Épidémiologie des maladies Animales et zoonotiques

Wildlife species as reservoirs of infectious pathogens represent a serious constraint in the implementation of disease management strategies. In the Mediterranean island of Corsica, the dynamics of hepatitis E virus (HEV) and Aujeszky's disease virus (ADV) are suspected to be influenced by interactions between wild and domestic pigs. To improve our understanding of these influences, we first compared the seroprevalences of both viruses in domestic pig populations from different locations with contrasted levels of wild-domestic interactions, ADV vaccination, biosafety, and farm husbandry. Second, we performed an analysis at a more restricted geographical scale, to assess the matching of ADV or HEV prevalence between sympatric wild boar and outdoor pig farms most exposed to interactions with wildlife. Logistic models were adjusted to the observed data. A high seroprevalence of HEV (>80%) and ADV (40%) in pigs, with no significant difference according to the region, confirms that both pathogens are enzootic in Corsica. Vaccination against ADV had a strong protective effect, even when performed voluntarily by farmers. Farm biosafety had an additional effect on pigs' exposure, suggesting that contact between wild boars and pigs were involved in disease transmission. A strong correlation in HEV seroprevalence was observed between pigs and wild boars that were in close contact, and significantly lower seroprevalence was observed in pigs when they had little contact with wild boars due to spatial segregation. These results suggest a regular HEV circulation between sympatric wild boar and domestic pigs. The high HEV seroprevalence observed in domestic pigs (>80%) suggests a spillover of the virus from domestic to wild populations through environmental contamination, but this hypothesis has to be confirmed. Conversely, even though avoiding sows' release on pasture during estrus showed some protecting effect in the free ranging pig farms regarding ADV, ADV seroprevalence was not dependent on the swine populations (wild or domestic) or on the wild-domestic spatial overlap, suggesting two quasi-separate enzootic cycles. This information will prove useful for designing more efficient disease management strategies in Corsica and similar contexts.

With the exception of Aelurostrongylus abstrusus, feline lungworms have been poorly studied. Information on their distribution is patchy and mostly limited to case reports. In this study, the occurrence of feline lungworms and co-infecting gastrointestinal parasites has been investigated in 12 European countries (i.e. Austria, Belgium, Bulgaria, France, Greece, Hungary, Italy, Portugal, Romania, Spain, Switzerland and the United Kingdom). An average of 10 domestic cats, with regular outdoor access, was sampled each month for 12months, and freshly passed faeces were collected. Stools were processed using a McMaster assay and a quantitative Baermann-Wetzel method. Animals positive for lungworms and/or gastrointestinal parasites were treated with a formulation containing fipronil, (S)-methoprene, eprinomectin, and praziquantel (Broadline®, Merial), and re-sampled 28days post-treatment. The association between lungworm infection and risk factors was analysed using statistical medians/means and the efficacy of the treatment against each lungworm species was assessed. Of 1990 cats sampled, 613 (30.8%) were positive for at least one parasite, while 210 (10.6%) were infected by lungworms. The prevalence of lungworm infection varied between the sampled sites, with the highest recorded in Bulgaria (35.8%) and the lowest in Switzerland (0.8%). None of the cats from Austria or the United Kingdom were infected by lungworms. Aelurostrongylus abstrusus was the species most frequently detected (78.1%), followed by Troglostrongylus brevior (19.5%), Eucoleus aerophilus (14.8%) and Oslerus rostratus (3.8%). The overall efficacy of the treatment was 99% for A. abstrusus and 100% for T. brevior, O. rostratus and E. aerophilus. Data presented provide a comprehensive account of the diagnosis, epidemiology and treatment of feline lungworms in Europe, as well as of the occurrence of co-infections by gastrointestinal parasites.

