One Health compartment analysis of ESBL-producing Escherichia coli reveals multiple transmission events in a rural area of Madagascar.

BACKGROUND: ESBL-producing Escherichia coli (ESBL-Ec) is considered a key indicator for antimicrobial resistance (AMR) epidemiological surveillance in animal, human and environment compartments. There is likelihood of ESBL-Ec animal-human transmission but proof of cross-compartment transmission is still unclear. OBJECTIVES: To characterize ESBL-Ec genetic similarity in various compartments (humans, animals and environment) from a rural area of Madagascar. METHODS: We collected ESBL-Ec isolates prospectively from humans, animals and the environment (water) between April and October 2018. These isolates were subject to WGS and analysed with cutting-edge phylogenomic methods to characterize population genetic structure and infer putative transmission events among compartments. RESULTS: Of the 1454 samples collected, 512 tested positive for ESBL-Ec. We successfully sequenced 510 samples, and a phylogenomic tree based on 179 365 SNPs was produced. Phylogenetic distances between and amongst compartments were indistinguishable, and 104 clusters of recent transmission events between compartments were highlighted. Amongst a large diversity of ESBL-Ec genotypes, no lineage host specificity was observed, indicating the regular occurrence of ESBL-Ec transfer among compartments in rural Madagascar. CONCLUSIONS: Our findings stress the importance of using a phylogenomic approach on ESBL-Ec samples in various putative compartments to obtain a clear baseline of AMR transmissions in rural settings, where one wants to identify risk factors associated with transmission or to measure the effect of 'One Health' interventions in low- and middle-income countries.

Antimicrobial Resistance in Africa-How to Relieve the Burden on Family Farmers.

Although currently available data indicate that Africa has the lowest usage of antimicrobials in animals in the world (adjusted by animal biomass), data show a high prevalence of antimicrobial resistance in foodborne pathogens isolated from animals and animal products. Apart from the lack of solid data on antimicrobial use in many countries in Africa, different hypotheses could explain this situation. Qualitative interviews of farmers show a lack of knowledge and uninformed use of antimicrobials. Considering the development of animal farming to meet an increasing demand for proteins, this deficiency represents a serious public health issue. We advocate for policies that consider the specific challenges faced by family farmers in Africa, to simultaneously improve access to veterinary drugs while strengthening the regulation of their use. We propose a global approach targeting the agri-food system, offering innovative social and technical interventions on antimicrobial usage, adapted to family farmers.

A dynamic model of transmission and elimination of peste des petits ruminants in Ethiopia.

Peste des petits ruminants (PPR), a devastating viral disease of sheep and goats, has been targeted by the global community for eradication within the next 15 years. Although an efficacious attenuated live vaccine is available, the lack of knowledge about the transmission potential of PPR virus (PPRV) may compromise eradication efforts. By fitting a metapopulation model simulating PPRV spread to the results of a nationwide serological survey in Ethiopia, we estimated the level of viral transmission in an endemic setting and the vaccination coverage required for elimination. Results suggest that the pastoral production system as a whole acts as a viral reservoir, from which PPRV spills over into the sedentary production system, where viral persistence is uncertain. Estimated levels of PPRV transmission indicate that viral spread could be prevented if the proportion of immune small ruminants is kept permanently above 37% in at least 71% of pastoral village populations. However, due to the high turnover of these populations, maintaining the fraction of immune animals above this threshold would require high vaccine coverage within villages, and vaccination campaigns to be conducted annually. Adapting vaccination strategies to the specific characteristics of the local epidemiological context and small ruminant population dynamics would result in optimized allocation of limited resources and increase the likelihood of PPR eradication.

MERS coronaviruses from camels in Africa exhibit region-dependent genetic diversity.

