Institut Pasteur De Madagascar Research Articles

Antimicrobial susceptibility profile of Neisseria gonorrhoeae from patients attending a medical laboratory, Institut Pasteur de Madagascar between 2014 and 2020: phenotypical and genomic characterisation in a subset of Neisseria gonorrhoeae isolates

ObjectivesAntimicrobial-resistant Neisseria gonorrhoeae (NG) is a concern. Little is known about antimicrobial susceptibility profiles and associated genetic resistance mechanisms of NG in Madagascar. We report susceptibility data of NG isolates...

Rabies surveillance in Madagascar from 2011 to 2021: can we reach the target?

Rabies is endemic in Madagascar and a neglected disease. The aim of this study was to summarize human and animal rabies surveillance activities in Madagascar from 2011 to 2021. Samples from terrestrial mammals and humans were tested for rabies virus infection using direct fluorescent antibody, RT-PCR and virus isolation by the National Reference Laboratory (NRL) for rabies at the Institut Pasteur de Madagascar. Among 964 animal and 47 human samples tested, 66.7 and 70.2% were positive, respectively. The NRL received these suspect rabies samples from 48 of 114 districts of Madagascar. Most of them were submitted from the district of the capital city Antananarivo (26.3%) and mainly from its region Analamanga (68.9%). Animal samples were mainly from dogs (83%), cats (9.5%) and cattle (5.8%). Pigs, lemurs, goats accounted for less than 1%. During the 11 years of surveillance, 48 human skin and/or brain biopsy samples were received from 20 districts, mainly from Antananarivo and its surroundings (N = 13), Toamasina and its surroundings (N = 8) and Moramanga (N = 6). The high positivity rate for all species and the non-homogeneous spatial distribution of samples suggests substantial underreporting of rabies cases. There is a clear need to better understand the reasons for underreporting and prioritize rabies surveillance, prevention and control in Madagascar, with improvements in budget, education and infrastructure. A joint animal and human health rabies control program including vaccination of at least 70% of the dog population, is needed to achieve the goal of eliminating dog-transmitted human rabies by 2030 from Madagascar.

Epidemiological characteristics of an urban plague epidemic in Madagascar, August–November, 2017: an outbreak report

SummaryBackgroundMadagascar accounts for 75% of global plague cases reported to WHO, with an annual incidence of 200–700 suspected cases (mainly bubonic plague). In 2017, a pneumonic plague epidemic of unusual size occurred. The extent of this epidemic provides a unique opportunity to better understand the epidemiology of pneumonic plagues, particularly in urban settings.MethodsClinically suspected plague cases were notified to the Central Laboratory for Plague at Institut Pasteur de Madagascar (Antananarivo, Madagascar), where biological samples were tested. Based on cases recorded between Aug 1, and Nov 26, 2017, we assessed the epidemiological characteristics of this epidemic. Cases were classified as suspected, probable, or confirmed based on the results of three types of diagnostic tests (rapid diagnostic test, molecular methods, and culture) according to 2006 WHO recommendations.Findings2414 clinically suspected plague cases were reported, including 1878 (78%) pneumonic plague cases, 395 (16%) bubonic plague cases, one (<1%) septicaemic case, and 140 (6%) cases with unspecified clinical form. 386 (21%) of 1878 notified pneumonic plague cases were probable and 32 (2%) were confirmed. 73 (18%) of 395 notified bubonic plague cases were probable and 66 (17%) were confirmed. The case fatality ratio was higher among confirmed cases (eight [25%] of 32 cases) than probable (27 [8%] of 360 cases) or suspected pneumonic plague cases (74 [5%] of 1358 cases) and a similar trend was seen for bubonic plague cases (16 [24%] of 66 confirmed cases, four [6%] of 68 probable cases, and six [2%] of 243 suspected cases). 351 (84%) of 418 confirmed or probable pneumonic plague cases were concentrated in Antananarivo, the capital city, and Toamasina, the main seaport. All 50 isolated Yersinia pestis strains were susceptible to the tested antibiotics.InterpretationThis predominantly urban plague epidemic was characterised by a large number of notifications in two major urban areas and an unusually high proportion of pneumonic forms, with only 23% having one or more positive laboratory tests. Lessons about clinical and biological diagnosis, case definition, surveillance, and the logistical management of the response identified in this epidemic are crucial to improve the response to future plague outbreaks.FundingUS Agency for International Development, WHO, Institut Pasteur, US Department of Health and Human Services, Laboratoire d'Excellence Integrative Biology of Emerging Infectious Diseases, Models of Infectious Disease Agent Study of the National Institute of General Medical Sciences, AXA Research Fund, and the INCEPTION programme.