BACKGROUND: Leptospirosis is a worldwide zoonotic bacterial disease caused by infection with leptospires. Leptospirosis in humans and livestock is an endemic and epidemic disease in Thailand. Livestock may act as reservoirs for leptospires and source for human infection. METHODOLOGY/PRINCIPAL FINDINGS: Data on leptospirosis infection in humans and livestock (Buffaloes, Cattle, and Pigs) species during 2010 to 2015 were analyzed. Serum samples were examined using Microscopic Agglutination Test (MAT) to identify antibodies against Leptospira serovars using a cut-off titer ≥ 1:100. The seroprevalence was 23.7% in humans, 24.8% in buffaloes, 28.1% in cattle, and 11.3% in pigs. Region specific prevalence among humans and livestock was found in a wide range. The most predominant serovars were Shermani, followed by Bratislava, Panama, and Sejroe in human, Shermani, Ranarum, and Tarassovi in buffaloes, and Shermani and Ranarum in cattle and pigs. Equally highest MAT titers against multiple serovars per one sample were found mainly in buffaloes and cattle showing equally titers against Ranarum and Shermani. The correlations of distribution of serovars across Thailand's regions were found to be similar in pattern for cattle but not for buffaloes. In humans, the serovar distribution in the south differed from other regions. By logistic regression, the results indicated that livestock is more susceptible to infection by serovar Shermani when compared to humans. CONCLUSIONS/SIGNIFICANCE: This study gives a detailed picture of the predominance of Leptospira serovars in relation to region, humans and typical livestock. The broad spatial distribution of seroprevalence was analyzed across and within species as well as regions in Thailand. Our finding may guide public health policy makers to implement appropriate control measures and help to reduce the impact of leptospirosis in Thailand.

Abstract Deforestation and associated changing landscapes are major components of environmental changes, with important implications for ecosystem functioning and biodiversity conservation. Tropical forests are hot spots of biodiversity and provide multiple goods and ecosystem services which benefit people in many ways. Forests also play an important role in health-related legends, myths, and fairy tales from all over the world, and are important sources of new potential emerging microbial threats to humans. Although plausibly numerous abundant microbial forms with a forest origin may exist, our systematic literature review shows that forest-derived infection studies are relatively unexplored, and both taxonomically and geographically biased. Since biodiversity has been associated with emergence of novel infectious diseases at macro-scale, we describe the main biogeographical patterns in the emerging infection-biodiversity-forest loss nexus. Then, we illustrate four fine-scale case studies to decipher the underlying processes of increased infection risk in changing forest clearing landscapes. Finally, we identify scientific challenges and regional management measures required to mitigate these important new emerging threats.

Biodiversity is of critical value to human societies, but recent evidence that biodiversity may mitigate infectious-disease risk has sparked controversy among researchers. The majority of work on this topic has focused on direct assessments of the relationship between biodiversity and endemic-pathogen prevalence, without disentangling intervening mechanisms; thus study outcomes often differ, fuelling more debate. Here, we suggest two critical changes to the approach researchers take to understanding relationships between infectious disease, both endemic and emerging, and biodiversity that may help clarify sources of controversy. First, the distinct concepts of hazards versus risks need to be separated to determine how biodiversity and its drivers may act differently on each. This distinction is particularly important since it illustrates that disease emergence drivers in humans could be quite different to the general relationship between biodiversity and transmission of endemic pathogens. Second, the interactive relationship among biodiversity, anthropogenic change and zoonotic disease risk, including both direct and indirect effects, needs to be recognized and accounted for. By carefully disentangling these interactions between humans' activities and pathogen circulation in wildlife, we suggest that conservation efforts could mitigate disease risks and hazards in novel ways that complement more typical disease control efforts.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

In dairy cattle, mastitis is the most frequent bacterial disease, and the routine use of antibiotics for treatment and prevention can drive antimicrobial resistance (AMR). The aim of our study was to estimate the levels of AMR of the 3 main bacteria isolated from dairy cattle with mastitis in France (Streptococcus uberis, Escherichia coli, and coagulase-positive staphylococci) and to investigate their changes over time. Data collected between 2006 and 2016 by the French surveillance network for AMR in pathogenic bacteria of animal origin (called RESAPATH) were analyzed. The proportions of mono- and multidrug resistance were calculated and the trends were investigated using nonlinear analyses applied to time series. Over the whole period, the lowest proportions of resistance in S. uberis isolates were observed for oxacillin (2.2%) and gentamicin (2.4%) and most resistance levels were below 20%. The trends in resistance showed some significant variation, mainly for S. uberis, but without a common pattern across the various antibiotics examined. For only 2 combinations of bacteria-antibiotic the trend in resistance showed a continuous increase from 2006 to 2016: tetracycline resistance in S. uberis isolates and third-generation cephalosporin resistance in E. coli isolates. In E. coli, the highest proportions of resistance were observed for amoxicillin (28.1%) and tetracycline (23.1%). Resistance to third-generation cephalosporins in E. coli from dairy cattle was almost nil in 2006, but reached 2.4% in December 2016. This increase is particularly concerning because these antibiotics constitute one of the latest therapeutic alternatives to fight severe infectious diseases in humans. Except for penicillin (33.9%), the proportions of resistance in coagulase-positive staphylococci were below 11% during the whole study period. Multidrug resistance (isolates with acquired resistance to at least one antibiotic in 3 or more antibiotic classes) ranged from 2.4% for coagulase-positive staphylococci to 9.9% for S. uberis. These findings can serve as guidelines for practitioners in the choice of the most appropriate antibiotic according to the prevailing epidemiological context. Ultimately, our results contribute to risk assessment of AMR and provide a baseline for setting up and evaluating control measures and designing strategies to limit AMR.

