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1. Reduction of SARS-CoV-2 intra-household child-to-parent transmission associated with ventilation: results from a case–control study

Author: Simon Galmiche, Tiffany Charmet, Yoann Madec, Arthur Rakover, Laura Schaeffer, Olivia Chény, Faïza Omar, Sophie Martin, Alexandra Mailles, Fabrice Carrat, and Arnaud Fontanet
Subjects: SARS-CoV-2, Home environment, Family, Patient isolation, Ventilation, Public aspects of medicine, RA1-1270
Abstract: Abstract Purpose Our objective was to describe circumstances of SARS-CoV-2 household transmission and to identify factors associated with a lower risk of transmission in a nationwide case–control study in France. Methods In a descriptive analysis, we analysed cases reporting transmission from someone in the household (source case). Index cases could invite a non-infected household member to participate as a related control. In such situations, we compared the exposures of the index case and related control to the source case by conditional logistic regression matched for household, restricted to households in which the source case was a child, and the index case and related control were the infected child’s parents. Results From October 27, 2020 to May 16, 2022, we included 104 373 cases for the descriptive analysis with a documented infection from another household member. The source case was mostly the index case’s child (46.9%) or partner (45.7%). In total, 1026 index cases invited a related control to participate in the study. In the case–control analysis, we included 611 parental pairs of cases and controls exposed to the same infected child. COVID-19 vaccination with 3 + doses versus no vaccination (OR 0.1, 95%CI: 0.04–0.4), isolation from the source case (OR 0.6, 95%CI: 0.4–0.97) and the ventilation of indoor areas (OR 0.6, 95%CI: 0.4–0.9) were associated with lower risk of infection. Conclusion Household transmission was common during the SARS-CoV-2 pandemic in France. Mitigation strategies, including isolation and ventilation, decreased the risk of secondary transmission within the household. Trial registration ClinicalTrials.gov registration number: NCT04607941.
Published: 2023
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2. National Monkeypox Surveillance, Central African Republic, 2001–2021

Author: Camille Besombes, Festus Mbrenga, Laura Schaeffer, Christian Malaka, Ella Gonofio, Jordi Landier, Ulrich Vickos, Xavier Konamna, Benjamin Selekon, Joella Namsenei Dankpea, Cassandre Von Platen, Franck Gislain Houndjahoue, Daniel Sylver Ouaïmon, Alexandre Hassanin, Nicolas Berthet, Jean-Claude Manuguerra, Antoine Gessain, Arnaud Fontanet, and Emmanuel Nakouné-Yandoko
Subjects: monkeypox, monkeypox virus, Central Africa, Central African Republic, national surveillance, outbreak investigation, Medicine, Infectious and parasitic diseases, RC109-216
Abstract: We analyzed monkeypox disease surveillance in Central African Republic (CAR) during 2001–2021. Surveillance data show 95 suspected outbreaks, 40 of which were confirmed as monkeypox, comprising 99 confirmed and 61 suspected monkeypox cases. After 2018, CAR’s annual rate of confirmed outbreaks increased, and 65% of outbreaks occurred in 2 forested regions bordering the Democratic Republic of the Congo. The median patient age for confirmed cases was 15.5 years. The overall case-fatality ratio was 7.5% (12/160) for confirmed and suspected cases, 9.6% (8/83) for children
Published: 2022
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3. Changes in Systemic Regulatory T Cells, Effector T Cells, and Monocyte Populations Associated With Early-Life Stunting

Author: Zo Andriamanantena, Fanirisoa Randrianarisaona, Maheninasy Rakotondrainipiana, Prisca Andriantsalama, Ravaka Randriamparany, Rindra Randremanana, Frédérique Randrianirina, Sophie Novault, Darragh Duffy, François Huetz, Milena Hasan, Matthieu Schoenhals, Philippe J. Sansonetti, Pascale Vonaesch, Inès Vigan-Womas, Afribiota Investigators, Laurence Barbot-Trystram, Robert Barouki, Alexandra Bastaraud, Jean-Marc Collard, Maria Doria, Serge Ghislain Djorie, Tamara Giles-Vernick, Bolmbaye Privat Gondje, Jean-Chrysostome Gody, Jean-Michel Héraud, Francis Allan Hunald, Nathalie Kapel, Jean-Pierre Lombart, Alexandre Manirakiza, Synthia Nazita Nigatoloum, Laura Wegener Parfrey, Lisette Raharimalala, Rindra Vatosoa Randremanana, Harifetra Mamy Richard Randriamizao, Frédérique Randrianirina, Annick Lalaina Robinson, Pierre-Alain Rubbo, Philippe Sansonetti, Laura Schaeffer, Ionela Gouandjika-Vassilache, Sonia Sandrine Vondo, and Inès Vigan-Womas
Subjects: stunting, environmental enteric dysfunction, flow cytometry, monocytes, regulatory T cells, Madagascar, Immunologic diseases. Allergy, RC581-607
Abstract: Stunting and environmental enteric dysfunction (EED) may be responsible for altered gut and systemic immune responses. However, their impact on circulating immune cell populations remains poorly characterized during early life. A detailed flow cytometry analysis of major systemic immune cell populations in 53 stunted and 52 non-stunted (2 to 5 years old) children living in Antananarivo (Madagascar) was performed. Compared to age-matched non-stunted controls, stunted children aged 2-3 years old had a significantly lower relative proportion of classical monocytes. No significant associations were found between stunting and the percentages of effector T helper cell populations (Th1, Th2, Th17, Th1Th17, and cTfh). However, we found that HLA-DR expression (MFI) on all memory CD4+ or CD8+ T cell subsets was significantly lower in stunted children compared to non-stunted controls. Interestingly, in stunted children compared to the same age-matched non-stunted controls, we observed statistically significant age-specific differences in regulatory T cells (Treg) subsets. Indeed, in 2- to 3-year-old stunted children, a significantly higher percentage of memory Treg, whilst a significantly lower percentage of naive Treg, was found. Our results revealed that both innate and adaptive systemic cell percentages, as well as activation status, were impacted in an age-related manner during stunting. Our study provides valuable insights into the understanding of systemic immune system changes in stunted children.
Published: 2022
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4. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France

Author: Rebecca Grant, Tiffany Charmet, Laura Schaeffer, Simon Galmiche, Yoann Madec, Cassandre Von Platen, Olivia Chény, Faïza Omar, Christophe David, Alexandra Rogoff, Juliette Paireau, Simon Cauchemez, Fabrice Carrat, Alexandra Septfons, Daniel Levy-Bruhl, Alexandra Mailles, and Arnaud Fontanet
Subjects: Public aspects of medicine, RA1-1270
Abstract: Summary: Background: We aimed to assess the settings and activities associated with SARS-CoV-2 infection in the context of B.1.617.2 (Delta) variant circulation in France, as well as the protection against symptomatic Delta infection. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 23 May and 13 August 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire and multivariable logistic regression analysis was used to determine the association between acute SARS-CoV-2 infection and recent activity-related exposures, past history of SARS-CoV-2 infection, and COVID-19 vaccination. Findings: We did not find any differences in the settings and activities associated with Delta versus non-Delta infections and grouped them for subsequent analyses. In multivariable analysis involving 12634 cases (8644 Delta and 3990 non-Delta) and 5560 controls, we found individuals under 40 years and attending bars (aOR:1.9; 95%CI:1.6-2.2) or parties (aOR:3.4; 95%CI:2.8-4.2) to be at increased risk of infection. In those aged 40 years and older, having children attend daycare (aOR:1.9; 95%CI:1.1-3.3), kindergarten (aOR:1.6; 95%CI:1.2-2.1), primary school (aOR:1.4; 95%CI:1.2-1.6) or middle school (aOR:1.3; 95%CI:1.2-1.6) were associated with increased risk of infection. We found strong protection against symptomatic Delta infection for those with prior infection whether it was recent (2-6 months) (95%; 95%CI:90-97) or associated with one dose (85%; 95%CI:78-90) or two doses of mRNA vaccine (96%; 95%CI:87-99). For those without past infection, protection was lower with two doses of mRNA vaccine (67%; 95%CI:63-71). Interpretation: In line with other observational studies, we find reduced vaccine effectiveness against symptomatic Delta infections. The settings and activities at increased risk of infection indicate where efforts to reinforce individual and public health measures need to be concentrated.
Published: 2022
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5. Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France

Author: Tiffany Charmet, Laura Schaeffer, Rebecca Grant, Simon Galmiche, Olivia Chény, Cassandre Von Platen, Alexandra Maurizot, Alexandra Rogoff, Faïza Omar, Christophe David, Alexandra Septfons, Simon Cauchemez, Alexandre Gaymard, Bruno Lina, Louise H Lefrancois, Vincent Enouf, Sylvie van der Werf, Alexandra Mailles, Daniel Levy-Bruhl, Fabrice Carrat, and Arnaud Fontanet
Subjects: COVID-19, Vaccine effectiveness, SARS-CoV-2 variants, epidemiology, case-control study, Public aspects of medicine, RA1-1270
Abstract: Background: We aimed to assess the effectiveness of two doses of mRNA COVID-19 vaccines against COVID-19 with the original virus and other lineages circulating in France. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults with onset of symptoms between 14 February and 3 May 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire on recent activity-related exposures and vaccination history. Information about the infecting virus was based on a screening RT-PCR for either B.1.1.7 or B.1.351/P.1 variants. Findings: Included in our analysis were 7 288 adults infected with the original SARS-CoV-2 virus, 31 313 with the B.1.1.7 lineage, 2 550 with B.1.351/P1 lineages, and 3 644 controls. In multivariable analysis, the vaccine effectiveness (95% confidence interval) seven days after the second dose of mRNA vaccine was estimated at 88% (81-92), 86% (81-90) and 77% (63-86) against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Recent (2 to 6 months) history of virologically confirmed SARS-CoV-2 infection was found to be 83% (76-88), 88% (85-91) and 83% (71-90) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively; and more distant (> 6 months) infections were 76% (54-87), 84% (75-90), and 74% (41-89) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Interpretation: In real-life settings, two doses of mRNA vaccines proved to be effective against COVID-19 with the original virus, B.1.1.7 lineage and B.1.351/P.1 lineages. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance “Tous unis contre le virus”).
Published: 2021
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6. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study

Author: Simon Galmiche, Tiffany Charmet, Laura Schaeffer, Juliette Paireau, Rebecca Grant, Olivia Chény, Cassandre Von Platen, Alexandra Maurizot, Carole Blanc, Annika Dinis, Sophie Martin, Faïza Omar, Christophe David, Alexandra Septfons, Simon Cauchemez, Fabrice Carrat, Alexandra Mailles, Daniel Levy-Bruhl, and Arnaud Fontanet
Subjects: Public aspects of medicine, RA1-1270
Abstract: Summary: Background: We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures. Findings: Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75). Interpretation: Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance” Tous unis contre le virus”).
Published: 2021
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7. Acceptability of a COVID-19 pre-exposure prophylaxis trial with hydroxychloroquine in French healthcare workers during the first wave of COVID-19 pandemic