Middle East respiratory syndrome coronavirus (MERS-CoV) causes a zoonotic respiratory disease of global public health concern, and dromedary camels are the only proven source of zoonotic infection. Although MERS-CoV infection is ubiquitous in dromedaries across Africa as well as in the Arabian Peninsula, zoonotic disease appears confined to the Arabian Peninsula. MERS-CoVs from Africa have hitherto been poorly studied. We genetically and phenotypically characterized MERS-CoV from dromedaries sampled in Morocco, Burkina Faso, Nigeria, and Ethiopia. Viruses from Africa (clade C) are phylogenetically distinct from contemporary viruses from the Arabian Peninsula (clades A and B) but remain antigenically similar in microneutralization tests. Viruses from West (Nigeria, Burkina Faso) and North (Morocco) Africa form a subclade, C1, that shares clade-defining genetic signatures including deletions in the accessory gene ORF4b Compared with human and camel MERS-CoV from Saudi Arabia, virus isolates from Burkina Faso (BF785) and Nigeria (Nig1657) had lower virus replication competence in Calu-3 cells and in ex vivo cultures of human bronchus and lung. BF785 replicated to lower titer in lungs of human DPP4-transduced mice. A reverse genetics-derived recombinant MERS-CoV (EMC) lacking ORF4b elicited higher type I and III IFN responses than the isogenic EMC virus in Calu-3 cells. However, ORF4b deletions may not be the major determinant of the reduced replication competence of BF785 and Nig1657. Genetic and phenotypic differences in West African viruses may be relevant to zoonotic potential. There is an urgent need for studies of MERS-CoV at the animal-human interface.

Diversity of Dromedary Camel Coronavirus HKU23 in African Camels Revealed Multiple Recombination Events among Closely Related Betacoronaviruses of the Subgenus Embecovirus.

Genetic recombination has frequently been observed in coronaviruses. Here, we sequenced multiple complete genomes of dromedary camel coronavirus HKU23 (DcCoV-HKU23) from Nigeria, Morocco, and Ethiopia and identified several genomic positions indicative of cross-species virus recombination events among other betacoronaviruses of the subgenus Embecovirus (clade A beta-CoVs). Recombinant fragments of a rabbit coronavirus (RbCoV-HKU14) were identified at the hemagglutinin esterase gene position. Homolog fragments of a rodent CoV were also observed at 8.9-kDa open reading frame 4a at the 3' end of the spike gene. The patterns of recombination differed geographically across the African region, highlighting a mosaic structure of DcCoV-HKU23 genomes circulating in dromedaries. Our results highlighted active recombination of coronaviruses circulating in dromedaries and are also relevant to the emergence and evolution of other betacoronaviruses, including Middle East respiratory syndrome coronavirus (MERS-CoV).IMPORTANCE Genetic recombination is often demonstrated in coronaviruses and can result in host range expansion or alteration in tissue tropism. Here, we showed interspecies events of recombination of an endemic dromedary camel coronavirus, HKU23, with other clade A betacoronaviruses. Our results supported the possibility that the zoonotic pathogen MERS-CoV, which also cocirculates in the same camel species, may have undergone similar recombination events facilitating its emergence or may do so in its future evolution.

Survey of Ebola Viruses in Frugivorous and Insectivorous Bats in Guinea, Cameroon, and the Democratic Republic of the Congo, 2015-2017.

To clarify the role of bats in the ecology of Ebola viruses, we assessed the prevalence of Ebola virus antibodies in a large-scale sample of bats collected during 2015-2017 from countries in Africa that have had previous Ebola outbreaks (Guinea, the Democratic Republic of the Congo) or are at high risk for outbreaks (Cameroon). We analyzed 4,022 blood samples of bats from >12 frugivorous and 27 insectivorous species; 2-37 (0.05%-0.92%) bats were seropositive for Zaire and 0-30 (0%-0.75%) bats for Sudan Ebola viruses. We observed Ebola virus antibodies in 1 insectivorous bat genus and 6 frugivorous bat species. Certain bat species widespread across Africa had serologic evidence of Zaire and Sudan Ebola viruses. No viral RNA was detected in the subset of samples tested (n = 665). Ongoing surveillance of bats and other potential animal reservoirs are required to predict and prepare for future outbreaks.

Risk factors for MERS coronavirus infection in dromedary camels in Burkina Faso, Ethiopia, and Morocco, 2015.

