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McCann N, Paganotti Vicentine M, Kim YC, Pollard AJ. The use of controlled human infection models to identify correlates of protection for invasive Salmonella vaccines. Front Immunol 2024; 15:1457785. [PMID: 39257585 PMCID: PMC11385307 DOI: 10.3389/fimmu.2024.1457785] [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: 07/01/2024] [Accepted: 08/08/2024] [Indexed: 09/12/2024] Open
Abstract
Controlled human infection model (CHIM) studies, which involve deliberate exposure of healthy human volunteers to an infectious agent, are recognised as important tools to advance vaccine development. These studies not only facilitate estimates of vaccine efficacy, but also offer an experimental approach to study disease pathogenesis and profile vaccine immunogenicity in a controlled environment, allowing correlation with clinical outcomes. Consequently, the data from CHIMs can be used to identify immunological correlates of protection (CoP), which can help accelerate vaccine development. In the case of invasive Salmonella infections, vaccination offers a potential instrument to prevent disease. Invasive Salmonella disease, caused by the enteric fever pathogens Salmonella enterica serovar Typhi (S. Typhi) and S. Paratyphi A, B and C, and nontyphoidal Salmonella (iNTS), remains a significant cause of mortality and morbidity in low- and middle-income countries, resulting in over 200,000 deaths and the loss of 15 million DALYs annually. CHIM studies have contributed to the understanding of S. Typhi infection and provided invaluable insight into the development of vaccines and CoP following vaccination against S. Typhi. However, CoP are less well understood for S. Paratyphi A and iNTS. This brief review focuses on the contribution of vaccine-CHIM trials to our understanding of the immune mechanisms associated with protection following vaccines against invasive Salmonella pathogens, particularly in relation to CoP.
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Affiliation(s)
- Naina McCann
- Oxford Vaccine Group, Department of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Margarete Paganotti Vicentine
- Oxford Vaccine Group, Department of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Young Chan Kim
- Oxford Vaccine Group, Department of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, Centre for Clinical Vaccinology and Tropical Medicine, Churchill Hospital, Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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2
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Naidu A, Garg V, Balakrishnan D, C R V, Sundararajan V, Lulu S S. Systems and Computational Screening identifies SRC and NKIRAS2 as Baseline Correlates of Risk (CoR) for Live Attenuated Oral Typhoid Vaccine (TY21a) associated Protection. Mol Immunol 2024; 169:99-109. [PMID: 38552286 DOI: 10.1016/j.molimm.2024.03.005] [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: 12/01/2023] [Revised: 03/01/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
AIM We investigated the molecular underpinnings of variation in immune responses to the live attenuated typhoid vaccine (Ty21a) by analyzing the baseline immunological profile. We utilized gene expression datasets obtained from the Gene Expression Omnibus (GEO) database (accession number: GSE100665) before and after immunization. We then employed two distinct computational approaches to identify potential baseline biomarkers associated with responsiveness to the Ty21a vaccine. MAIN METHODS The first pipeline (knowledge-based) involved the retrieval of differentially expressed genes (DEGs), functional enrichment analysis, protein-protein interaction network construction, and topological network analysis of post-immunization datasets before gauging their pre-vaccination expression levels. The second pipeline utilized an unsupervised machine learning algorithm for data-driven feature selection on pre-immunization datasets. Supervised machine-learning classifiers were employed to computationally validate the identified biomarkers. KEY FINDINGS Baseline activation of NKIRAS2 (a negative regulator of NF-kB signalling) and SRC (an adaptor for immune receptor activation) was negatively associated with Ty21a vaccine responsiveness, whereas LOC100134365 exhibited a positive association. The Stochastic Gradient Descent (SGD) algorithm accurately distinguished vaccine responders and non-responders, with 88.8%, 70.3%, and 85.1% accuracy for the three identified genes, respectively. SIGNIFICANCE This dual-pronged novel analytical approach provides a comprehensive comparison between knowledge-based and data-driven methods for the prediction of baseline biomarkers associated with Ty21a vaccine responsiveness. The identified genes shed light on the intricate molecular mechanisms that influence vaccine efficacy from the host perspective while pushing the needle further towards the need for development of precise enteric vaccines and on the importance of pre-immunization screening.
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Affiliation(s)
- Akshayata Naidu
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Varin Garg
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Deepna Balakrishnan
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Vinaya C R
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Vino Sundararajan
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India..
| | - Sajitha Lulu S
- Integrative Multi Omics Lab, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India..
