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Braunack-Mayer L, Malinga J, Masserey T, Nekkab N, Sen S, Schellenberg D, Tchouatieu AM, Kelly SL, Penny MA. Design and selection of drug properties to increase the public health impact of next-generation seasonal malaria chemoprevention: a modelling study. Lancet Glob Health 2024; 12:e478-e490. [PMID: 38365418 PMCID: PMC10882206 DOI: 10.1016/s2214-109x(23)00550-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 02/18/2024]
Abstract
BACKGROUND Seasonal malaria chemoprevention (SMC) is recommended for disease control in settings with moderate to high Plasmodium falciparum transmission and currently depends on the administration of sulfadoxine-pyrimethamine plus amodiaquine. However, poor regimen adherence and the increased frequency of parasite mutations conferring sulfadoxine-pyrimethamine resistance might threaten the effectiveness of SMC. Guidance is needed to de-risk the development of drug compounds for malaria prevention. We aimed to provide guidance for the early prioritisation of new and alternative SMC drugs and their target product profiles. METHODS In this modelling study, we combined an individual-based malaria transmission model that has explicit parasite growth with drug pharmacokinetic and pharmacodynamic models. We modelled SMC drug attributes for several possible modes of action, linked to their potential public health impact. Global sensitivity analyses identified trade-offs between drug elimination half-life, maximum parasite killing effect, and SMC coverage, and optimisation identified minimum requirements to maximise malaria burden reductions. FINDINGS Model predictions show that preventing infection for the entire period between SMC cycles is more important than drug curative efficacy for clinical disease effectiveness outcomes, but similarly important for impact on prevalence. When children younger than 5 years receive four SMC cycles with high levels of coverage (ie, 69% of children receiving all cycles), drug candidates require a duration of protection half-life higher than 23 days (elimination half-life >10 days) to achieve reductions higher than 75% in clinical incidence and severe disease (measured over the intervention period in the target population, compared with no intervention across a range of modelled scenarios). High coverage is crucial to achieve these targets, requiring more than 60% of children to receive all SMC cycles and more than 90% of children to receive at least one cycle regardless of the protection duration of the drug. INTERPRETATION Although efficacy is crucial for malaria prevalence reductions, chemoprevention development should select drug candidates for their duration of protection to maximise burden reductions, with the duration half-life determining cycle timing. Explicitly designing or selecting drug properties to increase community uptake is paramount. FUNDING Bill & Melinda Gates Foundation and the Swiss National Science Foundation.
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Affiliation(s)
- Lydia Braunack-Mayer
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Josephine Malinga
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Thiery Masserey
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Narimane Nekkab
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Swapnoleena Sen
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - David Schellenberg
- Department of Disease Control, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sherrie L Kelly
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Melissa A Penny
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland; Telethon Kids Institute, Nedlands, WA, Australia; Centre for Child Health Research, The University of Western Australia, Perth, WA, Australia.
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Price DJ, Nekkab N, Monteiro WM, Villela DAM, Simpson JA, Lacerda MVG, White MT, Devine A. Tafenoquine following G6PD screening versus primaquine for the treatment of vivax malaria in Brazil: A cost-effectiveness analysis using a transmission model. PLoS Med 2024; 21:e1004255. [PMID: 38194420 PMCID: PMC10775976 DOI: 10.1371/journal.pmed.1004255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/29/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Malaria transmission modelling has demonstrated the potential impact of semiquantitative glucose-6-phosphate dehydrogenase (G6PD) testing and treatment with single-dose tafenoquine for Plasmodium vivax radical cure but has not investigated the associated costs. This study evaluated the cost-effectiveness of P. vivax treatment with tafenoquine after G6PD testing using a transmission model. METHODS AND FINDINGS We explored the cost-effectiveness of using tafenoquine after G6PD screening as compared to usual practice (7-day low-dose primaquine (0.5 mg/kg/day) without G6PD screening) in Brazil using a 10-year time horizon with 5% discounting considering 4 scenarios: (1) tafenoquine for adults only assuming 66.7% primaquine treatment adherence; (2) tafenoquine for adults and children aged >2 years assuming 66.7% primaquine adherence; (3) tafenoquine for adults only assuming 90% primaquine adherence; and (4) tafenoquine for adults only assuming 30% primaquine adherence. The incremental cost-effectiveness ratios (ICERs) were estimated by dividing the incremental costs by the disability-adjusted life years (DALYs) averted. These were compared to a willingness to pay (WTP) threshold of US$7,800 for Brazil, and one-way and probabilistic sensitivity analyses were performed. All 4 scenarios were cost-effective in the base case analysis using this WTP threshold with ICERs ranging from US$154 to US$1,836. One-way sensitivity analyses showed that the results were most sensitive to severity and mortality due to vivax malaria, the lifetime and number of semiquantitative G6PD analysers needed, cost per malaria episode and per G6PD test strips, and life expectancy. All scenarios had a 100% likelihood of being cost-effective at the WTP threshold. The main limitations of this study are due to parameter uncertainty around our cost estimates for low transmission settings, the costs of G6PD screening, and the severity of vivax malaria. CONCLUSIONS In our modelling study that incorporated impact on transmission, tafenoquine prescribed after a semiquantitative G6PD testing was highly likely to be cost-effective in Brazil. These results demonstrate the potential health and economic importance of ensuring safe and effective radical cure.