Author: Amandine Gagneux-Brunon, Clémentine Schilte, Arnauld Garcin, Nathalie Jolly, Muriel Vray, Laura Schaeffer, Xavier Duval, Bruno Hoen, and Elisabeth Botelho-Nevers
Subjects: Pre-exposure chemoprophylaxis trial, SARS-CoV-2 infection, Healthcare workers, Acceptability, Hydroxychloroquine, Medicine (General), R5-920
Published: 2021
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8. Impact of Introducing Hepatitis B Birth Dose Vaccines into the Infant Immunization Program in Burkina Faso: Study Protocol for a Stepped Wedge Cluster Randomized Trial (NéoVac Study)

Author: Haoua Tall, Pierrick Adam, Abdoul Salam Eric Tiendrebeogo, Jeanne Perpétue Vincent, Laura Schaeffer, Cassandre von Platen, Sandrine Fernandes-Pellerin, François Sawadogo, Alkadri Bokoum, Ghislain Bouda, Seydou Ouattara, Issa Ouédraogo, Magali Herrant, Pauline Boucheron, Appolinaire Sawadogo, Edouard Betsem, Alima Essoh, Lassané Kabore, Amariane Ouattara, Nicolas Méda, Hervé Hien, Andréa Gosset, Tamara Giles-Vernick, Sylvie Boyer, Dramane Kania, Muriel Vray, and Yusuke Shimakawa
Subjects: hepatitis B vaccine, mother-to-child transmission, birth dose vaccination, complex intervention, mixed method, stepped wedge cluster randomized trial, Medicine
Abstract: To achieve global hepatitis elimination by 2030, it is critical to prevent the mother-to-child transmission (MTCT) of hepatitis B virus (HBV). Since 2009, the WHO has recommended administering hepatitis B vaccine to all neonates within 24 h of birth to prevent MTCT. However, many countries in sub-Saharan Africa only provide hepatitis B immunization at the age of 6, 10, and 14 weeks or 8, 12, and 16 weeks using a combined vaccine. To accelerate the introduction of the hepatitis B birth dose vaccine (HepB-BD) into sub-Saharan Africa, it is critical to establish to what extent the addition of HepB-BD can further reduce HBV transmission in areas where three-dose infant vaccination has been implemented. We therefore designed a study to evaluate the impact, acceptability, and cost-effectiveness of incorporating the HepB-BD into the routine immunization program in a real-life field condition in Burkina Faso, where the hepatitis B vaccination is currently scheduled at 8-12-16 weeks. Through a multidisciplinary approach combining epidemiology, anthropology, and health economics, the Neonatal Vaccination against Hepatitis B in Africa (NéoVac) study conducts a pragmatic stepped wedge cluster randomized controlled trial in rural areas of the Hauts-Bassins Region. The study was registered in ClinicalTrials.gov (identifier: NCT04029454). A health center is designated as a cluster, and the introduction of HepB-BD will be rolled out sequentially in 24 centers. Following an initial period in which no health center administers HepB-BD, one center will be randomly allocated to incorporate HepB-BD. Then, at a regular interval, another center will be randomized to cross from the control to the intervention period, until all 24 centers integrate HepB-BD. Pregnant women attending antenatal care will be systematically invited to participate. Infants born during the control period will follow the conventional immunization schedule (8-12-16 weeks), while those born in the interventional period will receive HepB-BD in addition to the routine vaccines (0-8-12-16 weeks). The primary outcome, the proportion of hepatitis B surface antigen (HBsAg) positivity in infants aged at 9 months, will be compared between children born before and after HepB-BD introduction. The study will generate data that may assist governments and stakeholders in sub-Saharan Africa to make evidence-based decisions about whether to add HepB-BD into the national immunization programs.
Published: 2021
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9. Systematic Booster after Rabies Pre-Exposure Prophylaxis to Alleviate Rabies Antibody Monitoring in Individuals at Risk of Occupational Exposure

Author: Perrine Parize, Jérémie Sommé, Laura Schaeffer, Florence Ribadeau-Dumas, Sheherazade Benabdelkader, Agnès Durand, Arnaud Tarantola, Johann Cailhol, Julia Goesch, Lauriane Kergoat, Anne-Sophie Le Guern, Marie-Laurence Mousel, Laurent Dacheux, Paul-Henri Consigny, Arnaud Fontanet, Beata Francuz, and Hervé Bourhy
Subjects: rabies, pre-exposure prophylaxis, humoral immunity, booster immunization, occupational health, Medicine
Abstract: Pre-exposure rabies prophylaxis (PrEP) is recommended for people at frequent or increased risk of professional exposure to lyssavirus (including rabies virus). PrEP provides protection against unrecognized exposure. After the primary vaccination, one’s immune response against rabies may decline over time. We aimed to evaluate the immune response to rabies in individuals immunized for occupational reasons before and after a booster dose of the rabies vaccine. With this aim, we retrospectively documented factors associated with an inadequate response in individuals vaccinated for occupational purposes. Our findings analyzed data from 498 vaccinated individuals and found that 17.2% of participants had an inadequate antibody titration documented after their primary vaccination without the booster, while inadequate response after an additional booster of the vaccine was evidenced in 0.5% of tested participants. This study showed that a single booster dose of vaccine after PrEP conferred a high and long-term immune response in nearly all individuals except for rare, low responders. A systematic rabies booster after primary vaccination may result in alleviating the monitoring strategy of post-PrEP antibody titers among exposed professionals.
Published: 2021
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10. SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study

Author: Simon Galmiche, Thomas Cortier, Tiffany Charmet, Laura Schaeffer, Olivia Chény, Cassandre von Platen, Anne Lévy, Sophie Martin, Faïza Omar, Christophe David, Alexandra Mailles, Fabrice Carrat, Simon Cauchemez, and Arnaud Fontanet
Subjects: Microbiology (medical), Infectious Diseases, Virology, Microbiology
Published: 2023
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11. SARS-CoV-2 self-test uptake and factors associated with self-testing during Omicron BA.1 and BA.2 waves in France, January to May 2022

Author: Olivier Supplisson, Tiffany Charmet, Simon Galmiche, Laura Schaeffer, Olivia Chény, Anne Lévy, Nathan Jeandet, Faïza Omar, Christophe David, Alexandra Mailles, and Arnaud Fontanet
Subjects: Epidemiology, Virology, Public Health, Environmental and Occupational Health
Abstract: Background Following the SARS-CoV-2 Omicron variant spread, the use of unsupervised antigenic rapid diagnostic tests (self-tests) increased. Aim This study aimed to measure self-test uptake and factors associated with self-testing. Methods In this cross-sectional study from 20 January to 2 May 2022, the case series from a case–control study on factors associated with SARS-CoV-2 infection were used to analyse self-testing habits in France. A multivariable quasi-Poisson regression was used to explore the variables associated with self-testing among symptomatic cases who were not contacts of another infected individual. The control series from the same study was used as a proxy for the self-test background rate in the non-infected population of France. Results During the study period, 179,165 cases who tested positive through supervised tests were recruited. Of these, 64.7% had performed a self-test in the 3 days preceding this supervised test, of which 79,038 (68.2%) were positive. The most frequently reported reason for self-testing was the presence of symptoms (64.6%). Among symptomatic cases who were not aware of being contacts of another case, self-testing was positively associated with being female, higher education, household size, being a teacher and negatively associated with older age, not French by birth, healthcare-related work and immunosuppression. Among the control series, 12% self-tested during the 8 days preceding questionnaire filling, with temporal heterogeneity. Conclusion The analysis showed high self-test uptake in France with some inequalities which must be addressed through education and facilitated access (cost and availability) for making it a more efficient epidemic control tool.
Published: 2023
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12. Factors Associated with Stunted Growth in Children Under Five Years in Antananarivo, Madagascar and Bangui, Central African Republic