Integrating entomoligical covariates in a predictive model of malaria incidence in Farafangana, Madagascar: Limitations and benefits

Introduction Malaria is one of the leading causes of morbidity in Farafangana, an urban area in the southeastern coast of Madagascar with around 35,000 inhabitants. Predictive models of incidence are needed to strengthen prevention measures in case of an epidemic risk. In a context of large scale vector-control interventions, with changing mosquito density and behaviour, entomological surveillance data could be useful to better forecast malaria incidence. Our primary objective was to build a predictive model of malaria incidence (up to two months in advance) in the primary healthcare center (PHC) of Farafangana, including past incidence (at least two months back), climatic, environmental, vector-control and entomological covariates. Our secondary objective was to quantify how entomological covariates might have improved the model fit. Methods Diagnosed malaria incidence data at the PHC of Farafangana came from the Fever Sentinel Surveillance Network of the Institut Pasteur de Madagascar. Climatic data (temperature and precipitations) and environmental data (Normalized Difference Vegetation Index - NDVI) were extracted from the International Research Institute for Climate and Society (missing values were imputed by exponential smoothing). Vector-control covariates, insecticide treated nets from mass distributions and indoor residual spraying, were binary (1 value means effective). From January 2014 until March 2017, human landing mosquito collections were performed every two months for two consecutive nights (from 6 pm to 6 am), inside and outside five houses spread over one central district, close to the PHC. As entomological data were not measured continuously, we made the hypothesis that they could be repeated until the next capture session. We focused our work on the three most abundant vectors: Anopheles gambiae (n = 209), An. coustani (n = 215) and An. funestus (n = 19). Aggressiveness was calculated for each vector species and capture time [number of bites per human and per evening (from 6 to 10 pm), night (from 10 pm to 2 am) or morning (from 2 to 6 am)]. Exophagy percentage was calculated for each species as the number of captures outside houses on the total number of captures (except for An. funestus due to a small number of captures). These entomological data were transformed on a weekly-basis, resulting in 167 weeks of observations. Lags between incidence and non-entomological covariates were determined by cross-correlation maps for quantitative variables and by univariate analyses for binary variables. Accordingly, lagged covariates were built. Only non-correlated lagged covariates were kept (|Pearson's correlation coefficient| Results Lagged NDVI was excluded because of a correlation with lagged temperature and a negative correlation with incidence. Entomological covariates in the reduced model included the evening aggressiveness of An. gambiae, the night and morning aggressiveness of An. funestus and the exophagy percentage of An. gambiae. The model with entomological covariates (R2 = 0.619 and RMSE = 11.607 malaria cases per week) had a better fit than the model without (R2 = 0.406 and RMSE = 14.654 malaria cases per week). Conclusion Entomological surveillance data may improve the prediction of malaria incidence, even in a context of large scale vector-control and when mosquitos are only captured every two months and from one town district. More frequent captures may generate a better predictive model. However, field Anopheles surveillance remains time-and-money consuming. More studies in various transmission contexts are needed to confirm these results and assess benefits in terms of malaria control and prevention.

Low cost, low tech SNP genotyping tools for resource-limited areas: Plague in Madagascar as a model.