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Affiliation(s)
- David J. Price
- Department of Infectious Diseases, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Narimane Nekkab
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Wuelton M. Monteiro
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Daniel A. M. Villela
- Programa de Computacão Científica, Fundacão Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Julie A. Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Marcus V. G. Lacerda
- Instituto de Pesquisa Clínica Carlos Borborema, Fundação de Medicina Tropical Dr Heitor Vieira Dourado, Manaus, Brazil
- Instituto Leônidas & Maria Deane–ILMD, Fundação Oswaldo Cruz, Manaus, Brazil
| | - Michael T. White
- Institut Pasteur, Université de Paris, G5 Épidémiologie et Analyse des Maladies Infectieuses, Département de Santé Globale, F-75015 Paris, France
| | - Angela Devine
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Melbourne Health Economics, Centre for Health Policy, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
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Nekkab N, Obadia T, Monteiro WM, Lacerda MV, White M, Mueller I. Accelerating towards P. vivax elimination with a novel serological test-and-treat strategy: a modelling case study in Brazil. Lancet Reg Health Am 2023; 22:100511. [PMID: 37250687 PMCID: PMC10209700 DOI: 10.1016/j.lana.2023.100511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/05/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Background Plasmodium vivax malaria is challenging to control and eliminate. Treatment with radical cure drugs fails to target the hidden asymptomatic and hypnozoite reservoirs in populations. PvSeroTAT, a novel serological test-and-treat intervention using a serological diagnostic to screen hypnozoite carriers for radical cure eligibility and treatment, could accelerate P. vivax elimination. Methods Using a previously developed mathematical model of P. vivax transmission adapted to the Brazilian context as a case study for implementation, we evaluate the public health impact of various deployment strategies of PvSeroTAT as a mass campaign. We compare relative reductions in prevalence, cases averted, glucose-6-phosphate dehydrogenase (G6PD) tests, and treatment doses of PvSeroTAT campaigns to strengthened case management alone or mass drug administration (MDA) campaigns across different settings. Findings Deploying a single round of PvSeroTAT with 80% coverage to treat cases with a high efficacy radical cure regimen with primaquine is predicted to reduce point population prevalence by 22.5% [95% UI: 20.2%-24.8%] in a peri-urban setting with high transmission and by 25.2% [95% UI: 9.6%-42.2%] in an occupational setting with moderate transmission. In the latter example, while a single PvSeroTAT achieves 9.2% less impact on prevalence and averts 300 less cases per 100,000 than a single MDA (25.2% [95% UI: 9.6%-42.2%] point prevalence reduction versus 34.4% [95% UI: 24.9%-44%]), PvSeroTAT requires 4.6 times less radical cure treatments and G6PD tests. Layering strengthened case management and deploying four rounds of PvSeroTAT six months apart is predicted to reduce point prevalence by a mean of 74.1% [95% UI: 61.3%-86.3%] or more in low transmission settings with less than 10 cases per 1000 population. Interpretation Modelling predicts that mass campaigns with PvSeroTAT are predicted to reduce P. vivax parasite prevalence across a range of transmission settings and require fewer resources than MDA. In combination with strengthened case management, mass campaigns of serological test-and-treat interventions can accelerate towards P. vivax elimination. Funding This project was funded in part by the Bill and Melinda Gates Foundation and the National Health and Medical Research Council.
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Affiliation(s)
- Narimane Nekkab
- Institut Pasteur, Université Paris Cité, G5 Épidémiologie et Analyse des Maladies Infectieuses, Paris, France
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Thomas Obadia
- Institut Pasteur, Université Paris Cité, G5 Épidémiologie et Analyse des Maladies Infectieuses, Paris, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Wuelton M. Monteiro
- Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Manaus, Brazil
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
| | - Marcus V.G. Lacerda
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
| | - Michael White
- Institut Pasteur, Université Paris Cité, G5 Épidémiologie et Analyse des Maladies Infectieuses, Paris, France
| | - Ivo Mueller
- Population Health & Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
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Nekkab N, Malinga J, Braunack-Mayer L, Kelly SL, Miller RS, Penny MA. Modelling to inform next-generation medical interventions for malaria prevention and treatment. Commun Med (Lond) 2023; 3:41. [PMID: 36966272 PMCID: PMC10039673 DOI: 10.1038/s43856-023-00274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 03/10/2023] [Indexed: 03/27/2023] Open
Abstract
Global progress against malaria has stagnated and novel medical interventions to prevent malaria are needed to fill gaps in existing tools and improve protection against infection and disease. Candidate selection for next-generation interventions should be supported by the best available evidence. Target product profiles and preferred product characteristics play a key role in setting selection criteria requirements and early endorsement by health authorities. While clinical evidence and expert opinion often inform product development decisions, integrating modelling evidence early and iteratively into this process provides an opportunity to link product characteristics with expected public health outcomes. Population models of malaria transmission can provide a better understanding of which, and at what magnitude, key intervention characteristics drive public health impact, and provide quantitative evidence to support selection of use-cases, transmission settings, and deployment strategies. We describe how modelling evidence can guide and accelerate development of new malaria vaccines, monoclonal antibodies, and chemoprevention.
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Affiliation(s)
- Narimane Nekkab
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Josephine Malinga
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Lydia Braunack-Mayer
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sherrie L Kelly
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Melissa A Penny
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
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Nekkab N, Penny MA. Accelerated development of malaria monoclonal antibodies. Cell Rep Med 2022; 3:100786. [PMID: 36260982 PMCID: PMC9589116 DOI: 10.1016/j.xcrm.2022.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
L9LS, a potent and safe antimalarial monoclonal antibody, demonstrated 88% protective efficacy against infection in a phase 1 trial in healthy adults.1 These promising results are the first of many to usher in a potential new era of malaria prevention.
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Affiliation(s)
- Narimane Nekkab
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland,University of Basel, Basel, Switzerland
| | - Melissa A. Penny
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland,University of Basel, Basel, Switzerland,Corresponding author
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Rosado J, Carrasco-Escobar G, Nolasco O, Garro K, Rodriguez-Ferruci H, Guzman-Guzman M, Llanos-Cuentas A, Vinetz JM, Nekkab N, White MT, Mueller I, Gamboa D. Malaria transmission structure in the Peruvian Amazon through antibody signatures to Plasmodium vivax. PLoS Negl Trop Dis 2022; 16:e0010415. [PMID: 35533146 PMCID: PMC9119515 DOI: 10.1371/journal.pntd.0010415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 05/19/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The landscape of malaria transmission in the Peruvian Amazon is temporally and spatially heterogeneous, presenting different micro-geographies with particular epidemiologies. Most cases are asymptomatic and escape routine malaria surveillance based on light microscopy (LM). Following the implementation of control programs in this region, new approaches to stratify transmission and direct efforts at an individual and community level are needed. Antibody responses to serological exposure markers (SEM) to Plasmodium vivax have proven diagnostic performance to identify people exposed in the previous 9 months. METHODOLOGY We measured antibody responses against 8 SEM to identify recently exposed people and determine the transmission dynamics of P. vivax in peri-urban (Iquitos) and riverine (Mazán) communities of Loreto, communities that have seen significant recent reductions in malaria transmission. Socio-demographic, geo-reference, LM and qPCR diagnosis data were collected from two cross-sectional surveys. Spatial and multilevel analyses were implemented to describe the distribution of seropositive cases and the risk factors associated with exposure to P. vivax. PRINCIPAL FINDINGS Low local transmission was detected by qPCR in both Iquitos (5.3%) and Mazán (2.7%); however, seroprevalence indicated a higher level of (past) exposure to P. vivax in Mazán (56.5%) than Iquitos (38.2%). Age and being male were factors associated with high odds of being seropositive in both sites. Higher antibody levels were found in individuals >15 years old. The persistence of long-lived antibodies in these individuals could overestimate the detection of recent exposure. Antibody levels in younger populations (<15 years old) could be a better indicator of recent exposure to P. vivax. CONCLUSIONS The large number of current and past infections detected by SEMs allows for detailed local epidemiological analyses, in contrast to data from qPCR prevalence surveys which did not produce statistically significant associations. Serological surveillance will be increasingly important in the Peruvian Amazon as malaria transmission is reduced by continued control and elimination efforts.
