Infection of Wildlife by Mycobacterium bovis in France Assessment Through a National Surveillance System, Sylvatub.

Mycobacterium bovis infection was first described in free-ranging wildlife in France in 2001, with subsequent detection in hunter-harvested ungulates and badgers in areas where outbreaks of bovine tuberculosis (TB) were also detected in cattle. Increasing concerns regarding TB in wildlife led the French General Directorate for Food (DGAL) and the main institutions involved in animal health and wildlife management, to establish a national surveillance system for TB in free-ranging wildlife. This surveillance system is known as "Sylvatub." The system coordinates the activities of various national and local partners. The main goal of Sylvatub is to detect and monitor M. bovis infection in wildlife through a combination of passive and active surveillance protocols adapted to the estimated risk level in each area of the country. Event-base surveillance relies on M. bovis identification (molecular detection) (i) in gross lesions detected in hunter-harvested ungulates, (ii) in ungulates that are found dead or dying, and (iii) in road-killed badgers. Additional targeted surveillance in badgers, wild boars and red deer is implemented on samples from trapped or hunted animals in at-risk areas. With the exception of one unexplained case in a wild boar, M. bovis infection in free-living wildlife has always been detected in the vicinity of cattle TB outbreaks with the same genotype of the infectious M. bovis strains. Since 2012, M. bovis was actively monitored in these infected areas and detected mainly in badgers and wild boars with apparent infection rates of 4.57-5.14% and 2.37-3.04%, respectively depending of the diagnostic test used (culture or PCR), the period and according to areas. Sporadic infection has also been detected in red deer and roe deer. This surveillance has demonstrated that M. bovis infection, in different areas of France, involves a multi-host system including cattle and wildlife. However, infection rates are lower than those observed in badgers in the United Kingdom or in wild boars in Spain.

Emerging highly pathogenic H5 avian influenza viruses in France during 2015/16: phylogenetic analyses and markers for zoonotic potential.

Several new highly pathogenic (HP) H5 avian influenza virus (AIV) have been detected in poultry farms from south-western France since November 2015, among which an HP H5N1. The zoonotic potential and origin of these AIVs immediately became matters of concern. One virus of each subtype H5N1 (150169a), H5N2 (150233) and H5N9 (150236) was characterised. All proved highly pathogenic for poultry as demonstrated molecularly by the presence of a polybasic cleavage site in their HA protein - with a sequence (HQRRKR/GLF) previously unknown among avian H5 HPAI viruses - or experimentally by the in vivo demonstration of an intravenous pathogenicity index of 2.9 for the H5N1 HP isolate. Phylogenetic analyses based on the full genomes obtained by NGS confirmed that the eight viral segments of the three isolates were all part of avian Eurasian phylogenetic lineage but differed from the Gs/Gd/1/96-like lineage. The study of the genetic characteristics at specific amino acid positions relevant for modulating the adaptation to and the virulence for mammals showed that presently, these viruses possess most molecular features characteristic of AIV and lack some major characteristics required for efficient respiratory transmission to or between humans. The three isolates are therefore predicted to have no significant pandemic potential.

Spread and impact of the Schmallenberg virus epidemic in France in 2012-2013.

BACKGROUND: The Schmallenberg virus (SBV) emerged in Europe in 2011 and caused a widespread epidemic in ruminants.In France, SBV emergence was monitored through a national multi-stakeholder surveillance and investigation system. Based on the monitoring data collected from January 2012 to August 2013, we describe the spread of SBV in France during two seasons of dissemination (vector seasons 2011 and 2012) and we provide a large-scale assessment of the impact of this new disease in ruminants. RESULTS: SBV impact in infected herds was primarily due to the birth of stillborns or deformed foetuses and neonates. Congenital SBV morbidity level was on average moderate, although higher in sheep than in other ruminant species. On average, 8% of lambs, 3% of calves and 2% of kids born in SBV-infected herds showed typical congenital SBV deformities. In addition, in infected herds, farmers reported retrospectively a lower prolificacy during the vector season, suggesting a potential impact of acute SBV infection during mating and early stages of gestation. CONCLUSIONS: Due to the lack of available control and prevention measures, SBV spread quickly in the naive ruminant population. France continues to monitor for SBV, and updated information is made available online on a regular basis [http://www.plateforme-esa.fr/]. Outbreaks of congenital SBV are expected to occur sporadically from now on, but further epidemics may also occur if immunity at population level declines.

