Unexpected interfarm transmission dynamics during a highly pathogenic avian influenza epidemic

Next-generation sequencing technology is now being increasingly applied to study the within- and between-host population dynamics of viruses. However, information on avian influenza virus evolution and transmission during a naturally occurring epidemic is still limited. Here, we use deep-sequencing data obtained from clinical samples collected from five industrial holdings and a backyard farm infected during the 2013 highly pathogenic avian influenza (HPAI) H7N7 epidemic in Italy to unravel (i) the epidemic virus population diversity, (ii) the evolution of virus pathogenicity, and (iii) the pathways of viral transmission between different holdings and sheds. We show a high level of genetic diversity of the HPAI H7N7 viruses within a single farm as a consequence of separate bottlenecks and founder effects. In particular, we identified the cocirculation in the index case of two viral strains showing a different insertion at the hemagglutinin cleavage site, as well as nine nucleotide differences at the consensus level and 92 minority variants. To assess interfarm transmission, we combined epidemiological and genetic data and identified the index case as the major source of the virus, suggesting the spread of different viral haplotypes from the index farm to the other industrial holdings, probably at different time points. Our results revealed interfarm transmission dynamics that the epidemiological data alone could not unravel and demonstrated that delay in the disease detection and stamping out was the major cause of the emergence and the spread of the HPAI strain

West Nile virus circulation in Veneto region in 2008-2009.

SUMMARYWest Nile virus (WNV) was detected in Italy, in late summer 2008 in horses and birds in the Po valley. As a consequence, an intense WNV surveillance was implemented in that area involving Emilia-Romagna, Veneto and Lombardy. This paper presents the results of the September 2008–November 2009 surveillance on equines, mosquitoes, wild birds, dogs and cattle in Veneto. WNV was detected in equines and dogs, and, to a lesser extent in cattle and wild birds. Simultaneous circulation of Usutu virus was detected by testing wild birds found dead. Usutu virus but not WNV was also found in mosquitoes monitored during 2009. Equine practices monitoring allowed the definition of an area of WNV circulation and the 2008–2009 westward and northward spread of the infection. Although a relatively low number of human cases and a low virus circulation in vectors and birds detected in Veneto region could be considered favourable conditions for a limited risk of human exposure, it remains difficult to predict the possible evolution of the epidemiological situation

Impact of emergency oral rabies vaccination of foxes in northeastern Italy, 28 December 2009-20 January 2010: preliminary evaluation.

Fox rabies re-emerged in northeastern Italy in 2008, in an area bordering Slovenia. In 2009, the infection spread westward to Veneto region and in 2010 to the provinces of Trento and Bolzano. Aerial emergency oral fox vaccination was implemented in the winter 2009-10. Since this vaccination was performed at altitudes below the freezing level, a statistical analysis was conducted to evaluate its impact. Of the foxes sampled following the vaccination campaign, 77% showed a rabies antibody titre of ≥0.5 IU/ml

Geographical information systems in the management of the 2009-2010 emergency oral anti-rabies vaccination of foxes in north-eastern Italy

Emergency oral fox vaccination campaigns, targeting a recent rabies epidemic in wild foxes (Vulpes vulpes) in north-eastern Italy, were implemented twice, first in the winter of 2009 and then in the spring of 2010. Following on an unsuccessful manual bait distribution campaign, vaccine baits were aerially distributed by helicopters using a satellite-navigated, computer-supported, automatic bait drop system. The flight paths were traced with distance of 500-1,000 m from one another to optimise helicopter missions and guarantee homogeneous coverage of the vaccination area. The vaccine distribution was evaluated by superimposing a 1 km-step grid and weighing the number of baits per cell. The implementation of a geographical information system for the management of vaccine distribution proved to be useful, both for the planning and execution phases, of the campaigns. It supported effective management of the flights and allowed near real-time monitoring of the campaigns. In addition, it facilitated the identification of areas with suboptimal bait density that would require additional flights or supplementary, manual distributio

Natural immunity in conventionally and organically reared turkeys and its relation with antimicrobial resistance.