Abstract Antimicrobial-resistant bacteria in dogs can be transmitted to humans and close contact between dogs and people might foster dissemination of resistance determinants. The aim of our study was to describe the antimicrobial resistance (AMR) pattern of the major causative agents of canine otitis – one of the most common diseases in dogs – isolated in France. Data collected between 2012 and 2016 by the French national surveillance network for AMR, referred to as RESAPATH, were analysed. Resistance trends were investigated using non-linear analysis (generalised additive models). A total of 7021 antibiograms were analysed. The four major causative agents of canine otitis in France were coagulase-positive staphylococci, Pseudomonas aeruginosa , Proteus mirabilis and streptococci. Since 2013, resistance to fluoroquinolones has been on the decrease in both P. aeruginosa and Staphylococcus pseudintermedius isolates. For P. aeruginosa , 19.4% of isolates were resistant to both enrofloxacin and gentamicin. The levels of multidrug resistance (acquired resistance to at least one antibiotic in three or more antibiotic classes) ranged between 11.9% for P. mirabilis and 16.0% for S. pseudintermedius. These results are essential to guide prudent use of antibiotics in veterinary medicine. They will also help in designing efficient control strategies and in measuring their effectiveness.

Ticks transmit the most diverse array of disease agents and harbor one of the most diverse microbial communities. Major progress has been made in the characterization of the taxonomic profiles of tick microbiota. However, the functional profiles of tick microbiome have been comparatively less studied. In this proof of concept we used state-of-the-art functional metagenomics analytical tools to explore previously reported datasets of bacteria found in male and female Ixodes ovatus, Ixodes persulcatus and Amblyomma variegatum. Results showed that both taxonomic and functional profiles have differences between sexes of the same species. KEGG pathway analysis revealed that male and female of the same species had major differences in the abundance of genes involved in different metabolic pathways including vitamin B, amino acids, carbohydrates, nucleotides and antibiotics among others. Partial reconstruction of metabolic pathways using KEGG enzymes suggests that tick microbiome form a complex metabolic network that may increase microbial community resilience and adaptability. Linkage analysis between taxonomic and functional profiles showed that among the KEGG enzymes with differential abundance in male and female ticks only 12% were present in a single bacterial genera. The rest of these enzymes were found in more than two bacterial genera, and 27% of them were found in five up to ten bacterial genera. Comparison of bacterial genera contributing to the differences in the taxonomic and functional profiles of males and females revealed that while a small group of bacteria has a dual-role, most of the bacteria contribute only to functional or taxonomic differentiation between sexes. Results suggest that the different life styles of male and female ticks exert sex-specific evolutionary pressures that act independently on the phenomes (set of phenotypes) and genomes of bacteria in tick gut microbiota. We conclude that functional redundancy is a fundamental property of male and female tick microbiota and propose that functional metagenomics should be combined with taxonomic profiling of microbiota because both analyses are complementary.