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3
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Igiri BE, Okoduwa SIR, Munirat SA, Otu-Bassey IB, Bashir A, Onyiyioza OM, Enang IA, Okoduwa UJ. Diversity in Enteric Fever Diagnostic Protocols and Recommendation for Composite Reference Standard. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2023; 17:22-38. [DOI: 10.30699/ijmm.17.1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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4
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J Barton A, Hill J, J Blohmke C, J Pollard A. Host restriction, pathogenesis and chronic carriage of typhoidal Salmonella. FEMS Microbiol Rev 2021; 45:6159486. [PMID: 33733659 PMCID: PMC8498562 DOI: 10.1093/femsre/fuab014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 03/03/2021] [Indexed: 12/16/2022] Open
Abstract
While conjugate vaccines against typhoid fever have recently been recommended by the World Health Organization for deployment, the lack of a vaccine against paratyphoid, multidrug resistance and chronic carriage all present challenges for the elimination of enteric fever. In the past decade, the development of in vitro and human challenge models has resulted in major advances in our understanding of enteric fever pathogenesis. In this review, we summarise these advances, outlining mechanisms of host restriction, intestinal invasion, interactions with innate immunity and chronic carriage, and discuss how this knowledge may progress future vaccines and antimicrobials.
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Affiliation(s)
- Amber J Barton
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK.,Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Jennifer Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford OX3 7LE, UK.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
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5
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Dhingra D, Marathe SA, Sharma N, Marathe A, Chakravortty D. Modeling the immune response to Salmonella during typhoid. Int Immunol 2021; 33:281-298. [PMID: 33406267 DOI: 10.1093/intimm/dxab003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/05/2021] [Indexed: 11/13/2022] Open
Abstract
Several facets of the host immune response to Salmonella infection have been studied independently at great depths to understand the progress and pathogenesis of Salmonella infection. The circumstances under which a Salmonella-infected individual succumbs to an active disease, evolves as a persister or clears the infection are not understood in detail. We have adopted a system-level approach to develop a continuous-time mechanistic model. We considered key interactions of the immune system state variables with Salmonella in the mesenteric lymph node to determine the final disease outcome deterministically and exclusively temporally. The model accurately predicts the disease outcomes and immune response trajectories operational during typhoid. The results of the simulation confirm the role of anti-inflammatory (M2) macrophages as a site for persistence and relapsing infection. Global sensitivity analysis highlights the importance of both bacterial and host attributes in influencing the disease outcome. It also illustrates the importance of robust phagocytic and anti-microbial potential of M1 macrophages and dendritic cells (DCs) in controlling the disease. Finally, we propose therapeutic strategies for both antibiotic-sensitive and antibiotic-resistant strains (such as IFN-γ therapy, DC transfer and phagocytic potential stimulation). We also suggest prevention strategies such as improving the humoral response and macrophage carrying capacity, which could complement current vaccination schemes for enhanced efficiency.
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Affiliation(s)
- Divy Dhingra
- Department of Mechanical Engineering, Birla Institute of Technology & Science, Pilani, Rajasthan, India
| | - Sandhya Amol Marathe
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Rajasthan, India
| | - Nandita Sharma
- Department of Biological Sciences, Birla Institute of Technology & Science, Pilani, Rajasthan, India
| | - Amol Marathe
- Department of Mechanical Engineering, Birla Institute of Technology & Science, Pilani, Rajasthan, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
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Creighton R, Schuch V, Urbanski AH, Giddaluru J, Costa-Martins AG, Nakaya HI. Network vaccinology. Semin Immunol 2020; 50:101420. [PMID: 33162295 DOI: 10.1016/j.smim.2020.101420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/31/2020] [Indexed: 01/21/2023]
Abstract
The structure and function of the immune system is governed by complex networks of interactions between cells and molecular components. Vaccination perturbs these networks, triggering specific pathways to induce cellular and humoral immunity. Systems vaccinology studies have generated vast data sets describing the genes related to vaccination, motivating the use of new approaches to identify patterns within the data. Here, we describe a framework called Network Vaccinology to explore the structure and function of biological networks responsible for vaccine-induced immunity. We demonstrate how the principles of graph theory can be used to identify modules of genes, proteins, and metabolites that are associated with innate and adaptive immune responses. Network vaccinology can be used to assess specific and shared molecular mechanisms of different types of vaccines, adjuvants, and routes of administration to direct rational design of the next generation of vaccines.
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Affiliation(s)
- Rachel Creighton
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Viviane Schuch
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alysson H Urbanski
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jeevan Giddaluru
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Andre G Costa-Martins
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Scientific Platform Pasteur USP, São Paulo, Brazil
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil; Scientific Platform Pasteur USP, São Paulo, Brazil.
