cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28218693.v2
title: Genetic and structural factors contributing to the dominance and persistence of goose astrovirus type 2

description: Goose astrovirus (GoAstV) has emerged as a significant pathogen affecting the goose industry in China, with GoAstV-2 becoming the dominant genotype since 2017. This study explored the genetic and structural factors underlying the prevalence of GoAstV-2, focusing on codon usage bias, spike protein variability, and structural stability. Phylogenetic and effective population size analyses revealed that GoAstV-2 underwent rapid expansion between 2017 and 2018, followed by population stabilization. Codon usage analysis indicated that GoAstV-2 exhibited a weaker codon usage bias compared to GoAstV-1, suggesting greater flexibility in synonymous codon usage and potentially enhanced adaptability across host environments. Additionally, the lower codon adaptation index values of GoAstV-2 point to a divergence from the host’s optimal codon usage, which may reduce competition with host tRNA pools and facilitate viral replication. The spike protein of GoAstV-2 demonstrated significantly lower variability than GoAstV-1, as shown by Shannon entropy analysis, indicating greater structural stability. This stability may reduce the need for frequent mutations, allowing GoAstV-2 to persist in host populations without undergoing constant evolution. The lower antigenic variability likely decreases immune-driven selective pressure, contributing to the sustained viral transmission and long-term persistence. These findings provide new insights into the evolutionary advantages of GoAstV-2 and its epidemiological success, which could inform future control strategies aimed at mitigating its impact on poultry populations. Goose astrovirus type 2 (GoAstV-2) became the dominant strain in China post-2017.GoAstV-2 exhibits weaker codon usage bias, enhancing adaptability across hosts.The stability of GoAstV-2 spike protein reduces mutation needs and selective pressure.GoAstV-2 low spike protein variability supports long-term persistence in host populations. Goose astrovirus type 2 (GoAstV-2) became the dominant strain in China post-2017. GoAstV-2 exhibits weaker codon usage bias, enhancing adaptability across hosts. The stability of GoAstV-2 spike protein reduces mutation needs and selective pressure. GoAstV-2 low spike protein variability supports long-term persistence in host populations.
DOI: 10.6084/m9.figshare.28269451.v1
title: Comparative Genomic Analysis Reveals the Emergence and Dissemination of Different <i>Salmonella enterica</i> serovar Gallinarum biovar Gallinarum Lineages in Brazil

description: <i>Salmonella enterica</i> serovar Gallinarum biovar Gallinarum is a pathogenic bacterium that causes fowl typhoid (FT), affecting chicken flocks worldwide. This study aimed to evaluate the emergence, dissemination and genomic profile of <i>S.</i> Gallinarum lineages from Brazil. Twelve whole-genomes sequences (WGS) of different <i>S</i>. Gallinarum strains isolated from Brazilian poultry farms (2014 to 2018) were obtained and used to construct a dataset with other 31 previously published data (five more from Brazil). Brazilian strains phylogenetic diversity, temporal evolution and antimicrobial resistance/virulence genomic profile were evaluated. Sixteen (94.1%) Brazilian strains were from sequence type ST78 and one (5.9%) was from ST331. All <i>S.</i> Gallinarum strains clustered into five different clades/lineages (I to V), all circulating in South America and four (I, II, III, IV) in Brazil. The time of most recent common ancestor (tMRCA) of all strains was many centuries ago, but the lineages detected in South America (II and V) had tMRCA in recent decades. IncFIC(FII), IncFII(S) and ColRNAI were plasmid replicons frequently found in the lineages from Brazil, but antimicrobial resistance genes were scarce. Only two resistance genes (<i>aac(6’)-Iaa</i> and <i>mdf(A)</i>) were detected in most strains, while other two (<i>blaTEM-106</i> and <i>fosA3</i>) were present in some isolates. It was also observed important differences in the virulence genomic profile of the different lineages, highlighting lineage IV, which does not carry the very important <i>Salmonella</i> pathogenicity island 1 (SPI1) genes cluster. In summary, this study reveals the emergence and dissemination of four different lineages of <i>S.</i> Gallinarum in Brazil.
DOI: 10.6084/m9.figshare.28218693.v1
title: Genetic and Structural Factors Contributing to the Dominance and Persistence of Goose Astrovirus Type 2