BackgroundGenetic analysis of pathogenic organisms is a useful tool for linking human cases together and/or to potential environmental sources. The resulting data can also provide information on evolutionary patterns within a targeted species and phenotypic traits. However, the instruments often used to generate genotyping data, such as single nucleotide polymorphisms (SNPs), can be expensive and sometimes require advanced technologies to implement. This places many genotyping tools out of reach for laboratories that do not specialize in genetic studies and/or lack the requisite financial and technological resources. To address this issue, we developed a low cost and low tech genotyping system, termed agarose-MAMA, which combines traditional PCR and agarose gel electrophoresis to target phylogenetically informative SNPs.Methodology/Principal findingsTo demonstrate the utility of this approach for generating genotype data in a resource-constrained area (Madagascar), we designed an agarose-MAMA system targeting previously characterized SNPs within Yersinia pestis, the causative agent of plague. We then used this system to genetically type pathogenic strains of Y. pestis in a Malagasy laboratory not specialized in genetic studies, the Institut Pasteur de Madagascar (IPM). We conducted rigorous assay performance validations to assess potential variation introduced by differing research facilities, reagents, and personnel and found no difference in SNP genotyping results. These agarose-MAMA PCR assays are currently employed as an investigative tool at IPM, providing Malagasy researchers a means to improve the value of their plague epidemiological investigations by linking outbreaks to potential sources through genetic characterization of isolates and to improve understanding of disease ecology that may contribute to a long-term control effort.ConclusionsThe success of our study demonstrates that the SNP-based genotyping capacity of laboratories in developing countries can be expanded with manageable financial cost for resource constraint laboratories. This is a practical formula that reduces resource-driven limitations to genetic research and promises to advance global collective knowledge of infectious diseases emanating from resource limited regions of the world.

Evaluation of the influenza sentinel surveillance system in Madagascar, 2009-2014.

ProblemEvaluation of influenza surveillance systems is poor, especially in Africa.ApproachIn 2007, the Institut Pasteur de Madagascar and the Malagasy Ministry of Public Health implemented a countrywide system for the prospective syndromic and virological surveillance of influenza-like illnesses. In assessing this system’s performance, we identified gaps and ways to promote the best use of resources. We investigated acceptability, data quality, flexibility, representativeness, simplicity, stability, timeliness and usefulness and developed qualitative and/or quantitative indicators for each of these attributes.Local settingUntil 2007, the influenza surveillance system in Madagascar was only operational in Antananarivo and the observations made could not be extrapolated to the entire country.Relevant changesBy 2014, the system covered 34 sentinel sites across the country. At 12 sites, nasopharyngeal and/or oropharyngeal samples were collected and tested for influenza virus. Between 2009 and 2014, 177 718 fever cases were detected, 25 809 (14.5%) of these fever cases were classified as cases of influenza-like illness. Of the 9192 samples from patients with influenza-like illness that were tested for influenza viruses, 3573 (38.9%) tested positive. Data quality for all evaluated indicators was categorized as above 90% and the system also appeared to be strong in terms of its acceptability, simplicity and stability. However, sample collection needed improvement.Lessons learntThe influenza surveillance system in Madagascar performed well and provided reliable and timely data for public health interventions. Given its flexibility and overall moderate cost, this system may become a useful platform for syndromic and laboratory-based surveillance in other low-resource settings.

Bubonic Plague Outbreak Investigation in the Endemic District of Tsiroanomandidy - Madagascar, October 2014

Background: Plague remains a major public health problem in Madagascar. Faced with reports of plague cases and deaths in Tsiroanomandidy district, we performed an investigation in October 2014.List of Abbreviations: BHCS: Basic Health Center; CDC: Control and prevention Diseases Center; DHS: District Health Service; IPM: Institut Pasteur de Madagascar; MOH: Ministry of Health; SMZ-TMP: Sulfamethoxazole Trimethoprim; WHO: World Health Organization Methods: We used the National plague control program case definition. We identified cases from outpatient registers and collected socio-demographic and clinical information. Plague circulation was determined through a retrospective environmental survey of rodents and vectors. Results: From August 1st to October 12th 2014, we identified 30 cases of which 13 deaths in 7 out of 17 municipalities; 18 were confirmed, 6 probable, and 6 suspected cases. The sex ratio (M/F) was 4:1. Yersinia pestis was isolated from Rattus rattus in one municipality. Flea index was 2.3. We collected 45 fleas through a trap set in a house 6 hours after insecticide spraying. Our aim was to describe the plague outbreak and to improve the national plague control strategies. Conclusion: The presence of infected flea and rodent maintain the persistence of plague in the municipalities investigated. There is a high risk of plague transmission to humans. This study showed that rodent and flea information are important for plague control strategies.

Susceptibility status of Anopheles arabiensis (Diptera: Culicidae) commonly used as biological materials for evaluations of malaria vector control tools in Madagascar.