Understanding Middle East respiratory syndrome coronavirus (MERS-CoV) transmission in dromedary camels is important, as they consitute a source of zoonotic infection to humans. To identify risk factors for MERS-CoV infection in camels bred in diverse conditions in Burkina Faso, Ethiopia and Morocco, blood samples and nasal swabs were sampled in February-March 2015. A relatively high MERS-CoV RNA rate was detected in Ethiopia (up to 15.7%; 95% confidence interval (CI): 8.2-28.0), followed by Burkina Faso (up to 12.2%; 95% CI: 7-20.4) and Morocco (up to 7.6%; 95% CI: 1.9-26.1). The RNA detection rate was higher in camels bred for milk or meat than in camels for transport (p = 0.01) as well as in younger camels (p = 0.06). High seropositivity rates (up to 100%; 95% CI: 100-100 and 99.4%; 95% CI: 95.4-99.9) were found in Morocco and Ethiopia, followed by Burkina Faso (up to 84.6%; 95% CI: 77.2-89.9). Seropositivity rates were higher in large/medium herds (≥51 camels) than small herds (p = 0.061), in camels raised for meat or milk than for transport (p = 0.01), and in nomadic or sedentary herds than in herds with a mix of these lifestyles (p < 0.005).

Seroprevalence of contagious bovine pleuropneumonia (CBPP) in Mali.

A serological survey to determine the prevalence of contagious bovine pleuropneumonia (CBPP) in Mali was carried out by using the competitive enzyme linked-immunosorbent test (c-ELISA) on 8007 serum samples systematically collected from 199 cattle herds collected throughout the whole country. Results showed a national prevalence of 18.11 % at the individual level and 85.93 % at the herd level. Significant variations in the individual prevalence were observed between regions of the country and ranged from 4.63 % in Tombouctou to 54.88 % in Kidal. At the herd level, although there were variations between regions, a high prevalence was constantly observed ranging from 60 to 100 %, hence confirming the endemic nature of the disease across the country. The CBPP risk varied also between regions and was very low in Tombouctou (odds ratio (OR) = 0.4) but very high in Kidal (OR = 9.8). Similarly, the risk seemed higher in the animals of the over 3-year age group (OR = 1.6) compared to the other age groups. It was also observed that there was a slightly higher risk (OR = 1.3) in the females than in the males. This study confirms the presence of CBPP across the country and should help to elaborate strategies for the effective control of the disease.

Application of loop analysis for the qualitative assessment of surveillance and control in veterinary epidemiology.

BACKGROUND: Systems for animal disease mitigation involve both surveillance activities and interventions to control the disease. They are complex organizations that are described by partial or imprecise data, making it difficult to evaluate them or make decisions to improve them. A mathematical method, called loop analysis, can be used to model qualitatively the structure and the behavior of dynamic systems; it relies on the study of the sign of the interactions between the components of the system. This method, currently widely used by ecologists, has to our knowledge never been applied in the context of animal disease mitigation systems. The objective of the study was to assess whether loop analysis could be applied to this new context. We first developed a generic model that restricted the applicability of the method to event-based surveillance systems of endemic diseases, excluding the emergence and eradication phases. Then we chose the mitigation system of highly pathogenic avian influenza (HPAI) H5N1 in Cambodia as an example of such system to study the application of loop analysis to a real disease mitigation system. RESULTS: Breaking down the generic model, we constructed a 6-variables model to represent the HPAI H5N1 mitigation system in Cambodia. This construction work improved our understanding of this system, highlighting the link between surveillance and control which is unclear in traditional representations of this system. Then we analyzed the effect of the perturbations to this HPAI H5N1 mitigation system that we interpreted in terms of investment in a given compartment. This study suggested that increasing intervention at a local level can optimize the system's efficiency. Indeed, this perturbation both decreases surveillance and intervention costs and reduces the disease's occurrence. CONCLUSION: Loop analysis can be applied to disease mitigation systems. Its main strength is that it is easy to design, focusing on the signs of the interactions. It is a simple and flexible tool that could be used as a precursor to large-scale quantitative studies, to support reflection about disease mitigation systems structure and functioning.

Avian influenza vaccination of poultry and passive case reporting, Egypt.

We investigated the influence of a mass poultry vaccination campaign on passive surveillance of highly pathogenic avian influenza subtype (H5N1) outbreaks among poultry in Egypt. Passive reporting dropped during the campaign, although probability of infection remained unchanged. Future poultry vaccination campaigns should consider this negative impact on reporting for adapting surveillance strategies.