Author: Pascale, Vonaesch, Serge Ghislain, Djorie, Kaleb Jephté Estimé, Kandou, Maheninasy, Rakotondrainipiana, Laura, Schaeffer, Prisca Vega, Andriatsalama, Ravaka, Randriamparany, Bolmbaye Privat, Gondje, Synthia, Nigatoloum, Sonia Sandrine, Vondo, Aurélie, Etienne, Annick, Robinson, Francis Allen, Hunald, Lisette, Raharimalala, Tamara, Giles-Vernick, Laura, Tondeur, Frédérique, Randrianirina, Alexandra, Bastaraud, Jean-Chrysostome, Gody, Philippe Jean, Sansonetti, Rindra Vatosoa, Randremanana, Inès, Vigan-Womas, Pathogénie microbienne moléculaire, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Unité d'Epidémiologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Centre pédiatrique de Bangui, Centre Hospitalier Universitaire Mère-Enfant de Tsaralalàna (CHUMET), Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHUJRA), Anthropologie et écologie de l’émergence des maladies - Anthropology and Ecology of Disease Emergence, Institut Pasteur [Paris], Centre de Biologie Clinique [Antananarivo] (IPM), Laboratoire d'hygiène des aliments et de l'environnement [Antananarivo, Madagascar] (IPM), Unité d’Épidémiologie et de Recherche clinique [Antananarivo, Madagascar], The epidemiological part of AFRIBIOTA was funded by the Total Foundation and the Fondation Petram. PV was supported by an Early Postdoctoral Fellowship (Grant No. P2EZP3_152159), an Advanced Postdoctoral Fellowship (Grant No. P300PA_177876) as well as a Return Grant (Grant No. P3P3PA_17877) from the Swiss National Science Foundation, a Roux-Cantarini Fellowship (2016) and a L’Oréal-UNESCO for Women in Science France Fellowship (2017). PJS is a HHMI Senior Foreign Scholar. The funders had no role in study design or collection, analysis, and interpretation of data and in writing this manuscript., AFRIBIOTA Investigators: Laurence Barbot-Trystram, Hôpital Pitié-Salpêtrière, Paris, France, Robert Barouki, Hôpital Necker-Enfants maladies, Paris, France, Alexandra Bastaraud, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Jean-Marc Collard, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Maria Doria, Institut Pasteur, Paris, France, Aurélie Etienne, Institut Pasteur, Paris, France/Institut Pasteur de Madagascar, Madagascar, Serge Ghislain Djorie, Institut Pasteur de Bangui, Bangui, Central African Republic, Tamara Giles-Vernick, Institut Pasteur, Paris, France, Bolmbaye Privat Gondje, Complexe Pédiatrique de Bangui, Bangui, Central African Republic, Jean-Chrysostome Gody, Complexe Pédiatrique de Bangui, Bangui, Central African Republic, Francis Allen Hunald, Service de Chirurgie pédiatrique, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar, Nathalie Kapel, Hôpital Pitié-Salpêtrière, Paris, France, Jean-Pierre Lombart, Institut Pasteur de Bangui, Bangui, Central African Republic, Alexandre Manirakiza, Institut Pasteur de Bangui, Bangui, Central African Republic, Synthia Nazita Nigatoloum, Complexe Pédiatrique de Bangui, Bangui, Central African Republic, Lisette Raharimalala, Centre de Santé Materno-Infantile, Tsaralalana, Antananarivo, Madagascar, Maheninasy Rakotondrainipiana, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Rindra Randremanana, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Harifetra Mamy Richard Randriamizao, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar, Frédérique Randrianirina, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Annick Robinson, Centre Hospitalier Universitaire Mère Enfant de Tsaralalana, Antananarivo, Madagascar, Pierre-Alain Rubbo, Institut Pasteur de Bangui, Bangui, République Centrafricaine, Philippe Sansonetti, Institut Pasteur, Paris, France, Laura Schaeffer, Institut Pasteur, Paris, France, Ionela Gouandjika-Vassilache, Institut Pasteur de Bangui, Bangui, République Centrafricaine, Pascale Vonaesch, Institut Pasteur, Paris, France, Sonia Sandrine Vondo, Complexe Pédiatrique de Bangui, Bangui, Central African Republic, Inès Vigan-Womas, Institut Pasteur de Madagascar, Antananarivo, Madagascar. We wish to thank further all families and fieldworkers who contributed to this study, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Cité (UPCité)-Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Université Paris Cité (UPCité)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), and Vigan-Womas, Inès
Subjects: [SDV.IMM] Life Sciences [q-bio]/Immunology, Stunted growth, Nutritional Status, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Article, MESH: Madagascar, MESH: Pregnancy, Pregnancy, MESH: Risk Factors, MESH: Child, Prevalence, Madagascar, Humans, Child, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, Children, Growth Disorders, MESH: Prevalence, MESH: Humans, digestive, oral, and skin physiology, MESH: Child, Preschool, Infant, Undernutrition, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Growth Disorders, MESH: Nutritional Status, MESH: Case-Control Studies, MESH: Infant, Central African Republic, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Risk factors, MESH: Central African Republic, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Case-Control Studies, Child, Preschool, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Female
Abstract: Objectives With a fourth of all under-five children affected, stunting remains one of the biggest health challenges worldwide. Even though the main underlying factors are known, the exact pathways to stunting varying in affected regions, and interventions thus need to be tailored to the local contexts. This study aimed assessing and comparing factors associated with stunting in two understudied sub-Saharan urban contexts with some of the highest stunting prevalence globally: Bangui, Central African Republic (~ 36%) and Antananarivo, Madagascar (42%). Methods We performed a case–control study on 175 + 194 stunted and 237 + 230 non-stunted control children aged 2–5 years and matched for age, gender and district of residency. Factors associated with stunting were identified using a standardized, paper questionnaire delivered by trained interviewers. Statistical analysis was done using logistic regression modelling. Results In both sites, formal maternal education lowered the risk of being stunted and restricted access to soap, suffering of anaemia and low birth weight were associated with higher risk of stunting. Short maternal stature, household head different from parents, diarrhoea and coughing were associated with an increased risk and continuing breastfeeding was associated with a lower risk of stunting in Antananarivo. Previous severe undernutrition and dermatitis/ fungal skin infections were associated with higher and changes in diet during pregnancy with lower risk of stunting in Bangui. Conclusions Our results suggest maternal education, antenatal care, iron supplementation and simple WASH interventions such as using soap and infection control as general and breastfeeding (Antananarivo) or better nutrition (Bangui) as area-specified interventions. Supplementary Information The online version contains supplementary material available at 10.1007/s10995-021-03201-8.
Published: 2021
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13. SARS-CoV-2 Exposures of Healthcare Workers from Primary Care, Long-Term Care Facilities and Hospitals: A Nationwide Matched Case-Control Study

Author: Martin Belan, Tiffany Charmet, Laura Schaeffer, Sarah Tubiana, Xavier Duval, Jean-Christophe Lucet, Arnaud Fontanet, Gabriel Birgand, and Solen Kernéis
Subjects: Microbiology (medical), Infectious Diseases, SARS-CoV-2, Case-Control Studies, Health Personnel, Humans, COVID-19, General Medicine, Long-Term Care, Hospitals
Abstract: ObjectivesHealthcare workers (HCWs) are at higher risk of contracting coronavirus disease-19 (COVID-19) than the general population. This study assessed the roles of various exposures and personal protective equipment (PPE) use on that risk for HCWs working in primary care, long-term-care facilities (LTCFs) or hospitals.MethodsWe conducted a matched case-control (1:1) study (10 April–9 July 2021). Cases (HCWs with confirmed COVID-19) and controls (HCWs without any COVID-19-positive test or symptoms) recruited by email were invited to complete an online questionnaire on their exposures and PPE use. Questions covered the 10 days preceding symptom onset for cases (or testing if asymptomatic) or inclusion for controls.ResultsA total of 4152 matched cases and controls were included. The multivariable conditional logistic regression analysis retained exposure to an infected person outside work (adjusted odds ratio, 19.9 [95% confidence intervaI, 12.4–31.9]), an infected colleague (2.26 [1.53–3.33]) or COVID-19 patients (2.37 [1.66–3.40]), as independent predictors of COVID-19 in HCWs, while partial or complete immunization was protective. Eye protection (0.57 [0.37–0.87]) and wearing a gown (0.58 [0.34–0.97]) during COVID-19 patient care were protective, while wearing an apron slightly increased the risk of infection (1.47 [1.00–2.18]). N95-respirator protection was comparable to that of surgical masks. Results were consistent across healthcare-facility categories.ConclusionsHCWs were more likely to get COVID-19 in their personal sphere than during occupational activities. Our results suggest that eye protection for HCWs during patient care should be actively promoted.
Published: 2022
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14. Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France

Author: Alexandra Septfons, Simon Galmiche, Daniel Lévy-Bruhl, Simon Cauchemez, Sylvie van der Werf, Rebecca Grant, Alexandra Rogoff, Alexandra Maurizot, Cassandre Von Platen, Laura Schaeffer, Faïza Omar, Vincent Enouf, Olivia Chény, Christophe David, Alexandra Mailles, Fabrice Carrat, Bruno Lina, Louise H Lefrancois, Tiffany Charmet, Arnaud Fontanet, Alexandre Gaymard, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Sorbonne Université (SU), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris], Caisse Nationale d'Assurance Maladie des Travailleurs salariés (CNAMTS), Ministère de l'économie et des finances, Ipsos, Santé publique France - French National Public Health Agency [Saint-Maurice, France], Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR), Institut des Agents Infectieux [Lyon] (IAI), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Virology and human respiratory Pathologies - Virology and human respiratory Pathologies (VirPath), Centre International de Recherche en Infectiologie - UMR (CIRI), Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR), Plateforme de Microbiologie Mutualisée (PIBnet) - Mutualized Platform for Microbiology (P2M), Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), The study was funded by Institut Pasteur and Research & Action Emerging Infectious Diseases (REACTing). AF's laboratory receives support from the Labex IBEID (ANR-10-LABX-62-IBEID) and the INCEPTION project (PIA/ANR-16-CONV-0005) for studies on emerging viruses. TC is funded by the Fondation de France (Alliance 'Tous unis contre le virus'). SW's laboratory receives support from Institut Pasteur, CNRS, Université de Paris, Santé publique France, Labex IBEID (ANR-10-LABX-62-IBEID), REACTing (Research & Action Emerging Infectious Diseases), and by the H2020 project 101003589 (RECOVER)., We would like to thank the Action Coordonnée transmission group of the ANRS-MIE for helpful discussions on the study design, and Violette Mouro (Conseil d'Orientation de la Stratégie Vaccinale) for providing us with data on vaccine distribution in France., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CONV-0005,INCEPTION,Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs(2016), European Project: 101003589, H2020-SC1-PHE-CORONAVIRUS-2020,RECOVER(2020), Gestionnaire, HAL Sorbonne Université 5, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Institut Convergences pour l'étude de l'Emergence des Pathologies au Travers des Individus et des populatiONs - - INCEPTION2016 - ANR-16-CONV-0005 - CONV - VALID, Rapid European COVID-19 Emergency Response research - RECOVER - - H2020-SC1-PHE-CORONAVIRUS-20202020-02-14 - 2022-02-13 - 101003589 - VALID, Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Centre National de Référence des Virus des Infections Respiratoires (dont la Grippe) [Lyon] (CNR - laboratoire associé), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur)
Subjects: medicine.medical_specialty, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Lineage (evolution), case-control study, Biology, Virus, 03 medical and health sciences, 0302 clinical medicine, Epidemiology, Internal Medicine, medicine, 030212 general & internal medicine, 030304 developmental biology, Vaccine effectiveness, 0303 health sciences, Messenger RNA, SARS-CoV-2 variants, Health Policy, Case-control study, COVID-19, Virology, Confidence interval, 3. Good health, Vaccination, Oncology, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, epidemiology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, Public aspects of medicine, RA1-1270, Research Paper
Abstract: Background: We aimed to assess the effectiveness of two doses of mRNA COVID-19 vaccines against COVID-19 with the original virus and other lineages circulating in France. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults with onset of symptoms between 14 February and 3 May 2021. Controls were non-infected adults from a national representative panel matched to cases by age, sex, region, population density and calendar week. Participants completed an online questionnaire on recent activity-related exposures and vaccination history. Information about the infecting virus was based on a screening RT-PCR for either B.1.1.7 or B.1.351/P.1 variants. Findings: Included in our analysis were 7 288 adults infected with the original SARS-CoV-2 virus, 31 313 with the B.1.1.7 lineage, 2 550 with B.1.351/P1 lineages, and 3 644 controls. In multivariable analysis, the vaccine effectiveness (95% confidence interval) seven days after the second dose of mRNA vaccine was estimated at 88% (81-92), 86% (81-90) and 77% (63-86) against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Recent (2 to 6 months) history of virologically confirmed SARS-CoV-2 infection was found to be 83% (76-88), 88% (85-91) and 83% (71-90) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively; and more distant (> 6 months) infections were 76% (54-87), 84% (75-90), and 74% (41-89) protective against COVID-19 with the original virus, the B.1.1.7 lineage, and the B.1.351/P.1 lineages, respectively. Interpretation: In real-life settings, two doses of mRNA vaccines proved to be effective against COVID-19 with the original virus, B.1.1.7 lineage and B.1.351/P.1 lineages. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance “Tous unis contre le virus”).
Published: 2021
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15. Cost-effectiveness of adding a birth dose of hepatitis B vaccine in the Dafra district of the Hauts-Bassins Region in Burkina Faso (NéoVac Study)

