cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.26879003
title: Seroprevalence and risk factors of bluetongue virus in domestic cattle, sheep, goats and camels in Africa: a systematic review and meta-analysis

description: Bluetongue (BT) is a vector-borne disease affecting wild and domestic ruminants in many parts of the world. Although bluetongue virus (BTV) is widespread in ungulates in Africa, available epidemiological information on BT in this continent is limited. This systematic review and meta-analysis aimed to estimate the seroprevalence of BTV and summarize information on associated risk factors in domestic ruminants and camels in Africa. Systematic searches were conducted from the inception of the database to November 2022 on PubMed/MEDLINE, ScienceDirect, Web of Science, and Google/Google Scholar. Forty-four eligible publications were identified, published in the range from 1973 to 2020, and statistically analyzed. The pooled overall seroprevalence of BTV was 45.02% (95% confidence interval [CI]: 36.00-54.00%). The pooled seroprevalence was 49.70% (95% CI: 34.50-65.00%) in cattle, 47.00% (95% CI: 29.90-64.50%) in goats, 40.80% (95% CI: 19.60-63.90%) in camels, and 36.30% (95% CI: 29.00-44.90%) in sheep. The pooled seroprevalence decreased after 1990 and increased again after 2010. The highest pooled overall seroprevalence was found in the southeastern region, and the highest pooled overall seroprevalence was obtained by Competitive Enzyme-Linked Immunosorbent Assay. Finally, the seroprevalence in females (53.30%, 95% CI: 34.80-71.00%) was significantly higher than in males (28.10%, 95% CI: 17.40-40.30%) (<i>p</i> &lt; 0.05). We showed that antibodies against BTV were common in African ruminants and camels. Monitoring the seroprevalence of BTV, as well as systematic and continuous surveillance of the <i>Culicoides</i> population, are encouraged to prevent and control the spread of BT.
DOI: 10.6084/m9.figshare.25727446
title: Antimicrobial susceptibility and resistome of <i>Actinobacillus pleuropneumoniae</i> in Taiwan: a next-generation sequencing analysis

description: <i>Actinobacillus pleuropneumoniae</i> infection causes a high mortality rate in porcine animals. Antimicrobial resistance poses global threats to public health. The current study aimed to determine the antimicrobial susceptibilities and probe the resistome of <i>A. pleuropneumoniae</i> in Taiwan. Herein, 133 isolates were retrospectively collected; upon initial screening, 38 samples were subjected to next-generation sequencing (NGS). Over the period 2017–2022, the lowest frequencies of resistant isolates were found for ceftiofur, cephalexin, cephalothin, and enrofloxacin, while the highest frequencies of resistant isolates were found for oxytetracycline, streptomycin, doxycycline, ampicillin, amoxicillin, kanamycin, and florfenicol. Furthermore, most isolates (71.4%) showed multiple drug resistance. NGS-based resistome analysis revealed aminoglycoside- and tetracycline-related genes at the highest prevalence, followed by genes related to beta-lactam, sulfamethoxazole, florphenicol, and macrolide. A plasmid replicon (repUS47) and insertion sequences (IS10R and ISVAp11) were identified in resistant isolates. Notably, the multiple resistance roles of the insertion sequence IS10R were widely proposed in human medicine; however, this is the first time IS10R has been reported in veterinary medicine. Concordance analysis revealed a high consistency of phenotypic and genotypic susceptibility to florphenicol, tilmicosin, doxycycline, and oxytetracycline. The current study reports the antimicrobial characterization of <i>A. pleuropneumoniae</i> for the first time in Taiwan using NGS.
DOI: 10.6084/m9.figshare.26879003.v1
title: Seroprevalence and risk factors of bluetongue virus in domestic cattle, sheep, goats and camels in Africa: a systematic review and meta-analysis

