Training convolutional neural networks to score pneumonia in slaughtered pigs

The slaughterhouse can act as a valid checkpoint to estimate the prevalence and the economic impact of diseases in farm animals. At present, scoring lesions is a challenging and time‐consuming activity, which is carried out by veterinarians serving the slaughter chain. Over recent years, artificial intelligence(AI) has gained traction in many fields of research, including livestock production. In particular, AI‐based methods appear able to solve highly repetitive tasks and to consistently analyze large amounts of data, such as those collected by veterinarians during postmortem inspection in high‐throughput slaughterhouses. The present study aims to develop an AI‐based method capable of recognizing and quantifying enzootic pneumonia‐like lesions on digital images captured from slaughtered pigs under routine abattoir conditions. Overall, the data indicate that the AI‐based method proposed herein could properly identify and score enzootic pneumonia‐like lesions without interfering with the slaughter chain routine. According to European legislation, the application of such a method avoids the handling of carcasses and organs, decreasing the risk of microbial contamination, and could provide further alternatives in the field of food hygiene

Whole mitochondrial genome sequencing provides new insights into the phylogeography of loggerhead turtles (Caretta caretta) in the Mediterranean Sea

Population structure and phylogeography of the loggerhead sea turtle (Caretta caretta) have so far been assessed mainly by mitochondrial DNA (mtDNA) single-gene sequencing studies. However, phylogenetic relationships amongst matrilines, genetic characterisation of rookeries and mixed-stock analyses have suffered from the limited resolution obtained by comparison of relatively short sequences such as from the mtDNA control region. Whole mitogenome sequencing can significantly improve population genetics, particularly in marine organisms showing female natal philopatry. Despite mitogenomics becoming increasingly common in biodiversity monitoring and conservation, only a few complete mitogenomes are available for C. caretta. In this study, we sequenced the complete mtDNA of 61 loggerhead turtles sampled between 2008 and 2021 along the Italian coastline and central Mediterranean Sea. We assigned complete mtDNA haplotypes to dead embryos and bycatch samples, and introduced a first nomenclature for loggerhead mitogenomes. Analysis of mtDNA diversity, Maximum Parsimony and Bayesian phylogenetic reconstruction allowed improved resolution of lineages with respect to studies reporting on partial mtDNA control region sequence comparisons, and we were able to further inform previous analyses on loggerhead ancestry based on control region haplogroups. Overall, whole mitogenome analysis has potential for considerable improvement of evolutionary history and phylogeographic investigations as well as mixed-stock surveys of loggerhead turtles

Avian viral pathogens in swallows, Zimbabwe infectious diseases in <em>Hirundinidae</em>: A risk to swallow?

International audienceWe sampled 417 swallows in a wetland ecosystem of Zimbabwe in February 2010 and October 2011. RT-PCR tests revealed circulation of avian paramyxovirus type I, avian influenza and West Nile disease viruses in these populations. We discuss the relevance of these findings in relation to what is known on the epidemiology of these viruses in these hosts and in relation to the host ecology. We conclude with recommendations to focus more research on Passeriformes in disease ecology and in particular on the hirundinidae family