Author: Muriel Vray, Nicolas Meda, Laura Schaeffer, Roger Sombié, Mamadou Yaya Diallo, Edouard Betsem, Andréa Gosset, Sylvie Boyer, Yusuke Shimakawa, Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut des sciences de la santé publique [Marseille] (ISSPAM), Agence de Médecine Préventive [Burkina Faso], Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Centre Muraz [Bobo-Dioulasso, Burkina Faso], Centre Hospitalier Universitaire Yalgado Ouédraogo (CHUYO), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Malbec, Odile
Subjects: Marginal cost, Hepatitis B vaccine, Cost effectiveness, Cost-Benefit Analysis, [SDV]Life Sciences [q-bio], Gross domestic product, law.invention, 03 medical and health sciences, 0302 clinical medicine, law, Pregnancy, Burkina Faso, Medicine, Humans, Hepatitis B Vaccines, 030212 general & internal medicine, Unit cost, Discounting, Hepatitis B Surface Antigens, General Veterinary, General Immunology and Microbiology, business.industry, Mother-to-child transmission, Public Health, Environmental and Occupational Health, Infant, Newborn, Hepatitis B, Infectious Disease Transmission, Vertical, 3. Good health, Vaccination, [SDV] Life Sciences [q-bio], Infectious Diseases, Transmission (mechanics), Africa, Molecular Medicine, Birth dose, 030211 gastroenterology & hepatology, Female, Cost-effectiveness, business, Demography
Abstract: International audience; Background: The World Health Organization (WHO) recommends a first hepatitis B vaccine dose within 24 h of birth (HepB-BD) to prevent mother-to-child transmission. Evidence for this strategy's economic value in Africa is limited. We assessed the costs and cost-effectiveness of adding HepB-BD to the current three-dose pentavalent schedule (HepB3) in the Dafra district of the Hauts-Bassins Region in Burkina Faso.Methods: Using a decision tree combined with a Markov model, we estimated the expected number of life-years (LY) and disability-adjusted life-years (DALYs) saved, incremental costs, and incremental cost-effectiveness ratios (ICER) of HepB-BD + HepB3 versus HepB3 alone in Dafra's 2017 birth cohort (n = 11,462). Institutional delivery rates, vaccine coverage, and vaccination costs from a health system perspective were estimated from field-collected data. We estimated the effectiveness of HepB-BD, age-specific transition probabilities, and horizontal transmission risks using data from previous African studies. Costs and health outcomes were discounted at an annual rate of 3%. We conducted one-way and probabilistic sensitivity analyses to assess uncertainty.Results: In the base-case analysis without discounting, HepB-BD + HepB3 yielded a net cost saving of US$18,979 and saved 163 DALYs compared with HepB3 alone. With discounting, HepB-BD + HepB3 compared with HepB3 resulted in an incremental cost of US$554 and 31 DALYs averted, translating into an ICER of US$18/DALY averted. In one-way sensitivity analyses, HepB-BD + HepB3 remained cost-effective (at the cost-effectiveness threshold of US$671 i.e. the Burkina Faso per-capita gross domestic product) for all parameter changes. However, results were very sensitive to variations in HepB-BD unit cost per vaccinated neonate and perinatal transmission risk in mothers carrying the hepatitis B e antigen. The probabilities of HepB-BD + HepB3 being cost-effective were 71.7% and 86.7%, at the cost-effectiveness thresholds of US$335 and US$671, respectively.Conclusion: Introducing HepB-BD in Burkina Faso is likely to be cost-effective.
Published: 2021
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16. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study

Author: Cassandre Von Platen, Simon Galmiche, Alexandra Maurizot, Sophie Martin, Faïza Omar, Laura Schaeffer, Olivia Chény, Juliette Paireau, Annika Dinis, Alexandra Septfons, Rebecca Grant, Fabrice Carrat, Carole Blanc, Simon Cauchemez, Arnaud Fontanet, Alexandra Mailles, Christophe David, Tiffany Charmet, Daniel Lévy-Bruhl, Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Modélisation mathématique des maladies infectieuses - Mathematical modelling of Infectious Diseases, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Santé publique France - French National Public Health Agency [Saint-Maurice, France], Sorbonne Université (SU), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris], Caisse Nationale d'Assurance Maladie des Travailleurs salariés (CNAMTS), Ministère de l'économie et des finances, Ipsos, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance' Tous unis contre le virus')., We would like to thank the AC transmission group of REACTing (Research & Action Emerging Infectious Diseases) for helpful discussions about the study design, Xavier Duval and Sarah Tubiana for pilot testing the questionnaire, and Nathalie Bajos and Dominique Costagliola for their critical review of an earlier version of the manuscript., Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), and Limouzin, Cécile
Subjects: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], 030231 tropical medicine, Computer-assisted web interviewing, 03 medical and health sciences, 0302 clinical medicine, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Environmental health, Internal Medicine, Medicine, Infection control, 030212 general & internal medicine, Sports activity, [MATH.MATH-ST] Mathematics [math]/Statistics [math.ST], business.industry, Health Policy, Risk of infection, Case-control study, 3. Good health, [SDV] Life Sciences [q-bio], Increased risk, Oncology, Public aspects of medicine, RA1-1270, business, Research Paper
Abstract: Summary: Background: We aimed to assess the role of different setting and activities in acquiring SARS-CoV-2 infection. Methods: In this nationwide case-control study, cases were SARS-CoV-2 infected adults recruited between 27 October and 30 November 2020. Controls were individuals from the Ipsos market research database matched to cases by age, sex, region, population density and time period. Participants completed an online questionnaire on recent activity-related exposures. Findings: Among 3426 cases and 1713 controls, in multivariable analysis, we found an increased risk of infection associated with any additional person living in the household (adjusted-OR: 1•16; 95%CI: 1•11-1•21); having children attending day-care (aOR: 1•31; 95%CI: 1•02-1•62), kindergarten (aOR: 1•27; 95%CI: 1•09-1•45), middle school (aOR: 1•30; 95%CI: 1•15-1•47), or high school (aOR: 1•18; 95%CI: 1•05-1•34); with attending professional (aOR: 1•15; 95%CI: 1•04-1•26) or private gatherings (aOR: 1•57; 95%CI: 1•45-1•71); and with having frequented bars and restaurants (aOR: 1•95; 95%CI: 1•76-2•15), or having practiced indoor sports activities (aOR: 1•36; 95%CI: 1•15-1•62). We found no increase in risk associated with frequenting shops, cultural or religious gatherings, or with transportation, except for carpooling (aOR: 1•47; 95%CI: 1•28-1•69). Teleworking was associated with decreased risk of infection (aOR: 0•65; 95%CI: 0•56-0•75). Interpretation: Places and activities during which infection prevention and control measures may be difficult to fully enforce were those with increased risk of infection. Children attending day-care, kindergarten, middle and high schools, but not primary schools, were potential sources of infection for the household. Funding: Institut Pasteur, Research & Action Emerging Infectious Diseases (REACTing), Fondation de France (Alliance” Tous unis contre le virus”).
Published: 2021
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17. Impact of Introducing Hepatitis B Birth Dose Vaccines into the Infant Immunization Program in Burkina Faso: Study Protocol for a Stepped Wedge Cluster Randomized Trial (NéoVac Study)

Author: François Sawadogo, A. Sawadogo, Andréa Gosset, Alima T. Essoh, Dramane Kania, Lassané Kabore, Tamara Giles-Vernick, Yusuke Shimakawa, Nicolas Meda, Cassandre Von Platen, Pierrick Adam, Issa Ouedraogo, Alkadri Bokoum, Muriel Vray, Sandrine Fernandes-Pellerin, Magali Herrant, Amariane Ouattara, Ghislain Bouda, Haoua Tall, Laura Schaeffer, Hervé Hien, Jeanne Perpétue Vincent, Edouard Betsem, Pauline Boucheron, Seydou Ouattara, Sylvie Boyer, Abdoul Salam Eric Tiendrebeogo, Agence de Médecine Préventive [Burkina Faso], Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Centre de Recherche Translationnelle - Center for Translational Science (CRT), Institut Pasteur [Paris] (IP), Ministère de la Santé [Burkina Faso], Direction Internationale de l'Institut Pasteur, Centre Hospitalier Universitaire Souro Sanou [Bobo-Dioulasso] (CHUSS), Centre Muraz [Bobo-Dioulasso, Burkina Faso], Sciences Economiques et Sociales de la Santé & Traitement de l'Information Médicale (SESSTIM - U1252 INSERM - Aix Marseille Univ - UMR 259 IRD), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM), Anthropologie et écologie de l’émergence des maladies - Anthropology and Ecology of Disease Emergence, Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Institut Pasteur [Paris], and Malbec, Odile
Subjects: sub-Saharan Africa, HBsAg, Pediatrics, medicine.medical_specialty, Hepatitis B vaccine, [SDV]Life Sciences [q-bio], 030231 tropical medicine, Immunology, medicine.disease_cause, Article, complex intervention, law.invention, 03 medical and health sciences, 0302 clinical medicine, Randomized controlled trial, law, Drug Discovery, medicine, Pharmacology (medical), 030212 general & internal medicine, Cluster randomised controlled trial, stepped wedge cluster randomized trial, mixed method, 2. Zero hunger, Pharmacology, Hepatitis B virus, Hepatitis, implementation science, business.industry, birth dose vaccination, mother-to-child transmission, Hepatitis B, medicine.disease, 3. Good health, [SDV] Life Sciences [q-bio], Infectious Diseases, Immunization, Medicine, business, hepatitis B vaccine
Abstract: International audience; To achieve global hepatitis elimination by 2030, it is critical to prevent the mother-to-child transmission (MTCT) of hepatitis B virus (HBV). Since 2009, the WHO has recommended administering hepatitis B vaccine to all neonates within 24 h of birth to prevent MTCT. However, many countries in sub-Saharan Africa only provide hepatitis B immunization at the age of 6, 10, and 14 weeks or 8, 12, and 16 weeks using a combined vaccine. To accelerate the introduction of the hepatitis B birth dose vaccine (HepB-BD) into sub-Saharan Africa, it is critical to establish to what extent the addition of HepB-BD can further reduce HBV transmission in areas where three-dose infant vaccination has been implemented. We therefore designed a study to evaluate the impact, acceptability, and cost-effectiveness of incorporating the HepB-BD into the routine immunization program in a real-life field condition in Burkina Faso, where the hepatitis B vaccination is currently scheduled at 8-12-16 weeks. Through a multidisciplinary approach combining epidemiology, anthropology, and health economics, the Neonatal Vaccination against Hepatitis B in Africa (NéoVac) study conducts a pragmatic stepped wedge cluster randomized controlled trial in rural areas of the Hauts-Bassins Region. The study was registered in ClinicalTrials.gov (identifier: NCT04029454). A health center is designated as a cluster, and the introduction of HepB-BD will be rolled out sequentially in 24 centers. Following an initial period in which no health center administers HepB-BD, one center will be randomly allocated to incorporate HepB-BD. Then, at a regular interval, another center will be randomized to cross from the control to the intervention period, until all 24 centers integrate HepB-BD. Pregnant women attending antenatal care will be systematically invited to participate. Infants born during the control period will follow the conventional immunization schedule (8-12-16 weeks), while those born in the interventional period will receive HepB-BD in addition to the routine vaccines (0-8-12-16 weeks). The primary outcome, the proportion of hepatitis B surface antigen (HBsAg) positivity in infants aged at 9 months, will be compared between children born before and after HepB-BD introduction. The study will generate data that may assist governments and stakeholders in sub-Saharan Africa to make evidence-based decisions about whether to add HepB-BD into the national immunization programs.
Published: 2021
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18. Comparative Immuno-Virological and Clinical Responses to Antiretroviral Therapy between HIV-1 Group O- and HIV-1 Group M-Infected Patients (ANRS 12168 DynaMO Study)

