cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28558357
title: Integrative and conjugative elements associated with antimicrobial resistance in multidrug resistant <i>Pasteurella multocida</i> isolates from bovine respiratory disease (BRD)-affected animals in Spanish feedlots

description: The emergence of multidrug-resistance (MDR) in Pasteurella multocida, a major contributor to bovine respiratory disease (BRD) is being increasingly reported, often linked to the carriage of antimicrobial resistance genes (ARGs) on integrative and conjugative elements (ICEs). The resistance phenotype for 19 antimicrobials was determined using broth microdilution in 75 Pasteurella multocida isolates from healthy and BRD-affected cattle from five feedlots. The genomes of 32 isolates were sequenced to identify ARG) and mobile genetic elements (MGEs) and assess their genetic diversity. MDR isolates (with phenotypic resistance to aminoglycosides, macrolides, fluoroquinolones and/or tetracyclines) were primarily found among BRD-affected compared to healthy animals. Non-susceptible isolates, belonging to ST79 and ST13, harbored point mutations and four to nine ARGs, including rarely reported mechanisms in Europe (mph(E), msr(E) and aadA31 ARGs and newly described mutations in the gyrA/parC genes). All ARGs were linked to the presence of MGEs including two ICEs, Tn7407 and the novel Tn7809, a prophage and a putative composite transposon. Clonally related isolates were found in different batches from the same feedlot, suggesting maintenance of MDR strains. Our findings demonstrate the diverse genetic basis of AMR in P. multocida from BRD-affected cattle in Spain, emphasizing the role of MGEs in the ARG dissemination.
DOI: 10.6084/m9.figshare.28558357.v1
title: Integrative and conjugative elements associated with antimicrobial resistance in multidrug resistant <i>Pasteurella multocida</i> isolates from bovine respiratory disease (BRD)-affected animals in Spanish feedlots

description: The emergence of multidrug-resistance (MDR) in Pasteurella multocida, a major contributor to bovine respiratory disease (BRD) is being increasingly reported, often linked to the carriage of antimicrobial resistance genes (ARGs) on integrative and conjugative elements (ICEs). The resistance phenotype for 19 antimicrobials was determined using broth microdilution in 75 Pasteurella multocida isolates from healthy and BRD-affected cattle from five feedlots. The genomes of 32 isolates were sequenced to identify ARG) and mobile genetic elements (MGEs) and assess their genetic diversity. MDR isolates (with phenotypic resistance to aminoglycosides, macrolides, fluoroquinolones and/or tetracyclines) were primarily found among BRD-affected compared to healthy animals. Non-susceptible isolates, belonging to ST79 and ST13, harbored point mutations and four to nine ARGs, including rarely reported mechanisms in Europe (mph(E), msr(E) and aadA31 ARGs and newly described mutations in the gyrA/parC genes). All ARGs were linked to the presence of MGEs including two ICEs, Tn7407 and the novel Tn7809, a prophage and a putative composite transposon. Clonally related isolates were found in different batches from the same feedlot, suggesting maintenance of MDR strains. Our findings demonstrate the diverse genetic basis of AMR in P. multocida from BRD-affected cattle in Spain, emphasizing the role of MGEs in the ARG dissemination.
DOI: 10.6084/m9.figshare.30383563.v1
title: Characteristics of an emerging canine respiratory coronavirus in China

description: Canine respiratory coronavirus (CRCoV) is a prevalent pathogen implicated in canine infectious respiratory disease, yet information on its genomic characteristics and pathogenicity remains scarce. To address this situation, we investigated the genetic evolution and pathogenic potential of CRCoV strains circulating in China. Five complete CRCoV genomes (GenBank: PQ725948–PQ725952) were obtained from clinical samples, and phylogenetic analysis showed these strains formed a distinct genetic branch. The evolutionary trees for ORF1ab, HE, and S genes closely mirrored the full genome tree, indicating key roles for these genes in CRCoV evolution. Multiple unique amino acid mutations were identified in the ORF1ab, HE, S, M, and N proteins. Notably, molecular docking analysis suggests that mutations S158F and L161F in the HE lectin domain are associated with improved docking scores, indicating a potential increase in receptor-binding affinity. Consecutive nucleotide deletions in two non-coding regions between non-structural protein genes—which were also identified in strains of a Thai lineage (OQ621707.1–OQ621727.1)—were observed. A CRCoV strain (10<sup>6</sup> TCID<sub>50</sub>/mL) was isolated, and experimental infection confirmed its ability to induce pneumonia and tracheal cilia loss in dogs. These findings reveal the emergence and unique genetic diversity of a novel CRCoV variant in China, highlighting the need for ongoing epidemiological surveillance.
DOI: 10.6084/m9.figshare.28375160
title: The secretomes of bovine mammary epithelial cell subpopulations differentially modulate macrophage function