Exposure of wild boar to Mycobacterium tuberculosis complex in France since 2000 is consistent with the distribution of bovine tuberculosis outbreaks in cattle.

The Eurasian wild boar (Sus scrofa) is increasingly considered as a relevant actor in the epidemiology of animal tuberculosis (TB). Therefore, monitoring TB in wild boar becomes a key tool for establishing comprehensive control schemes for this disease. To estimate the exposure of free living wild boar to Mycobacterium tuberculosis complex (MTC) in France, a bovine-purified protein derivative based ELISA was used to test 2,080 archived serum samples of hunter-harvested animals in 58 French "départements". Two cut-off values were used for diagnostic interpretation: 0.2, recommended by the manufacturer (specificity: 96.43%; sensitivity: 72.6%), and 0.5 (specificity: 100%; sensitivity: 64%). During the same period, at the 0.2 cut-off, global true seroprevalence was 5.9% (IC95%: 4.3%-7.7%) and 76% of the sampled "départements" had seropositive wild boar, including seven cattle TB-free "départements. At the 0.5 cut-off, global true seroprevalence was 2.2% (IC95%: 1.5-3.2) and positive wild boar belonged to 21% of the "départements". All but one of these positive "départements" had reported at least one cattle TB outbreak since 2000. A good consistence between seropositive wild boar and TB outbreaks in cattle was found, especially at the 0.5 cut-off value (the mean distance to the nearest cattle TB outbreak was 13 km and 27 km for seropositive and seronegative wild boar, respectively; P<0.05). The use of an ELISA to detect MTC antibodies in wild boar has permitted the description of the geographic distribution of MTC contact in wild boar in France. Our results suggest that the ELISA could be used as a first screening tool to conduct TB surveillance in wild boar at a population level. High-risk wild boar populations (e.g. overabundant) could be tested and if identified positive by ELISA they should be surveyed in detail by combining pathology and culture.

Quantitative estimation of genetic risk for atypical scrapie in French sheep and potential consequences of the current breeding programme for resistance to scrapie on the risk of atypical scrapie.

BACKGROUND: Since 2002, active surveillance programmes have detected numerous atypical scrapie (AS) and classical scrapie cases (CS) in French sheep with almost all the PrP genotypes. The aim of this study was 1) to quantify the genetic risk of AS in French sheep and to compare it with the risk of CS, 2) to quantify the risk of AS associated with the increase of the ARR allele frequency as a result of the current genetic breeding programme against CS. METHODS: We obtained genotypes at codons 136, 141, 154 and 171 of the PRNP gene for representative samples of 248 AS and 245 CS cases. We used a random sample of 3,317 scrapie negative animals genotyped at codons 136, 154 and 171 and we made inferences on the position 141 by multiple imputations, using external data. To estimate the risk associated with PrP genotypes, we fitted multivariate logistic regression models and we estimated the prevalence of AS for the different genotypes. Then, we used the risk of AS estimated for the ALRR-ALRR genotype to analyse the risk of detecting an AS case in a flock homogenous for this genotype. RESULTS: Genotypes most at risk for AS were those including an AFRQ or ALHQ allele while genotypes including a VLRQ allele were less commonly associated with AS. Compared to ALRQ-ALRQ, the ALRR-ALRR genotype was significantly at risk for AS and was very significantly protective for CS. The prevalence of AS among ALRR-ALRR animals was 0.6 per thousand and was not different from the prevalence in the general population. CONCLUSION: In conclusion, further selection of ALRR-ALRR animals will not result in an overall increase of AS prevalence in the French sheep population although this genotype is clearly susceptible to AS. However the probability of detecting AS cases in flocks participating in genetic breeding programme against CS should be considered.

The prevalence of atypical scrapie in sheep from positive flocks is not higher than in the general sheep population in 11 European countries.