Author: Elodie Alessandri-Gradt, Rose Mougnutou, Laura Schaeffer, Eric Delaporte, Jean-Christopher Plantier, Anfumbom Kfutwah, Charles Kouanfack, Muriel Vray, Avelin F. Aghokeng, Nathalie Noumsi, François Simon, and Guillemette Unal
Subjects: medicine.medical_specialty, HBsAg, education.field_of_study, biology, business.industry, Population, virus diseases, Context (language use), biology.organism_classification, Antiretroviral therapy, Clinical trial, Internal medicine, Clinical endpoint, Medicine, business, Sida, education, Viral load
Abstract: Backgroud: HIV-1/O presents a high level of genetic divergence relative to HIV-1/M which impacts viral load monitoring and drug susceptibility; however, its impact on therapeutic outcomes is still poorly known. The aim of this study was to determine if responses to standardised cART based on 2NRTIs 1IP/r were similar between group O and M infections despite strain divergence. Methods: We performed an open non-randomised study comparing the immunological, virological and clinical responses to cART, in naive and paired HIV-1/O- versus HIV-1/M-infected patients. Each HIV-1/O patient was matched to two HIV-1/M patients on sex, age, CD4 cell count, haemoglobin level, and HBsAg status. The primary endpoint was the proportion of patients with an undetectable plasma viral load (pVL
Published: 2018
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19. Simian Immunodeficiency Virus seroreactivity in inhabitants from rural Cameroon frequently in contact with non-human primates

Author: Arnaud Fontanet, Antoine Gessain, Claudia Filippone, Fabienne De Oliveira, Edouard Betsem, Jean-Christophe Plantier, Laura Schaeffer, Véronique Lemée, Epidémiologie et Physiopathologie des Virus Oncogènes (EPVO (UMR_3569 / U-Pasteur_3)), Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Institut Pasteur [Paris], Unité de Virologie [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), CHU Rouen, Normandie Université (NU), University of Yaoundé [Cameroun], Epidémiologie des Maladies Emergentes - Emerging Diseases Epidemiology, Pasteur-Cnam Risques infectieux et émergents (PACRI), Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM)-Institut Pasteur [Paris]-Conservatoire National des Arts et Métiers [CNAM] (CNAM), Groupe de Recherche sur l'Adaptation Microbienne (GRAM 2.0), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU)-Université de Caen Normandie (UNICAEN), This work was supported by the Institut Pasteur and the Investissement d’ Avenir program, as part of a Laboratoire d’ Excellence (LabEx) research program: Integrative Biology of Emerging Infectious Diseases (IBEID), and the CHU de Rouen. Claudia Filippone was supported by the European programs EDENext (No. 261504) and EMPERIE (No. 223498). Edouard Betsem was supported by the 'Service de Coopération et de l'Action Culturelle (SCAC) ’of the French embassy in Yaounde, Cameroon and the ‘Institut National pour le Cancer ’ (France)., European Project: 261504,EC:FP7:HEALTH,FP7-HEALTH-2010-single-stage,EDENEXT(2011), European Project: 223498,EC:FP7:HEALTH,FP7-HEALTH-2007-B,EMPERIE(2009), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-Institut Pasteur [Paris] (IP)-Conservatoire National des Arts et Métiers [CNAM] (CNAM), HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM)-HESAM Université - Communauté d'universités et d'établissements Hautes écoles Sorbonne Arts et métiers université (HESAM), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Epidémiologie des Maladies Emergentes, and Pasteur-Cnam risques infectieux et émergents (PACRI)
Subjects: 0301 basic medicine, Male, Cross-sectional study, viruses, [SDV]Life Sciences [q-bio], Cross-species transmission, Simian foamy virus, MESH: Pan troglodytes, Simian, Seroreactivity, medicine.disease_cause, MESH: Simian foamy virus, Bite, MESH: Aged, 80 and over, Risk Factors, MESH: Risk Factors, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Surveys and Questionnaires, Zoonoses, MESH: Child, MESH: Animals, Bites and Stings, Cameroon, Young adult, Child, Aged, 80 and over, MESH: Aged, education.field_of_study, Pygmies, Central Africa, MESH: Middle Aged, biology, virus diseases, Middle Aged, 3. Good health, MESH: Bites and Stings, SIV, MESH: Young Adult, Child, Preschool, MESH: Retroviridae Infections, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Female, Simian Immunodeficiency Virus, MESH: Cercopithecus, Simian T-lymphotropic virus 1, MESH: Zoonoses, Adult, Adolescent, Pan troglodytes, MESH: Simian T-lymphotropic virus 1, Population, MESH: Simian Immunodeficiency Virus, Cercopithecus, 03 medical and health sciences, Young Adult, MESH: Cross-Sectional Studies, Virology, medicine, Animals, Humans, Risk factor, MESH: Surveys and Questionnaires, education, Aged, MESH: Adolescent, Gorilla gorilla, MESH: Humans, MESH: Gorilla gorilla, MESH: Child, Preschool, HIV, MESH: Adult, Simian immunodeficiency virus, MESH: Cameroon, biology.organism_classification, Non-human primate, MESH: Male, 030104 developmental biology, Cross-Sectional Studies, Immunology, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Female, Retroviridae Infections
Abstract: International audience; Central African tropical forests are home to several species of non-human primates (NHPs), infected by Simian Immunodeficiency Virus (SIV). It is well-known that HIV-1 epidemic is due to cross-transmission and adaptation of SIV to humans. The main goal of this work was to investigate if a NHP bite is a risk factor for SIV acquisition. A cross-sectional study was performed in rural Cameroon on 246 bitten individuals (mostly by adult NHPs), matched, according to sex, age, and ethnicity (Bantus and Pygmies), with an equal number of not-bitten subjects. Following a serological assay for a wide range of SIVs, we observed a high level of indeterminate seroreactivity (25.8%) in the total population, whereas 68.9% were sero-negative and 5.3% HIV-1 positive. Bites do not appear to be a risk factor for SIV seroreactivity, in contrast to Simian Foamy Virus and Simian T-Lymphotropic Virus type 1 in the same studied population.
Published: 2017
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20. How to estimate exposure when studying the temperature-mortality relationship? A case study of the Paris area

Author: Julien Desplat, Perrine De Crouy-Chanel, Laura Schaeffer, Vérène Wagner, Mathilde Pascal, Institut de Veille Sanitaire (INVS), Météo-France [Paris], and Météo France
Subjects: Risk, Paris, Atmospheric Science, Percentile, MESH: Air Pollution, 010504 meteorology & atmospheric sciences, Health, Toxicology and Mutagenesis, Population, Poison control, 010501 environmental sciences, 01 natural sciences, Weather station, symbols.namesake, Heat wave, Air Pollution, Statistics, MESH: Humidity, Humans, Climate change, Poisson regression, Time series, Mortality, education, Aged, 0105 earth and related environmental sciences, Exposure assessment, MESH: Aged, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, education.field_of_study, MESH: Humans, MESH: Risk, Ecology, MESH: Mortality, MESH: Paris, Environmental engineering, Temperature, Humidity, MESH: Temperature, 13. Climate action, Relative risk, symbols, Environmental science
Abstract: International audience; Time series studies assessing the effect of temperature on mortality generally use temperatures measured by a single weather station. In the Paris region, there is a substantial measurement network, and a variety of exposure indicators created from multiple stations can be tested. The aim of this study is to test the influence of exposure indicators on the temperature-mortality relationship in the Paris region. The relationship between temperature and non-accidental mortality was assessed based on a time series analysis using Poisson regression and a generalised additive model. Twenty-five stations in Paris and its three neighbouring departments were used to create four exposure indicators. These indicators were (1) the temperature recorded by one reference station, (2) a simple average of the temperatures of all stations, (3) an average weighted on the departmental population and (4) a classification of the stations based on land use and an average weighted on the population in each class. The relative risks and the Akaike criteria were similar for all the exposure indicators. The estimated temperature-mortality relationship therefore did not appear to be significantly affected by the indicator used, regardless of study zone (departments or region) or age group. The increase in temperatures from the 90(th) to the 99(th) percentile of the temperature distribution led to a significant increase in mortality over 75 years (RR = 1.10 [95% CI, 1.07; 1.14]). Conversely, the decrease in temperature between the 10(th) and 1(st) percentile had a significant effect on the mortality under 75 years (RR = 1.04 [95% CI, 1.01; 1.06]). In the Paris area, there is no added value in taking multiple climatic stations into account when estimating exposure in time series studies. Methods to better represent the subtle temperature variations in densely populated areas in epidemiological studies are needed.
Published: 2016
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21. Les enfants présentant un retard de croissance présentent une colonisation ectopique de l'intestin grêle par des bactéries buccales, qui provoquent une malabsorption des lipides dans des modèles expérimentaux

