Wild Boars as Reservoir of Highly Virulent Clone of Hybrid Shiga Toxigenic and Enterotoxigenic Escherichia coli Responsible for Edema Disease, France.

Edema disease is an often fatal enterotoxemia caused by specific strains of Shiga toxin-producing Escherichia coli (STEC) that affect primarily healthy, rapidly growing nursery pigs. Recently, outbreaks of edema disease have also emerged in France in wild boars. Analysis of STEC strains isolated from wild boars during 2013-2019 showed that they belonged to the serotype O139:H1 and were positive for both Stx2e and F18 fimbriae. However, in contrast to classical STEC O139:H1 strains circulating in pigs, they also possessed enterotoxin genes sta1 and stb, typical of enterotoxigenic E. coli. In addition, the strains contained a unique accessory genome composition and did not harbor antimicrobial-resistance genes, in contrast to domestic pig isolates. These data thus reveal that the emergence of edema disease in wild boars was caused by atypical hybrid of STEC and enterotoxigenic E. coli O139:H1, which so far has been restricted to the wildlife environment.

An outbreak of leptospirosis among kayakers in Brittany, North-West France, 2016.

In September 2016, a cluster of seven kayakers with clinical symptoms of leptospirosis with onset since July 2016 was reported to French health authorities. Human and animal investigations were undertaken to describe the outbreak, identify the likely place and source of infection and implement necessary control measures. We identified 103 patients with clinical symptoms of leptospirosis between 1 June and 31 October 2016 who lived in the Ille-et-Vilaine district in Brittany. Of these, 14 (including the original seven) reported contacts with the river Vilaine during the incubation period and were defined as outbreak cases: eight were confirmed by serology tests or PCR and six were probable without a laboratory confirmation for leptospirosis. All 14 cases were kayakers. Three distinct contamination sites were identified on a 30 km stretch of the river Vilaine. Nine cases reported having skin wounds while kayaking. None were vaccinated against leptospirosis. The outbreak was attributed to Leptospira kirschneri serogroup Grippotyphosa. Animal investigations did not allow identifying the possible reservoir. Leptospirosis outbreaks associated with freshwater sports are rare in temperate climates. The prevention of such outbreaks requires control of potential animal reservoirs in zones such as the Vilaine valley and that kayakers adopt the recommended individual prevention measures.

Large-scale lagovirus disease outbreaks in European brown hares (Lepus europaeus) in France caused by RHDV2 strains spatially shared with rabbits (Oryctolagus cuniculus).

Rabbit haemorrhagic disease virus (RHDV) is a lagovirus that causes rabbit haemorrhagic disease (RHD) in European rabbits (Oryctolagus cuniculus). In 2010, a new genotype called RHDV2 emerged in France. It exhibits a larger host range than classical RHDV strains by sporadically infecting different hare species, including the European hare (Lepus europaeus). Phylogenetic analyses revealed that closely related RHDV2 strains circulate locally in both hares and rabbits, and therefore that RHDV2 strains infecting hares do not belong to a lineage that has evolved only in this species. We showed that RHDV2 is widely distributed in France and that it was responsible for more than a third of cases of lagovirus disease in European hare populations in 2015. The oldest RHDV2 positive hare was sampled in November 2013 and we reported two hares co-infected by EBHSV and RHDV2. All together, our results raise important epidemiological and evolutionary issues. In particular, along with the potential emergence of recombinant EBHSV/RHDV2 strains in hares, the enlargement of the host range changes the host population structure of RHDV2 and may alter the impact of the virus on rabbit and hare populations.

Little field evidence of direct acute and short-term effects of current pesticides on the grey partridge.