BACKGROUND: Ixodes ricinus is the predominant tick species in Europe and the primary pathogen vector for both humans and animals. These ticks are frequently involved in the transmission of Borrelia burgdorferi (sensu lato), the causative agents of Lyme borreliosis. While much more is known about I. ricinus tick-borne pathogen composition, information about temporal tick-borne pathogen patterns remain scarce. These data are crucial for predicting seasonal/annual patterns which could improve understanding and prevent tick-borne diseases. METHODS: We examined tick-borne pathogen (TBP) dynamics in I. ricinus collected monthly in a peri-urban forest over three consecutive years. In total, 998 nymphs were screened for 31 pathogenic species using high-throughput microfluidic real-time PCR. RESULTS: We detected DNA from Anaplasma phagocytophilum (5.3%), Rickettsia helvetica (4.5%), Borrelia burgdorferi (s.l.) (3.7%), Borrelia miyamotoi (1.2%), Babesia venatorum (1.5%) and Rickettsia felis (0.1%). Among all analysed ticks, 15.9% were infected by at least one of these microorganisms, and 1.3% were co-infected. Co-infections with B. afzeli/B. garinii and B. garinii/B. spielmanii were significantly over-represented. Moreover, significant variations in seasonal and/or inter-annual prevalence were observed for several pathogens (R. helvetica, B. burgdorferi (s.l.), B. miyamotoi and A. phagocytophilum). CONCLUSIONS: Analysing TBP prevalence in monthly sampled tick over three years allowed us to assess seasonal and inter-annual fluctuations of the prevalence of TBPs known to circulate in the sampled area, but also to detect less common species. All these data emphasize that sporadic tick samplings are not sufficient to determine TBP prevalence and that regular monitoring is necessary.

Brown rats are one of the most widespread urban species worldwide. Despite the nuisances they induce and their potential role as a zoonotic reservoir, knowledge on urban rat populations remains scarce. The main purpose of this study was to characterize an urban brown rat population from Chanteraines park (Hauts-de-Seine, France), with regards to haematology, population genetics, immunogenic diversity, resistance to anticoagulant rodenticides, and community of parasites. Haematological parameters were measured. Population genetics was investigated using 13 unlinked microsatellite loci. Immunogenic diversity was assessed for Mhc-Drb. Frequency of the Y139F mutation (conferring resistance to rodenticides) and two linked microsatellites were studied, concurrently with the presence of anticoagulant residues in the liver. Combination of microscopy and molecular methods were used to investigate the occurrence of 25 parasites. Statistical approaches were used to explore multiple parasite relationships and model parasite occurrence. Eighty-six rats were caught. The first haematological data for a wild urban R. norvegicus population was reported. Genetic results suggested high genetic diversity and connectivity between Chanteraines rats and surrounding population(s). We found a high prevalence (55.8%) of the mutation Y139F and presence of rodenticide residues in 47.7% of the sampled individuals. The parasite species richness was high (16). Seven potential zoonotic pathogens were identified, together with a surprisingly high diversity of Leptospira species (4). Chanteraines rat population is not closed, allowing gene flow and making eradication programs challenging, particularly because rodenticide resistance is highly prevalent. Parasitological results showed that co-infection is more a rule than an exception. Furthermore, the presence of several potential zoonotic pathogens, of which four Leptospira species, in this urban rat population raised its role in the maintenance and spread of these pathogens. Our findings should stimulate future discussions about the development of a long-term rat-control management program in Chanteraines urban park.

Since 2013, the French Animal Health Epidemic Intelligence System (in French: Veille Sanitaire Internationale, VSI) has been monitoring signals of the emergence of new and exotic animal infectious diseases worldwide. Once detected, the VSI team verifies the signals and issues early warning reports to French animal health authorities when potential threats to France are detected. To improve detection of signals from online news sources, we designed the Platform for Automated extraction of Disease Information from the web (PADI-web). PADI-web automatically collects, processes and extracts English-language epidemiological information from Google News. The core component of PADI-web is a combined information extraction (IE) method founded on rule-based systems and data mining techniques. The IE approach allows extraction of key information on diseases, locations, dates, hosts and the number of cases mentioned in the news. We evaluated the combined method for IE on a dataset of 352 disease-related news reports mentioning the diseases involved, locations, dates, hosts and the number of cases. The combined method for IE accurately identified (F-score) 95% of the diseases and hosts, respectively, 85% of the number of cases, 83% of dates and 80% of locations from the disease-related news. We assessed the sensitivity of PADI-web to detect primary outbreaks of four emerging animal infectious diseases notifiable to the World Organisation for Animal Health (OIE). From January to June 2016, PADI-web detected signals for 64% of all primary outbreaks of African swine fever, 53% of avian influenza, 25% of bluetongue and 19% of foot-and-mouth disease. PADI-web timely detected primary outbreaks of avian influenza and foot-and-mouth disease in Asia, i.e. they were detected 8 and 3 days before immediate notification to OIE, respectively.