description: Goose astrovirus (GoAstV) has emerged as a significant pathogen affecting the goose industry in China, with GoAstV-2 becoming the dominant genotype since 2017. This study explores the genetic and structural factors underlying the prevalence of GoAstV-2, focusing on codon usage bias, spike protein variability, and structural stability. Phylogenetic and effective population size analyses revealed that GoAstV-2 experienced rapid expansion between 2017 and 2018, followed by population stabilization. Codon usage analysis indicated that GoAstV-2 exhibited a weaker codon usage bias compared to GoAstV-1, suggesting greater flexibility in synonymous codon usage and potentially enhanced adaptability across host environments. Additionally, GoAstV-2's lower codon adaptation index values point to a divergence from the host’s optimal codon usage, which may reduce competition with host tRNA pools and facilitate viral replication. The spike protein of GoAstV-2 demonstrated significantly lower variability than GoAstV-1, as shown by Shannon entropy analysis, indicating greater structural stability. This stability may reduce the need for frequent mutations, allowing GoAstV-2 to persist in host populations without undergoing constant evolution. The lower antigenic variability likely decreases immune-driven selective pressure, contributing to the viral sustained transmission and long-term persistence. These findings provide new insights into the evolutionary advantages of GoAstV-2 and its epidemiological success, which could inform future control strategies aimed at mitigating its impact on poultry populations.
DOI: 10.6084/m9.figshare.28351010
title: Histomorphological characteristics of keel bone maturation and keel bone fractures in laying hens

description: The keel bone in laying hens is prone to fractures, especially on the caudal third of the keel, which is also the last part to ossify. Keel bone fractures (KBF) typically occur between 25 and 50 weeks of age (WOA). However, the keel is fully ossified at around 40 WOA, suggesting fractures can occur before ossification is complete. To better understand the relationship between KBF and ossification, this descriptive study examined keel bone morphology during maturation. Keel bones from 50 commercial aviary housed Dekalb White laying hens were collected at 10 timepoints from 17–53 WOA and prepared for histological analysis. The samples were stained with haematoxylin and eosin and Safranin O to show cartilage, ossification, bone tissue, and KBF. The results indicated an ossification process similar to endochondral ossification. The degree of ossification varied between individuals of the same age. The age at complete ossification varied from 28–49 WOA. None of the keels from hens aged 53 WOA were fully ossified. Cartilage canals were present in the keel cartilage. Medullary bone was observed in all age groups. Most fractures lacked tissue morphologies typical of high-impact collisions, suggesting the need for further research into the underlying causes. This is the first study to detail keel bone histomorphology in commercial laying hens, providing baseline data for future research.
DOI: 10.6084/m9.figshare.28246302.v1
title: Co-infections of <i>Enterococcus cecorum</i> and various avian pathogens resulted in varying rates of SPF broilers with an <i>E. cecorum</i> infection

