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Background In 2015, antimicrobial resistance was identified as a public health priority for the South-Western Indian Ocean (SWIO) (i.e. Comoros, Madagascar, Mauritius, Mayotte (France), Reunion Island (France), and Seychelles). However, in 2020, colonization rates of antimicrobial-resistant bacteria (ARB) in human populations on most islands in SWIO were still not known and neither hospital nor community colonization rates had been estimated. The aim of this study was to estimate the prevalence of colonization of six ARB groups in hospitalized patients residing in the SWIO territories. The six groups comprise extended-spectrum betalactamase producing Enterobacteriaceae (ESBL-E), carbapenem-resistant Enterobacteriaceae (CRE), methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and both ceftazidime and/or imipenem-resistant Acinetobacter spp. (ACB), and ceftazidime and/or imipenem-resistant Pseudomonas spp. (PSA)). Methods Based on comprehensive hospital laboratory ARB screening data, we provide the first estimation of ARB colonization rates in hospitalized patients residing in SWIO (2015–2017). Using ARB colonization rates in Reunion Island (France) as the reference for estimating odds ratio, we identified at risk patients based on their territory of residence. Results The survey pointed to significantly higher overall ARB colonization rates in patients from Comoros, Madagascar, Mayotte, and Seychelles compared to Reunion Island as the reference. Extended-spectrum betalactamase producing Enterobacteriaceae was found to be the most common ARB group colonizing patients from SWIO territories. The highest MRSA colonization rates were observed in patients from Mayotte and Seychelles. Colonization by carbapenem-resistant Enterobacteriaceae (CRE) was highest in patients from Mauritius. Conclusion These results identify high ARB colonization rates in hospitalized patients from SWIO territories that require further investigation, particularly CRE in Mauritius and MRSA in Seychelles and Mayotte. This study is the first step toward the implementation of a broader regional ARB surveillance system.

Spatio-temporal variations in environmental and socio-agricultural factors create heterogeneity in livestock disease transmission risk, raising challenges in identifying populations most at risk and how this risk changes over time. Consequently, effective vaccination strategies require careful planning to achieve optimal or equitable outcomes across regions. We developed a metapopulation model for Rift Valley fever transmission in livestock across the Comoros archipelago which incorporates livestock vaccination in addition to heterogeneity in viral transmission rates and animal movements. We used the model to evaluate three vaccine allocation strategies–proportional allocation, optimal allocation for maximising total infections averted across the archipelago, and optimal allocation for more equitable outcomes across islands—under different vaccination coverage levels and animal identification scenarios. We report that (i) both archipelago-wide and island-specific strategy effectiveness were impacted by vaccination rate, allocation strategy, and animal identification approach, (ii) optimally allocating vaccines improved strategy effectiveness compared with proportional allocation but resulted in inequitable outcomes between islands, and (iii) tagging animals post-vaccination boosted overall strategy effectiveness for all vaccination rates.

Rift Valley fever (RVF) is a vector-borne viral disease widespread in Africa. The primary cycle involves mosquitoes and wild and domestic ruminant hosts. Humans are usually contaminated after contact with infected ruminants. As many environmental, agricultural, epidemiological, and anthropogenic factors are implicated in RVF spread, the multidisciplinary One Health approach was needed to identify the drivers of RVF epidemics in Madagascar. We examined the environmental patterns associated with these epidemics, comparing human and ruminant serological data with environmental and cattle-trade data. In contrast to East Africa, environmental drivers did not trigger the epidemics: They only modulated local Rift Valley fever virus (RVFV) transmission in ruminants. Instead, RVFV was introduced through ruminant trade and subsequent movement of cattle between trade hubs caused its long-distance spread within the country. Contact with cattle brought in from infected districts was associated with higher infection risk in slaughterhouse workers. The finding that anthropogenic rather than environmental factors are the main drivers of RVF infection in humans can be used to design better prevention and early detection in the case of RVF resurgence in the region.