Author: Vonaesch, P., Araújo, J. R., Gody, J. C., Mbecko, J. R., Sanke, H., Andrianonimiadana, L., Naharimanananirina, T., Ningatoloum, S. N., Vondo, S. S., Gondje, P. B., Rodriguez-Pozo, A., Rakotondrainipiana, M., Kandou, K. J. E., Nestoret, A., Kapel, N., Djorie, S. G., Finlay, B. B., Wegener Parfrey, L., Collard, J. M., Randremanana, R. V., Sansonetti, P. J., Afribiota Investigators, Pathogénie microbienne moléculaire, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Swiss Tropical and Public Health Institute [Basel], Université de Lausanne = University of Lausanne (UNIL), University of Basel (Unibas), Centre pédiatrique de Bangui, Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Unité de Bactériologie Expérimentale [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHUJRA), Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of British Columbia (UBC), Collège de France (CdF (institution)), This project was funded by the Total Foundation, the Institut Pasteur, Bill and Melinda Gates Foundation Grant OPP1204689, the Fondation Petram, Nutricia Foundation Grant NRF 2016-10, and a donation from the Odyssey Re-Insurance Company. P.V. was supported by Swiss National Science Foundation Early Postdoctoral Fellowship P2EZP3_152159, Advanced Postdoctoral Fellowship P300PA_177876, and Return Grant P3P3PA_17877, a Roux-Cantarini fellowship (2016), a L’Oréal–UNESCO for Women in Science France fellowship (2017), and an Excellence Scholarship from the University of Basel (Forschungsfonds, 2019). Her group is funded through the NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation (grant number 180575). Work in the group of L.W.P. is funded by Human Frontier Science Program Grant RGY0078/2015. P.J.S. is a Howard Hughes Medical Institute Senior Foreign Scholar and CIFAR scholar in the human microbiome consortium., We thank all children and their families who participated in the Afribiota project. Further, we thank the Afribiota Consortium, the participating hospitals in Bangui and Antananarivo, the Institut Pasteur, the Institut Pasteur de Madagascar, the Institut Pasteur de Bangui, and members of the scientific advisory boards for their continuous support, and we thank the Centre de Recherche Translationelle and the Direction Internationale of the Institut Pasteur (especially Paméla Palvadeau, Jane Lynda Deuve, Cécile Artaud, Nathalie Jolly, Sophie Jarrijon, Mamy Ratsialonina, and Jean-François Damaras) for help in setting up and steering the Afribiota project. We also thank J.-M.C., Pierre-Alain Rubbo, Dieu-Merci Welekoi-Yapondo, L.A., Laurence Arowas, and Marie-Noelle Ungeheuer for managing the biobank, the members of the animal facility at the Institut Pasteur for taking care of the mice, the Centre d’Immunolgoie Humaine of the Institut Pasteur, especially Milena Hasan, Tarshana Stephen, and Esma Karkeni, for help with setting up the LUMINEX assays at their platform, Asmaa Tazi for identification of the bacteria by MALDI-TOF spectroscopy, Estelle Martineau at the Platform Spectrometries Capacités at the University of Nantes for quantification of the fermentation products, Kelsey Huus for critical reading of the manuscript, and Munir Winkel for streamlining of the R code., and Liste of Afribiota Inverstigators : Laurence Barbot-Trystram, Hôpital Pitié-Salpêtrière, Paris, France Robert Barouki, Hôpital Necker- Enfants maladies, Paris, France Alexandra Bastaraud, Institut Pasteur de Madagascar, Antananarivo, Madagascar Jean-Marc Collard, Institut Pasteur de Madagascar, Antananarivo, Madagascar Maria Doria, Institut Pasteur, Paris, France Darragh Duffy, Institut Pasteur, Paris, France B. Brett Finlay, University of British Columbia, Vancouver, Canada Serge Ghislain Djorie, Institut Pasteur de Bangui, Bangui, Central African Republic Tamara Giles-Vernick, Institut Pasteur, Paris, France Bolmbaye Privat Gondje, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Jean-Chrysostome Gody, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Milena Hasan, Institut Pasteur, France Francis Allen Hunald, Service de Chirurgie pédiatrique, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar Nathalie Kapel, Hôpital Pitié-Salpêtrière, Paris, France Jean-Pierre Lombart, Institut Pasteur de Bangui, Bangui, Central African Republic Alexandre Manirakiza, Institut Pasteur de Bangui, Bangui, Central African Republic Synthia Nazita Nigatoloum, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Laura Wegener Parfrey, University of British Columbia, Vancouver, Canada Lisette Raharimalala, Centre de Santé Materno-Infantile, Tsaralalana, Antananarivo, Madagascar Maheninasy Rakotondrainipiana, Institut Pasteur de Madagascar, Antananarivo, Madagascar Rindra Vatosoa Randremanana, Institut Pasteur de Madagascar, Antananarivo, Madagascar Harifetra Mamy Richard Randriamizao, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar Frédérique Randrianirina, Institut Pasteur de Madagascar, Antananarivo, Madagascar Annick Robinson, Centre Hospitalier Universitaire Mère Enfant de Tsaralalana, Antananarivo, Madagascar Pierre-Alain Rubbo, Institut Pasteur de Bangui, Bangui, République Centrafricaine Philippe Sansonetti, Institut Pasteur, Paris, France Laura Schaeffer, Institut Pasteur, Paris, France Ionela Gouandjika-Vassilache, Institut Pasteur de Bangui, Bangui, République Centrafricaine Pascale Vonaesch, Institut Pasteur, Paris, France Sonia Sandrine Vondo, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Inès Vigan-Womas, Institut Pasteur de Madagascar, Antananarivo, Madagasca
Subjects: Mouth, Multidisciplinary, Bacteria, lipid malabsorption, [SDV]Life Sciences [q-bio], [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, Models, Theoretical, Lipid Metabolism, Lipids, Gastrointestinal Microbiome, Mice, Cross-Sectional Studies, Malabsorption Syndromes, stunted child growth, Child, Preschool, Intestine, Small, environmental enteric dysfunction, low-grade inflammation, Animals, Humans, Leukocyte L1 Antigen Complex, small intestine, Growth Disorders
Abstract: International audience; Environmental enteric dysfunction (EED) is an inflammatory syndrome postulated to contribute to stunted child growth and to be associated with intestinal dysbiosis and nutrient malabsorption. However, the small intestinal contributions to EED remain poorly understood. This study aimed to assess changes in the proximal and distal intestinal microbiota in the context of stunting and EED and to test for a causal role of these bacterial isolates in the underlying pathophysiology. We performed a cross-sectional study in two African countries recruiting roughly 1,000 children aged 2 to 5 years and assessed the microbiota in the stomach, duodenum, and feces. Upper gastrointestinal samples were obtained from stunted children and stratified according to stunting severity. Fecal samples were collected. We then investigated the role of clinical isolates in EED pathophysiology using tissue culture and animal models. We find that small intestinal bacterial overgrowth (SIBO) is extremely common (>80%) in stunted children. SIBO is frequently characterized by an overgrowth of oral bacteria, leading to increased permeability and inflammation and to replacement of classical small intestinal strains. These duodenal bacterial isolates decrease lipid absorption in both cultured enterocytes and mice, providing a mechanism by which they may exacerbate EED and stunting. Further, we find a specific fecal signature associated with the EED markers fecal calprotectin and alpha-antitrypsin. Our study shows a causal implication of ectopic colonization of oral bacterial isolated from the small intestine in nutrient malabsorption and gut leakiness in vitro. These findings have important therapeutic implications for modulating the microbiota through microbiota-targeted interventions.
Published: 2022
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22. Stunted children display ectopic small intestinal colonization by oral bacteria, which cause lipid malabsorption in experimental models