description: <i>Enterococcus cecorum</i> infections can be experimentally reproduced after oral inoculation. Co-infections of <i>E. cecorum</i> with other avian pathogens might increase the proportion of broilers with <i>E. cecorum</i> infections. The aim of the study was to examine via which infection routes <i>E. cecorum</i> is capable of causing infections, and which co-infections exacerbate <i>E. cecorum</i> infections. Two experiments, each with 12 groups, were conducted. Per group, 40 SPF broilers were inoculated intravenously, orally or via aerosol with <i>E. cecorum</i> alone, a negative control group was included, and in eight groups the effect of co-infections was studied. In experiment 1, infectious bronchitis virus (IBV), Newcastle disease virus (NDV) vaccine, reovirus, and chicken anaemia virus (CAV) were inoculated before oral or aerosol challenge with <i>E. cecorum</i>. In experiment 2, <i>E. cecorum</i> was given after the administration of dexamethasone, or inoculation of CAV, or combinations of IBV or NDV with <i>Mycoplasma synoviae</i> (M.s.). Typical <i>E. cecorum</i> lesions were reproduced via all applied infection routes. The proportion of lesions was highest in the intravenously inoculated groups, being 0.25 (95% confidence interval (CI):0.127–0.412) and 0.275 (95% CI:0.146–0.439) in experiments 1 and 2, respectively. More lesions were observed in experiment 2, while the proportion of lesions after oral and aerosol inoculation did not differ in either experiment. The proportion of lesions was not exacerbated after co-infections of <i>E. cecorum</i> with various avian pathogens. Only the proportion of <i>E. cecorum</i> reisolations was exacerbated after inoculation with CAV or M.s. in combination with IBV or NDV. Typical <i>E. cecorum</i> lesions can be reproduced in SPF broilers after intravenous, aerosol and oral inoculations.The respiratory route is potentially an infection route for pathogenic <i>E. cecorum</i> bacteria.Co-infections tested in this study or dexamethasone do not exacerbate the proportion of <i>E. cecorum</i> lesions.M.s. in combination with IBV or NDV vaccines exacerbates the proportion of positive reisolations.Immunosuppression induced by early CAV infection increases the proportion of positive reisolations. Typical <i>E. cecorum</i> lesions can be reproduced in SPF broilers after intravenous, aerosol and oral inoculations. The respiratory route is potentially an infection route for pathogenic <i>E. cecorum</i> bacteria. Co-infections tested in this study or dexamethasone do not exacerbate the proportion of <i>E. cecorum</i> lesions. M.s. in combination with IBV or NDV vaccines exacerbates the proportion of positive reisolations. Immunosuppression induced by early CAV infection increases the proportion of positive reisolations.
DOI: 10.6084/m9.figshare.28351010.v1
title: Histomorphological characteristics of keel bone maturation and keel bone fractures in laying hens

description: The keel bone in laying hens is prone to fractures, especially on the caudal third of the keel, which is also the last part to ossify. Keel bone fractures (KBF) typically occur between 25 and 50 weeks of age (WOA). However, the keel is fully ossified at around 40 WOA, suggesting fractures can occur before ossification is complete. To better understand the relationship between KBF and ossification, this descriptive study examined keel bone morphology during maturation. Keel bones from 50 commercial aviary housed Dekalb White laying hens were collected at 10 timepoints from 17–53 WOA and prepared for histological analysis. The samples were stained with haematoxylin and eosin and Safranin O to show cartilage, ossification, bone tissue, and KBF. The results indicated an ossification process similar to endochondral ossification. The degree of ossification varied between individuals of the same age. The age at complete ossification varied from 28–49 WOA. None of the keels from hens aged 53 WOA were fully ossified. Cartilage canals were present in the keel cartilage. Medullary bone was observed in all age groups. Most fractures lacked tissue morphologies typical of high-impact collisions, suggesting the need for further research into the underlying causes. This is the first study to detail keel bone histomorphology in commercial laying hens, providing baseline data for future research.
DOI: 10.6084/m9.figshare.28246302
title: Co-infections of <i>Enterococcus cecorum</i> and various avian pathogens resulted in varying rates of SPF broilers with an <i>E. cecorum</i> infection