Performance evaluation of two serological tests for contagious bovine pleuropneumonia (CBPP) detection in an enzootic area using a Bayesian framework.

A Bayesian approach, allowing for conditional dependence between two tests was used to estimate without gold standard the sensitivities of complement fixation test (CFT) and competitive enzyme-linked immunosorbent assay test (cELISA) and the serological prevalence of CBPP in a cattle population of the Central Delta of the Niger River in Mali, where CBPP is enzootic and the true prevalence and animals serological state were unknown. A significant difference (P = 0.99) was observed between the sensitivities of the two tests, estimated at 73.7% (95% probability interval [PI], 63.4-82.7) for cELISA and 42.3% (95% PI, 33.3-53.7) for CFT. Individual-level serological prevalence in the study population was estimated at 14.1% (95% PI, 10.8-16.9). Our results indicate that in enzootic areas, cELISA performs better in terms of sensitivity than CFT. However, negative conditional sensitivity dependence between the two tests was detected, implying that to achieve maximum sensitivity, the two tests should be applied in parallel.

COVID-19 in Africa: Underreporting, demographic effect, chaotic dynamics, and mitigation strategy impact.

The epidemic of COVID-19 has shown different developments in Africa compared to the other continents. Three different approaches were used in this study to analyze this situation. In the first part, basic statistics were performed to estimate the contribution of the elderly people to the total numbers of cases and deaths in comparison to the other continents; Similarly, the health systems capacities were analysed to assess the level of underreporting. In the second part, differential equations were reconstructed from the epidemiological time series of cases and deaths (from the John Hopkins University) to analyse the dynamics of COVID-19 in seventeen countries. In the third part, the time evolution of the contact number was reconstructed since the beginning of the outbreak to investigate the effectiveness of the mitigation strategies. Results were compared to the Oxford stringency index and to the mobility indices of the Google Community Mobility Reports. Compared to Europe, the analyses show that the lower proportion of elderly people in Africa enables to explain the lower total numbers of cases and deaths by a factor of 5.1 on average (from 1.9 to 7.8). It corresponds to a genuine effect. Nevertheless, COVID-19 numbers are effectively largely underestimated in Africa by a factor of 8.5 on average (from 1.7 to 20. and more) due to the weakness of the health systems at country level. Geographically, the models obtained for the dynamics of cases and deaths reveal very diversified dynamics. The dynamics is chaotic in many contexts, including a situation of bistability rarely observed in dynamical systems. Finally, the contact number directly deduced from the epidemiological observations reveals an effective role of the mitigation strategies on the short term. On the long term, control measures have contributed to maintain the epidemic at a low level although the progressive release of the stringency did not produce a clear increase of the contact number. The arrival of the omicron variant is clearly detected and characterised by a quick increase of interpeople contact, for most of the African countries considered in the analysis.

Seroprevalence of African swine fever in Senegal, 2006.

In Senegal, during 2002-2007, 11 outbreaks of African swine fever (ASF) were reported to the World Organisation for Animal Health. Despite this, little was known of the epidemiology of ASF in the country. To determine the prevalence of ASF in Senegal in 2006, we tested serum specimens collected from a sample of pigs in the 3 main pig-farming regions for antibodies to ASF virus using an ELISA. Of 747 serum samples examined, 126 were positive for ASF, suggesting a prevalence of 16.9%. The estimated prevalences within each of the regions (Fatick, Kolda, and Ziguinchor) were 13.3%, 7.8%, and 22.1%, respectively, with statistical evidence to suggest that the prevalence in Ziguinchor was higher than in Fatick or Kolda. This regional difference is considered in relation to different farming systems and illegal trade with neighboring countries where the infection is endemic.

Risk assessment of the introduction of Rift Valley fever from the Horn of Africa to Yemen via legal trade of small ruminants.

Rift Valley fever (RVF) is a mosquito-borne viral zoonosis of increasing global importance. Occurring since 1930 across Africa, it was detected for the first time in Saudi Arabia and Yemen in September 2000, leading to human deaths and major losses in livestock populations. Assuming the virus has not survived in Yemen or has been circulating at a low level, authors qualitatively assessed the likelihood of "re-introduction" of RVF into Yemen through the legal importation of small ruminants from the Horn of Africa. The overall probability of introduction was assessed very low to medium, increasing during festival periods and higher when considering a direct transmission exposure as compared to a vectorial transmission exposure. The uncertainty was considered to be medium underlining important gaps in information that need to be fulfilled in the region. Options to reduce the risk are proposed and discussed, including possible improvements of the current Yemeni quarantine system.

