Tuberculosis (TB) remains a public health problem in Madagascar. A crucial element of TB control is the development of an easy and rapid method for the orientation of TB control strategies in the country. Our main objective was to develop a TB spatial hotspot identification method by combining spatial analysis and TB genotyping method in Antananarivo. Sputa of new pulmonary TB cases from 20 TB diagnosis and treatment centers (DTCs) in Antananarivo were collected from August 2013 to May 2014 for culture. Mycobacterium tuberculosis complex (MTBC) clinical isolates were typed by spoligotyping on a Luminex® 200 platform. All TB patients were respectively localized according to their neighborhood residence and the spatial distribution of all pulmonary TB patients and patients with genotypic clustered isolates were scanned respectively by the Kulldorff spatial scanning method for identification of significant spatial clustering. Areas exhibiting spatial clustering of patients with genotypic clustered isolates were considered as hotspot TB areas for transmission. Overall, 467 new cases were included in the study, and 394 spoligotypes were obtained (84.4%). New TB cases were distributed in 133 of the 192 Fokontany (administrative neighborhoods) of Antananarivo (1 to 15 clinical patients per Fokontany) and patients with genotypic clustered isolates were distributed in 127 of the 192 Fokontany (1 to 13 per Fokontany). A single spatial focal point of epidemics was detected when ignoring genotypic data (p = 0.039). One Fokontany of this focal point and three additional ones were detected to be spatially clustered when taking genotypes into account (p < 0.05). These four areas were declared potential TB transmission hotspots in Antananarivo and will be considered as priority targets for surveillance in the future. This method, combining spatial analysis and TB genotyping will now be used for further focused clinical and epidemiological studies in Madagascar and will allow better TB control strategies by public health authorities.

Pertussis is a highly contagious infectious disease and remains an important cause of mortality and morbidity worldwide. Over the last decade, vaccination has greatly reduced the burden of pertussis. Yet, uncertainty in individual vaccination coverage and ineffective case surveillance systems make it difficult to estimate burden and the related quantity of population-level susceptibility, which determines population risk. These issues are more pronounced in low-income settings where coverage is often overestimated, and case numbers are under-reported. Serological data provide a direct characterisation of the landscape of susceptibility to infection; and can be combined with vaccination coverage and basic theory to estimate rates of exposure to natural infection. Here, we analysed cross-sectional data on seropositivity against pertussis to identify spatial and age patterns of susceptibility in children in Madagascar. A large proportion of individuals surveyed were seronegative; however, there were patterns suggestive of natural infection in all the regions analysed. Improvements in vaccination coverage are needed to help prevent additional burden of pertussis in the country.

Background: The world is facing a 2019 coronavirus (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this context, efficient serological assays are needed to accurately describe the humoral responses against the virus. These tools could potentially provide temporal and clinical characteristics and are thus paramount in developing-countries lacking sufficient ongoing COVID-19 epidemic descriptions. Methods: We developed and validated a Luminex xMAP® multiplex serological assay targeting specific IgM and IgG antibodies against the SARS-CoV-2 Spike subunit 1 (S1), Spike subunit 2 (S2), Spike Receptor Binding Domain (RBD) and the Nucleocapsid Protein (NP). Blood samples collected periodically for 12 months from 43 patients diagnosed with COVID-19 in Madagascar were tested for these antibodies. A random forest algorithm was used to build a predictive model of time since infection and symptom presentation. Findings: The performance of the multiplex serological assay was evaluated for the detection of SARS-CoV-2 anti-IgG and anti-IgM antibodies. Both sensitivity and specificity were equal to 100% (89.85-100) for S1, RBD and NP (S2 had a lower specificity = 95%) for IgG at day 14 after enrolment. This multiplex assay compared with two commercialized ELISA kits, showed a higher sensitivity. Principal Component Analysis was performed on serologic data to group patients according to time of sample collection and clinical presentations. The random forest algorithm built by this approach predicted symptom presentation and time since infection with an accuracy of 87.1% (95% CI = 70.17-96.37, p-value = 0.0016), and 80% (95% CI = 61.43-92.29, p-value = 0.0001) respectively. Interpretation: This study demonstrates that the statistical model predicts time since infection and previous symptom presentation using IgM and IgG response to SARS-CoV2. This tool may be useful for global surveillance, discriminating recent- and past- SARS-CoV-2 infection, and assessing disease severity. Funding: This study was funded by the French Ministry for Europe and Foreign Affairs through the REPAIR COVID-19-Africa project coordinated by the Pasteur International Network association. WANTAI reagents were provided by WHO AFRO as part of a Sero-epidemiological "Unity" Study Grant/Award Number: 2020/1019828-0 P.O 202546047 and Initiative 5% grant n°AP-5PC–2018–03-RO. Declaration of Interest: We declare no competing interests. Ethical Approval: This study protocol obtained ethical approval from the Biomedical Research Ethics Committee of Madagascar (n°. 058/MSANP/SG/AGMED/CERBM, March 30, 2020 and amendment n°109/MSANP/SG/AGMED/CERBM, June 24, 2020).