description: Bluetongue (BT) is a vector-borne disease affecting wild and domestic ruminants in many parts of the world. Although bluetongue virus (BTV) is widespread in ungulates in Africa, available epidemiological information on BT in this continent is limited. This systematic review and meta-analysis aimed to estimate the seroprevalence of BTV and summarize information on associated risk factors in domestic ruminants and camels in Africa. Systematic searches were conducted from the inception of the database to November 2022 on PubMed/MEDLINE, ScienceDirect, Web of Science, and Google/Google Scholar. Forty-four eligible publications were identified, published in the range from 1973 to 2020, and statistically analyzed. The pooled overall seroprevalence of BTV was 45.02% (95% confidence interval [CI]: 36.00-54.00%). The pooled seroprevalence was 49.70% (95% CI: 34.50-65.00%) in cattle, 47.00% (95% CI: 29.90-64.50%) in goats, 40.80% (95% CI: 19.60-63.90%) in camels, and 36.30% (95% CI: 29.00-44.90%) in sheep. The pooled seroprevalence decreased after 1990 and increased again after 2010. The highest pooled overall seroprevalence was found in the southeastern region, and the highest pooled overall seroprevalence was obtained by Competitive Enzyme-Linked Immunosorbent Assay. Finally, the seroprevalence in females (53.30%, 95% CI: 34.80-71.00%) was significantly higher than in males (28.10%, 95% CI: 17.40-40.30%) (<i>p</i> &lt; 0.05). We showed that antibodies against BTV were common in African ruminants and camels. Monitoring the seroprevalence of BTV, as well as systematic and continuous surveillance of the <i>Culicoides</i> population, are encouraged to prevent and control the spread of BT.
DOI: 10.6084/m9.figshare.26942135
title: Pathological, immunological and molecular epidemiological analysis of lumpy skin disease virus in Indian cattle during a high-mortality epidemic

description: Lumpy skin disease (LSD) is an economically significant, emerging viral disease of Cattle and Buffaloes. This study aimed to investigate the causes of high mortality in a recent LSD epidemic in India. We examined 1618 animals across seventy outbreaks and conducted post-mortem on 48 cattle out of 513 clinically suspected LSD cases. The morbidity, mortality and case fatality rates recorded were 31.70%, 2.97 and 9.37% respectively. Disease stages were categorized as early (20.81%), mid (42.02%), and late (37.17%) and the distribution of skin lesions was classified as mild (34.14%), moderate (39.39%), and severe (26.47%). Post-mortem findings revealed systemic infection with necrotic and ulcerative nodules on multiple internal organs. Histologically, necrotizing vasculitis and mononuclear cell infiltration with intracytoplasmic inclusions were observed in various organs. The highest viral load was found in skin nodules/scabs, trachea, tongue, and lymph nodes. The viral load was significantly higher in mid- and late-stages of skin nodules and internal organs; whereas, blood from early-stage showed high viral load. The expression of Th1-type and Th2-type cytokines varied significantly across different stages of the disease. The downregulation of the apoptotic intrinsic and upregulation of the extrinsic pathway genes, suggesting that the latter plays a role in LSDV infection. Genetic analysis revealed that the LSD virus (LSDV) isolates were derived from a Kenyan ancestral strain with unique nucleotide changes in RPO30 and P32 gene. In conclusion, the high mortality in the recent Indian LSD epidemic can be attributed to a newly identified, highly virulent strain of LSDV causing systemic infection.
DOI: 10.6084/m9.figshare.24942350
title: First detection of Omicron variant BA.4.1 lineage in dogs, Chile

description: SARS-CoV-2’s rapid global spread caused the declaration of COVID-19 as a pandemic in March 2020. Alongside humans, domestic dogs and cats are also susceptible to infection. However, limited reports on pet infections in Chile prompted a comprehensive study to address this knowledge gap. Between March 2021 and March 2023, the study assessed 65 pets (26 dogs and 39 cats) from 33 COVID-19+ households alongside 700 nasal swabs from animals in households with unknown COVID-19 status. Using RT-PCR, nasal, fecal, and environmental samples were analyzed for the virus. In COVID-19+ households, 6.06% tested positive for SARS-CoV-2, belonging to 3 dogs, indicating human-to-pet transmission. Pets from households with unknown COVID-19 status tested negative for the virus. We obtained 2 SARS-CoV-2 genomes from animals, that belonged to Omicron BA.4.1 variant, marking the first report of pets infected with this lineage globally. Phylogenetic analysis showed these sequences clustered with human sequences collected in Chile during the same period when the BA.4.1 variant was prevalent in the country. The prevalence of SARS-CoV-2 in Chilean pets was relatively low, likely due to the country’s high human vaccination rate. Our study highlights the importance of upholding and strengthening human vaccination strategies to mitigate the risk of interspecies transmission. It underscores the critical role of the One Health approach in addressing emerging zoonotic diseases, calling for further research on infection dynamics and risk factors for a comprehensive understanding.
DOI: 10.6084/m9.figshare.24942350.v1
title: First detection of Omicron variant BA.4.1 lineage in dogs, Chile

