Long-term dynamics of trematode infections in common birds that use farmlands as their feeding habitats

Background The biodiversity of farmland habitats is witnessing unprecedented change, mostly in declines and simplification of assemblages that were established during centuries of the use of traditional agricultural techniques. In Central Europe, conspicuous changes are evident in populations of common farmland birds, in strong contrast to forest birds in the same region. However, there is a lack of information on longitudinal changes in trematodes that are associated with common farmland birds, despite the fact that diversity of trematodes is directly linked to the preservation of long-established food webs and habitat use adaptations of their hosts. Methods We analyzed the population trends of trematodes for the period 1963–2020 in six bird species that use Central European farmlands as their predominant feeding habitats. Namely, we examined Falco tinnunculus, Vanellus vanellus, winter populations of Buteo buteo, Ciconia ciconia, extravilan population of Pica pica, and Asio otus, all originating from the Czech Republic. Results We observed dramatic population losses of all trematode species in C. ciconia and V. vanellus; the changes were less prominent in the other examined hosts. Importantly, the declines in prevalence and intensity of infection affected all previously dominant species. These included Tylodelphys excavata and Chaunocephalus ferox in C. ciconia, Lyperosomum petiolatum in P. pica, Strigea strigis in A. otus, Neodiplostomum attenuatum and Strigea falconis in B. buteo (χ2 test P < 0.001 each), and Echinoparyphium agnatum and Uvitellina adelpha in V. vanellus (completely absent in 2011–2000). In contrast, the frequency and spectrum of isolated records of trematode species did not change to any large extent except those in V. vanellus. Conclusions The analysis of six unrelated common bird species that use farmlands as their feeding habitats revealed a previously unreported collapse of previously dominant trematode species. The previously dominant trematode species declined in terms of both prevalence and intensity of infection. The causes of the observed declines are unclear; of note is, however, that some of the broadly used agrochemicals, such as azole fungicides, are well known for their antihelminthic activity. Further research is needed to provide direct evidence for effects of field-realistic concentrations of azole fungicides on the survival and fitness of trematodes. Graphical abstract

Genome evolution and the emergence of pathogenicity in avian Escherichia coli

Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.

CBNWI-50: A Deep Learning Bird Dataset for Image Translation and Resolution Improvement using Generative Adversarial Network

Generative Adversarial Networks have gained prominence in a short span of time as they can synthesize images from latent noise by minimizing the adversarial cost function. New variants of GANs have been developed to perform specific tasks using state-of-the-art GAN models, like image translation, single image super resolution, segmentation, classification, style transfer etc. However, a combination of two GANs to perform two different applications in one model has been sparsely explored. Hence, this paper concatenates two GANs and aims to perform Image Translation using Cycle GAN model on bird images and improve their resolution using SRGAN. During the extensive survey, it is observed that most of the deep learning databases on Aves were built using the new world species (i.e. species found in North America). Hence, to bridge this gap, a new Ave database, 'Common Birds of North - Western India' (CBNWI-50), is also proposed in this work.