BackgroundMadagascar is a malaria-endemic country with an increase in cases in recent years. In vector control using insecticide, a susceptible strain is necessary to evaluate insecticide efficacy, either for spraying or on nets. The susceptibility of Anopheles arabiensis from Antananarivo, Madagascar to two organophosphate, three pyrethroid, two carbamate, and one organochlorine insecticides was investigated. Since 2010, An. arabiensis strain has been maintained away from insecticide source during 110 generations with optimal insectarium conditions.MethodsBioassay were performed on adult mosquitoes to assess the susceptibility of An. arabiensis to insecticide-impregnated papers (malathion 5 %, fenitrothion 1 %, deltamethrin 0.05 %, permethrin 0.75 %, alphacypermethrin 0.05 %, bendiocarb 0.1 %, propoxur 0.01 %, and DDT 4 %) following World Health Organization Pesticide Evaluation Scheme guidelines. Bioassay using Center for Disease Control bottle tests were also used to detect mortality. Molecular assay were carried out to detect the presence of knock down resistance (kdr) mutation using PCR techniques.ResultsAnopheles arabiensis is fully susceptible with 100 % mortality to malathion, fenitrothion, deltamethrin, permethrin, alphacypermethrin, bendiocarb, propoxur, and DDT. No kdr gene was detected using PCR method.ConclusionThe strain An. arabiensis maintained in the insectarium of Institut Pasteur de Madagascar is a fully susceptible strain and can be used for insecticide evaluation.

Early-warning health and process indicators for sentinel surveillance in Madagascar 2007-2011.

Background: Epidemics pose major threats in resource-poor countries, and surveillance tools for their early detection and response are often inadequate. In 2007, a sentinel surveillance system was established in Madagascar, with the aim of rapidly identifying potential epidemics of febrile or diarrhoeal syndromes and issuing alerts. We present the health and process indicators for the five years during which this system was constructed, showing the spatiotemporal trends, early-warning sign detection capability and process evaluation through timely analyses of high-quality data.Methods: The Malagasy sentinel surveillance network is currently based on data for fever and diarrhoeal syndromes collected from 34 primary health centres and reported daily via the transmission of short messages from mobile telephones. Data are analysed daily at the Institut Pasteur de Madagascar to make it possible to issue alerts more rapidly, and integrated process indicators (timeliness, data quality) are used to monitor the system.Results: From 2007 to 2011, 917,798 visits were reported. Febrile syndromes accounted for about 11% of visits annually, but the trends observed differed between years and sentinel sites. From 2007 to 2011, 21 epidemic alerts were confirmed. However, delays in data transmission were observed (88% transmitted within 24 hours in 2008; 67% in 2011) and the percentage of forms transmitted each week for validity control decreased from 99.9% in 2007 to 63.5% in 2011.Conclusion: A sentinel surveillance scheme should take into account both epidemiological and process indicators. It must also be governed by the main purpose of the surveillance and by local factors, such as the motivation of healthcare workers and telecommunication infrastructure. Permanent evaluation indicators are required for regular improvement of the system.

First results of hormone receptors’ status in Malagasy women with invasive breast cancer

IntroductionBreast cancer is the most common malignancy tumor amongst Malagasy women registered at the pathology unit of the “Institut Pasteur de Madagascar”. In Madagascar, there is no laboratory practicing hormone receptors' status on these tumors. Until now no study about hormone receptors' status of Malagasy women with invasive breast cancer was performed. So it will be the first study talking about this topic. The aim of this study was to determine hormone receptors' status in Malagasy women with invasive breast cancer.MethodsThis retrospective and descriptive study was based on patients' medical files from 2009 to 2011. It included all invasive breast cancer diagnosed in Malagasy women at the pathology laboratory located at the “Institut Pasteur de Madagascar”, in Antananarivo. Along this period this laboratory has sent paraffin blocks of invasive breast carcinoma in two pathological laboratories in France.ResultsWe collected 77 cases of invasive breast cancer along this period. The mean age was 48.8 +/- 10.7, ranging from 26 years to 70 years. There were 46.8 % (n = 36) women with progesterone receptor positive (PR+), 53.2 % (n = 41) with progesterone receptor negative (PR-). For the estrogen receptor, 61.0 % (n = 47) were positive and 36.4 % (n = 28) were negative. ER+/PR+ represented 44.2 % (n = 34); ER-/PR- 33.8 % (n = 26); ER +/ PR- 16.8 % (n = 13); ER-/PR+ and ER-/PR- represented respectively 2.6 % (n = 2).ConclusionPatients in our study had more important rate of ER-, PR- and a less important rate of ER+/PR+, PR+. These results suggest that more study related to Hormone Receptor profile should be conducted in Malagasy women with breast cancer.