description: Bovine mammosphere-derived epithelial cell (MDEC) cultures are heterogeneous and enriched for stem and progenitor cells. We previously reported that the bovine MDEC secretome, comprised of all bioactive factors secreted by the cells, displays regenerative properties, exerts antimicrobial effects, and modulates neutrophil activity, positioning it as a promising non-antibiotic biologic therapy for infectious diseases important to the dairy industry, like mastitis. Mastitis is defined as inflammation of the udder, and it is typically caused by bacterial infection. The effect of the MDEC secretome on macrophages, a first line of defense against bacterial infections in the udder, is unknown and could impact the utility of the secretome as a therapy for mastitis. To address this, we isolated bovine monocytes from peripheral blood and maintained them as an unpolarized (M0) population or polarized them into M1 or M2 phenotypes. Macrophages cultured with the secretome of bovine MDECs were assessed for their ability to phagocytose labeled bacterial particles and accumulate reactive oxygen species (ROS). We used single-cell RNA sequencing (scRNA-seq) and fluorescence-activated cell sorting (FACS) to isolate a subpopulation of MDECs that exert enhanced effects on macrophages. We found that the secretome of MDECs that do not express cluster of differentiation (CD) 73, a cell surface enzyme used as a marker for mesenchymal stromal cells, most strongly increased macrophage phagocytosis and ROS accumulation. These findings will help optimize the generation of the bovine MDEC secretome as a suitable treatment option for mastitis.
DOI: 10.6084/m9.figshare.28375160.v1
title: The secretomes of bovine mammary epithelial cell subpopulations differentially modulate macrophage function

description: Bovine mammosphere-derived epithelial cell (MDEC) cultures are heterogeneous and enriched for stem and progenitor cells. We previously reported that the bovine MDEC secretome, comprised of all bioactive factors secreted by the cells, displays regenerative properties, exerts antimicrobial effects, and modulates neutrophil activity, positioning it as a promising non-antibiotic biologic therapy for infectious diseases important to the dairy industry, like mastitis. Mastitis is defined as inflammation of the udder, and it is typically caused by bacterial infection. The effect of the MDEC secretome on macrophages, a first line of defense against bacterial infections in the udder, is unknown and could impact the utility of the secretome as a therapy for mastitis. To address this, we isolated bovine monocytes from peripheral blood and maintained them as an unpolarized (M0) population or polarized them into M1 or M2 phenotypes. Macrophages cultured with the secretome of bovine MDECs were assessed for their ability to phagocytose labeled bacterial particles and accumulate reactive oxygen species (ROS). We used single-cell RNA sequencing (scRNA-seq) and fluorescence-activated cell sorting (FACS) to isolate a subpopulation of MDECs that exert enhanced effects on macrophages. We found that the secretome of MDECs that do not express cluster of differentiation (CD) 73, a cell surface enzyme used as a marker for mesenchymal stromal cells, most strongly increased macrophage phagocytosis and ROS accumulation. These findings will help optimize the generation of the bovine MDEC secretome as a suitable treatment option for mastitis.
DOI: 10.6084/m9.figshare.30383563
title: Characteristics of an emerging canine respiratory coronavirus in China