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Affiliation(s)
- Jason Rosado
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
- Sorbonne Université, ED 393, Paris, France
- Infectious Disease Epidemiology and Analytics G5 Unit, Institut Pasteur, Paris, France
- * E-mail:
| | - Gabriel Carrasco-Escobar
- School of Public Health, University of California San Diego, La Jolla, California, United States of America
- Health Innovation Laboratory, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Peru
| | - Oscar Nolasco
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Katherine Garro
- Laboratorio de Malaria, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Mitchel Guzman-Guzman
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Llanos-Cuentas
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Narimane Nekkab
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
| | - Michael T. White
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
- Infectious Disease Epidemiology and Analytics G5 Unit, Institut Pasteur, Paris, France
| | - Ivo Mueller
- Unit of Malaria: Parasites and hosts, Institut Pasteur, Paris, France
- Department of Medical Biology, University of Melbourne, Melbourne, Australia
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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Huber JH, Koepfli C, España G, Nekkab N, White MT, Alex Perkins T. How radical is radical cure? Site-specific biases in clinical trials underestimate the effect of radical cure on Plasmodium vivax hypnozoites. Malar J 2021; 20:479. [PMID: 34930278 PMCID: PMC8686294 DOI: 10.1186/s12936-021-04017-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/08/2021] [Indexed: 12/01/2022] Open
Abstract
Background Plasmodium vivax blood-stage relapses originating from re-activating hypnozoites are a major barrier for control and elimination of this disease. Radical cure is a form of therapy capable of addressing this problem. Recent clinical trials of radical cure have yielded efficacy estimates ranging from 65 to 94%, with substantial variation across trial sites. Methods An analysis of simulated trial data using a transmission model was performed to demonstrate that variation in efficacy estimates across trial sites can arise from differences in the conditions under which trials are conducted. Results The analysis revealed that differences in transmission intensity, heterogeneous exposure and relapse rate can yield efficacy estimates ranging as widely as 12–78%, despite simulating trial data under the uniform assumption that treatment had a 75% chance of clearing hypnozoites. A longer duration of prophylaxis leads to a greater measured efficacy, particularly at higher transmission intensities, making the comparison between the protection of different radical cure treatment regimens against relapse more challenging. Simulations show that vector control and parasite genotyping offer two potential means to yield more standardized efficacy estimates that better reflect prevention of relapse. Conclusions Site-specific biases are likely to contribute to variation in efficacy estimates both within and across clinical trials. Future clinical trials can reduce site-specific biases by conducting trials in low-transmission settings where re-infections from mosquito bite are less common, by preventing re-infections using vector control measures, or by identifying and excluding likely re-infections that occur during follow-up, by using parasite genotyping methods. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-021-04017-1.
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Affiliation(s)
- John H Huber
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
| | - Cristian Koepfli
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Guido España
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
| | - Narimane Nekkab
- Unité Malaria: Parasites et Hôtes, Département Parasites et Insectes Vecteur, Institut Pasteur, Paris, France
| | - Michael T White
- Unité Malaria: Parasites et Hôtes, Département Parasites et Insectes Vecteur, Institut Pasteur, Paris, France
| | - T Alex Perkins
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA
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Chotirat S, Nekkab N, Kumpitak C, Hietanen J, White MT, Kiattibutr K, Sa-angchai P, Brewster J, Schoffer K, Takashima E, Tsuboi T, Harbers M, Chitnis CE, Healer J, Tham WH, Nguitragool W, Mueller I, Sattabongkot J, Longley RJ. Application of 23 Novel Serological Markers for Identifying Recent Exposure to Plasmodium vivax Parasites in an Endemic Population of Western Thailand. Front Microbiol 2021; 12:643501. [PMID: 34276583 PMCID: PMC8279756 DOI: 10.3389/fmicb.2021.643501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/03/2021] [Indexed: 01/24/2023] Open
Abstract
Thailand is aiming for malaria elimination by the year 2030. However, the high proportion of asymptomatic infections and the presence of the hidden hypnozoite stage of Plasmodium vivax are impeding these efforts. We hypothesized that a validated surveillance tool utilizing serological markers of recent exposure to P. vivax infection could help to identify areas of ongoing transmission. The objective of this exploratory study was to assess the ability of P. vivax serological exposure markers to detect residual transmission "hot-spots" in Western Thailand. Total IgG levels were measured against a panel of 23 candidate P. vivax serological exposure markers using a multiplexed bead-based assay. A total of 4,255 plasma samples from a cross-sectional survey conducted in 2012 of endemic areas in the Kanchanaburi and Ratchaburi provinces were assayed. We compared IgG levels with multiple epidemiological factors that are associated with an increased risk of P. vivax infection in Thailand, including age, gender, and spatial location, as well as Plasmodium infection status itself. IgG levels to all proteins were significantly higher in the presence of a P. vivax infection (n = 144) (T-test, p < 0.0001). Overall seropositivity rates varied from 2.5% (PVX_097625, merozoite surface protein 8) to 16.8% (PVX_082670, merozoite surface protein 7), with 43% of individuals seropositive to at least 1 protein. Higher IgG levels were associated with older age (>18 years, p < 0.05) and males (17/23 proteins, p < 0.05), supporting the paradigm that men have a higher risk of infection than females in this setting. We used a Random Forests algorithm to predict which individuals had exposure to P. vivax parasites in the last 9-months, based on their IgG antibody levels to a panel of eight previously validated P. vivax proteins. Spatial clustering was observed at the village and regional level, with a moderate correlation between PCR prevalence and sero-prevalence as predicted by the algorithm. Our data provides proof-of-concept for application of such surrogate markers as evidence of recent exposure in low transmission areas. These data can be used to better identify geographical areas with asymptomatic infection burdens that can be targeted in elimination campaigns.