Direct lethal and sublethal effects of pesticides on farmland birds' populations are recurring questions and largely debated. In this context, we conducted an innovative study combining radiotelemetry, farmer surveys, residue analyses on carcasses and modelling to assess the unintentional effects of pesticides on terrestrial birds. We chose the grey partridge Perdix perdix as a case study because this typical bird of European cereal ecosystems is highly exposed to pesticides. In this paper we focused on acute and short-term impacts of pesticides on adult mortality during spring and summer in a one-substance approach (multiple exposure were not studied here) but for a large variety of active substances (a.s.) actually used in cultivated farmland of Northern France. The fate and the location of 529 partridges were monitored twice a day from early March to late August 2010 and 2011 on 12 sites (14,500 ha). Their daily potential exposure to 183 a.s. was determined by overlapping birds' habitat use and daily pesticide application data. Based on this procedure, we calculated mortality rates within 10 days following a potential exposure for 157 different a.s.. 5 a.s. were associated with a "10-day mortality rate" higher than 10% but a single one (thiacloprid) is reported to be highly toxic to birds. We recorded 261 mortalities among which 94 carcasses were in suitable condition for residue analyses. We detected at least one a.s in 39.4% of carcasses. However, only 2 mortality cases were attributed to poisoning (carbofuran). Furthermore, modelling results showed that these lethal pesticide-related poisonings decreased the population growth rate by less than 1%. In conclusion, we did not point out important direct acute and short-term effects of pesticides currently used by farmers during the breeding season on the grey partridge. This is discussed with regards to the complexity of potential effects in operational conditions.

Unintentional wildlife poisoning and proposals for sustainable management of rodents.

In Europe, bromadiolone, an anticoagulant rodenticide authorized for plant protection, may be applied intensively in fields to control rodents. The high level of poisoning of wildlife that follows such treatments over large areas has been frequently reported. In France, bromadiolone has been used to control water voles (Arvicola terrestris) since the 1980s. Both regulation and practices of rodent control have evolved during the last 15 years to restrict the quantity of poisoned bait used by farmers. This has led to a drastic reduction of the number of cases of poisoned wildlife reported by the French surveillance network SAGIR. During the autumn and winter 2011, favorable weather conditions and high vole densities led to the staging of several hundreds of Red Kites (Milvus milvus) in the Puy-de-Dôme department (central France). At the same time, intensive treatments with bromadiolone were performed in this area. Although no misuse has been mentioned by the authorities following controls, 28 Red Kites and 16 Common Buzzards (Buteo buteo) were found dead during surveys in November and December 2011. For all these birds, poisoning by bromadiolone as the main cause of death was either confirmed or highly suspected. Other observations suggest a possible impact of bromadiolone on the breeding population of Red Kites in this area during the spring 2011. French regulation of vole control for plant protection is currently under revision, and we believe this event calls for more sustainable management of rodent outbreaks. Based on large-scale experiments undertaken in eastern France, we propose that direct control of voles at low density (with trapping or limited chemical treatments) and mechanical destruction of vole tunnels, mole control, landscape management, and predator fostering be included in future regulation because such practices could help resolve conservation and agricultural issues.

Protostrongylus pulmonalis (Frölich, 1802) and P. oryctolagi Babos, 1955 (Nematoda: Protostrongylidae), parasites of the lungs of European hare (Lepus europaeus L.) in France: morphological and molecular approaches.

Pulmonary protostrongyliasis of hare is a parasitic disease caused by nematodes belonging to the genus Protostrongylus (Nematoda, Protostrongylidae). During survey of wildlife disease in the South-East of France, pathologic examination of lungs from European hares found dead or hunter-killed between 2009 and 2012 was performed. Adult male worms were morphologically characterized and the identification confirmed by molecular biology (D2 domain of the 28S and ITS2 of rDNA). Two different species were identified: the first one, Protostrongylus pulmonalis, is identical with the haplotype previously deposited in GenBank. Based on morphological criteria of copulatory bursa of adult male worms (especially length of spicules and gubernaculum structure), we identified a second species found in France as Protostrongylus oryctolagi. This is the first report of P. oryctolagi in France from European hare and rabbit. P. oryctolagi was isolated from 248 hares and 3 rabbits in the South of France. P. pulmonalis was isolated from four hares found dead in the Northern France and from one hare in the South, which was co-parasitized by P. oryctolagi and P. pulmonalis. It's the first coinfection observed with these two species from a lung of hare in France.

Tracking potential Leptospira sources following human cases of leptospirosis: A One Health approach applied to an ecosystem in Brittany, France.