Flaviviruses have become increasingly important pathogens in Europe over the past few decades. A better understanding of the spatiotemporal distribution of flaviviruses in France is needed to better define risk areas and to gain knowledge of the dynamics of virus transmission cycles. Serum samples from 1014 wild boar and 758 roe deer from 16 departments (administrative units) in France collected from 2009 to 2014 were screened for flavivirus antibodies using a competitive ELISA (cELISA) technique. Serum samples found to be positive or doubtful by cELISA were then tested for antibodies directed against West Nile virus (WNV), Usutu virus (USUV), Bagaza virus (BAGV), and tick-borne encephalitis/Louping ill viruses (TBEV/LIV) by microsphere immunoassays (except BAGV) and micro-neutralization tests. USUV antibodies were detected only in southeastern and southwestern areas. TBEV/LIV antibodies were detected in serum samples from eastern, southwestern and northern departments. The results indicate continuous circulation of USUV in southern France from 2009 to 2014, which was unnoticed by the French monitoring system for bird mortality. The findings also confirm wider distribution of TBEV in the eastern part of the country than of human clinical cases. However, further studies are needed to determine the tick-borne flavivirus responsible for the seroconversion in southwestern and northern France.

Intestinal strongyles are the most problematic endoparasites of equids as a result of their wide distribution and the spread of resistant isolates throughout the world. While abundant literature can be found on the extent of anthelmintic resistance across continents, empirical knowledge about associated risk factors is missing. This study brought together results from anthelmintic efficacy testing and risk factor analysis to provide evidence-based guidelines in the field. It involved 688 horses from 39 French horse farms and riding schools to both estimate Faecal Egg Count Reduction (FECR) after anthelmintic treatment and to interview farm and riding school managers about their practices. Risk factors associated with reduced anthelmintic efficacy in equine strongyles were estimated across drugs using a marginal modelling approach. Results demonstrated ivermectin efficacy (96.3% ± 14.5% FECR), the inefficacy of fenbendazole (42.8% ± 33.4% FECR) and an intermediate profile for pyrantel (90.3% ± 19.6% FECR). Risk factor analysis provided support to advocate for FEC-based treatment regimens combined with individual anthelmintic dosage and the enforcement of tighter biosecurity around horse introduction. The combination of these measures resulted in a decreased risk of drug resistance (relative risk of 0.57, p = 0.02). Premises falling under this typology also relied more on their veterinarians suggesting practitionners play an important role in the sustainability of anthelmintic usage. Similarly, drug resistance risk was halved in premises with frequent pasture rotation and with stocking rate below five horses/ha (relative risk of 0.53, p < 0.01). This is the first empirical risk factor analysis for anthelmintic resistance in equids. Our findings should guide the implementation of more sustained strongyle management in the field.

BACKGROUND: In the last two decades, recurrent epizootics of bluetongue virus and Schmallenberg virus have been reported in the western Palearctic region. These viruses affect domestic cattle, sheep, goats and wild ruminants and are transmitted by native hematophagous midges of the genus Culicoides (Diptera: Ceratopogonidae). Culicoides dispersal is known to be stratified, i.e. due to a combination of dispersal processes occurring actively at short distances and passively or semi-actively at long distances, allowing individuals to jump hundreds of kilometers. METHODS: Here, we aim to identify the environmental factors that promote or limit gene flow of Culicoides obsoletus, an abundant and widespread vector species in Europe, using an innovative framework integrating spatial, population genetics and statistical approaches. A total of 348 individuals were sampled in 46 sites in France and were genotyped using 13 newly designed microsatellite markers. RESULTS: We found low genetic differentiation and a weak population structure for C. obsoletus across the country. Using three complementary inter-individual genetic distances, we did not detect any significant isolation by distance, but did detect significant anisotropic isolation by distance on a north-south axis. We employed a multiple regression on distance matrices approach to investigate the correlation between genetic and environmental distances. Among all the environmental factors that were tested, only cattle density seems to have an impact on C. obsoletus gene flow. CONCLUSIONS: The high dispersal capacity of C. obsoletus over land found in the present study calls for a re-evaluation of the impact of Culicoides on virus dispersal, and highlights the urgent need to better integrate molecular, spatial and statistical information to guide vector-borne disease control.