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Affiliation(s)
- Sadudee Chotirat
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narimane Nekkab
- Malaria Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Chalermpon Kumpitak
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jenni Hietanen
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Michael T. White
- Malaria Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Kirakorn Kiattibutr
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Patiwat Sa-angchai
- Department of Tropical Hygiene, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jessica Brewster
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Kael Schoffer
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Eizo Takashima
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Takafumi Tsuboi
- Division of Malaria Research, Proteo-Science Center, Ehime University, Matsuyama, Japan
| | - Matthias Harbers
- CellFree Sciences Co., Ltd., Yokohama, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chetan E. Chitnis
- Malaria Parasite Biology and Vaccines Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Julie Healer
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Wai-Hong Tham
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Wang Nguitragool
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ivo Mueller
- Malaria Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rhea J. Longley
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
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9
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Roux J, Nekkab N, Colomb-Cotinat M, Astagneau P, Crépey P. Time-series modelling for the quantification of seasonality and forecasting antibiotic-resistant episodes: application to carbapenemase-producing Enterobacteriaceae episodes in France over 2010-20. J Antimicrob Chemother 2021; 76:226-232. [PMID: 32929455 DOI: 10.1093/jac/dkaa388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/17/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Carbapenemase-producing Enterobacteriaceae (CPE) cause resistant healthcare-associated infections that jeopardize healthcare systems and patient safety worldwide. The number of CPE episodes has been increasing in France since 2009, but the dynamics are still poorly understood. OBJECTIVES To use time-series modelling to describe the dynamics of CPE episodes from August 2010 to December 2016 and to forecast the evolution of CPE episodes for the 2017-20 period. METHODS We used time series to analyse CPE episodes from August 2010 to November 2016 reported to the French national surveillance system. The impact of seasonality was quantified using seasonal-to-irregular ratios. Seven time-series models and three ensemble stacking models (average, convex and linear stacking) were assessed and compared with forecast CPE episodes during 2017-20. RESULTS During 2010-16, 3559 CPE episodes were observed in France. Compared with the average yearly trend, we observed a 30% increase in the number of CPE episodes in the autumn. We noticed a 1 month lagged seasonality of non-imported episodes compared with imported episodes. Average stacking gave the best forecasts and predicted an increase during 2017-20 with a peak up to 345 CPE episodes (95% prediction interval = 124-1158, 80% prediction interval = 171-742) in September 2020. CONCLUSIONS The observed seasonality of CPE episodes sheds light on potential factors associated with the increased frequency of episodes, which need further investigation. Our model predicts that the number of CPE episodes will continue to rise in the coming years in France, mainly due to local dissemination, associated with bacterial carriage by patients in the community, which is becoming an immediate challenge with regard to outbreak control.
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Affiliation(s)
- Jonathan Roux
- Univ Rennes, EHESP, REPERES (Pharmacoepidemiology and health services research) - EA 7449, Rennes, France
| | - Narimane Nekkab
- Laboratoire MESuRS, Conservatoire National des Arts et Métiers, Paris, France.,Institut Pasteur, Cnam, Unité PACRI, Paris, France
| | | | - Pascal Astagneau
- Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Paris, France.,Centre de prévention des infections associées aux soins, Paris, France
| | - Pascal Crépey
- Univ Rennes, EHESP, REPERES (Pharmacoepidemiology and health services research) - EA 7449, Rennes, France
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10
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Watson JA, Nekkab N, White M. Tafenoquine for the prevention of Plasmodium vivax malaria relapse. The Lancet Microbe 2021; 2:e175-e176. [DOI: 10.1016/s2666-5247(21)00062-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 11/29/2022] Open
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11
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Nekkab N, Lana R, Lacerda M, Obadia T, Siqueira A, Monteiro W, Villela D, Mueller I, White M. Estimated impact of tafenoquine for Plasmodium vivax control and elimination in Brazil: A modelling study. PLoS Med 2021; 18:e1003535. [PMID: 33891582 PMCID: PMC8064585 DOI: 10.1371/journal.pmed.1003535] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/06/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Despite recent intensification of control measures, Plasmodium vivax poses a major challenge for malaria elimination efforts. Liver-stage hypnozoite parasites that cause relapsing infections can be cleared with primaquine; however, poor treatment adherence undermines drug effectiveness. Tafenoquine, a new single-dose treatment, offers an alternative option for preventing relapses and reducing transmission. In 2018, over 237,000 cases of malaria were reported to the Brazilian health system, of which 91.5% were due to P. vivax. METHODS AND FINDINGS We evaluated the impact of introducing tafenoquine into case management practices on population-level transmission dynamics using a mathematical model of P. vivax transmission. The model was calibrated to reflect the transmission dynamics of P. vivax endemic settings in Brazil in 2018, informed by nationwide malaria case reporting data. Parameters for treatment pathways with chloroquine, primaquine, and tafenoquine with glucose-6-phosphate dehydrogenase deficiency (G6PDd) testing were informed by clinical trial data and the literature. We assumed 71.3% efficacy for primaquine and tafenoquine, a 66.7% adherence rate to the 7-day primaquine regimen, a mean 5.5% G6PDd prevalence, and 8.1% low metaboliser prevalence. The introduction of tafenoquine is predicted to improve effective hypnozoite clearance among P. vivax cases and reduce population-level transmission over time, with heterogeneous levels of impact across different transmission settings. According to the model, while achieving elimination in only few settings in Brazil, tafenoquine rollout in 2021 is estimated to improve the mean effective radical cure rate from 42% (95% uncertainty interval [UI] 41%-44%) to 62% (95% UI 54%-68%) among clinical cases, leading to a predicted 38% (95% UI 7%-99%) reduction in transmission and over 214,000 cumulative averted cases between 2021 and 2025. Higher impact is predicted in settings with low transmission, low pre-existing primaquine adherence, and a high proportion of cases in working-aged males. High-transmission settings with a high proportion of cases in children would benefit from a safe high-efficacy tafenoquine dose for children. Our methodological limitations include not accounting for the role of imported cases from outside the transmission setting, relying on reported clinical cases as a measurement of community-level transmission, and implementing treatment efficacy as a binary condition. CONCLUSIONS In our modelling study, we predicted that, provided there is concurrent rollout of G6PDd diagnostics, tafenoquine has the potential to reduce P. vivax transmission by improving effective radical cure through increased adherence and increased protection from new infections. While tafenoquine alone may not be sufficient for P. vivax elimination, its introduction will improve case management, prevent a substantial number of cases, and bring countries closer to achieving malaria elimination goals.
