The recent arrival of Batrachochytrium salamandrivorans in Europe was followed by rapid expansion of its geographical distribution and host range, confirming the unprecedented threat that this chytrid fungus poses to western Palaearctic amphibians. Mitigating this hazard requires a thorough understanding of the pathogen's disease ecology that is driving the extinction process. Here, we monitored infection, disease and host population dynamics in a Belgian fire salamander (Salamandra salamandra) population for two years immediately after the first signs of infection. We show that arrival of this chytrid is associated with rapid population collapse without any sign of recovery, largely due to lack of increased resistance in the surviving salamanders and a demographic shift that prevents compensation for mortality. The pathogen adopts a dual transmission strategy, with environmentally resistant non-motile spores in addition to the motile spores identified in its sister species B. dendrobatidis. The fungus retains its virulence not only in water and soil, but also in anurans and less susceptible urodelan species that function as infection reservoirs. The combined characteristics of the disease ecology suggest that further expansion of this fungus will behave as a 'perfect storm' that is able to rapidly extirpate highly susceptible salamander populations across Europe.

Urbanisation represents one of the most radical forms of terrestrial land use change and has been shown to lead to alterations in ecosystem functioning and community dynamics and changes in individual phenotypic traits. While the recent surge in microbiome studies has brought about a paradigm shift by which individuals cannot truly be considered independently of the bacterial communities they host, the role of gut microbiota in organismal response to human-induced environmental change is still scarcely studied. Here, we applied a metabarcoding approach to examine the impact of urbanisation on the gut microbiota of Passer domesticus. We found urbanisation to be associated to lower microbiota species diversity, modifications in taxonomic composition and community structure, and changes in functional composition. The strength of these relationships, however, depended on the spatial scale and season at which they were considered. Such spatio-temporal effect suggests that urbanisation may dampen the natural seasonal variation of the gut microbiota observed in more pristine habitats, potentially influencing the fitness of urban organisms. Our results hence shed light on a hitherto little considered perspective, i.e. that the negative effects of urbanisation on city-dwelling organisms may extend to their microbiomes, causing potential dysbioses.

Mycoplasma gallisepticum is the most important pathogenic avian Mycoplasma species and causes chronic respiratory disease in poultry. In addition, the prevalence of Mycoplasma synoviae is of increasing concern in several EU member states. We investigated the prevalence of M. gallisepticum in commercial poultry (5220 layers, 1224 broilers and 1020 meat turkeys), 56 racing pigeons and 890 wild birds (Order Anseriformes, Galliformes, Pelecaniformes, Accipitriformes, Gruiformes, Charadriiformes, Columbiformes, Strigiformes, Falconiformes and Passeriformes). Broilers and wild birds were also evaluated for Mycoplasma synoviae. Dependent on the bird lifespan and the nature of the sample, different diagnostic tests were used including the rapid plate agglutination test, enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction and real-time polymerase chain reaction. A low prevalence of M. gallisepticum was found in both layers (0.9%; 95% CI: 0.7-1.2%) and broilers (2.7%; 95% CI: 1.9-3.8%) possibly due to reduced vertical transmission by breeder farms, which are under official surveillance. None of the samples from turkeys or racing pigeons tested positive. In wild birds, we found five birds were positive (1.7%; 95% CI: 0.7-3.9%): one wood pigeon, two grey herons, one mallard and one Eurasian magpie. For M. synoviae a high prevalence was found in broilers (12.9%: 95% CI: 11.1-14.9%). Four samples collected by hunters gave a positive result for M. synoviae (4%: 95% CI: 1.6-9.8%): one carrion crow and three wood pigeons. In addition, 12 house sparrows were found to be positive (3%; 95% CI: 1.7-5.2%). Wild birds probably play a limited role as a reservoir but we cannot exclude a possible impact on transmission of Mycoplasmas.

Chytridiomycosis caused by the chytrid fungus Batrachochytrium salamandrivorans (Bsal) poses a serious threat to urodelan diversity worldwide. Antimycotic treatment of this disease using protocols developed for the related fungus Batrachochytrium dendrobatidis (Bd), results in therapeutic failure. Here, we reveal that this therapeutic failure is partly due to different minimum inhibitory concentrations (MICs) of antimycotics against Bsal and Bd. In vitro growth inhibition of Bsal occurs after exposure to voriconazole, polymyxin E, itraconazole and terbinafine but not to florfenicol. Synergistic effects between polymyxin E and voriconazole or itraconazole significantly decreased the combined MICs necessary to inhibit Bsal growth. Topical treatment of infected fire salamanders (Salamandra salamandra), with voriconazole or itraconazole alone (12.5 μg/ml and 0.6 μg/ml respectively) or in combination with polymyxin E (2000 IU/ml) at an ambient temperature of 15 °C during 10 days decreased fungal loads but did not clear Bsal infections. However, topical treatment of Bsal infected animals with a combination of polymyxin E (2000 IU/ml) and voriconazole (12.5 μg/ml) at an ambient temperature of 20 °C resulted in clearance of Bsal infections. This treatment protocol was validated in 12 fire salamanders infected with Bsal during a field outbreak and resulted in clearance of infection in all animals.

At the end of the summer of 2016, unusually high levels of mortality were detected in Passeriformes and Strigiformes in Flanders, Belgium, mainly in Eurasian Blackbirds ( Turdus merula). A passive surveillance program demonstrated a widespread Usutu virus outbreak and revealed a coinfection with Plasmodium in 99% of the dead passerine birds that were necropsied.