Wild birds of Anseriformes and Charadriiformes are natural reservoirs of influenza A viruses (IAVs). Occasionally, IAVs transmit and adapt to mammalian hosts, and are maintained as epidemic strains in their new hosts. Viral adaptions to mammalian hosts include altered receptor preference of host epithelial sialylated oligosaccharides from terminal α2,3-linked sialic acid (SA) towards α2,6-linked SA. However, α2,3-linked SA has been found in human respiratory tract epithelium, and human infections by avian IAVs (AIVs) have been reported. To further explore the attachment properties of AIVs, four AIVs of different subtypes were investigated on human and pig tissues using virus histochemistry. Additionally, glycan array analysis was performed for further characterization of IAVs' receptor structure tropism. Generally, AIV attachment was more abundant to human tissues than to pig tissues. The attachment pattern was very strong to human conjunctiva and upper respiratory tract, but variable to the lower respiratory tract. AIVs mainly attached to α2,3-linked SA, but also to combinations of α2,3- and α2,6-linked SA. The low attachment of these AIV isolates to pig tissues, but high attachment to human tissues, addresses the question whether AIVs in general require passage through pigs to obtain adaptions towards mammalian receptor structures.

A study was carried out, from 2012 to 2015, in 10 French départements to estimate the serological prevalence of Q fever and the frequency of abortive episodes potentially related to Coxiella burnetii in a large sample of cattle, sheep and goat herds. The serological survey covered 731 cattle, 522 sheep and 349 goat herds, randomly sampled. The frequency of abortive episodes potentially related to C. burnetii was estimated by investigating series of abortions in 2695 cattle, 658 sheep and 105 goat herds using quantitative polymerase chain reaction analyses and complementary serological results when needed. The average between-herd seroprevalence was significantly lower for cattle (36·0%) than for sheep (55·7%) and goats (61·0%) and significantly higher for dairy herds (64·9% for cattle and 75·6% for sheep) than for meat herds (18·9% for cattle and 39·8% for sheep). Within-herd seroprevalence was also significantly higher for goats (41·5%) than for cattle (22·2%) and sheep (25·7%). During the study period, we estimated that 2·7% (n = 90), 6·2% (n = 48) and 16·7% (n = 19) of the abortive episodes investigated could be 'potentially related to C. burnetii'in cattle, sheep and goat herds, respectively. Overall, strong variability was observed between départements and species, suggesting that risk factors such as herd density and farming practices play a role in disease transmission and maintenance.

BACKGROUND: Horses are one of the potential reservoirs of antimicrobial resistance (AMR) determinants that could be transferred to human subjects. OBJECTIVE: To describe the AMR patterns of major bacteria isolated from diseased horses in France. STUDY DESIGN: Retrospective observational study. METHODS: Data collected between 2012 and 2016 by RESAPATH, the French national surveillance network for AMR, were analysed. Only antimicrobials relevant in veterinary and human medicine for the isolated bacteria were considered. Mono- and multidrug resistance were calculated. The resistance proportions of major equine diseases were assessed and compared. Where data permitted, resistance trends were investigated using nonlinear analysis (generalised additive models). RESULTS: A total of 12,695 antibiograms were analysed. The five most frequently isolated bacteria were Streptococcus spp., Escherichia coli, Pseudomonas spp., Staphylococcus aureus, Pantoea spp. and Klebsiella spp. The highest proportions of resistance to gentamicin were found for S. aureus (22.1%) and Pseudomonas spp. (26.9%). Klebsiella spp. and E. coli had the highest proportions of resistance to trimethoprim-sulfamethoxazole (15.5 and 26.2%, respectively). Proportions of resistance to tetracycline were among the highest for all the bacteria considered. Resistance to third-generation cephalosporins was below 10% for all Enterobacteriaceae. The highest proportions of multidrug resistance (22.5%) were found among S. aureus isolates, which is worrying given their zoonotic potential. From 2012 to 2016, resistance proportions decreased in Pseudomonas spp. isolates, but remained the same for S. aureus. For Streptococcus spp. and E. coli, resistance proportions to trimethoprim-sulfamethoxazole increased. MAIN LIMITATIONS: Since antibiograms are not systematic analyses, any selection bias could impact the results. CONCLUSIONS: Such studies are essential to estimate the magnitude of the potential threat of AMR to public health, to design efficient control strategies and to measure their effectiveness. These findings may also guide the initial empirical treatment of horse diseases.