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Affiliation(s)
- Narimane Nekkab
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Raquel Lana
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Marcus Lacerda
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- Instituto Leônidas e Maria Deane, Fundação Oswaldo Cruz, Manaus, Brazil
| | - Thomas Obadia
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - André Siqueira
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Wuelton Monteiro
- Diretoria de Ensino e Pesquisa, Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Brazil
- School of Health Sciences, Universidade do Estado do Amazonas, Manaus, Brazil
| | - Daniel Villela
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ivo Mueller
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- Population Health & Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Michael White
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
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12
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Lana R, Nekkab N, Siqueira AM, Peterka C, Marchesini P, Lacerda M, Mueller I, White M, Villela D. The top 1%: quantifying the unequal distribution of malaria in Brazil. Malar J 2021; 20:87. [PMID: 33579298 PMCID: PMC7880522 DOI: 10.1186/s12936-021-03614-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background As malaria endemic countries strive towards elimination, intensified spatial heterogeneities of local transmission could undermine the effectiveness of traditional intervention policy. Methods The dynamic nature of large-scale and long-term malaria heterogeneity across Brazilian Amazon basin were explored by (1) exploratory analysis of Brazil’s rich clinical malaria reporting database from 2004 to 2018, and (2) adapting Gini coefficient to study the distribution of malaria cases in the region. Results As transmission declined, heterogeneity increased with cases clustering into smaller subpopulations across the territory. In 2004, the 1% of health units with the greatest number of cases accounted for 46% of all reported Plasmodium vivax cases, whereas in 2018 52% of P. vivax cases occurred in the top 1% of health units. Plasmodium falciparum had lower levels of transmission than P. vivax, and also had greater levels of heterogeneity with 75% of cases occurring in the top 1% of health units. Age and gender stratification of cases revealed peri-domestic and occupational exposure settings that remained relatively stable. Conclusion The pathway to decreasing incidence is characterized by higher proportions of cases in males, in adults, due to importation, and caused by P. vivax. Characterization of spatio-temporal heterogeneity and risk groups can aid stratification for improved malaria control towards elimination with increased heterogeneity potentially allowing for more efficient and cost-effective targeting. Although distinct epidemiological phenomena were clearly observed as malaria transmission declines, the authors argue that there is no canonical path to malaria elimination and a more targeted and dynamic surveillance will be needed if Brazil decides to adopt the elimination target.
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Affiliation(s)
- Raquel Lana
- Scientific Computing Programme, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-360, Brazil
| | - Narimane Nekkab
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Andre M Siqueira
- Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-360, Brazil
| | - Cassio Peterka
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, AM, Brasil.,Programa de Pós-Graduação Em Medicina Tropical, Universidade Do Estado Do Amazonas, Manaus, AM, Brasil.,Programa Nacional de Controle da Malária, Ministério da Saúde, Brasília, DF, Brasil
| | - Paola Marchesini
- Department of Transmissible Diseases Surveillance, Ministry of Health, Brasília, Brazil
| | - Marcus Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, AM, Brasil.,Programa de Pós-Graduação Em Medicina Tropical, Universidade Do Estado Do Amazonas, Manaus, AM, Brasil.,Instituto de Pesquisas Leônidas and Maria Deane, Fundação Oswaldo Cruz, Manaus, AM, Brasil
| | - Ivo Mueller
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.,Division of Population Health and Immunity, Walter and Eliza Hall Institute, Melbourne, Australia
| | - Michael White
- Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France.
| | - Daniel Villela
- Scientific Computing Programme, Fundação Oswaldo Cruz, Rio de Janeiro, 21040-360, Brazil.
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13
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Rosado J, Pelleau S, Cockram C, Merkling SH, Nekkab N, Demeret C, Meola A, Kerneis S, Terrier B, Fafi-Kremer S, de Seze J, Bruel T, Dejardin F, Petres S, Longley R, Fontanet A, Backovic M, Mueller I, White MT. Multiplex assays for the identification of serological signatures of SARS-CoV-2 infection: an antibody-based diagnostic and machine learning study. Lancet Microbe 2021; 2:e60-e69. [PMID: 33521709 PMCID: PMC7837364 DOI: 10.1016/s2666-5247(20)30197-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induces an antibody response targeting multiple antigens that changes over time. This study aims to take advantage of this complexity to develop more accurate serological diagnostics. METHODS A multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples collected up to 39 days after symptom onset from 215 adults in four French hospitals (53 patients and 162 health-care workers) with quantitative RT-PCR-confirmed SARS-CoV-2 infection, and negative control serum samples collected from healthy adult blood donors before the start of the SARS-CoV-2 epidemic (335 samples from France, Thailand, and Peru). Machine learning classifiers were trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection, with the best classification performance displayed by a random forests algorithm. A Bayesian mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate time-varying antibody responses and assess the sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low-transmission settings. FINDINGS IgG antibody responses to trimeric spike protein (Stri) identified individuals with previous SARS-CoV-2 infection with 91·6% (95% CI 87·5-94·5) sensitivity and 99·1% (97·4-99·7) specificity. Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98·8% (96·5-99·6) sensitivity and 99·3% (97·6-99·8) specificity. Informed by existing data from other coronaviruses, we estimate that 1 year after infection, a monoplex assay with optimal anti-Stri IgG cutoff has 88·7% (95% credible interval 63·4-97·4) sensitivity and that a four-antigen multiplex assay can increase sensitivity to 96·4% (80·9-100·0). When applied to population-level serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 2%, below the false-positivity rate of many other assays. INTERPRETATION Serological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected more than 6 months ago and measuring seroprevalence in serological surveys in very low-transmission settings. FUNDING European Research Council. Fondation pour la Recherche Médicale. Institut Pasteur Task Force COVID-19.