The persistence mechanisms of Rift Valley fever (RVF), a zoonotic arboviral haemorrhagic fever, at both local and broader geographical scales have yet to be fully understood and rigorously quantified. We developed a mathematical metapopulation model describing RVF virus transmission in livestock across the four islands of the Comoros archipelago, accounting for island-specific environments and inter-island animal movements. By fitting our model in a Bayesian framework to 2004–2015 surveillance data, we estimated the importance of environmental drivers and animal movements on disease persistence, and tested the impact of different control scenarios on reducing disease burden throughout the archipelago. Here we report that (i) the archipelago network was able to sustain viral transmission in the absence of explicit disease introduction events after early 2007, (ii) repeated outbreaks during 2004–2020 may have gone under-detected by local surveillance, and (iii) co-ordinated within-island control measures are more effective than between-island animal movement restrictions. Rift Valley fever is a zoonotic haemorrhagic fever with complex transmission dynamics influenced by environmental variables and animal movements. Here, the authors develop a metapopulation model incorporating these factors and use it to identify the main drivers of transmission in the Comoros archipelago.

Peste des petits ruminants (PPR) is a highly contagious disease affecting mainly sheep and goats. Livestock movements contribute to the spread of the disease by introducing it to naive areas or exposing susceptible animals to it in infected regions. Because of its socio-economic impact, the Food and Agriculture Organisation (FAO) and the World Organization for Animal Health (WOAH) have set the goal to eradicate it by 2030, one of the key steps being the improvement of surveillance networks. The present study aimed to provide tools to identify areas that could serve as sentinel nodes, i.e. areas that may be rapidly infected at the onset of epidemics. Using data from a market survey conducted in Northern Nigeria, we reconstructed the small ruminants mobility network and simulated the diffusion of PPR virus through animal movement. From the analysis of simulation outcomes, we investigated which nodes could act as sentinel nodes under specific conditions for disease transmission. We considered several modified networks to get around the problem of data only being available for part of the overall network structure and to account for potential errors made during the field study. For each configuration, we simulated the spread of PPR using a stochastic Susceptible-Infectious (SI) model based on animal movements to assess the epidemics’ extent and the presence of recurrent patterns to identify potential sentinel nodes. We extracted the backbone of the reference network and checked for the presence of sentinel nodes within it. We investigated how the origin ( seed ) of the epidemics could affect the propagation pattern by comparing and grouping seeds based on their respective transmission paths. Results showed that the isolated backbone contains 45% of sentinel nodes that remain stable or undergo only minor changes in 9 out of 11 configurations. On top of that, the characteristics of sentinel nodes identified in the backbone are not influenced by the severity of the disease. The H index, in-degree, and eigenvector are the most essential variables. This study provides an overview of the major axes of animal movements in Nigeria and the most vulnerable locations that should be prioritized for monitoring livestock diseases like PPR.

Rift Valley fever (RVF) is a vector-borne viral disease of major animal and public health importance. In 2018–19, it caused an epidemic in both livestock and human populations of the island of Mayotte. Using Bayesian modelling approaches, we assessed the spatio-temporal pattern of RVF virus (RVFV) infection in livestock and human populations across the island, and factors shaping it. First, we assessed if (i) livestock movements, (ii) spatial proximity from communes with infected animals, and (iii) livestock density were associated with the temporal sequence of RVFV introduction into Mayotte communes’ livestock populations. Second, we assessed whether the rate of human infection was associated with (a) spatial proximity from and (b) livestock density of communes with infected animals. Our analyses showed that the temporal sequence of RVFV introduction into communes’ livestock populations was associated with livestock movements and spatial proximity from communes with infected animals, with livestock movements being associated with the best model fit. Moreover, the pattern of human cases was associated with their spatial proximity from communes with infected animals, with the risk of human infection sharply increasing if livestock in the same or close communes were infected. This study highlights the importance of understanding livestock movement networks in informing the design of risk-based RVF surveillance programs.

Our understanding of the drivers of the temporal dynamics of livestock mobility networks is currently limited, despite their significant implications for the surveillance and control of infectious diseases. We analyzed the effect of time-varying environmental and economic variables—biomass production, rainfall, livestock market prices, and religious calendar on long-distance movements of cattle and small ruminant herds in Senegal in the years 2014 and 2019. We used principal component analysis to explore the variation of the hypothesized explanatory variables in space and time and a generalized additive modelling approach to assess the effect of those variables on the likelihood of herd movement between pairs of administrative units. Contrary to environmental variables, the patterns of variation of market prices show significant differences across locations. The explanatory variables at origin had the highest contribution to the model deviance reduction. Biomass production and rainfall were found to affect the likelihood of herd movement for both species on at least 1 year. Market price at origin had a strong and consistent effect on the departure of small ruminant herds. Our study shows the potential benefits of regular monitoring of market prices for future efforts at forecasting livestock movements and associated sanitary risks.