Pathogenic Leptospira can cause leptospirosis: a widespread, potentially fatal bacterial zoonosis whose risk is mediated by the soil and water features, animal host distributions, meaning the local ecosystem. When human cases of leptospirosis occur, it is challenging to track down their source because ecosystem-level epidemiological knowledge on Leptospira is needed. Between 2016 and 2019 in a focal riparian ecosystem, the human population experienced an outbreak and successive cases of leptospirosis attributable to L. kirschneri and L. interrogans. The epidemiological investigation was carried out using the One Health approach, as described in international health guidelines. As a first step in this process, we investigated leptospiral carriage in the main animal hosts found in the region. We sampled 143 nutrias, 17 muskrats, and 10 Norway rats using convenient trapping. DNA was extracted from their kidneys, lungs, and urine and subjected to real-time PCR (RT-PCR) targeting the Leptospira 16S rDNA and lfb1 genes. In the farms along the river's stretch of interest, we sampled serum from 439 cattle and used a microscopic agglutination test to detect the presence of antibodies against Leptospira. Urine samples were concomitantly obtained from 145 cattle and were used in two analyses: RT-PCR targeting the Leptospira 16S rDNA gene and Leptospira culturing. We found th, wt rodents were the most likely source of the L. interrogans behind the human cases. The cattle tested negative for Leptospira DNA but positive for antibodies against the serogroups implicated in the human cases. We failed to identify the potential source of the L. kirschneri responsible for several human cases of leptospirosis. Our results call for further clarification of the Leptospira maintenance community, which may comprise known maintenance hosts, such as rodents, as well as taxa not commonly considered to be maintenance hosts but that can still spread Leptospira. The resulting research network will collaboratively conduct future eco-epidemiological surveys to illuminate the leptospirosis risks faced by humans and animals within ecosystems.

Emergence of a new lagovirus related to Rabbit Haemorrhagic Disease Virus.

Since summer 2010, numerous cases of Rabbit Haemorrhagic Disease (RHD) have been reported in north-western France both in rabbitries, affecting RHD-vaccinated rabbits, and in wild populations. We demonstrate that the aetiological agent was a lagovirus phylogenetically distinct from other lagoviruses and which presents a unique antigenic profile. Experimental results show that the disease differs from RHD in terms of disease duration, mortality rates, higher occurrence of subacute/chronic forms and that partial cross-protection occurs between RHDV and the new RHDV variant, designated RHDV2. These data support the hypothesis that RHDV2 is a new member of the Lagovirus genus. A molecular epidemiology study detected RHDV2 in France a few months before the first recorded cases and revealed that one year after its discovery it had spread throughout the country and had almost replaced RHDV strains. RHDV2 was detected in continental Italy in June 2011, then four months later in Sardinia.

How to Strengthen Wildlife Surveillance to Support Freedom From Disease: Example of ASF Surveillance in France, at the Border With an Infected Area.

Using a risk-based approach, the SAGIR network (dedicated to wildlife disease surveillance) had to strengthen surveillance activities after ASF was confirmed in Belgium in September 2018, very near the French border. Three new active dead wild boars search protocols supplemented opportunistic surveillance in Level III risk areas: patrols by volunteer hunters, professional systematic combing, and dog detection. Those protocols were targeted in terms of location and time and complemented each other. The main objectives of the designed surveillance system were (i) to assure early detection in case of introduction of the disease and (ii) to support the free status of the zone. Compiling the surveillance effort was thus a necessity to assure authorities and producer representatives that the sometimes low number of carcasses detected was not a consequence of no surveillance activities. The human involvement in implementing those activities was significant: more than 1000 8-h days just for the time spent in the field on active search activities. We calculated a specific indicator to enable a comparison of the surveillance results from different zones, including non-infected Belgian zones with strengthened surveillance activities. This was a first step in the evaluation of the efficacy of our surveillance activities in a WB population. Field experiments and modelling dead WB detection probability are planned to supplement this evaluation. Belgium regained its ASF-free status in November 2020, and ASF was not detected in France in either the WB or domestic pig populations.