Reliable data on whooping cough, a highly contagious disease sometimes fatal for infants, are largely lacking in low- and middle-income countries. We conducted a hospital-based prospective study (PS) on infants, and a household contact-case investigation (CCI) for positive cases throughout Cambodia and in the city of Antananarivo, Madagascar, between 2017 and 2019. The PS, in which Bordetella diagnostics (qPCR) were performed, included infants aged ≤6 months presenting with ≥5 days of cough associated with one pertussis-like symptom. CCI was performed using qPCR and serology regardless of clinical signs. In this study, 207 and 173 participants from Cambodia and Antananarivo were respectively enrolled. Respectively 26.1% (54/207) and 22.0% (38/173) of the infants were infected in the cohorts from Cambodia and Antananarivo. Cough longer than 10 days appeared as a risk factor in both countries, as well as coughing spells, apnea and normal pulmonary auscultation, having a coughing contact in Cambodia. In Antananarivo, being clinically well between coughing spells appeared as a risk factor. Five infants, all positive, died during the study. In Cambodia and Antananarivo respectively, 50.9% (118/232) and 67.8% (82/121) of the contact cases were positive. Respectively 94.4% (51/54) and 90.3% (28/31) of the households had at least one positive contact case. The data show that pertussis circulates at high levels among infants and in their households both in Cambodia and in Antananarivo. Given the vulnerability of youngest infants, who are too young to receive fully primary vaccination, they need to be protected through boosters breaking transmission chains. Molecular diagnosis, as well as trained medical human resources to detect the disease early, are absolutely key to protect populations.

Sentinel animals may play a key role in the surveillance of arbovirus circulation, particularly in developing countries. This study aimed to assess the relevance of using dogs as sentinel animals for Rift Valley fever virus (RVFV) surveillance in Madagascar. Serological surveys were conducted on 513 dogs and 135 cattle in the Ifanadiana district, southeastern Madagascar. In addition, 486 human dry blood samples available from the same area were used. Antibodies against RVFV were detected in 23 of 513 dogs, in 86 of 486 humans, and in 33 of 135 cattle. Serocatalytic models fitted to age-stratified serological data were developed to estimate the RVFV force of infection (FOI) under several hypotheses, ranging from no relationship to proportional RVFV FOIs between humans, cattle, and dogs. The best supported model indicated that RVFV FOI in humans and cattle was proportional to RVFV FOI in dogs. Proportionality parameters were estimated at 2.6 (95% credible interval: [1.4–5.1]) for humans and 3.5 (95% credible interval: [1.3–6.4]) for cattle. Our findings suggested that dog blood samples could be used to identify RVFV circulation in RVF endemic areas and infer the exposure of humans and cattle in these areas in Madagascar.

Background: Amidst a global resurgence of diphtheria cases with numerous outbreaks recorded worldwide since 2000, a better understanding of this vaccine-preventable disease's circulation is needed. Methods: We retrospectively analyzed sera from 2 sero-epidemiological cross-sectional studies in Madagascar and Cambodia on fully primo-vaccinated 3- to 15-year-olds. Using enzyme-linked immunosorbent assay (ELISA) and seroneutralization (Vero Cell TNT) for the 3- to 8-year-olds with low ELISA titration values (6 years postvaccination. Results: Seven hundred forty-five children in Cambodia and 949 children in Madagascar were included. Our results show significantly more unprotected children among the 5- to 6-year-olds than among the 3- to 4-year-olds, with 41.1% (39/95) vs 26.7% (27/101; P = .03) in Cambodia and 21.4% (27/126) vs 8.0% (9/113; P < .01) in Madagascar. In Cambodia and Madagascar, respectively, 27.8% and 20.7% of the participants whose primary vaccination was performed >6 years earlier were seropositive, suggesting diphtheria infection. In both countries, we observed a higher rate of infected children when the last vaccine injection had been received 7–8 years or 11–12 years earlier vs 5–6 years earlier. Conclusions: Our data show that the disease is present at high levels in Cambodia and Madagascar and that the national recommendation—primary vaccination—is not sufficient: Booster doses appear necessary at around 6 years of age and for adolescents, as recommended by the World Health Organization.