Mapping of Ebola virus spillover: Suitability and seasonal variability at the landscape scale.

The unexpected Ebola virus outbreak in West Africa in 2014 involving the Zaire ebolavirus made clear that other regions outside Central Africa, its previously documented niche, were at risk of future epidemics. The complex transmission cycle and a lack of epidemiological data make mapping areas at risk of the disease challenging. We used a Geographic Information System-based multicriteria evaluation (GIS-MCE), a knowledge-based approach, to identify areas suitable for Ebola virus spillover to humans in regions of Guinea, Congo and Gabon where Ebola viruses already emerged. We identified environmental, climatic and anthropogenic risk factors and potential hosts from a literature review. Geographical data layers, representing risk factors, were combined to produce suitability maps of Ebola virus spillover at the landscape scale. Our maps show high spatial and temporal variability in the suitability for Ebola virus spillover at a fine regional scale. Reported spillover events fell in areas of intermediate to high suitability in our maps, and a sensitivity analysis showed that the maps produced were robust. There are still important gaps in our knowledge about what factors are associated with the risk of Ebola virus spillover. As more information becomes available, maps produced using the GIS-MCE approach can be easily updated to improve surveillance and the prevention of future outbreaks.

Typological analysis of public-private partnerships in the veterinary domain.

Public-Private Partnerships (PPPs) are defined as a collaborative approach in which the public and private sector share resources, responsibilities and risks to achieve common objectives and mutual benefits in a sustainable manner. PPPs are identified as a key solution to reinforce Veterinary Services. However only limited information is available on the scope, added value and enabling factors of PPPs in this sector. The aims of this study were to develop a typology of PPPs in the veterinary field and to identify key success factors and obstacles to their implementation. A structured questionnaire was sent to all 181 World Organisation for Animal Health (OIE) Member Countries and to 47 private contacts. 36 different variables characterizing PPP initiatives were collected. 97 examples of PPPs were retrieved from 76 countries. Dimensionality reduction techniques were combined with clustering and discrimination methods to establish a typology of PPPs and to derive a set of simple rules to classify new instances of PPPs. Three clusters were identified, separated according to two main variables: the type of private partners and the type of interaction. Cluster 1, transactional PPPs, represented the traditional understanding of PPPs by Veterinary Services, initiated and funded by the public sector, giving service delivery accreditation to mostly private veterinarians; cluster 2, collaborative PPPs, included partnerships between producer associations and public Veterinary Services, driven by trade interests; cluster 3, transformational PPPs, represented joint programs initiated and funded by private companies and initially driven by business development objectives. Specific success factors and key obstacles affecting the performances and sustainability of these initiatives were identified for each cluster. This study represents the first practical attempt to develop a meaningful typology of PPPs in the field of animal health and to identify fundamental obstacles currently inhibiting the development of PPPs, and suggests ways to support national Veterinary Services in overcoming these obstacles.

Epidemiological Survey of Peste des Petits Ruminants in Ethiopia: Cattle as Potential Sentinel for Surveillance.