DNA Extracted from Stained Sputum Smears Can Be Used in the MTBDR plus Assay

We examined the feasibility of using DNA extracted from stained sputum smears for the detection of rifampin and isoniazid resistance with the commercial MTBDRplus assay from Hain Lifescience GmbH, Nehren, Germany. Overall sensitivity was initially low (70.0%) but increased to 96.7% when a multiplex PCR preamplification step was added. We then tested stored Mycobacterium tuberculosis-positive stained smears prepared from 297 patients' sputum samples. Species identification and drug susceptibility testing (DST) had been performed at the Institut Pasteur de Madagascar. Overall, the performance of the MTBDRplus assay applied to slide DNA was similar to that obtained in other studies with DNA extracted from clinical specimens. With the ready availability of stained smears in routine diagnostic laboratories and their easy transport and storage at room temperature, this approach should be useful for optimizing the treatment of multidrug-resistant tuberculosis and for conducting resistance surveys aimed at identifying hot-spot regions and breaking chains of transmission.

Further evidence for malaria elimination failutre on the island of Sainte Marie (Madagascar)

Since 2006, the new malaria elimination programme has been implemented on Sainte Marie Island – a district of approximately 20,000 inhabitants, on the eastern coast of Madagascar. Key malaria interventions include mass distribution of long lasting insecticide-treated nets (LLINs), intermittent preventive treatment using sulfadoxine-pyrimethamine in pregnant women (IPTp) and ACT for treating uncomplicated malaria cases. Over 20,000 LLINs were distributed in 2006. The implementation of this programme on Sainte Marie is expected to generate useful and usable information to inform malaria elimination strategies in the entire country. As part of the routine monitoring at the health district level, active detection of malaria was carried out in primary school children in Sainte Marie during the rainy season from January 27 to March 3, 2009. Giemsa stained blood smears were examined for malaria parasite at the Institut Pasteur de Madagascar. Also, blood spots were collected. The presence/absence of pfdhfr S108N and S108T mutations in Plasmodium falciparum isolates was detected by PCR/RFLP method. Asymptomatic and consenting 524 children participated in this survey. The mean age was 8.8 ± 2.1 years. The malaria prevalence was 20.2% (95%CI: 16.9 – 23.9%) with a predominance of P. falciparum malaria (105/106) and a single case of P. vivax. Of the 105 isolates P. falciparum isolates, two (1.9%) harboured the S108N mutation at position 108 in pfDHFR. Our findings demonstrate that in three years following the malaria treatment policy change, mutant P. falciparum strains potentially resistant to sulfadoxine-pyrimethamine emerge in Sainte Marie. This is considered as an alarming situation given the importance of the IPTp to control malaria in pregnancy. Also, the prevalence of malaria among children above five is still high. This is a further proof of the malaria elimination failure. Overall, this situation resulted from weaknesses in malaria control measures. A single massive distribution round of LLINs in 2006 is not enough. Besides, cyclones hit Sainte Marie every year and most of the nets disappeared with broken houses. We believe that key approaches to achieve malaria elimination in Madagascar are (i) coupling malaria surveillance with interventions with additive innovative approaches such as treating asymptomatic malaria cases with ACT and (ii) on-going maintenance of malaria prevention including the unfailing renewal of LLINs coverage and in door spraying of insecticide.

Atelier paludisme: an international malaria training course held in Madagascar

The Atelier Paludisme (Malaria Workshop) is an international training course organized by the Institut Pasteur de Madagascar, which has been held annually for the past five years. The course was designed for both young and experienced researchers, as well as for healthcare professionals, mostly from malaria-endemic countries. Its objective is to provide participants with a broad knowledge of all features of malaria, to improve their skills in project management, to break geographical isolation by using the Internet as a source of documentary information. This six-week course makes use of concepts of andragogy and problem-based learning, i.e. a relationship between participants and tutors, which promotes a process of exchange rather than the simple transmission of knowledge, where participants have to search actively for information. This approach to training, combined with the wide background and experience of those involved, creates positive dynamics and enables participants to acquire new skills, develop their critical and analytical abilities. This paper describes the course and the lessons learned from its evaluation.