BACKGROUND: During the last decade, active surveillance for transmissible spongiform encephalopathies in small ruminants has been intensive in Europe. In many countries this has led to the detection of cases of atypical scrapie which, unlike classical scrapie, might not be contagious. EU legislation requires, that following detection of a scrapie case, control measures including further testing take place in affected flocks, including the culling of genotype susceptible to classical scrapie. This might result in the detection of additional cases. The aim of this study was to investigate the occurrence of additional cases in flocks affected by atypical scrapie using surveillance data collected in Europe in order to ascertain whether atypical scrapie, is contagious. RESULTS: Questionnaires were used to collect, at national level, the results of active surveillance and testing associated with flock outbreaks in 12 European countries. The mean prevalence of atypical scrapie was 5.5 (5.0-6.0) cases per ten thousand in abattoir surveillance and 8.1 (7.3-9.0) cases per ten thousand in fallen stock. By using meta-analysis, on 11 out of the 12 countries, we found that the probability of detecting additional cases of atypical scrapie in positive flocks was similar to the probability observed in animals slaughtered for human consumption (odds ratio, OR = 1.07, CI95%: 0.70-1.63) or among fallen stock (OR = 0.78, CI95%: 0.51-1.2). In contrast, when comparing the two scrapie types, the probability of detecting additional cases in classical scrapie positive flocks was significantly higher than the probability of detecting additional cases in atypical scrapie positive flocks (OR = 32.4, CI95%: 20.7-50.7). CONCLUSIONS: These results suggest that atypical scrapie is not contagious or has a very low transmissibility under natural conditions compared with classical scrapie. Furthermore this study stressed the importance of standardised data collection to make good use of the analyses undertaken by European countries in their efforts to control atypical and classical scrapie.

Discrepant epidemiological patterns between classical and atypical scrapie in sheep flocks under French TSE control measures.

The occurrence of secondary cases of atypical and classical scrapie was examined in 340 outbreaks of atypical and 296 of classical sheep scrapie detected in France during active surveillance programmes between 2002 and 2007. The prevalence of atypical scrapie in these flocks was 0.05% under selective culling and 0.07% under intensified monitoring i.e. not significantly different from that detected during active surveillance of the general population (P>0.5), whereas these figures were much higher for classical scrapie (3.67% and 0.25%, respectively, P<10(-5)). In addition the number of atypical scrapie cases per outbreak did not indicate clustering. The results suggest that atypical scrapie occurs spontaneously or is not particularly contagious, and that the control measures in force allowed appropriate control of classical scrapie but were not more efficient than active surveillance in detecting cases of atypical scrapie.

A case-control study on the origin of atypical scrapie in sheep, France.

A matched case-control study (95 cases and 220 controls) was designed to study risk factors for atypical scrapie in sheep in France. We analyzed contacts with animals from other flocks, lambing and feeding practices, and exposure to toxic substances. Data on the prnp genotype were collected for some case and control animals and included in a complementary analysis. Sheep dairy farms had a higher risk for scrapie (odds ratio [OR] 15.1, 95% confidence interval [CI] 3.3-69.7). Lower risk was associated with organic farms (OR 0.15, 95% CI 0.02-1.26), feeding corn silage (OR 0.16, 95% CI 0.05-0.53), and feeding vitamin and mineral supplements (OR 0.6, 95% CI 0.32-1.14). Genetic effects were quantitatively important but only marginally changed estimates of other variables. We did not find any risk factor associated with an infectious origin of scrapie. Atypical scrapie could be a spontaneous disease influenced by genetic and metabolic factors.

A descriptive study of the prevalence of atypical and classical scrapie in sheep in 20 European countries.

BACKGROUND: The development of active surveillance programmes for transmissible spongiform encephalopathies of small ruminants across Europe has led to the recent identification of a previously undetected form of ovine prion disease, 'atypical' scrapie. Knowledge of the epidemiology of this disease is still limited, as is whether it represents a risk for animal and/or public health. The detection of atypical scrapie has been related to the use of only some of the EU agreed rapid tests. Information about the rapid tests used is not, as yet, available from public reports on the surveillance of transmissible spongiform encephalopathies in small ruminants. We collected detailed results of active surveillance from European countries to estimate and to compare the prevalence of atypical scrapie and classical scrapie in sheep for each country stratified by each surveillance stream; healthy slaughtered and found dead adult sheep. RESULTS: From the 20 participating countries, it appeared that atypical scrapie was detected in Europe wherever the conditions necessary for its diagnosis were present. In most countries, atypical scrapie and classical scrapie occurred at low prevalence level. The classical scrapie prevalence estimates were more variable than those for atypical scrapie, which appeared remarkably homogeneous across countries, surveillance streams and calendar years of surveillance. Differences were observed in the age and genotype of atypical scrapie and classical scrapie cases that are consistent with previous published findings. CONCLUSION: This work suggests that atypical scrapie is not rare compared to classical scrapie. The homogeneity of its prevalence, whatever the country, stream of surveillance or year of detection, contrasts with the epidemiological pattern of classical scrapie. This suggests that the aetiology of atypical scrapie differs from that of classical scrapie.