Suboptimal animal welfare may affect natural immunity, rendering animals more susceptible to environmentally conditioned diseases, including those requiring antimicrobial treatment, which may promote antimicrobial resistance (AMR) in bacterial populations. Herewith, we tested the hypothesis that conventionally raised turkeys have higher levels of AMR in indicator Escherichia coli bacteria, but lower levels of natural immunity, as compared to turkeys reared under organic conditions. Litter and serum samples were collected from 28 conventional and 4 organic turkey farms: E. coli isolates from litter were tested for resistance to 14 antimicrobials, while 3 parameters of natural immunity (i.e., lysozyme, hemolytic complement levels, and serum bactericidal activity) were assessed in the sera. Resistant E. coli isolates were identified in both conventional and organic farms but generally more frequently in conventional farms. High rates of resistance to ampicillin (96%), tetracycline (95%), streptomycin (82%), sulfamethoxazole (80%), ciprofloxacin (73%), and trimethoprim (71%), as well as high rates of multiresistance, were observed in conventional farms. Organically raised turkeys had significantly higher levels of lysozyme and serum bactericidal activity than conventional turkeys, and these levels were also higher in turkeys housed in farms where AMR frequency was lower. Findings support the hypothesis that conventional farming conditions may affect turkeys' natural immunity, rendering the animals more susceptible to environmentally conditioned diseases requiring antimicrobial treatment, which would in turn promote AMR. Reducing AMR in turkey farming is therefore more likely to be successful when considering animal welfare as an option to reduce the need of antimicrobial use

Natural immunity in conventionally and organically reared turkeys and its relation with antimicrobial resistance

Suboptimal animal welfare may affect natural immunity, rendering animals more susceptible to environmentally conditioned diseases, including those requiring antimicrobial treatment, which may promote antimicrobial resistance (AMR) in bacterial populations. Herewith, we tested the hypothesis that conventionally raised turkeys have higher levels of AMR in indicator Escherichia coli bacteria, but lower levels of natural immunity, as compared to turkeys reared under organic conditions. Litter and serum samples were collected from 28 conventional and 4 organic turkey farms: E. coli isolates from litter were tested for resistance to 14 antimicrobials, while 3 parameters of natural immunity (i.e., lysozyme, hemolytic complement levels, and serum bactericidal activity) were assessed in the sera. Resistant E. coli isolates were identified in both conventional and organic farms but generally more frequently in conventional farms. High rates of resistance to ampicillin (96%), tetracycline (95%), streptomycin (82%), sulfamethoxazole (80%), ciprofloxacin (73%), and trimethoprim (71%), as well as high rates of multiresistance, were observed in conventional farms. Organically raised turkeys had significantly higher levels of lysozyme and serum bactericidal activity than conventional turkeys, and these levels were also higher in turkeys housed in farms where AMR frequency was lower. Findings support the hypothesis that conventional farming conditions may affect turkeys' natural immunity, rendering the animals more susceptible to environmentally conditioned diseases requiring antimicrobial treatment, which would in turn promote AMR. Reducing AMR in turkey farming is therefore more likely to be successful when considering animal welfare as an option to reduce the need of antimicrobial use

Environmental correlates of H5N2 low pathogenicity avian influenza outbreak heterogeneity in domestic poultry in Italy.

Italy has experienced recurrent incursions of H5N2 avian influenza (AI) viruses in different geographical areas and varying sectors of the domestic poultry industry. Considering outbreak heterogeneity rather than treating all outbreaks of low pathogenicity AI (LPAI) viruses equally is important given their interactions with the environment and potential to spread, evolve and increase pathogenicity. This study aims at identifying potential environmental drivers of H5N2 LPAI outbreak occurrence in time, space and poultry populations. Thirty-four environmental variables were tested for association with the characteristics of 27 H5N2 LPAI outbreaks (i.e. time, place, flock type, number and species of birds affected) occurred among domestic poultry flocks in Italy in 2010-2012. This was done by applying a recently proposed analytical approach based on a combined non-metric multidimensional scaling, clustering and regression analysis. Results indicated that the pattern of (dis)similarities among the outbreaks entailed an underlying structure that may be the outcome of large-scale, environmental interactions in ecological dimension. Increased densities of poultry breeders, and increased land coverage by industrial, commercial and transport units were associated with increased heterogeneity in outbreak characteristics. In areas with high breeder densities and with many infrastructures, outbreaks affected mainly industrial turkey/layer flocks. Outbreaks affecting ornamental, commercial and rural multi-species flocks occurred mainly in lowly infrastructured areas of northern Italy. Outbreaks affecting rural layer flocks occurred mainly in areas with low breeder densities in south-central Italy. In savannah-like environments, outbreaks affected mainly commercial flocks of galliformes. Suggestive evidence that ecological ordination makes sense genetically was also provided, as virus strains showing high genetic similarity clustered into ecologically similar outbreaks. Findings were informed by hypotheses about how ecological interactions among poultry populations, viruses and their environments can be related to the observed patterns of H5N2 LPAI occurrence. This may prove useful in enhancing future interventions by developing site-specific, ecologically-grounded strategies