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Affiliation(s)
- Jason Rosado
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- ED 393, Sorbonne Université, Paris, France
| | - Stéphane Pelleau
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Charlotte Cockram
- Spatial Regulation of Genomes Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Sarah Hélène Merkling
- Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Narimane Nekkab
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Caroline Demeret
- Molecular Genetics of RNA Viruses Unit, Department of Virology, Institut Pasteur, Paris, France
| | - Annalisa Meola
- Structural Virology Unit, Department of Virology and CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Solen Kerneis
- Epidemiology and Modelling of Bacterial Escape to Antimicrobials Unit, Department of Global Health, Institut Pasteur, Paris, France
- Equipe Mobile d'Infectiologie, APHP Centre-Université de Paris, Paris, France
| | - Benjamin Terrier
- Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hôpitaux de Paris-Centre (APHP-CUP), Université de Paris, Paris, France
- Paris-Cardiovascular Research Center, INSERM U970, Paris, France
| | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France
- Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Jerome de Seze
- Centre d'Investigation Clinique - INSERM CIC-1434, Strasbourg, France
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, Paris, France
- Vaccine Research Institute, Creteil, France
| | - François Dejardin
- Production and Purification of Recombinant Proteins Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Stéphane Petres
- Production and Purification of Recombinant Proteins Technological Platform, Center for Technological Resources and Research, Institut Pasteur, Paris, France
| | - Rhea Longley
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Arnaud Fontanet
- Epidemiology of Emerging Diseases Unit, Department of Global Health, Institut Pasteur, Paris, France
| | - Marija Backovic
- Structural Virology Unit, Department of Virology and CNRS UMR 3569, Institut Pasteur, Paris, France
| | - Ivo Mueller
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
- Division of Population Health and Immunity, The Walter and Eliza Hall Institute, Melbourne, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Michael T White
- Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
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14
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Duchemin T, Bastard J, Ante-Testard PA, Assab R, Daouda OS, Duval A, Garsi JP, Lounissi R, Nekkab N, Neynaud H, Smith DRM, Dab W, Jean K, Temime L, Hocine MN. Monitoring sick leave data for early detection of influenza outbreaks. BMC Infect Dis 2021; 21:52. [PMID: 33430793 PMCID: PMC7799403 DOI: 10.1186/s12879-020-05754-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/28/2020] [Indexed: 12/03/2022] Open
Abstract
Background Workplace absenteeism increases significantly during influenza epidemics. Sick leave records may facilitate more timely detection of influenza outbreaks, as trends in increased sick leave may precede alerts issued by sentinel surveillance systems by days or weeks. Sick leave data have not been comprehensively evaluated in comparison to traditional surveillance methods. The aim of this paper is to study the performance and the feasibility of using a detection system based on sick leave data to detect influenza outbreaks. Methods Sick leave records were extracted from private French health insurance data, covering on average 209,932 companies per year across a wide range of sizes and sectors. We used linear regression to estimate the weekly number of new sick leave spells between 2016 and 2017 in 12 French regions, adjusting for trend, seasonality and worker leaves on historical data from 2010 to 2015. Outbreaks were detected using a 95%-prediction interval. This method was compared to results from the French Sentinelles network, a gold-standard primary care surveillance system currently in place. Results Using sick leave data, we detected 92% of reported influenza outbreaks between 2016 and 2017, on average 5.88 weeks prior to outbreak peaks. Compared to the existing Sentinelles model, our method had high sensitivity (89%) and positive predictive value (86%), and detected outbreaks on average 2.5 weeks earlier. Conclusion Sick leave surveillance could be a sensitive, specific and timely tool for detection of influenza outbreaks. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05754-5.
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Affiliation(s)
- Tom Duchemin
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France. .,Malakoff Humanis, 21 Rue Laffitte, 75009, Paris, France.
| | - Jonathan Bastard
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,PACRI unit, Conservatoire National des Arts et Métiers, Institut Pasteur, Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
| | - Pearl Anne Ante-Testard
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,PACRI unit, Conservatoire National des Arts et Métiers, Institut Pasteur, Paris, France
| | - Rania Assab
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France
| | - Oumou Salama Daouda
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France
| | - Audrey Duval
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France.,Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Jérôme-Philippe Garsi
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France
| | | | - Narimane Nekkab
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,Malaria: Parasites and Hosts, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Helene Neynaud
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France
| | - David R M Smith
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
| | - William Dab
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France
| | - Kevin Jean
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,PACRI unit, Conservatoire National des Arts et Métiers, Institut Pasteur, Paris, France
| | - Laura Temime
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France.,PACRI unit, Conservatoire National des Arts et Métiers, Institut Pasteur, Paris, France
| | - Mounia N Hocine
- MESuRS laboratory, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, 75003, Paris, France
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15
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Nekkab N, Crépey P, Astagneau P, Opatowski L, Temime L. Assessing the role of inter-facility patient transfer in the spread of carbapenemase-producing Enterobacteriaceae: the case of France between 2012 and 2015. Sci Rep 2020; 10:14910. [PMID: 32913244 PMCID: PMC7483561 DOI: 10.1038/s41598-020-71212-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 07/31/2020] [Indexed: 11/09/2022] Open
Abstract
The spread of carbapenemase-producing Enterobacteriaceae (CPE) in healthcare settings is a major public health threat that has been associated with cross-border and local patient transfers between healthcare facilities. Since the impact of transfers on spread may vary, our study aimed to assess the contribution of a patient transfer network on CPE incidence and spread at a countrywide level, with a case study of France from 2012 to 2015. Our results suggest a transition in 2013 from a CPE epidemic sustained by internationally imported episodes to an epidemic sustained by local transmission events through patient transfers. Incident episodes tend to occur within close spatial distance of their potential infector. We also observe an increasing frequency of multiple spreading events, originating from a limited number of regional hubs. Consequently, coordinated prevention and infection control strategies should focus on transfers of carriers of CPE to reduce regional and inter-regional transmission.