Polymorphism of the alpha-1-fucosyltransferase (FUT1) gene in several wild boar (Sus scrofa) populations in France and link to edema disease.

BACKGROUND: In 2013, an outbreak of edema disease in a population of wild boars (Sus scrofa) took place. This was the first described case as reported worldwide. An enterotoxigenic Escherichia coli (presenting the Stx2e and F18 virulence factors) is the main pathogen for this disease in wild boar. The alpha-1-fucosyltransferase gene (FUT1) has been identified as the gene regulating the expression of the receptor for E. coli stx2e F18 bacteria in domestic pigs affected by the disease. The genotypic frequencies of the FUT1 gene in European wild boars have not yet been investigated. The genotypes of wild boars for this gene were determined in four French departments with or without edema diseases cases. RESULTS: All of the wild boars analyzed had a genotype susceptible to the disease (GG or AG). The recessive, resistant A allele was found for the first time in wild boars, but in a very small proportion of individuals (7/222). No statistical differences were found between healthy hunted wild boars versus wild boars found dead by edema disease or among the four French departments. CONCLUSIONS: These results suggest that further mortality due to edema disease remains possible in wild boars in France.

Field evidence of bird poisonings by imidacloprid-treated seeds: a review of incidents reported by the French SAGIR network from 1995 to 2014.

The large-scale use of neonicotinoid insecticides has raised growing concerns about their potential adverse effects on farmland birds, and more generally on biodiversity. Imidacloprid, the first neonicotinoid commercialized, has been identified as posing a risk for seed-eating birds when it is used as seed treatment of some crops since the consumption of a few dressed seeds could cause mortality. But evidence of direct effects in the field is lacking. Here, we reviewed the 103 wildlife mortality incidents reported by the French SAGIR Network from 1995 to 2014, for which toxicological analyses detected imidacloprid residues. One hundred and one incidents totalling at least 734 dead animals were consistent with an agricultural use as seed treatment. Grey partridges (Perdix perdix) and "pigeons" (Columba palumbus, Columba livia and Columba oenas) were the main species found. More than 70% of incidents occurred during autumn cereal sowings. Furthermore, since there is no biomarker for diagnosing neonicotinoid poisonings, we developed a diagnostic approach to estimate the degree of certainty that these mortalities were due to imidacloprid poisoning. By this way, the probability that mortality was due to poisoning by imidacloprid-treated seeds was ranked as at least "likely" in 70% of incidents. As a result, this work provides clear evidence to risk managers that lethal effects due to the consumption by birds of imidacloprid-treated seeds regularly occur in the field. This in turn raises the question of the effectiveness of the two main factors (seed burying and imidacloprid-treated seeds avoidance) that are supposed to make the risk to birds negligible. Risk factors and the relevance of mitigation measures are discussed.

First Draft Genome Sequences of Three Strains of Francisella tularensis subsp. holarctica, Isolated from Hares and a Tick in France.

Here, we report the complete genome sequences of three strains of Francisella tularensis subsp. holarctica (11-789-5S, 11-935-13S, and 11-930-9S), isolated from brown hares and a tick during a tularemia outbreak in France, where tularemia is endemic.

Residues of plant protection products in grey partridge eggs in French cereal ecosystems.

The contamination of the eggs of farmland birds by currently used plant protection products (PPPs) is poorly documented despite a potential to adversely impact their breeding performance. In this context, 139 eggs of 52 grey partridge Perdix perdix clutches, collected on 12 intensively cultivated farmlands in France in 2010-2011, were analysed. Given the great diversity of PPPs applied on agricultural fields, we used exploratory GC/MS-MS and LC/MS-MS screenings measuring ca. 500 compounds. The limit of quantification was 0.01 mg/kg, a statutory reference. A total of 15 different compounds were detected in 24 clutches. Nine of them have been used by farmers to protect crops against fungi (difenoconazole, tebuconazole, cyproconazole, fenpropidin and prochloraz), insects (lambda-cyhalothrin and thiamethoxam/clothianidin) and weeds (bromoxynil and diflufenican). Some old PPPs were also detected (fipronil(+sulfone), HCH(α,ß,δ isomers), diphenylamine, heptachlor(+epoxyde), DDT(Σisomers)), as well as PCBs(153, 180). Concentrations ranged between <0.01 and 0.05 mg/kg but reached 0.067 (thiamethoxam/clothianidin), 0.11 (heptachlor + epoxyde) and 0.34 (fenpropidin) mg/kg in some cases. These results testify an actual exposure of females and/or their eggs to PPPs in operational conditions, as well as to organochlorine pollutants or their residues, banned in France since several years if not several decades, that persistently contaminate the environment.Routes of exposure, probability to detect a contamination in the eggs, and effects on egg/embryo characteristics are discussed with regard to the scientific literature.