description: SARS-CoV-2’s rapid global spread caused the declaration of COVID-19 as a pandemic in March 2020. Alongside humans, domestic dogs and cats are also susceptible to infection. However, limited reports on pet infections in Chile prompted a comprehensive study to address this knowledge gap. Between March 2021 and March 2023, the study assessed 65 pets (26 dogs and 39 cats) from 33 COVID-19+ households alongside 700 nasal swabs from animals in households with unknown COVID-19 status. Using RT-PCR, nasal, fecal, and environmental samples were analyzed for the virus. In COVID-19+ households, 6.06% tested positive for SARS-CoV-2, belonging to 3 dogs, indicating human-to-pet transmission. Pets from households with unknown COVID-19 status tested negative for the virus. We obtained 2 SARS-CoV-2 genomes from animals, that belonged to Omicron BA.4.1 variant, marking the first report of pets infected with this lineage globally. Phylogenetic analysis showed these sequences clustered with human sequences collected in Chile during the same period when the BA.4.1 variant was prevalent in the country. The prevalence of SARS-CoV-2 in Chilean pets was relatively low, likely due to the country’s high human vaccination rate. Our study highlights the importance of upholding and strengthening human vaccination strategies to mitigate the risk of interspecies transmission. It underscores the critical role of the One Health approach in addressing emerging zoonotic diseases, calling for further research on infection dynamics and risk factors for a comprehensive understanding.
DOI: 10.6084/m9.figshare.25727446.v1
title: Antimicrobial susceptibility and resistome of <i>Actinobacillus pleuropneumoniae</i> in Taiwan: a next-generation sequencing analysis

description: <i>Actinobacillus pleuropneumoniae</i> infection causes a high mortality rate in porcine animals. Antimicrobial resistance poses global threats to public health. The current study aimed to determine the antimicrobial susceptibilities and probe the resistome of <i>A. pleuropneumoniae</i> in Taiwan. Herein, 133 isolates were retrospectively collected; upon initial screening, 38 samples were subjected to next-generation sequencing (NGS). Over the period 2017–2022, the lowest frequencies of resistant isolates were found for ceftiofur, cephalexin, cephalothin, and enrofloxacin, while the highest frequencies of resistant isolates were found for oxytetracycline, streptomycin, doxycycline, ampicillin, amoxicillin, kanamycin, and florfenicol. Furthermore, most isolates (71.4%) showed multiple drug resistance. NGS-based resistome analysis revealed aminoglycoside- and tetracycline-related genes at the highest prevalence, followed by genes related to beta-lactam, sulfamethoxazole, florphenicol, and macrolide. A plasmid replicon (repUS47) and insertion sequences (IS10R and ISVAp11) were identified in resistant isolates. Notably, the multiple resistance roles of the insertion sequence IS10R were widely proposed in human medicine; however, this is the first time IS10R has been reported in veterinary medicine. Concordance analysis revealed a high consistency of phenotypic and genotypic susceptibility to florphenicol, tilmicosin, doxycycline, and oxytetracycline. The current study reports the antimicrobial characterization of <i>A. pleuropneumoniae</i> for the first time in Taiwan using NGS.
DOI: 10.6084/m9.figshare.27029132
title: Predictive value of <i>TP53</i> RNAscope<sup>®</sup> <i>in situ</i> hybridization and p53 immunohistochemistry for <i>TP53</i> mutational status in canine diffuse large B-cell lymphoma

description: <i>TP53</i> mutations are associated with short survival and poor treatment response in canine diffuse large B-cell lymphoma (cDLBCL). The expression of <i>TP53</i> by RNAscope<sup>®</sup> <i>in situ</i> hybridization and p53 by immunohistochemistry (IHC) was investigated in 37 formalin-fixed paraffin-embedded cDLBCL, to assess their correlation with <i>TP53</i> mutational status and to evaluate their prognostic value. <i>TP53</i> was detected in all samples by RNAscope<sup>®</sup>. Ten of 37 (27%) cases expressed p53 by IHC, with highly variable percentage of positive cells. <i>TP53</i> RNAscope<sup>®</sup> scores and p53 IHC results were not correlated. The expression of <i>TP53</i> by RNAscope<sup>®</sup> was not influenced by its mutational status. Conversely, p53 IHC and <i>TP53</i> mutations were significantly associated. p53 IHC predicted <i>TP53</i> genetic mutations with high accuracy (97.3%). All <i>TP53-</i>mutated samples carrying missense mutations exhibited p53 expression by IHC, while all wild-type cases and a single case with frameshift insertion were negative. In univariable analysis, p53 IHC was associated with shorter time to progression (TTP) and lymphoma-specific survival (LSS). Nevertheless, in multivariable analysis, only treatment significantly affected TTP and LSS. These findings suggest p53 IHC is an accurate, cost-effective tool for predicting <i>TP53</i> mutations in cDLBCL, unlike <i>TP53</i> RNAscope<sup>®</sup>, though its prognostic value requires further validation.
DOI: 10.6084/m9.figshare.27029132.v2
title: Predictive value of <i>TP53</i> RNAscope<sup>®</sup> <i>in situ</i> hybridization and p53 immunohistochemistry for <i>TP53</i> mutational status in canine diffuse large B-cell lymphoma