description: <i>Enterococcus cecorum</i> infections can be experimentally reproduced after oral inoculation. Co-infections of <i>E. cecorum</i> with other avian pathogens might increase the proportion of broilers with <i>E. cecorum</i> infections. The aim of the study was to examine via which infection routes <i>E. cecorum</i> is capable of causing infections, and which co-infections exacerbate <i>E. cecorum</i> infections. Two experiments, each with 12 groups, were conducted. Per group, 40 SPF broilers were inoculated intravenously, orally or via aerosol with <i>E. cecorum</i> alone, a negative control group was included, and in eight groups the effect of co-infections was studied. In experiment 1, infectious bronchitis virus (IBV), Newcastle disease virus (NDV) vaccine, reovirus, and chicken anaemia virus (CAV) were inoculated before oral or aerosol challenge with <i>E. cecorum</i>. In experiment 2, <i>E. cecorum</i> was given after the administration of dexamethasone, or inoculation of CAV, or combinations of IBV or NDV with <i>Mycoplasma synoviae</i> (M.s.). Typical <i>E. cecorum</i> lesions were reproduced via all applied infection routes. The proportion of lesions was highest in the intravenously inoculated groups, being 0.25 (95% confidence interval (CI):0.127–0.412) and 0.275 (95% CI:0.146–0.439) in experiments 1 and 2, respectively. More lesions were observed in experiment 2, while the proportion of lesions after oral and aerosol inoculation did not differ in either experiment. The proportion of lesions was not exacerbated after co-infections of <i>E. cecorum</i> with various avian pathogens. Only the proportion of <i>E. cecorum</i> reisolations was exacerbated after inoculation with CAV or M.s. in combination with IBV or NDV. Typical <i>E. cecorum</i> lesions can be reproduced in SPF broilers after intravenous, aerosol and oral inoculations.The respiratory route is potentially an infection route for pathogenic <i>E. cecorum</i> bacteria.Co-infections tested in this study or dexamethasone do not exacerbate the proportion of <i>E. cecorum</i> lesions.M.s. in combination with IBV or NDV vaccines exacerbates the proportion of positive reisolations.Immunosuppression induced by early CAV infection increases the proportion of positive reisolations. Typical <i>E. cecorum</i> lesions can be reproduced in SPF broilers after intravenous, aerosol and oral inoculations. The respiratory route is potentially an infection route for pathogenic <i>E. cecorum</i> bacteria. Co-infections tested in this study or dexamethasone do not exacerbate the proportion of <i>E. cecorum</i> lesions. M.s. in combination with IBV or NDV vaccines exacerbates the proportion of positive reisolations. Immunosuppression induced by early CAV infection increases the proportion of positive reisolations.
DOI: 10.6084/m9.figshare.28089744
title: Epidemiological investigation and drug resistance analysis of avian pathogenic <i>Escherichia coli</i> (APEC) of Wenchang chickens in Hainan, China

description: Avian pathogenic <i>Escherichia coli</i> (APEC) is one of the major causes of poultry morbidity worldwide, severely reducing egg production and embryo hatchability in laying hens. Hainan Wenchang chicken is an important poultry breed in Hainan, China, and production of these chickens has been affected by APEC for a long time. In this study, in order to investigate the causes of low hatchability and a large number of weak chicks during the breeding of Wenchang chickens, a total of 130 strains of APEC were isolated from 591 chicken embryo samples collected from five large-scale farms of Wenchang chicken in Hainan area. The APEC isolates from Hainan Wenchang chicken embryos were analysed in terms of serotypes, drug resistance, genomes and evolutionary relationships. O8 was the main prevalent serotype of APEC from embryos, and the isolates were highly resistant to antibiotics and were multi-drug resistant. Of the isolates, 19.2% were resistant to 14 antibiotics with a resistance rate of more than 73%. The number of resistance genes carried by APEC isolates from embryos was stabilized at 53. The results of pan-genomic analysis showed that the genomes of Hainan Wenchang chicken embryo APEC isolates are concentrated in two evolutionary clusters, and isolates of the same serotype had extremely close evolutionary relationships. This study is the first large-scale isolation and analysis of APEC isolated from Wenchang chicken embryos, which can provide a reference for the prevention and control of APEC and antibiotic use in Hainan Wenchang chickens. Type O8 is the most prevalent serotype of APEC isolated from Wenchang chicken embryos (Hainan, China).The isolates were more than 90% resistant to erythromycin, amoxicillin, ampicillin, and tetracycline.19.2% of the isolates were multi-resistant to more than 14 antibiotics.APEC of the same serotype isolated from Hainan Wenchang embryos have close relationships in the evolutionary tree of the core genome. Type O8 is the most prevalent serotype of APEC isolated from Wenchang chicken embryos (Hainan, China). The isolates were more than 90% resistant to erythromycin, amoxicillin, ampicillin, and tetracycline. 19.2% of the isolates were multi-resistant to more than 14 antibiotics. APEC of the same serotype isolated from Hainan Wenchang embryos have close relationships in the evolutionary tree of the core genome.
DOI: 10.6084/m9.figshare.28089744.v2
title: Epidemiological investigation and drug resistance analysis of avian pathogenic <i>Escherichia coli</i> (APEC) of Wenchang chickens in Hainan, China