Ashworthius sidemi Schulz, 1933 and Haemonchus contortus (Rudolphi, 1803) in cervids in France: integrative approach for species identification.

Among gastro-intestinal nematodes, the blood-sucking worms belonging to the subfamily of Haemonchinae are considered to be of pathogenic and economic great importance, particularly in small ruminants. Haemonchus contortus, primary found in domestic ruminants and wild bovines (Mouflon, Chamois), is probably the most studied, but occurrence of Ashworthius sidemi has gradually increased over recent years, especially in Cervids and free roaming wild bovid as the European bison in eastern Europe, and some cases of co-infestation were recently observed on five Roe deer (Capreolus capreolus) and one Red deer (Cervus elaphus) in France. If the diagnosis is possible on the morphological features for adult worms for helminthologists, the identification on some stages (female, subadult, eggs and larvae) is difficult or impossible. Sequencing ND4 domain from the mitochondrial DNA of H. contortus and A. sidemi worms, we observed clearly two distinct clades, with an inter-specific divergence of 28.1%. Basing on this specific domain, a multiplex PCR-based method was developed: new primers were designed and used pooled in one mix PCR, producing amplicons of 454bp for H. contortus and 330bp for A. sidemi, allowing a trivial and an inexpensive taxonomic affiliation after migration. This multiplex PCR-based method was developed here to distinguish H. contortus and A. sidemi regardless their developmental stage, easy to use for highlighting co-infestation cases in both wild and domestic ruminants. It is a non-invasive approach appearing as a good diagnostic tool relevant to coprological cultures.

Spatio-temporal dynamics of tularemia in French wildlife: 2002-2013.

Tularemia, caused by Francisella tularensis, is endemic in France. The surveillance of this disease in wildlife is operated by the SAGIR Network and by the National Reference Laboratory for Tularemia. Wild animals found dead or dying collected by the SAGIR network are necropsied and when tularemia is suspected culture and/or PCR are performed to confirm the diagnosis. The aim of this study was to present the results of tularemia surveillance in wildlife and to investigate the spatial and temporal pattern of tularemia observed between the 2002-2003 and 2012-2013 hunting seasons in French wildlife. Fourty-one to 121 cases were collected each hunting season for a total of 693 confirmed cases and 46 additional suspected cases. The main species affected was the European Brown Hare (Lepus europaeus) but 4 rabbits (Oryctolagus cuniculus), 2 roe deer (Capreolus capreolus) and one wild boar (Sus scrofa) were also found positive. The Standard Mortality Ratio was mapped and Kulldorff's retrospective space-time scan statistic was implemented and allowed the detection of several clusters: the nationwide outbreak of 2007-2008; 2 clusters in northern and central-western France in high hare-abundance areas and another in North-eastern France where the abundance of hares is low. Our results confirm the usefulness of brown hare as a sentinel of environmental risk.

Evaluation of a Multivariate Syndromic Surveillance System for West Nile Virus.