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Affiliation(s)
- Narimane Nekkab
- Laboratoire MESuRS, Conservatoire National Des Arts Et Métiers, Paris, France. .,Unité PACRI, Institut Pasteur, Conservatoire National Des Arts Et Métiers, Paris, France. .,EHESP, REPERES (Recherche en pharmaco-épidémiologie et recours aux soins) - EA 7449, University Rennes, Rennes, France.
| | - Pascal Crépey
- EHESP, REPERES (Recherche en pharmaco-épidémiologie et recours aux soins) - EA 7449, University Rennes, Rennes, France
| | - Pascal Astagneau
- Centre régional de prévention Des Infections associées Aux Soins (CPias), Paris, France.,INSERM, Institut Pierre Louis D'Epidémiologie Et de Santé Publique, Sorbonne Université, 75013, Paris, France
| | - Lulla Opatowski
- UMR 1181, «Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases» (B2PHI), University Versailles Saint Quentin en Yvelines, Saint Quentin en Yvelines, France.,Pharmacoepidemiology and Infectious Diseases Unit, Institut Pasteur, Paris, France.,Inserm UMR 1181 (B2PHI), Paris, France
| | - Laura Temime
- Laboratoire MESuRS, Conservatoire National Des Arts Et Métiers, Paris, France.,Unité PACRI, Institut Pasteur, Conservatoire National Des Arts Et Métiers, Paris, France
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16
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Tan BK, Crabol Y, Tasse J, Laurent F, Nekkab N, Vinter C, Puéchal X, Guillevin L. No evident association of nasal carriage of Staphylococcus aureus or its small-colony variants with cotrimoxazole use or ANCA-associated vasculitis relapses. Rheumatology (Oxford) 2020; 59:77-83. [PMID: 31834404 DOI: 10.1093/rheumatology/kez236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/14/2019] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE To identify the role of Staphylococcus aureus (SA) or its intracellular small-colony variant phenotype (SCV) with co-trimoxazole (CTX) or ANCA-associated vasculitis (AAV) activity. METHODS All consecutive AAV patients with granulomatosis with polyangiitis (GPA), eosinophilic GPA or microscopic polyangiitis, followed at the French National Vasculitis Referral Center (09/2012-05/2013), and hospitalized non-AAV controls, exclusively for SA/SCV carriage comparisons, were enrolled. All had bilateral anterior nasal swab cultures. Nasal SA or SCV carriage was determined and associations with relapse(s), BVAS, ANCA-positivity, anti-staphylococcal and immunosuppressant use, were analysed ⩾4 years post-inclusion. RESULTS Nasal SA carriage rates did not differ among AAVs (P = 0.53): GPA (24/80; 30%), EGPA (7/28; 25%) and microscopic polyangiitis (3/11; 27.3%); and the rate was less frequent in controls than in GPA patients not taking CTX (P = 0.04). AAV patients taking CTX prophylaxis had less nasal SA carriage (8.7% vs 36.2%; P = 0.02). Nasal SA carriage or CTX use did not modify relapse rates, BVAS or ANCA-positivity at inclusion or during follow-up. Nasal SCV carriage, found in 15/207 (7.2%) patients, was similar for GPA (10/24; 41.7%), microscopic polyangiitis (2/7; 28.6%) and eosinophilic GPA (2/3; 66.7%), but higher (P = 0.02) than controls (1/14; 7.1%). SCV carriage by AAV groups did not modify relapse rates or ANCA positivity at inclusion or during follow-up; a trend towards higher BVAS was observed only for anti-PR3 ANCA patients. CONCLUSION Nasal SA or SCV carriage was comparable among AAVs but more frequent than in controls. Nasal SA or SCV carriage and CTX use did not modify AAV relapse rates.
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Affiliation(s)
- Boun Kim Tan
- Department of Internal Medicine, Referral Center for Rare Systemic and Autoimmune Diseases, Hôpital Cochin, APHP, Université Paris-Descartes, Paris Cedex 14, France
| | - Yoann Crabol
- Department of Internal Medicine, Referral Center for Rare Systemic and Autoimmune Diseases, Hôpital Cochin, APHP, Université Paris-Descartes, Paris Cedex 14, France
| | - Jason Tasse
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, International Center of Infectiology Research, Lyon, France
| | - Frédéric Laurent
- Department of Microbiology, French National Reference Centre for Staphylococci, Hospices Civils de Lyon, International Center of Infectiology Research, Lyon, France
| | - Narimane Nekkab
- Conservatoire National des Arts et Métiers, MESuRS Laboratory, Paris, France
| | - Christine Vinter
- Department of Internal Medicine, Referral Center for Rare Systemic and Autoimmune Diseases, Hôpital Cochin, APHP, Université Paris-Descartes, Paris Cedex 14, France
| | - Xavier Puéchal
- Department of Internal Medicine, Referral Center for Rare Systemic and Autoimmune Diseases, Hôpital Cochin, APHP, Université Paris-Descartes, Paris Cedex 14, France
| | - Loïc Guillevin
- Department of Internal Medicine, Referral Center for Rare Systemic and Autoimmune Diseases, Hôpital Cochin, APHP, Université Paris-Descartes, Paris Cedex 14, France
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Roux J, Nekkab N, Astagneau P, Crépey P. Modeling Carbapenemase-producing Enterobacteriaceae episodes’ evolution in France over 2010-2020. Eur J Public Health 2019. [DOI: 10.1093/eurpub/ckz185.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Incidence of Carbapenemase-Producing Enterobacteriaceae (CPE) episodes within hospitals is rising at an alarming rate and threaten health systems and patient safety worldwide. Their number is growing in France since 2009 associated with inter-regional dissemination and importation of international cases. This study aimed at describing the dynamics of CPE episodes in France over 2010-2016 and forecasting their evolution for 2017-2020.