Author: Vonaesch, Pascale, Araújo, João, Gody, Jean-Chrysostome, Mbecko, Jean-Robert, Sanke, Hugues, Andrianonimiadana, Lova, Naharimanananirina, Tanteliniaina, Ningatoloum, Synthia Nazita, Vondo, Sonia Sandrine, Gondje, Privat Bolmbaye, Rodriguez-Pozo, Andre, Rakotondrainipiana, Maheninasy, Kandou, Kaleb Jephté Estimé, Nestoret, Alison, Kapel, Nathalie, Djorie, Serge Ghislain, Finlay, B. Brett, Wegener Parfrey, Laura, Collard, Jean-Marc, Randremanana, Rindra Vatosoa, Sansonetti, Philippe, Collard, Jean-Marc, Pathogénie microbienne moléculaire, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Swiss Tropical and Public Health Institute [Basel], Université de Lausanne = University of Lausanne (UNIL), University of Basel (Unibas), Centre pédiatrique de Bangui, Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Unité de Bactériologie Expérimentale [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHUJRA), Immunologie Translationnelle - Translational Immunology lab, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), CHU Pitié-Salpêtrière [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), University of British Columbia (UBC), Collège de France (CdF (institution)), This project was funded by the Total Foundation, the Institut Pasteur, Bill and Melinda Gates Foundation Grant OPP1204689, the Fondation Petram, Nutricia Foundation Grant NRF 2016-10, and a donation from the Odyssey Re-Insurance Company. P.V. was supported by Swiss National Science Foundation Early Postdoctoral Fellowship P2EZP3_152159, Advanced Postdoctoral Fellowship P300PA_177876, and Return Grant P3P3PA_17877, a Roux-Cantarini fellowship (2016), a L’Oréal–UNESCO for Women in Science France fellowship (2017), and an Excellence Scholarship from the University of Basel (Forschungsfonds, 2019). Her group is funded through the NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation (grant number 180575). Work in the group of L.W.P. is funded by Human Frontier Science Program Grant RGY0078/2015. P.J.S. is a Howard Hughes Medical Institute Senior Foreign Scholar and CIFAR scholar in the human microbiome consortium., We thank all children and their families who participated in the Afribiota project. Further, we thank the Afribiota Consortium, the participating hospitals in Bangui and Antananarivo, the Institut Pasteur, the Institut Pasteur de Madagascar, the Institut Pasteur de Bangui, and members of the scientific advisory boards for their continuous support, and we thank the Centre de Recherche Translationelle and the Direction Internationale of the Institut Pasteur (especially Paméla Palvadeau, Jane Lynda Deuve, Cécile Artaud, Nathalie Jolly, Sophie Jarrijon, Mamy Ratsialonina, and Jean-François Damaras) for help in setting up and steering the Afribiota project. We also thank J.-M.C., Pierre-Alain Rubbo, Dieu-Merci Welekoi-Yapondo, L.A., Laurence Arowas, and Marie-Noelle Ungeheuer for managing the biobank, the members of the animal facility at the Institut Pasteur for taking care of the mice, the Centre d’Immunolgoie Humaine of the Institut Pasteur, especially Milena Hasan, Tarshana Stephen, and Esma Karkeni, for help with setting up the LUMINEX assays at their platform, Asmaa Tazi for identification of the bacteria by MALDI-TOF spectroscopy, Estelle Martineau at the Platform Spectrometries Capacités at the University of Nantes for quantification of the fermentation products, Kelsey Huus for critical reading of the manuscript, and Munir Winkel for streamlining of the R code., and Liste of Afribiota Inverstigators : Laurence Barbot-Trystram, Hôpital Pitié-Salpêtrière, Paris, France Robert Barouki, Hôpital Necker- Enfants maladies, Paris, France Alexandra Bastaraud, Institut Pasteur de Madagascar, Antananarivo, Madagascar Jean-Marc Collard, Institut Pasteur de Madagascar, Antananarivo, Madagascar Maria Doria, Institut Pasteur, Paris, France Darragh Duffy, Institut Pasteur, Paris, France B. Brett Finlay, University of British Columbia, Vancouver, Canada Serge Ghislain Djorie, Institut Pasteur de Bangui, Bangui, Central African Republic Tamara Giles-Vernick, Institut Pasteur, Paris, France Bolmbaye Privat Gondje, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Jean-Chrysostome Gody, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Milena Hasan, Institut Pasteur, France Francis Allen Hunald, Service de Chirurgie pédiatrique, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar Nathalie Kapel, Hôpital Pitié-Salpêtrière, Paris, France Jean-Pierre Lombart, Institut Pasteur de Bangui, Bangui, Central African Republic Alexandre Manirakiza, Institut Pasteur de Bangui, Bangui, Central African Republic Synthia Nazita Nigatoloum, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Laura Wegener Parfrey, University of British Columbia, Vancouver, Canada Lisette Raharimalala, Centre de Santé Materno-Infantile, Tsaralalana, Antananarivo, Madagascar Maheninasy Rakotondrainipiana, Institut Pasteur de Madagascar, Antananarivo, Madagascar Rindra Vatosoa Randremanana, Institut Pasteur de Madagascar, Antananarivo, Madagascar Harifetra Mamy Richard Randriamizao, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar Frédérique Randrianirina, Institut Pasteur de Madagascar, Antananarivo, Madagascar Annick Robinson, Centre Hospitalier Universitaire Mère Enfant de Tsaralalana, Antananarivo, Madagascar Pierre-Alain Rubbo, Institut Pasteur de Bangui, Bangui, République Centrafricaine Philippe Sansonetti, Institut Pasteur, Paris, France Laura Schaeffer, Institut Pasteur, Paris, France Ionela Gouandjika-Vassilache, Institut Pasteur de Bangui, Bangui, République Centrafricaine Pascale Vonaesch, Institut Pasteur, Paris, France Sonia Sandrine Vondo, Complexe Pédiatrique de Bangui, Bangui, Central African Republic Inès Vigan-Womas, Institut Pasteur de Madagascar, Antananarivo, Madagasca
Subjects: [SDV] Life Sciences [q-bio], stunted child growth, lipid malabsorption, [SDV]Life Sciences [q-bio], environmental enteric dysfunction, low-grade inflammation, [SDV.MHEP.HEG]Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology, small intestine, [SDV.MHEP.HEG] Life Sciences [q-bio]/Human health and pathology/Hépatology and Gastroenterology
Abstract: International audience; Environmental enteric dysfunction (EED) is an inflammatory syndrome postulated to contribute to stunted child growth and to be associated with intestinal dysbiosis and nutrient malabsorption. However, the small intestinal contributions to EED remain poorly understood. This study aimed to assess changes in the proximal and distal intestinal microbiota in the context of stunting and EED and to test for a causal role of these bacterial isolates in the underlying pathophysiology. We performed a cross-sectional study in two African countries recruiting roughly 1,000 children aged 2 to 5 years and assessed the microbiota in the stomach, duodenum, and feces. Upper gastrointestinal samples were obtained from stunted children and stratified according to stunting severity. Fecal samples were collected. We then investigated the role of clinical isolates in EED pathophysiology using tissue culture and animal models. We find that small intestinal bacterial overgrowth (SIBO) is extremely common (>80%) in stunted children. SIBO is frequently characterized by an overgrowth of oral bacteria, leading to increased permeability and inflammation and to replacement of classical small intestinal strains. These duodenal bacterial isolates decrease lipid absorption in both cultured enterocytes and mice, providing a mechanism by which they may exacerbate EED and stunting. Further, we find a specific fecal signature associated with the EED markers fecal calprotectin and alpha-antitrypsin. Our study shows a causal implication of ectopic colonization of oral bacterial isolated from the small intestine in nutrient malabsorption and gut leakiness in vitro. These findings have important therapeutic implications for modulating the microbiota through microbiota-targeted interventions.
Published: 2022
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23. High prevalence of intestinal parasite infestations among stunted and control children aged 2 to 5 years old in two neighborhoods of Antananarivo, Madagascar

Author: Habib, Azimdine, Andrianonimiadana, Lova, Rakotondrainipiana, Maheninasy, Andriantsalama, Prisca, Randriamparany, Ravaka, Randremanana, Rindra, Rakotoarison, Rado, Vigan‑womas, Inès, Rafalimanantsoa, Armand, Vonaesch, Pascale, Sansonetti, Philippe, Collard, Jean-Marc, Investigators, The Afribiota, Vigan-Womas, Inès, Unité de Bactériologie Expérimentale [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Unité d’Épidémiologie et de Recherche clinique [Antananarivo, Madagascar], Unité d'immunologie des maladies infectieuses [Antananarivo, Madagascar] (IPM), Unité des Helminthiases [Antananarivo, Madagascar] (IPM), Pathogénie microbienne moléculaire, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), PV was supported by an Early Postdoctoral Fellowship (P2EZP3_152159), an Advanced Postdoctoral Fellowship (P300PA_177876) as well as a Return Grant (P3P3PA_17877) from the Swiss National Science Foundation, a Roux-Cantarini Fellowship (2016) and a L'Oréal-UNESCO for Women in Science France Fellowship (2017). The parasitology part of AFRIBIOTA was funded by the Total Foundation (2016) as well as the Fondation Petram (2014)., AFRIBIOTA Investigators (Group authorship in alphabetical order): Annick Robinson, Centre Hospitalier Universitaire Mère Enfant de Tsaralalana, Antananarivo, Madagascar, Aurélie Etienne, Institut Pasteur, Paris, France/ Institut Pasteur de Madagascar, Darragh Duffy, Institut Pasteur, Paris, France, Emilson Jean Andriatahirintsoa, Centre Hospitalier Universitaire Mère Enfant de Tsaralalana, Antananarivo, Francis Allan Hunald, Centre Hospitalier Universitaire Joseph Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar, Harifetra Mamy Richard Randriamizao, Centre Hospitalier Universitaire Joseph, Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar, Inès Vigan-Womas, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Jean-Chrysostome Gody, Complexe Pédiatrique de Bangui, Bangui, Central, African Republic, Jean-Marc Collard, Institut Pasteur de Madagascar Antananarivo, Madagascar, Laura Schaeffer, Institut Pasteur, Paris, France, Lisette Raharimalala, Centre social Materno-Infantile, Tsaralalana, Antananarivo, Madagascar, Maheninasy Rakotondrainipiana, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Milena Hasan, Institut Pasteur, Paris, France, Pascale Vonaesch, Institut Pasteur, Paris, France, Philippe Sansonetti, Institut Pasteur, Paris, France, Ravoahangy Andrianavalona (CHU-JRA), Antananarivo, Madagascar, Madagascar, Rindra Randremanana, Institut Pasteur de Madagascar, Antananarivo, Madagascar, Serge Ghislain Djorie, Institut Pasteur de Bangui, Bangui, Central African, Republic., and Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)
Subjects: Male, Nematoda, RC955-962, MESH: Logistic Models, Artificial Gene Amplification and Extension, Polymerase Chain Reaction, Feces, Families, 0302 clinical medicine, Medical Conditions, Arctic medicine. Tropical medicine, Medicine, MESH: Animals, Children, Protozoans, High prevalence, MESH: Feces, Eukaryota, 3. Good health, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Child, Preschool, Ascaris lumbricoides, Public aspects of medicine, [SDV.IMM] Life Sciences [q-bio]/Immunology, 03 medical and health sciences, Entamoeba histolytica, MESH: Cross-Sectional Studies, Madagascar, Humans, Parasites, Molecular Biology Techniques, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Molecular Biology, MESH: Prevalence, MESH: Humans, MESH: Child, Preschool, Public Health, Environmental and Occupational Health, Organisms, Biology and Life Sciences, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, Invertebrates, Cross-Sectional Studies, Logistic Models, Trichuris trichiura, Parasitology, Population Groupings, MESH: Female, Digestive System, Demography, Ascaris Lumbricoides, Water source, medicine.disease_cause, [SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, MESH: Madagascar, Intestinal Parasites, MESH: Risk Factors, Risk Factors, Poverty Areas, Prevalence, Medicine and Health Sciences, 030212 general & internal medicine, Intestinal Diseases, Parasitic, MESH: Poverty Areas, 2. Zero hunger, biology, Ascaris, 1. No poverty, Infectious Diseases, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, RA1-1270, Anatomy, Research Article, 030231 tropical medicine, Intestinal parasite, MESH: Parasitology, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Research and Analysis Methods, MESH: Multivariate Analysis, Entamoeba Histolytica, Helminths, Infestation, parasitic diseases, Parasitic Diseases, Animals, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, MESH: Parasites, Protozoan Infections, business.industry, biology.organism_classification, MESH: Intestinal Diseases, Parasitic, MESH: Male, Parasitic Protozoans, Gastrointestinal Tract, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, Age Groups, Multivariate Analysis, People and Places, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, business, Parasitic Intestinal Diseases, Zoology
Abstract: Background This study aimed to compare the prevalence of intestinal parasite infestations (IPIs) in stunted children, compared to control children, in Ankasina and Andranomanalina Isotry (two disadvantaged neighborhoods of Antananarivo, Madagascar), to characterize associated risk factors and to compare IPI detection by real-time PCR and standard microscopy techniques. Methodology/Principal findings Fecal samples were collected from a total of 410 children (171 stunted and 239 control) aged 2–5 years. A single stool sample per subject was examined by simple merthiolate-iodine-formaldehyde (MIF), Kato-Katz smear and real-time PCR techniques. A total of 96.3% of the children were infested with at least one intestinal parasite. The most prevalent parasites were Giardia intestinalis (79.5%), Ascaris lumbricoides (68.3%) and Trichuris trichiura (68.0%). For all parasites studied, real-time PCR showed higher detection rates compared to microscopy (G. intestinalis [77.6% (n = 318) versus 20.9% (n = 86)], Entamoeba histolytica [15.8% (n = 65) versus 1.9% (n = 8)] and A. lumbricoides [64.1% (n = 263) versus 50.7% (n = 208)]). Among the different variables assessed in the study, age of 4 to 5 years (AOR = 4.61; 95% CI, (1.35–15.77)) and primary and secondary educational level of the mother (AOR = 12.59; 95% CI, (2.76–57.47); AOR = 9.17; 95% CI, (2.12–39.71), respectively) were significantly associated with IPIs. Children drinking untreated water was associated with infestation with G. intestinalis (AOR = 1.85; 95% CI, (1.1–3.09)) and E. histolytica (AOR = 1.9; 95% CI, (1.07–3.38)). E. histolytica was also associated with moderately stunted children (AOR = 0.37; 95% CI, 0.2–0.71). Similarly, children aged between 4 and 5 years (AOR = 3.2; 95% CI (2.04–5.01)) and living on noncemented soil types (AOR = 1.85; 95% CI, (1.18–2.09)) were associated with T. trichiura infestation. Conclusions/Significance The prevalence of IPIs is substantial in the studied areas in both stunted and control children, despite the large-scale drug administration of antiparasitic drugs in the country. This high prevalence of IPIs warrants further investigation. Improved health education, environmental sanitation and quality of water sources should be provided., Author summary In populations living in adverse conditions due to poverty, a wide variety of intestinal parasite infestations can be observed. These infestations are usually diagnosed by stool microscopy but can be easily overlooked if the procedures used are inaccurate or performed in a suboptimal way. In the present study, we investigated the prevalence of intestinal parasite infestations in stunted and control children aged from 2 to 5 years living in two disadvantaged neighborhoods of Antananarivo Madagascar. We also assessed risk factors for infestations and the diagnostic performance of microscopic techniques and real-time PCR for the detection of parasites. Almost all individuals were found to be infested with at least one parasitic species. Children aged between 4 and 5 years and mothers with low educational levels were found to be associated with infestation. Similarly, children drinking untreated water were associated with G. intestinalis and E. histolytica infestation. This latter species was also associated with moderately stunted children. Children between 4 and 5 years old and with no cemented soil type were associated with T. trichiura infestation. The high prevalence of intestinal parasite infestations among the study participants requires the improvement of health education, environmental sanitation and quality of water sources.
Published: 2020
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24. Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study