BACKGROUND: Various methods are currently used for the early detection of West Nile virus (WNV) but their outputs are not quantitative and/or do not take into account all available information. Our study aimed to test a multivariate syndromic surveillance system to evaluate if the sensitivity and the specificity of detection of WNV could be improved. METHODS: Weekly time series data on nervous syndromes in horses and mortality in both horses and wild birds were used. Baselines were fitted to the three time series and used to simulate 100 years of surveillance data. WNV outbreaks were simulated and inserted into the baselines based on historical data and expert opinion. Univariate and multivariate syndromic surveillance systems were tested to gauge how well they detected the outbreaks; detection was based on an empirical Bayesian approach. The systems' performances were compared using measures of sensitivity, specificity, and area under receiver operating characteristic curve (AUC). RESULTS: When data sources were considered separately (i.e., univariate systems), the best detection performance was obtained using the data set of nervous symptoms in horses compared to those of bird and horse mortality (AUCs equal to 0.80, 0.75, and 0.50, respectively). A multivariate outbreak detection system that used nervous symptoms in horses and bird mortality generated the best performance (AUC = 0.87). CONCLUSIONS: The proposed approach is suitable for performing multivariate syndromic surveillance of WNV outbreaks. This is particularly relevant, given that a multivariate surveillance system performed better than a univariate approach. Such a surveillance system could be especially useful in serving as an alert for the possibility of human viral infections. This approach can be also used for other diseases for which multiple sources of evidence are available.

Quantification of potential exposure of gray partridge (Perdix perdix) to pesticide active substances in farmlands.

Estimating exposure of wild birds to plant protection products is of key importance in the risk assessment process evaluating their harmful potential. In this paper, we propose an ecologically-relevant methodology to estimate potential exposure to active substances (ASs) of a farmland focal bird, the gray partridge Perdix perdix. It is based on bird habitat use of fields at the time of pesticide applications. It accounts for spatio-temporal heterogeneity at population and landscape scales. We identify and quantify the potential exposure to 179 ASs of 140 clutches during pre-laying, laying, and incubation phases, and of 75 coveys. The data come from a large scale field study combining radiotelemetry and a farmer survey. They were collected in 12 different representative sites. The proportion of clutches potentially exposed to a given chemical was ≥5% for 32 ASs; prothioconazole and epoxiconazole ranking first. 71% of clutches were potentially exposed to ≥1 AS and 67% to ≥2 ASs. Mixtures involved 2 to 22 ASs. They emerged from commercial formulations, tank mixtures, bird habitat use, and combinations. ASs were fungicides (53%), herbicides (25%), and insecticides (16%) used on a variety of crops in April-June, when ground-nesting birds are breeding. The European Food Safety Authority conclusions report a long-term first-tier toxicity-to-exposure ratio (TERlt) <5 for 11 out of 19 documented ASs, and higher-tier TERlt <5 for 5 out of 10 ASs. This suggests a potential risk for bird reproduction in farmlands. Globally 13% of coveys were potentially exposed to 18 ASs during the first month (1-4 coveys per AS). The use of our field data in future research and risk assessment is discussed.

Intermediate hosts of Protostrongylus pulmonalis (Frölich, 1802) and P. oryctolagi Babos, 1955 under natural conditions in France.

BACKGROUND: Protostrongylus oryctolagi and P. pulmonalis are causative agents of pulmonary protostrongyliasis in Lagomorphs in France. These nematodes need usually one intermediate host for its life cycle, a terrestrial snail. However, some studies, mainly in experimental conditions, have identified the species of snails acting as intermediate hosts. METHODS: In total, 3315 terrestrial snails and 307 slugs were collected in the field in South-Eastern France and analyzed to detect the presence of parasites. Identification of nematode parasites and snails were performed according to morphological and molecular approaches (D2 domain of the 28S rDNA for parasites; 18S and ITS-1 rDNA, COI and 16S mtDNA for snails). RESULTS: Eighteen snails were found positive for Protostrongylids larvae. Haplotypes of the larvae corresponding to sequences of P. oryctolagi and P. pulmonalis were detected. Morphological identification of molluscs based on shell characters revealed 4 different morphotypes, and molecular results confirm the membership of these gastropods to the Hygromiidae and revealed 4 different species: Candidula gigaxii, 2 species of Cernuella sp. and Xeropicta derbentina. All infested snails were collected in wine cultures. CONCLUSION: This study displays the first description of intermediate hosts of P. oryctolagi and the first report of X. derbentina as natural intermediate host of P. pulmonalis.