description: Avian pathogenic <i>Escherichia coli</i> (APEC) is one of the major causes of poultry morbidity worldwide, severely reducing egg production and embryo hatchability in laying hens. Hainan Wenchang chicken is an important poultry breed in Hainan, China, and production of these chickens has been affected by APEC for a long time. In this study, in order to investigate the causes of low hatchability and a large number of weak chicks during the breeding of Wenchang chickens, a total of 130 strains of APEC were isolated from 591 chicken embryo samples collected from five large-scale farms of Wenchang chicken in Hainan area. The APEC isolates from Hainan Wenchang chicken embryos were analysed in terms of serotypes, drug resistance, genomes and evolutionary relationships. O8 was the main prevalent serotype of APEC from embryos, and the isolates were highly resistant to antibiotics and were multi-drug resistant. Of the isolates, 19.2% were resistant to 14 antibiotics with a resistance rate of more than 73%. The number of resistance genes carried by APEC isolates from embryos was stabilized at 53. The results of pan-genomic analysis showed that the genomes of Hainan Wenchang chicken embryo APEC isolates are concentrated in two evolutionary clusters, and isolates of the same serotype had extremely close evolutionary relationships. This study is the first large-scale isolation and analysis of APEC isolated from Wenchang chicken embryos, which can provide a reference for the prevention and control of APEC and antibiotic use in Hainan Wenchang chickens. Type O8 is the most prevalent serotype of APEC isolated from Wenchang chicken embryos (Hainan, China).The isolates were more than 90% resistant to erythromycin, amoxicillin, ampicillin, and tetracycline.19.2% of the isolates were multi-resistant to more than 14 antibiotics.APEC of the same serotype isolated from Hainan Wenchang embryos have close relationships in the evolutionary tree of the core genome. Type O8 is the most prevalent serotype of APEC isolated from Wenchang chicken embryos (Hainan, China). The isolates were more than 90% resistant to erythromycin, amoxicillin, ampicillin, and tetracycline. 19.2% of the isolates were multi-resistant to more than 14 antibiotics. APEC of the same serotype isolated from Hainan Wenchang embryos have close relationships in the evolutionary tree of the core genome.
DOI: 10.15468/dl.52e89v
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Material sample)"
 ]
 }
 },
 "TaxonKey is Fukomys amatus (Wroughton, 1907)",
 "Continent is one of (Africa)",
 "Year is greater than or equal to 1900"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032813-250525065834625/datasets/export for details.
DOI: 10.6084/m9.figshare.28089744.v1
title: Epidemiological investigation and drug resistance analysis of Avian pathogenic <i>Escherichia coli</i> (APEC) of Wenchang chickens in Hainan, China

description: Avian pathogenic <i>Escherichia coli</i> (APEC) is one of the major causes of poultry morbidity worldwide, severely reducing egg production and embryo hatchability in laying hens. Hainan Wenchang chicken is an important poultry breed in Hainan, China, and its culture has been affected by APEC for a long time. In this study, in order to investigate the causes of low hatchability and a large number of weak chicks during the breeding of Wenchang chicken, a total of 130 strains of APEC were isolated from 591 chicken embryo samples collected from five large-scale farms of Wenchang chicken in Hainan area. The APEC isolates from Hainan Wenchang chicken embryos were analyzed in terms of serotypes, drug resistance, genomes and evolutionary relationships. O8 was the main prevalent serotype of APEC from embryos, and the isolates were highly resistant to antibiotics and multi-drug resistant. 19.2% of the isolates were resistant to 14 antibiotics with a resistance rate of more than 73%. The number of resistance genes carried by APEC isolates from embryos was stabilized at 53. The results of pan-genomic analysis showed that the genomes of Hainan Wenchang chicken embryo APEC isolates would be concentrated in 2 evolutionary clusters, and the isolates of the same serotype had extremely close evolutionary relationships. This study is the first large-scale isolation and analysis of APEC isolated from Wenchang chicken embryos, which can provide a reference for the prevention and control of APEC and antibiotic use in Hainan Wenchang chickens.
DOI: 10.15468/dl.4xv4r3
title: Occurrence Download

description: A dataset containing 495276 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "OccurrenceStatus is Present",
 "TaxonKey is Erinaceus europaeus Linnaeus, 1758",
 "Year 1990-2023"
 ]
}

 The dataset includes 495276 records from 1353 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0032637-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.nfjkkw
title: Occurrence Download

description: A dataset containing 36120 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Senecio viscosus L."
 ]
}

 The dataset includes 36120 records from 209 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0021840-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.