Author: Pascale Vonaesch, Nathalie Kapel, Michel Dede, André Rodriguez-Pozo, Amee R. Manges, Alison Nestoret, Afribiota Investigators, Azimdine Habib, B. Brett Finlay, Philippe J. Sansonetti, Kelsey E. Huus, Jean-Marc Collard, University of British Columbia (UBC), Pathogénie microbienne moléculaire, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), CHU Pitié-Salpêtrière [AP-HP], Sorbonne Université (SU)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Unité des Helminthiases [Antananarivo, Madagascar] (IPM), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut Pasteur de Bangui, Réseau International des Instituts Pasteur (RIIP), Unité de Bactériologie Expérimentale [Antananarivo, Madagascar] (IPM), Chaire Microbiologie et Maladies infectieuses, Collège de France (CdF (institution)), This research was supported by grants from the Canadian Institutes of Health Research (CIHR), the Bill and Melinda Gates Foundation and the Total Foundation. Work in PJS’s laboratory is supported by grants from the European Research Commission. Work in BBF’s laboratory was supported by grants from CIHR. KEH was supported by a CIHR Vanier Graduate scholarship, a Killam fellowship and a Four-Year Fellowship. PV was supported by a Swiss National Science Foundation Early and Advanced Postdoctoral Fellowship as well as Return Grant, a Roux-Cantarini Postdoctoral Fellowship and a fellowship from L’Oréal-UNESCO for Women in Science., We are deeply grateful to the children and families who participated in Afribiota and to the large team of community health workers, nurses, doctors, technicians, administrators, and others without whom this study would not have been possible. We would like to thank Andy Johnson and Justin Wong at UBC for their invaluable assistance in the flow cytometry facility, as well as Lisa Thorson and Adrian Carney for their help in arranging and receiving sample shipments at the Michael Smith Laboratories. We are further grateful to Vincent Guillemot and Antoine Menard at the Institut Pasteur for their advice on biostatistic analysis and to the members of the Sansonetti research group and the Finlay laboratory for their support and feedback., The Afribiota Investigators are: (in alphabetical order): Emilson Jean Andriatahirintsoa, Alexandra Bastaraud, Jean-Marc Collard, Maria Doria, Serge Ghislain Djorie, Aurélie Etienne, Brett Finlay, Tamara Giles-Vernick, Jean-Chrysostome Gody, Bolmbaye Privat Godje, Ionela Gouandjika-Vassilache, Francis Allan Hunald, Nathalie Kapel, Jean-Pierre Lombart, Alexandre Manirakiza, Synthia Nazita Nigatoloum, Lisette Raharimalala, Maheninasy Rakotondrainipiana, Rindra Randremanana, Harifetra Mamy Richard Randriamizao, Frédérique Randrianirina, Annick Robinson, Pierre-Alain Rubbo, Philippe Sansonetti, Laura Schaeffer, Inès Vigan-Womas, Sonia Sandrine Vondo, Pascale Vonaesch & Laura Wegener-Parfrey, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Sorbonne Université (SU), and Collège de France - Chaire Microbiologie et Maladies infectieuses
Subjects: Male, Immunoglobulin A, medicine.disease_cause, Immunoglobulin G, Feces, Medical microbiology, RNA, Ribosomal, 16S, Growth Disorders, 2. Zero hunger, Stunting, 0303 health sciences, Sub-Saharan Africa, biology, Campylobacter, 3. Good health, Central African Republic, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, Child, Preschool, Environmental Enteric dysfunction, lcsh:QR100-130, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Microbiology (medical), medicine.medical_specialty, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Microbiology, lcsh:Microbial ecology, 03 medical and health sciences, Haemophilus, Madagascar, medicine, Humans, Microbiome, 030304 developmental biology, Bacteria, 030306 microbiology, Research, Malnutrition, Undernutrition, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, biology.organism_classification, medicine.disease, Fecal coliform, Immunology, biology.protein, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie
Abstract: Background Child undernutrition is a global health issue that is associated with poor sanitation and an altered intestinal microbiota. Immunoglobulin (Ig) A mediates host-microbial homeostasis in the intestine, and acutely undernourished children have been shown to have altered IgA recognition of the fecal microbiota. We sought to determine whether chronic undernutrition (stunting) or intestinal inflammation were associated with antibody recognition of the microbiota using two geographically distinct populations from the Afribiota project. Fecal bacteria from 200 children between 2 and 5 years old in Antananarivo, Madagascar, and Bangui, Central African Republic (CAR), were sorted into IgA-positive (IgA+) and IgA-negative (IgA−) populations by flow cytometry and subsequently characterized by 16S rRNA gene sequencing to determine IgA-bacterial targeting. We additionally measured IgG+ fecal bacteria by flow cytometry in a subset of 75 children. Results Stunted children (height-for-age z-score ≤ −2) had a greater proportion of IgA+ bacteria in the fecal microbiota compared to non-stunted controls. This trend was consistent in both countries, despite the higher overall IgA-targeting of the microbiota in Madagascar, but lost significance in each country individually. Two of the most highly IgA-recognized bacteria regardless of nutritional status were Campylobacter (in CAR) and Haemophilus (in both countries), both of which were previously shown to be more abundant in stunted children; however, there was no association between IgA-targeting of these bacteria and either stunting or inflammatory markers. IgG-bound intestinal bacteria were rare in both stunted and non-stunted children, similar to levels observed in healthy populations. Conclusions Undernourished children carry a high load of intestinal pathogens and pathobionts. Our data suggest that stunted children have a greater proportion of IgA-recognized fecal bacteria. We moreover identify two putative pathobionts, Haemophilus and Campylobacter, that are broadly targeted by intestinal IgA. This study furthers our understanding of host-microbiota interactions in undernutrition and identifies immune-recognized microbes for future study.
Published: 2020
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24 results on '"Laura Schaeffer"'

1. Reduction of SARS-CoV-2 intra-household child-to-parent transmission associated with ventilation: results from a case–control study

2. National Monkeypox Surveillance, Central African Republic, 2001–2021

3. Changes in Systemic Regulatory T Cells, Effector T Cells, and Monocyte Populations Associated With Early-Life Stunting

4. Impact of SARS-CoV-2 Delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in France

5. Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France

6. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study

7. Acceptability of a COVID-19 pre-exposure prophylaxis trial with hydroxychloroquine in French healthcare workers during the first wave of COVID-19 pandemic

8. Impact of Introducing Hepatitis B Birth Dose Vaccines into the Infant Immunization Program in Burkina Faso: Study Protocol for a Stepped Wedge Cluster Randomized Trial (NéoVac Study)

9. Systematic Booster after Rabies Pre-Exposure Prophylaxis to Alleviate Rabies Antibody Monitoring in Individuals at Risk of Occupational Exposure

10. SARS-CoV-2 incubation period across variants of concern, individual factors, and circumstances of infection in France: a case series analysis from the ComCor study

11. SARS-CoV-2 self-test uptake and factors associated with self-testing during Omicron BA.1 and BA.2 waves in France, January to May 2022

12. Factors Associated with Stunted Growth in Children Under Five Years in Antananarivo, Madagascar and Bangui, Central African Republic

13. SARS-CoV-2 Exposures of Healthcare Workers from Primary Care, Long-Term Care Facilities and Hospitals: A Nationwide Matched Case-Control Study

14. Impact of original, B.1.1.7, and B.1.351/P.1 SARS-CoV-2 lineages on vaccine effectiveness of two doses of COVID-19 mRNA vaccines: Results from a nationwide case-control study in France

15. Cost-effectiveness of adding a birth dose of hepatitis B vaccine in the Dafra district of the Hauts-Bassins Region in Burkina Faso (NéoVac Study)

16. Exposures associated with SARS-CoV-2 infection in France: A nationwide online case-control study

17. Impact of Introducing Hepatitis B Birth Dose Vaccines into the Infant Immunization Program in Burkina Faso: Study Protocol for a Stepped Wedge Cluster Randomized Trial (NéoVac Study)

18. Comparative Immuno-Virological and Clinical Responses to Antiretroviral Therapy between HIV-1 Group O- and HIV-1 Group M-Infected Patients (ANRS 12168 DynaMO Study)

19. Simian Immunodeficiency Virus seroreactivity in inhabitants from rural Cameroon frequently in contact with non-human primates

20. How to estimate exposure when studying the temperature-mortality relationship? A case study of the Paris area

21. Les enfants présentant un retard de croissance présentent une colonisation ectopique de l'intestin grêle par des bactéries buccales, qui provoquent une malabsorption des lipides dans des modèles expérimentaux

22. Stunted children display ectopic small intestinal colonization by oral bacteria, which cause lipid malabsorption in experimental models

23. High prevalence of intestinal parasite infestations among stunted and control children aged 2 to 5 years old in two neighborhoods of Antananarivo, Madagascar

24. Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study

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24 results on '"Laura Schaeffer"'

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