description: Canine respiratory coronavirus (CRCoV) is a prevalent pathogen implicated in canine infectious respiratory disease, yet information on its genomic characteristics and pathogenicity remains scarce. To address this situation, we investigated the genetic evolution and pathogenic potential of CRCoV strains circulating in China. Five complete CRCoV genomes (GenBank: PQ725948–PQ725952) were obtained from clinical samples, and phylogenetic analysis showed these strains formed a distinct genetic branch. The evolutionary trees for ORF1ab, HE, and S genes closely mirrored the full genome tree, indicating key roles for these genes in CRCoV evolution. Multiple unique amino acid mutations were identified in the ORF1ab, HE, S, M, and N proteins. Notably, molecular docking analysis suggests that mutations S158F and L161F in the HE lectin domain are associated with improved docking scores, indicating a potential increase in receptor-binding affinity. Consecutive nucleotide deletions in two non-coding regions between non-structural protein genes—which were also identified in strains of a Thai lineage (OQ621707.1–OQ621727.1)—were observed. A CRCoV strain (10<sup>6</sup> TCID<sub>50</sub>/mL) was isolated, and experimental infection confirmed its ability to induce pneumonia and tracheal cilia loss in dogs. These findings reveal the emergence and unique genetic diversity of a novel CRCoV variant in China, highlighting the need for ongoing epidemiological surveillance.
DOI: 10.6084/m9.figshare.28416745
title: Phylogenetic network of infectious bronchitis virus: exploring the impact of migratory birds on viral clustering, evolution, and recombination

description: Infectious bronchitis virus (IBV) presents a major threat to global poultry production, necessitating a thorough understanding of its evolutionary relationships for effective control measures. This study presents a novel distance-based Minimum Span Clustering (MSClustering) method to cluster 311 IBV strains, with a comparison of its results to the established IBV classification. Phylogenetic network and recombination analyses were employed to investigate IBV evolutionary relationships and transmission pathways. The phylogenetic network revealed distinct clusters reflecting relationships between IBV strains. Importantly, these network patterns, combined with recombination event analysis, suggest an unrecognized role for migratory birds in IBV dissemination, highlighting potential transmission pathways beyond established poultry trade routes. These findings contribute to advancing our understanding of IBV evolution and support the development of targeted strategies for controlling viral outbreaks in poultry populations. While statistical limitations may affect threshold estimation for smaller networks, our MSClustering method significantly accelerates processing speeds—approximately 100,000 times faster than PhyML when analyzing the dataset—enabling comprehensive-scale phylogenetic analysis of viruses.
DOI: 10.6084/m9.figshare.28416745.v1
title: Phylogenetic network of infectious bronchitis virus: exploring the impact of migratory birds on viral clustering, evolution, and recombination

description: Infectious bronchitis virus (IBV) presents a major threat to global poultry production, necessitating a thorough understanding of its evolutionary relationships for effective control measures. This study presents a novel distance-based Minimum Span Clustering (MSClustering) method to cluster 311 IBV strains, with a comparison of its results to the established IBV classification. Phylogenetic network and recombination analyses were employed to investigate IBV evolutionary relationships and transmission pathways. The phylogenetic network revealed distinct clusters reflecting relationships between IBV strains. Importantly, these network patterns, combined with recombination event analysis, suggest an unrecognized role for migratory birds in IBV dissemination, highlighting potential transmission pathways beyond established poultry trade routes. These findings contribute to advancing our understanding of IBV evolution and support the development of targeted strategies for controlling viral outbreaks in poultry populations. While statistical limitations may affect threshold estimation for smaller networks, our MSClustering method significantly accelerates processing speeds—approximately 100,000 times faster than PhyML when analyzing the dataset—enabling comprehensive-scale phylogenetic analysis of viruses.
DOI: 10.6084/m9.figshare.30528807
title: Towards a better understanding of clinical disease activity scores in dogs with chronic enteropathies