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7
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Baker S, Blohmke CJ, Maes M, Johnston PI, Darton TC. The Current Status of Enteric Fever Diagnostics and Implications for Disease Control. Clin Infect Dis 2020; 71:S64-S70. [PMID: 32725220 PMCID: PMC7388712 DOI: 10.1093/cid/ciaa503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Enteric (typhoid) fever remains a problem in low- and middle-income countries that lack the infrastructure to maintain sanitation and where inadequate diagnostic methods have restricted our ability to identify and control the disease more effectively. As we move into a period of potential disease elimination through the introduction of typhoid conjugate vaccine (TCV), we again need to reconsider the role of typhoid diagnostics in how they can aid in facilitating disease control. Recent technological advances, including serology, transcriptomics, and metabolomics, have provided new insights into how we can detect signatures of invasive Salmonella organisms interacting with the host during infection. Many of these new techniques exhibit potential that could be further explored with the aim of creating a new enteric fever diagnostic to work in conjunction with TCV. We need a sustained effort within the enteric fever field to accelerate, validate, and ultimately introduce 1 (or more) of these methods to facilitate the disease control initiative. The window of opportunity is still open, but we need to recognize the need for communication with other research areas and commercial organizations to assist in the progression of these diagnostic approaches. The elimination of enteric fever is now becoming a real possibility, but new diagnostics need to be part of the equation and factored into future calculations for disease control.
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Affiliation(s)
- Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Peter I Johnston
- Florey Institute for Host-Pathogen Interactions, Department for Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
| | - Thomas C Darton
- Florey Institute for Host-Pathogen Interactions, Department for Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry and Health, University of Sheffield, Sheffield, United Kingdom
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8
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Gonzalez-Dias P, Lee EK, Sorgi S, de Lima DS, Urbanski AH, Silveira EL, Nakaya HI. Methods for predicting vaccine immunogenicity and reactogenicity. Hum Vaccin Immunother 2019; 16:269-276. [PMID: 31869262 PMCID: PMC7062420 DOI: 10.1080/21645515.2019.1697110] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 12/28/2022] Open
Abstract
Subjects receiving the same vaccine often show different levels of immune responses and some may even present adverse side effects to the vaccine. Systems vaccinology can combine omics data and machine learning techniques to obtain highly predictive signatures of vaccine immunogenicity and reactogenicity. Currently, several machine learning methods are already available to researchers with no background in bioinformatics. Here we described the four main steps to discover markers of vaccine immunogenicity and reactogenicity: (1) Preparing the data; (2) Selecting the vaccinees and relevant genes; (3) Choosing the algorithm; (4) Blind testing your model. With the increasing number of Systems Vaccinology datasets being generated, we expect that the accuracy and robustness of signatures of vaccine reactogenicity and immunogenicity will significantly improve.
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Affiliation(s)
- Patrícia Gonzalez-Dias
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Eva K. Lee
- The Center for Operations Research in Medicine and HealthCare, Georgia Institute of Technology, Atlanta, GA, USA
| | - Sara Sorgi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Diógenes S. de Lima
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alysson H. Urbanski
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Eduardo Lv Silveira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
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9
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Blohmke CJ, Muller J, Gibani MM, Dobinson H, Shrestha S, Perinparajah S, Jin C, Hughes H, Blackwell L, Dongol S, Karkey A, Schreiber F, Pickard D, Basnyat B, Dougan G, Baker S, Pollard AJ, Darton TC. Diagnostic host gene signature for distinguishing enteric fever from other febrile diseases. EMBO Mol Med 2019; 11:e10431. [PMID: 31468702 PMCID: PMC6783646 DOI: 10.15252/emmm.201910431] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/30/2019] [Accepted: 08/09/2019] [Indexed: 12/19/2022] Open
Abstract
Misdiagnosis of enteric fever is a major global health problem, resulting in patient mismanagement, antimicrobial misuse and inaccurate disease burden estimates. Applying a machine learning algorithm to host gene expression profiles, we identified a diagnostic signature, which could distinguish culture-confirmed enteric fever cases from other febrile illnesses (area under receiver operating characteristic curve > 95%). Applying this signature to a culture-negative suspected enteric fever cohort in Nepal identified a further 12.6% as likely true cases. Our analysis highlights the power of data-driven approaches to identify host response patterns for the diagnosis of febrile illnesses. Expression signatures were validated using qPCR, highlighting their utility as PCR-based diagnostics for use in endemic settings.