Methods
Surveillance data of CPE episodes (imported and non-imported) from August 2010 to November 2016 were issued from the French national Healthcare-Associated Infections Early Warning and Response System. Impact of seasonality on the number of CPE episodes was analyzed using seasonal-to-irregular ratios. Seven models issued from time series analysis and three ensemble stacking models (average, convex and linear stacking) were used to describe and forecast CPE episodes. The model with the best forecasting’s quality was then trained on all available data (2010-2016) and used to predict CPE episodes over 2017-2020.
Results
Over 2010-2016, 3,559 CPE episodes were observed in France. Compared to the average yearly trend, we observed a 30% increase in the number of CPE episodes in September and October. On the opposite, a decrease of 20% was noticed in February compared to other months. We also noticed a 1-month lagged seasonality of non-imported episodes compared to imported ones. The number of non-imported episodes appeared to grow faster than imported ones starting from 2014. Average stacking gave the best forecasts and predicted an increase over 2017-2020 with a peak up to 345 CPE episodes (95% PI [124-1,158], 80% PI [171-742]) in September 2020.
Conclusions
The number of CPE episodes is predicted to rise in the next years in France because of non-imported episodes. These results could help public health authorities in the definition and evaluation of new containment strategies.
Key messages
Time series modeling predicts an increase in the number of CPE episodes in France in the next few years with a quicker rise of non-imported episodes. An increase of 30% in the number of CPE episodes was observed in September and October with a 1-month lagged seasonality impact of non-imported episodes compared to imported one.
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Affiliation(s)
- J Roux
- REPERES - EA 7449, University of Rennes, EHESP, Rennes, France
| | - N Nekkab
- Laboratoire MESuRS, Conservatoire National des Arts et Métiers (CNAM), Paris, France
- Unité PACRI, Institut Pasteur, CNAM, Paris, France
| | - P Astagneau
- CPias Ile-de-France, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine Pierre & Marie Curie, Sorbonne Université, Paris, France
| | - P Crépey
- REPERES - EA 7449, University of Rennes, EHESP, Rennes, France
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Nekkab N, Crépey P, Temime L. Assessing the role of a patient transfer network in the spread of carbapenemase-producing Enterobacteriaceae: The case of France between 2012 and 2015. Rev Epidemiol Sante Publique 2018. [DOI: 10.1016/j.respe.2018.05.080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Nekkab N, Astagneau P, Temime L, Crépey P. Spread of hospital-acquired infections: A comparison of healthcare networks. PLoS Comput Biol 2017; 13:e1005666. [PMID: 28837555 PMCID: PMC5570216 DOI: 10.1371/journal.pcbi.1005666] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 07/03/2017] [Indexed: 11/20/2022] Open
Abstract
Hospital-acquired infections (HAIs), including emerging multi-drug resistant organisms, threaten healthcare systems worldwide. Efficient containment measures of HAIs must mobilize the entire healthcare network. Thus, to best understand how to reduce the potential scale of HAI epidemic spread, we explore patient transfer patterns in the French healthcare system. Using an exhaustive database of all hospital discharge summaries in France in 2014, we construct and analyze three patient networks based on the following: transfers of patients with HAI (HAI-specific network); patients with suspected HAI (suspected-HAI network); and all patients (general network). All three networks have heterogeneous patient flow and demonstrate small-world and scale-free characteristics. Patient populations that comprise these networks are also heterogeneous in their movement patterns. Ranking of hospitals by centrality measures and comparing community clustering using community detection algorithms shows that despite the differences in patient population, the HAI-specific and suspected-HAI networks rely on the same underlying structure as that of the general network. As a result, the general network may be more reliable in studying potential spread of HAIs. Finally, we identify transfer patterns at both the French regional and departmental (county) levels that are important in the identification of key hospital centers, patient flow trajectories, and regional clusters that may serve as a basis for novel wide-scale infection control strategies. Hospital-acquired infections (HAIs), including emerging multi-drug resistant organisms, threaten healthcare systems worldwide. Efficient containment measures of HAIs must mobilize the entire healthcare network. Thus, to best understand how to reduce the scale of potential HAI epidemic spread, we explore patient transfer patterns in the French healthcare system. We construct and compare the characteristics of three different patient transfer networks based on data on transfers of patients with diagnosed HAIs, suspected HAIs, or of all patients. Our analyses show that these healthcare networks, the patient populations that comprise them and the patient movement patterns are heterogeneous and centralized. Despite the differences in patient populations, the HAI-specific and suspected-HAI healthcare networks have the same underlying structure as that of the general healthcare network. We identify key hospital centers, patient flow trajectories, at both the regional and department (county) level that may serve as a basis for proposing novel wide-scale infection control strategies.
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Affiliation(s)
- Narimane Nekkab
- Laboratoire MESuRS, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, Paris, France
- Institut Pasteur, Cnam, Unité PACRI, 25–28, rue du Docteur Roux, Paris, France
- Ecole des Hautes Etudes en Santé Publique, Département d'Epidémiologie et de Biostatistiques, 15 Avenue du Professeur-Léon-Bernard, Rennes, France
- * E-mail:
| | - Pascal Astagneau
- Ecole des Hautes Etudes en Santé Publique, Département d'Epidémiologie et de Biostatistiques, 15 Avenue du Professeur-Léon-Bernard, Rennes, France
- Centre de prévention des infections associées aux soins (C-CLIN), APHP, Paris, France
- Faculté de médecine Pierre et Marie Curie, Sorbonne Universités, Paris, France
| | - Laura Temime
- Laboratoire MESuRS, Conservatoire National des Arts et Métiers, 292 Rue Saint-Martin, Paris, France
- Institut Pasteur, Cnam, Unité PACRI, 25–28, rue du Docteur Roux, Paris, France
| | - Pascal Crépey
- Ecole des Hautes Etudes en Santé Publique, Département d'Epidémiologie et de Biostatistiques, 15 Avenue du Professeur-Léon-Bernard, Rennes, France
- UMR190, Emergence des Pathologies Virales, Marseille, France
- UPRES EA 7449 Reperes, Rennes, France
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