The role of microbial interactions in defining the properties of microbiota is a topic of key interest in microbial ecology. Microbiota contain hundreds to thousands of operational taxonomic units (OTUs), most of them rare. This feature of community structure can lead to methodological difficulties: simulations have shown that methods for detecting pairwise associations between OTUs, which presumably reflect interactions, yield problematic results. The performance of association detection tools is impaired when there is a high proportion of zeros in OTU tables. Our goal was to understand the impact of OTU rarity on the detection of associations. We explored the utility of common statistics for testing associations; the sensitivity of alternative association measures; and the performance of network inference tools. We found that a large proportion of pairwise associations, especially negative associations, cannot be reliably tested. This constraint could hamper the identification of candidate biological agents that could be used to control rare pathogens. Identifying testable associations could serve as an objective method for filtering datasets in lieu of current empirical approaches. This trimming strategy could significantly reduce the computational time needed to infer networks and network inference quality. Different possibilities for improving the analysis of associations within microbiota are discussed.

Avian influenza A viruses (AIVs) have a broad host range, but are most intimately associated with waterfowl (Anseriformes) and, in the case of the H13 and H16 subtypes, gulls (Charadriiformes). Host associations are multifactorial, but a key factor is the ability of the virus to bind host cell receptors and thereby initiate infection. The current study aims at investigating the tissue attachment pattern of a panel of AIVs, comprising H3N2, H6N1, H12N5, and H16N3, to avian trachea and colon tissue samples obtained from host species of different orders. Virus attachment was not restricted to the bird species or order from which the virus was isolated. Instead, extensive virus attachment was observed to several distantly related avian species. In general, more virus attachment and receptor expression were observed in trachea than in colon samples. Additionally, a human seasonal H3N2 virus was studied. Unlike the studied AIVs, this virus mainly attached to tracheae from Charadriiformes and a very limited set of avian cola. In conclusion, the reported results highlight the importance of AIV attachment to trachea in many avian species. Finally, the importance of chickens and mallards in AIVs dynamics was illustrated by the abundant AIV attachment observed.

Antimicrobial resistance (AMR) among bacteria isolated from food-producing animals is a growing concern with implications for public health. AMR surveillance is essential to identify resistance trends and help in the design of effective and efficient control strategies. The aim of the study was to describe the antimicrobial susceptibility of pathogenic Escherichia coli isolated from three livestock productions in France (cattle, swine and poultry). The trend in resistance to the most commonly prescribed antibiotics in animal health was analysed as follows: amoxicillin (penicillin), spectinomycin or streptomycin (aminoglycoside), tetracycline and trimethoprim-sulfamethoxazole/Enrofloxacin and ceftiofur were also taken into account as members of critically important antimicrobial families in human and veterinary medicine, that is fluoroquinolones and third-generation cephalosporins, respectively. Data collected between 2002 and 2015 by the French national surveillance network of AMR referred to as RESAPATH were analysed. Resistance trends were investigated using non-linear analysis (generalized additive models) applied to time-series stratified by livestock production and antibiotic. Irrespective of the species and the antibiotic considered, resistance signals over time showed no significant annual cycle. Resistance to third-generation cephalosporins emerged during the period of the study, with a peak at 22% [20.5; 24.0] in poultry in 2010, decreasing afterwards, while it remained consistently below 10% for the other species. The proportion of resistance to fluoroquinolones was broadly similar between species and remained under 30%, with a slight decreasing trend after 2009. Resistances to tetracycline and amoxicillin remained high, between 90% and 40% over time in cattle and swine. After 2010, there was a decrease in resistance to these antibiotics for all species, especially to tetracycline for poultry with a drop from 84% in 2009 to 43% in 2015. These results contribute to risk assessment and constitute objective evidence on which to evaluate the efficacy of control measures implemented to limit AMR occurrence.