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Affiliation(s)
- Christoph J Blohmke
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | | | - Malick M Gibani
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Hazel Dobinson
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Sonu Shrestha
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Soumya Perinparajah
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Celina Jin
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Harri Hughes
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Luke Blackwell
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Sabina Dongol
- Patan Academy of Healthy SciencesOxford University Clinical Research UnitKathmanduNepal
| | - Abhilasha Karkey
- Patan Academy of Healthy SciencesOxford University Clinical Research UnitKathmanduNepal
| | | | - Derek Pickard
- Infection Genomics ProgramThe Wellcome Trust Sanger InstituteHinxtonUK
| | - Buddha Basnyat
- Patan Academy of Healthy SciencesOxford University Clinical Research UnitKathmanduNepal
| | - Gordon Dougan
- Infection Genomics ProgramThe Wellcome Trust Sanger InstituteHinxtonUK
| | - Stephen Baker
- The Hospital for Tropical DiseasesWellcome Trust Major Overseas ProgrammeOxford University Clinical Research UnitHo Chi Minh CityVietnam
| | - Andrew J Pollard
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
| | - Thomas C Darton
- Department of PaediatricsCentre for Clinical Vaccinology and Tropical MedicineOxford Vaccine GroupOxfordUK
- Oxford National Institute of Health Research Biomedical CentreUniversity of OxfordOxfordUK
- The Hospital for Tropical DiseasesWellcome Trust Major Overseas ProgrammeOxford University Clinical Research UnitHo Chi Minh CityVietnam
- Department of Infection, Immunity and Cardiovascular DiseaseUniversity of SheffieldSheffieldUK
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10
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Abstract
BACKGROUND Typhoid fever and paratyphoid fever continue to be important causes of illness and death, particularly among children and adolescents in south-central and southeast Asia. Two typhoid vaccines are widely available, Ty21a (oral) and Vi polysaccharide (parenteral). Newer typhoid conjugate vaccines are at varying stages of development and use. The World Health Organization has recently recommended a Vi tetanus toxoid (Vi-TT) conjugate vaccine, Typbar-TCV, as the preferred vaccine for all ages. OBJECTIVES To assess the effects of vaccines for preventing typhoid fever. SEARCH METHODS In February 2018, we searched the Cochrane Infectious Diseases Group Specialized Register, CENTRAL, MEDLINE, Embase, LILACS, and mRCT. We also searched the reference lists of all included trials. SELECTION CRITERIA Randomized and quasi-randomized controlled trials (RCTs) comparing typhoid fever vaccines with other typhoid fever vaccines or with an inactive agent (placebo or vaccine for a different disease) in adults and children. Human challenge studies were not eligible. DATA COLLECTION AND ANALYSIS Two review authors independently applied inclusion criteria and extracted data, and assessed the certainty of the evidence using the GRADE approach. We computed vaccine efficacy per year of follow-up and cumulative three-year efficacy, stratifying for vaccine type and dose. The outcome addressed was typhoid fever, defined as isolation of Salmonella enterica serovar Typhi in blood. We calculated risk ratios (RRs) and efficacy (1 - RR as a percentage) with 95% confidence intervals (CIs). MAIN RESULTS In total, 18 RCTs contributed to the quantitative analysis in this review: 13 evaluated efficacy (Ty21a: 5 trials; Vi polysaccharide: 6 trials; Vi-rEPA: 1 trial; Vi-TT: 1 trial), and 9 reported on adverse events. All trials but one took place in typhoid-endemic countries. There was no information on vaccination in adults aged over 55 years of age, pregnant women, or travellers. Only one trial included data on children under two years of age.Ty21a vaccine (oral vaccine, three doses)A three-dose schedule of Ty21a vaccine probably prevents around half of typhoid cases during the first three years after vaccination (cumulative efficacy 2.5 to 3 years: 50%, 95% CI 35% to 61%, 4 trials, 235,239 participants, moderate-certainty evidence). These data include patients aged 3 to 44 years.Compared with placebo, this vaccine probably does not cause more vomiting, diarrhoea, nausea or abdominal pain (2 trials, 2066 participants; moderate-certainty evidence), headache, or rash (1 trial, 1190 participants; moderate-certainty evidence); however, fever (2 trials, 2066 participants; moderate-certainty evidence) is probably more common following vaccination.Vi polysaccharide vaccine (injection, one dose)A single dose of Vi polysaccharide vaccine prevents around two-thirds of typhoid cases in the first year after vaccination (year 1: 69%, 95% CI 63% to 74%; 3 trials, 99,979 participants; high-certainty evidence). In year 2, trial results were more variable, with the vaccine probably preventing between 45% and 69% of typhoid cases (year 2: 59%, 95% CI 45% to 69%; 4 trials, 194,969 participants; moderate-certainty evidence). These data included participants aged 2 to 55 years of