Peste des petits ruminants (PPR) is a highly contagious viral disease of small ruminants; it emerged in countries previously free of the disease following the eradication of rinderpest. PPR is classified by international organizations as the next priority animal disease for global eradication campaign. Assessment of the local situations is the first step in the eradication efforts. The objective of this study was to investigate and compare the seroprevalence of PPR in cattle, sheep, and goats under two livestock production systems in Ethiopia: North Shewa zone of Amhara region represents a highland sedentary life style characterized by mixed livestock-crop production system; Zone Three of Afar region represents a lowland nomadic life style characterized by pastoral livestock production system. N-competitive ELISA PPR test was performed on sera from 2,993 animals ≥6 months old sampled at watering and grazing points. Multivariable logistic regression models comparing the seropositivity between the two production systems were built by classifying doubtful results as positive, negative, or excluding them from the data. The odds ratio (OR) comparing overall PPR seroprevalence in the sedentary North Shewa Zone compared to the nomadic Zone Three ranged from 19 to 27 (P < 0.001), depending on how doubtful results were classified, which contrasts with what has been reported in the literature. This is not likely to be related solely to vaccination, since seroprevalences in cattle and small ruminants were similarly high or low in the respective zones (0-4% for Zone Three and 20-40% for North Shewa Zone), and cattle were not likely to be vaccinated. The OR of seropositivity for goats compared to cattle ranged from 1.9 [95% confidence interval (CI): 1.3-2.7; P < 0.001] to 2.2 (95% CI: 1.5-3.1; P < 0.001) when doubtful results were excluded or classified as negative, respectively. When doubtful results were classified as positive, association between seropositivity and animal species was not significant (P > 0.05). Our results suggest to further investigate cattle as sentinel animals for PPR surveillance.

Peste des petits ruminants (PPR) in Ethiopia: analysis of a national serological survey.

BACKGROUND: Peste des petits ruminants (PPR) is a contagious viral disease of small ruminants in Africa and Asia. In 1999, probably the largest survey on PPR ever conducted in Africa was initiated in Ethiopia where 13 651 serum samples from 7 out of the 11 regions were collected and analyzed by competitive enzyme-linked immunosorbent assay (cELISA). The objective of this paper is to present the results of this survey and discuss their practical implications for PPR-endemic regions. METHODS: We explored the spatial distribution of PPR in Ethiopia and we investigated risk factors for positive serological status. Intracluster correlation coefficients (rho), were calculated for 43 wereda (administrative units). RESULTS: Seroprevalence was very heterogeneous across regions and even more across wereda, with prevalence estimates ranging from 0% to 52.5%. Two groups of weredas could be distinguished on the basis of the estimated rho: a group with very low rho (rho < 0.12) and a group with very high rho (rho > 0.37). CONCLUSION: The results indicate that PPRV circulation has been very heterogeneous, the values for the rho may reflect the endemic or epidemic presence of the virus or the various degrees of mixing of animals in the different areas and production systems. Age appears as a risk factor for seropositive status, the linear effect seeming to confirm in the field that PPRV is highly immunogenic. Our estimates of intracluster correlation may prove useful in the design of serosurveys in other countries where PPR is of importance.

Using remote sensing to map larval and adult populations of Anopheles hyrcanus (Diptera: Culicidae) a potential malaria vector in Southern France.

BACKGROUND: Although malaria disappeared from southern France more than 60 years ago, suspicions of recent autochthonous transmission in the French Mediterranean coast support the idea that the area could still be subject to malaria transmission. The main potential vector of malaria in the Camargue area, the largest river delta in southern France, is the mosquito Anopheles hyrcanus (Diptera: Culicidae). In the context of recent climatic and landscape changes, the evaluation of the risk of emergence or re-emergence of such a major disease is of great importance in Europe. When assessing the risk of emergence of vector-borne diseases, it is crucial to be able to characterize the arthropod vector's spatial distribution. Given that remote sensing techniques can describe some of the environmental parameters which drive this distribution, satellite imagery or aerial photographs could be used for vector mapping. RESULTS: In this study, we propose a method to map larval and adult populations of An. hyrcanus based on environmental indices derived from high spatial resolution imagery. The analysis of the link between entomological field data on An. hyrcanus larvae and environmental indices (biotopes, distance to the nearest main productive breeding sites of this species i.e., rice fields) led to the definition of a larval index, defined as the probability of observing An. hyrcanus larvae in a given site at least once over a year. Independent accuracy assessments showed a good agreement between observed and predicted values (sensitivity and specificity of the logistic regression model being 0.76 and 0.78, respectively). An adult index was derived from the larval index by averaging the larval index within a buffer around the trap location. This index was highly correlated with observed adult abundance values (Pearson r = 0.97, p < 0.05). This allowed us to generate predictive maps of An. hyrcanus larval and adult populations from the landscape indices. CONCLUSION: This work shows that it is possible to use high resolution satellite imagery to map malaria vector spatial distribution. It also confirms the potential of remote sensing to help target risk areas, and constitutes a first essential step in assessing the risk of re-emergence of malaria in southern France.