description: <i>TP53</i> mutations are associated with short survival and poor treatment response in canine diffuse large B-cell lymphoma (cDLBCL). The expression of <i>TP53</i> by RNAscope<sup>®</sup> <i>in situ</i> hybridization and p53 by immunohistochemistry (IHC) was investigated in 37 formalin-fixed paraffin-embedded cDLBCL, to assess their correlation with <i>TP53</i> mutational status and to evaluate their prognostic value. <i>TP53</i> was detected in all samples by RNAscope<sup>®</sup>. Ten of 37 (27%) cases expressed p53 by IHC, with highly variable percentage of positive cells. <i>TP53</i> RNAscope<sup>®</sup> scores and p53 IHC results were not correlated. The expression of <i>TP53</i> by RNAscope<sup>®</sup> was not influenced by its mutational status. Conversely, p53 IHC and <i>TP53</i> mutations were significantly associated. p53 IHC predicted <i>TP53</i> genetic mutations with high accuracy (97.3%). All <i>TP53-</i>mutated samples carrying missense mutations exhibited p53 expression by IHC, while all wild-type cases and a single case with frameshift insertion were negative. In univariable analysis, p53 IHC was associated with shorter time to progression (TTP) and lymphoma-specific survival (LSS). Nevertheless, in multivariable analysis, only treatment significantly affected TTP and LSS. These findings suggest p53 IHC is an accurate, cost-effective tool for predicting <i>TP53</i> mutations in cDLBCL, unlike <i>TP53</i> RNAscope<sup>®</sup>, though its prognostic value requires further validation.
DOI: 10.6084/m9.figshare.25763979.v1
title: Evaluation of antimicrobial and non-steroidal anti-inflammatory treatments for BRD on health and welfare in fattening bulls: a cross-sectional study

description: Our study aimed to evaluate the effect of different treatments for BRD on health and welfare in fattening bulls. A total of 264 bulls were enrolled. Welfare was assessed on day 2 (T0) and day 15 (T1) after arrival. A decrease in the welfare level was observed from T0 to T1. All bulls were inspected clinically at T0 and T1 revealing an increase of skin lesions and lameness in T1. In both periods, a high incidence of respiratory disease was observed. A prevalence of 79.55% and 95.45% of <i>Mycoplasma bovis</i> using RT-PCR and culture at T0 and T1 respectively was observed. Blood samples were collected for haematology at T0 and T1. At T0, 36 animals were individually treated for BRD with an antimicrobial (IT), 54 received a metaphylactic treatment with tulathromycin (M), 150 received a metaphylactic treatment with tulathromycin plus a second antimicrobial (M + IT) whereas 24 were considered healthy and therefore not treated (NT). Additionally, 128 were treated with a non-steroid anti-inflammatory (NSAID). Neutrophils of M + IT were significantly higher than groups NT and M and the lymphocytes of M + IT were significantly lower than that of IT. White blood cells, neutrophils and N/L ratio of animals treated with an NSAID was significantly higher than that not treated. Lung inspection of 172 bulls at the abattoir indicated that 92.43% presented at least one lung lesion. A statistically significant effect of the NSAID treatment on the lung lesions was observed. Our findings indicate that BRD was a major welfare and health concern and evidence the difficulties of antimicrobial treatment of <i>M. bovis</i>.
DOI: 10.6084/m9.figshare.27029132.v1
title: Predictive value of <i>TP53</i> RNAscope<sup>®</sup><i>in situ</i> hybridization and p53 immunohistochemistry for <i>TP53</i> mutational status in canine diffuse large B-cell lymphoma