Cysticercosis in humans caused by the parasite Taenia solium is one of the World Health Organization’s Neglected Tropical Diseases. The parasite is transmitted between the human host and pigs. Efforts to prevent the disease have relied mainly on treatment of people with anthelmintics. However, to date, there is no practical and effective control method that has been delivered as a public health program. Here we describe a large-scale, minimum inputs T. solium control program implemented as a public health program in Madagascar. Initially all pigs were vaccinated for porcine cysticercosis and medicated with oxfendazole, after which only young piglets and pigs imported into the program area were targeted for interventions. After piglet interventions were in place and on-going, a single mass drug administration (MDA) was delivered to the human population with a taeniacide. The outcomes were assessed one year after the human treatment, by comparing pre-and post-intervention levels of porcine cysticercosis caused by T. solium and human T. solium taeniasis. Over a twenty-two-month period, 96,735 pig vaccinations and oxfendazole medications were delivered and during the MDA, 117,216 people received taeniacide. Ninety percent of the pig population were receiving vaccination and medication at the end of the intervention period. Coverage of the eligible human population by the MDA was 62.5%. Prior to the intervention 30.8% of slaughter-age pigs had viable T. solium infection, reduced to 8% after the program. Human taeniasis was found to be 1.25% prior to the MDA and 0.6% one year after the MDA. The program successfully demonstrated effective control of T. solium transmission to pigs using minimum inputs and delivered as a public health program. Sustained control and expansion of the program could potentially lead to the elimination of the disease being a public health problem in Madagascar.

Neurocysticercosis is recognized as an important health issue in the Malagasy population. To date, investigations into prevalence of infection with the causative agent, Taenia solium, in the parasite's natural animal intermediate hosts, have relied on serological methods which have been found to be non-specific. We determined the prevalence of porcine cysticercosis among pigs from a contiguous area of the Betafo and Mandoto administrative districts, Vakinankaratra Region, Madagascar. One hundred and four slaughter-weight pigs were examined by detailed necropsy examination including slicing of the heart, tongue, masseter muscles, diaphragm and carcase musculature. Thirty-seven animals (35.6%) were found infected with T. solium, representing one of the highest rates of infection ever reported, worldwide. These findings highlight the importance of T. solium in Madagascar and support the need for increased efforts to prevent the parasite's transmission to reduce its burden on the health of the Malagasy population.

West Nile virus is an arthropod-borne zoonosis transmitted by a large number of mosquito species, and birds play a key role as reservoir of the virus. Its distribution is largely widespread over Africa, Asia, the Americas and Europe. Since 1978, it has frequently been reported in Madagascar. Studies described a high seroprevalence level of the virus in humans in different areas of the island and a human fatal case of WNV infection was reported in 2011. Despite these reports, the epidemiology of WNV in Madagascar, in particular, viral circulation remains unclear. To explore the transmission of WNV in two rural human populations of Madagascar, we investigated local mosquitoes and poultry for evidence of current infections, and determined seroprevalence of candidate sentinel species among the local poultry. These 2 areas are close to lakes where domestic birds, migratory wild birds and humans coexist. Serological analysis revealed WNV antibodies in domestic birds (duck, chicken, goose, turkey and guinea fowl) sampled in both districts (Antsalova 29.4% and Mitsinjo 16.7%). West Nile virus nucleic acid was detected in one chicken and in 8 pools of mosquitoes including 2 mosquito species (Aedeomyia madagascarica and Anopheles pauliani) that have not been previously described as candidate vectors for WNV. Molecular analysis of WNV isolates showed that all viruses detected were part of the lineage 2 that is mainly distributed in Africa, and were most closely matched by the previous Malagasy strains isolated in 1988. Our study showed that WNV circulates in Madagascar amongst domestic birds and mosquitoes, and highlights the utility of poultry as a surveillance tool to detect WNV transmission in a peri-domestic setting.