description: The Canine Inflammatory Bowel Disease Activity Index (CIBDAI) and Canine Chronic Enteropathy Clinical Activity Index (CCECAI) are key tools for monitoring chronic enteropathies (CE) in dogs. Despite their widespread use, concerns persist regarding their intra-observer repeatability and inter-observer reproducibility, which may impact clinical and research applications. This study evaluated the reliability of these indices through a two-phase approach using anonymized clinical records. In Phase 1, two observers independently scored 41 consultation forms twice, one month apart, to assess repeatability and reproducibility. Phase 2 involved four observers with varying expertise who scored 59 forms using a standardized guide addressing Phase 1 inconsistencies. Statistical methods included Lin’s concordance correlation coefficient and Bland-Altman plots. High intra-observer repeatability was observed for most variables, but inter-observer reproducibility was limited for CIBDAI, CCECAI, and fluctuating parameters like stool consistency and defecation frequency. The standardized guide marginally improved consistency but did not resolve discrepancies. Expert evaluators did not consistently outperform non-experts. Reproducibility declined in more clinically severe cases. These findings highlight the need for standardized training, dynamic scoring systems, and digital tools to enhance reliability. Addressing these limitations is critical to improve clinical decision-making and research outcomes in canine CE.
DOI: 10.6084/m9.figshare.30528807.v1
title: Towards a better understanding of clinical disease activity scores in dogs with chronic enteropathies

description: The Canine Inflammatory Bowel Disease Activity Index (CIBDAI) and Canine Chronic Enteropathy Clinical Activity Index (CCECAI) are key tools for monitoring chronic enteropathies (CE) in dogs. Despite their widespread use, concerns persist regarding their intra-observer repeatability and inter-observer reproducibility, which may impact clinical and research applications. This study evaluated the reliability of these indices through a two-phase approach using anonymized clinical records. In Phase 1, two observers independently scored 41 consultation forms twice, one month apart, to assess repeatability and reproducibility. Phase 2 involved four observers with varying expertise who scored 59 forms using a standardized guide addressing Phase 1 inconsistencies. Statistical methods included Lin’s concordance correlation coefficient and Bland-Altman plots. High intra-observer repeatability was observed for most variables, but inter-observer reproducibility was limited for CIBDAI, CCECAI, and fluctuating parameters like stool consistency and defecation frequency. The standardized guide marginally improved consistency but did not resolve discrepancies. Expert evaluators did not consistently outperform non-experts. Reproducibility declined in more clinically severe cases. These findings highlight the need for standardized training, dynamic scoring systems, and digital tools to enhance reliability. Addressing these limitations is critical to improve clinical decision-making and research outcomes in canine CE.
DOI: 10.6084/m9.figshare.29163477
title: Transcriptomic insights into <i>Mycobacterium orygis</i> infection-associated pulmonary granulomas reveal multicellular immune networks and tuberculosis biomarkers in cattle

description: <i>Mycobacterium orygis</i>, a member of the <i>Mycobacterium tuberculosis</i> complex (MTBC), has emerged as a significant contributor to tuberculosis (TB) in cattle, wildlife, and humans. However, understanding about its pathogenesis and severity is limited, compounded by the lack of reliable TB biomarkers in cattle. This study delves into the comparative pathology and transcriptomic landscape of pulmonary granulomas in cattle naturally infected with <i>M. orygis</i>, using high-throughput RNA sequencing. Histopathological analysis revealed extensive, multistage granulomatous, necrotic, and cavitary lesions, indicative of severe lung pathology induced by <i>M. orygis</i>. Transcriptomic profiling highlighted numerous differentially expressed genes and dysregulated pathways related to immune response modulation and extracellular matrix remodelling. Additionally, cell type enrichment analysis provided insights into the multicellularity of the granulomatous niche, emphasising complex cell-cell interactions within TB granulomas. Via comparative transcriptomics leveraging publicly available bovine and human TB omics datasets, 14 key immunomodulators (SOD2, IL1α/β, IL15, IL18, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL8/MCP-2, CCL20/MIP-3α, CXCL2/MIP-2, CXCL10/IP-10, CXCL11, and IFN-γ) were identified as potential biomarkers for active TB in cattle. These findings significantly advance our understanding of <i>M. orygis</i> pathogenesis in bovine TB and highlight potential targets for the development of diagnostic tools for managing and controlling the disease.
DOI: 10.6084/m9.figshare.29163477.v1
title: Transcriptomic insights into <i>Mycobacterium orygis</i> infection-associated pulmonary granulomas reveal multicellular immune networks and tuberculosis biomarkers in cattle