age.The three-year cumulative efficacy of the vaccine may be around 55% (95% CI 30% to 70%; 11,384 participants, 1 trial; low-certainty evidence). These data came from a single trial conducted in South Africa in the 1980s in participants aged 5 to 15 years.Compared with placebo, this vaccine probably did not increase the incidence of fever (3 trials, 132,261 participants; moderate-certainty evidence) or erythema (3 trials, 132,261 participants; low-certainty evidence); however, swelling (3 trials, 1767 participants; moderate-certainty evidence) and pain at the injection site (1 trial, 667 participants; moderate-certainty evidence) were more common in the vaccine group.Vi-rEPA vaccine (two doses)Administration of two doses of the Vi-rEPA vaccine probably prevents between 50% and 96% of typhoid cases during the first two years after vaccination (year 1: 94%, 95% CI 75% to 99%; year 2: 87%, 95% CI 56% to 96%, 1 trial, 12,008 participants; moderate-certainty evidence). These data came from a single trial with children two to five years of age conducted in Vietnam.Compared with placebo, both the first and the second dose of this vaccine increased the risk of fever (1 trial, 12,008 and 11,091 participants, low-certainty evidence) and the second dose increase the incidence of swelling at the injection site (one trial, 11,091 participants, moderate-certainty evidence).Vi-TT vaccine (two doses)We are uncertain of the efficacy of administration of two doses of Vi-TT (PedaTyph) in typhoid cases in children during the first year after vaccination (year 1: 94%, 95% CI -1% to 100%, 1 trial, 1625 participants; very low-certainty evidence). These data come from a single cluster-randomized trial in children aged six months to 12 years and conducted in India. For single dose Vi-TT (Typbar-TCV), we found no efficacy trials evaluating the vaccine with natural exposure.There were no reported serious adverse effects in RCTs of any of the vaccines studied. AUTHORS' CONCLUSIONS The licensed Ty21a and Vi polysaccharide vaccines are efficacious in adults and children older than two years in endemic countries. The Vi-rEPA vaccine is just as efficacious, although data is only available for children. The new Vi-TT vaccine (PedaTyph) requires further evaluation to determine if it provides protection against typhoid fever. At the time of writing, there were only efficacy data from a human challenge setting in adults on the Vi-TT vaccine (Tybar), which clearly justify the ongoing field trials to evaluate vaccine efficacy.
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Affiliation(s)
- Rachael Milligan
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUKL3 5QA
| | - Mical Paul
- Rambam Health Care CampusDivision of Infectious DiseasesHa‐aliya 8 StHaifaIsrael33705
| | - Marty Richardson
- Liverpool School of Tropical MedicineCochrane Infectious Diseases GroupPembroke PlaceLiverpoolUKL3 5QA
| | - Ami Neuberger
- Rambam Health Care Campus and The Ruth and Bruce Rappaport Faculty of Medicine, Technion – Israel Institute of TechnologyDivision of Infectious DiseasesTel AvivIsrael
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Barton AJ, Hill J, Pollard AJ, Blohmke CJ. Transcriptomics in Human Challenge Models. Front Immunol 2017; 8:1839. [PMID: 29326715 PMCID: PMC5741696 DOI: 10.3389/fimmu.2017.01839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/05/2017] [Indexed: 12/22/2022] Open
Abstract
Human challenge models, in which volunteers are experimentally infected with a pathogen of interest, provide the opportunity to directly identify both natural and vaccine-induced correlates of protection. In this review, we highlight how the application of transcriptomics to human challenge studies allows for the identification of novel correlates and gives insight into the immunological pathways required to develop functional immunity. In malaria challenge trials for example, innate immune pathways appear to play a previously underappreciated role in conferring protective immunity. Transcriptomic analyses of samples obtained in human challenge studies can also deepen our understanding of the immune responses preceding symptom onset, allowing characterization of innate immunity and early gene signatures, which may influence disease outcome. Influenza challenge studies demonstrate that these gene signatures have diagnostic potential in the context of pandemics, in which presymptomatic diagnosis of at-risk individuals could allow early initiation of antiviral treatment and help limit transmission. Furthermore, gene expression analysis facilitates the identification of host factors contributing to disease susceptibility, such as C4BPA expression in enterotoxigenic Escherichia coli infection. Overall, these studies highlight the exceptional value of transcriptional data generated in human challenge trials and illustrate the broad impact molecular data analysis may have on global health through rational vaccine design and biomarker discovery.
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Affiliation(s)
- Amber J Barton
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Jennifer Hill
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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