description: <i>TP53</i> mutations are associated with short survival and poor treatment response in canine diffuse large B-cell lymphoma (cDLBCL). The expression of <i>TP53</i> by RNAscope<sup>®</sup> <i>in situ</i> hybridization and p53 by immunohistochemistry (IHC) was investigated in 37 formalin-fixed paraffin-embedded cDLBCL, to assess their correlation with <i>TP53</i> mutational status and to evaluate their prognostic value. <i>TP53</i> was detected in all samples by RNAscope<sup>®</sup>. Ten of 37 (27%) cases expressed p53 by IHC, with highly variable percentage of positive cells. <i>TP53</i> RNAscope<sup>®</sup> scores and p53 IHC results were not correlated. The expression of <i>TP53</i> by RNAscope<sup>®</sup> was not influenced by its mutational status. Conversely, p53 IHC and <i>TP53</i> mutations were significantly associated. p53 IHC predicted <i>TP53</i> genetic mutations with high accuracy (97.3%). All <i>TP53-</i>mutated samples carrying missense mutations exhibited p53 expression by IHC, while all wild-type cases and a single case with frameshift insertion were negative. In univariable analysis, p53 IHC was associated with shorter time to progression (TTP) and lymphoma-specific survival (LSS). Nevertheless, in multivariable analysis, only treatment significantly affected TTP and LSS. These findings suggest p53 IHC is an accurate, cost-effective tool for predicting <i>TP53</i> mutations in cDLBCL, unlike <i>TP53</i> RNAscope<sup>®</sup>, though its prognostic value requires further validation.
DOI: 10.6084/m9.figshare.25763979
title: Evaluation of antimicrobial and non-steroidal anti-inflammatory treatments for BRD on health and welfare in fattening bulls: a cross-sectional study

description: Our study aimed to evaluate the effect of different treatments for BRD on health and welfare in fattening bulls. A total of 264 bulls were enrolled. Welfare was assessed on day 2 (T0) and day 15 (T1) after arrival. A decrease in the welfare level was observed from T0 to T1. All bulls were inspected clinically at T0 and T1 revealing an increase of skin lesions and lameness in T1. In both periods, a high incidence of respiratory disease was observed. A prevalence of 79.55% and 95.45% of <i>Mycoplasma bovis</i> using RT-PCR and culture at T0 and T1 respectively was observed. Blood samples were collected for haematology at T0 and T1. At T0, 36 animals were individually treated for BRD with an antimicrobial (IT), 54 received a metaphylactic treatment with tulathromycin (M), 150 received a metaphylactic treatment with tulathromycin plus a second antimicrobial (M + IT) whereas 24 were considered healthy and therefore not treated (NT). Additionally, 128 were treated with a non-steroid anti-inflammatory (NSAID). Neutrophils of M + IT were significantly higher than groups NT and M and the lymphocytes of M + IT were significantly lower than that of IT. White blood cells, neutrophils and N/L ratio of animals treated with an NSAID was significantly higher than that not treated. Lung inspection of 172 bulls at the abattoir indicated that 92.43% presented at least one lung lesion. A statistically significant effect of the NSAID treatment on the lung lesions was observed. Our findings indicate that BRD was a major welfare and health concern and evidence the difficulties of antimicrobial treatment of <i>M. bovis</i>.
DOI: 10.6084/m9.figshare.27143209
title: Canine parvovirus in North-East India: a phylogenetic and evolutionary analysis

description: Canine parvovirus type 2 (CPV-2) infection in dogs is considered as one of the most common cause of morbidity and mortality in young dogs and continues to occur with high incidence worldwide. Despite a single-stranded DNA virus, CPV-2 possesses a high mutation rate which has led to the development of new variants from time to time. These variants are classically classified based on the amino acid markers present in the VP2 gene. In this study, we examined 20 different cases of CPV-2 infection from seven different states of the North East region (NER) of India. The near-complete genome sequences of all these isolates were subjected to phylodynamic and phylogeographic analysis to evaluate the genetic diversity and geographical spread of CPV-2 variants. Analysis of the deduced amino acid sequences revealed residues characteristic of the ‘Asian CPV-2c lineage’ in all the 20 sequences confirming it as the dominant strain circulating in NER, India. The phylogenetic analysis based on the whole genome showed that all 20 sequences formed a monophyletic clade together with other Asian CPV-2c sequences. Furthermore, phylogeographic analysis based on the VP2 gene showed the likely introduction of Asian CPV-2c strain to India from China. This study marks the first comprehensive report elucidating the molecular epidemiology of CPV-2 in India.