohort study. The households of a subset of these patients were geolocated, and 256 S. Typhi isolates were whole-genome sequenced. Pairwise single-nucleotide variant distances were incorporated into a geostatistical modeling framework using multidimensional scaling. RESULTS Typhoid fever was not evenly distributed across Blantyre, with estimated minimum incidence ranging across the city from <15 to >100 cases per 100 000 population per year. Pairwise single-nucleotide variant distance and physical household distances were significantly correlated (P = .001). We evaluated the ability of river catchment to explain the spatial patterns of genomics observed, finding that it significantly improved the fit of the model (P = .003). We also found spatial correlation at a smaller spatial scale, of households living <192 m apart. CONCLUSIONS These findings reinforce the emerging view that hydrological systems play a key role in the transmission of typhoid fever. By combining genomic and spatial data, we show how multifaceted data can be used to identify high incidence areas, explain the connections between them, and inform targeted environmental surveillance, all of which will be critical to shape local and regional typhoid control strategies.
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Affiliation(s)
- Jillian S Gauld
- Correspondence: Jillian S. Gauld, Institute for Disease Modeling, Bill and Melinda Gates Foundation, 500 Fifth Ave N, Seattle WA 98109 ()
| | - Franziska Olgemoeller
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom,Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - Eva Heinz
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom,Department of Vector Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Rose Nkhata
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | | | | | - Neil Kennedy
- Department of Paediatrics, University of Malawi the College of Medicine, Blantyre, Malawi,School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Jane Mallewa
- Adult Medicine, University of Malawi the College of Medicine, Blantyre, Malawi
| | - Melita A Gordon
- Malawi-Liverpool Wellcome Programme, Blantyre, Malawi,Institute of Infection, Veterinary and Ecological Sciences, The University of Liverpool, Liverpool, United Kingdom,Adult Medicine, University of Malawi the College of Medicine, Blantyre, Malawi
| | - Jonathan M Read
- Centre for Health Informatics, Computing, and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Cambridge, United Kingdom,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Peter J Diggle
- Centre for Health Informatics, Computing, and Statistics, Lancaster University, Lancaster, United Kingdom
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom,Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
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32
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Feikin DR, Widdowson MA, Mulholland K. Estimating the Percentage of a Population Infected with SARS-CoV-2 Using the Number of Reported Deaths: A Policy Planning Tool. Pathogens 2020; 9:E838. [PMID: 33066231 PMCID: PMC7602107 DOI: 10.3390/pathogens9100838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/08/2023] Open
Abstract
The magnitude of future waves of Covid19 in a population will depend, in part, on the percentage of that population already infected, recovered, and presumably immune. Sero-epidemiological surveys can define the prevalence of SARS-CoV-2 antibodies in various populations. However, sero-surveys are resource-intensive and methodologically challenging, limiting widespread use. We propose a relatively simple method for calculating the percentage of a population infected, which depends on the number of reported Covid19 deaths, a figure usually more reliable and less dependent on variable testing practices than the total number of reported Covid19 cases, and the infection fatality rate, a figure that is relatively stable in similar populations. The method can be applied in different sized areas, such as states, districts, or cities. Such an approach can provide useful, real-time estimates of probable population immunity in settings unable to undertake multiple sero-surveys. This method is applicable to low- and lower-middle-income country (LMIC) settings where sero-survey data will likely be limited; however, better estimates of infection fatality rates and Covid19 death counts in LMICs are needed to improve the method's accuracy. Information on the percentage of a population infected will help public health authorities in planning for future waves of Covid19, including where to most effectively deploy vaccines.
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Affiliation(s)
| | | | - Kim Mulholland
- Murdoch Children’s Research Institute, Royal Children’s Hospital, Flemington Road, Parkville, Melbourne 3051, Australia;
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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