description: <i>Mycobacterium orygis</i>, a member of the <i>Mycobacterium tuberculosis</i> complex (MTBC), has emerged as a significant contributor to tuberculosis (TB) in cattle, wildlife, and humans. However, understanding about its pathogenesis and severity is limited, compounded by the lack of reliable TB biomarkers in cattle. This study delves into the comparative pathology and transcriptomic landscape of pulmonary granulomas in cattle naturally infected with <i>M. orygis</i>, using high-throughput RNA sequencing. Histopathological analysis revealed extensive, multistage granulomatous, necrotic, and cavitary lesions, indicative of severe lung pathology induced by <i>M. orygis</i>. Transcriptomic profiling highlighted numerous differentially expressed genes and dysregulated pathways related to immune response modulation and extracellular matrix remodelling. Additionally, cell type enrichment analysis provided insights into the multicellularity of the granulomatous niche, emphasising complex cell-cell interactions within TB granulomas. Via comparative transcriptomics leveraging publicly available bovine and human TB omics datasets, 14 key immunomodulators (SOD2, IL1α/β, IL15, IL18, CCL2/MCP-1, CCL3/MIP-1α, CCL4/MIP-1β, CCL8/MCP-2, CCL20/MIP-3α, CXCL2/MIP-2, CXCL10/IP-10, CXCL11, and IFN-γ) were identified as potential biomarkers for active TB in cattle. These findings significantly advance our understanding of <i>M. orygis</i> pathogenesis in bovine TB and highlight potential targets for the development of diagnostic tools for managing and controlling the disease.
DOI: 10.6084/m9.figshare.28563857
title: Understanding zoonotic pathogens and risk factors from wildlife in Southeast Asia: a systematic literature review

description: The COVID-19 pandemic has demonstrated the significance of the human-animal interface in the emergence of zoonotic diseases, with wildlife serving as an important source of infection. A better understanding of the specific pathogens and mechanisms involved is vital to prepare against future outbreaks, especially in Southeast Asia, a hotspot for zoonotic diseases. This paper reviews the published literature on wildlife zoonoses in this region from 2012 to 2022. The results show a diverse range of potential zoonotic pathogens and the widespread occurrence of zoonotic diseases from wildlife. Drivers of zoonotic pathogen spillover include (i) environmental factors (e.g. animal habitat disruption, environmental conditions, exposure to contaminated water/food/soil), (ii) animal factors (e.g. movement patterns, age-related susceptibility), (iii) human factors (e.g. lack of awareness, poor hygiene practices, age, gender and income) and (iv) human-animal-environmental interface factors (e.g. close contact between humans and animals, exposure through visiting animals and presence of vectors). The diverse drivers of zoonoses in Southeast Asia put its communities at risk for infection. To mitigate these risks, global health efforts should consider adopting a One Health approach to foster collaboration across human, animal, and wildlife health sectors. This could involve educating communities on safe animal interactions and improving disease surveillance.
DOI: 10.6084/m9.figshare.28563857.v1
title: Understanding zoonotic pathogens and risk factors from wildlife in Southeast Asia: a systematic literature review

description: The COVID-19 pandemic has demonstrated the significance of the human-animal interface in the emergence of zoonotic diseases, with wildlife serving as an important source of infection. A better understanding of the specific pathogens and mechanisms involved is vital to prepare against future outbreaks, especially in Southeast Asia, a hotspot for zoonotic diseases. This paper reviews the published literature on wildlife zoonoses in this region from 2012 to 2022. The results show a diverse range of potential zoonotic pathogens and the widespread occurrence of zoonotic diseases from wildlife. Drivers of zoonotic pathogen spillover include (i) environmental factors (e.g. animal habitat disruption, environmental conditions, exposure to contaminated water/food/soil), (ii) animal factors (e.g. movement patterns, age-related susceptibility), (iii) human factors (e.g. lack of awareness, poor hygiene practices, age, gender and income) and (iv) human-animal-environmental interface factors (e.g. close contact between humans and animals, exposure through visiting animals and presence of vectors). The diverse drivers of zoonoses in Southeast Asia put its communities at risk for infection. To mitigate these risks, global health efforts should consider adopting a One Health approach to foster collaboration across human, animal, and wildlife health sectors. This could involve educating communities on safe animal interactions and improving disease surveillance.