cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29932152.v1
title: Isopropyl paraben targets type III secretion to inhibit <i>salmonella enterica</i> serovar typhimurium infection

description: <i>Salmonella enterica</i>, a food- and water-borne pathogen, triggers food poisoning and enteric infections. The effectiveness of antibiotics against <i>Salmonella</i> infections is decreasing due to bacterial resistance. Developing novel antimicrobial agents is crucial and urgent. Here, we screened 550 natural compounds and found that isopropyl paraben (IPPB) effectively inhibited <i>Salmonella enterica</i> serovar Typhimurium (ST) invasion of host cells without impacting bacterial growth, reducing the risk of developing bacterial resistance. Further investigation revealed that IPPB bound to the regulatory protein HilD and inhibited the transcription of the type III protein secretion system 1 (T3SS-1) regulatory genes <i>hilD</i>, <i>hilC</i> and <i>rtsA</i>. This interference blocked the production of T3SS-1 effectors. Importantly, IPPB exerted certain therapeutic effects on both <i>G. mellonella</i> larvae and murine models infected with ST and improved the ST-induced gut microbiota dysbiosis in mice. These findings suggest that IPPB has potential as a novel antimicrobial agent, targeting the T3SS-1 of <i>Salmonella</i>.
DOI: 10.6084/m9.figshare.28919743
title: <i>Stenotrophomonas maltophilia</i> of clinical origin display higher temperature tolerance comparing with environmental isolates

description: <i>Stenotrophomonas maltophilia</i> is a gram-negative, multidrug-resistant, opportunistic human pathogen responsible for hard-to-treat infections in immunocompromised individuals. Besides being recognized as an important clinical pathogen, <i>S. maltophilia</i> is also widespread in the natural environment, with knowledge of the pathogenic potential of the environmental <i>S. maltophilia</i> pool still lacking. In this study, we aimed to identify the differences in virulence-related traits between clinical and environmental <i>S. maltophilia</i> isolates by assessing their genotypic and phenotypic features. For this purpose, 40 <i>S. maltophilia</i> isolates from natural environment and 34 clinical isolates obtained from patients were analysed. We observed a high degree of genotypic diversity among the isolates irrespective of their origin. Although antibiotic resistance- and virulence-related genes were more prevalent in the clinical isolates, the majority of the analysed genes were also present in the environmental isolates. Most importantly, the phenotypic features, specifically the ability to form biofilms and display twitching motility at human body temperature were predominantly characteristic to the clinical isolates. Our study indicates that adaptation to endure human body temperature is a feature strongly linked to <i>S. maltophilia</i> strains of clinical origin, and is significant when differentiating harmless environmental bacteria from pathogenic <i>S. maltophilia</i> isolates.
DOI: 10.6084/m9.figshare.28919743.v2
title: <i>Stenotrophomonas maltophilia</i> of clinical origin display higher temperature tolerance comparing with environmental isolates

description: <i>Stenotrophomonas maltophilia</i> is a gram-negative, multidrug-resistant, opportunistic human pathogen responsible for hard-to-treat infections in immunocompromised individuals. Besides being recognized as an important clinical pathogen, <i>S. maltophilia</i> is also widespread in the natural environment, with knowledge of the pathogenic potential of the environmental <i>S. maltophilia</i> pool still lacking. In this study, we aimed to identify the differences in virulence-related traits between clinical and environmental <i>S. maltophilia</i> isolates by assessing their genotypic and phenotypic features. For this purpose, 40 <i>S. maltophilia</i> isolates from natural environment and 34 clinical isolates obtained from patients were analysed. We observed a high degree of genotypic diversity among the isolates irrespective of their origin. Although antibiotic resistance- and virulence-related genes were more prevalent in the clinical isolates, the majority of the analysed genes were also present in the environmental isolates. Most importantly, the phenotypic features, specifically the ability to form biofilms and display twitching motility at human body temperature were predominantly characteristic to the clinical isolates. Our study indicates that adaptation to endure human body temperature is a feature strongly linked to <i>S. maltophilia</i> strains of clinical origin, and is significant when differentiating harmless environmental bacteria from pathogenic <i>S. maltophilia</i> isolates.
DOI: 10.6084/m9.figshare.29900323
title: Pathogenic mechanisms and molecular features of a novel UL2 gene-deficient duck enteritis virus endemic to China

description: Duck enteritis virus (DEV) was identified as the etiological agent responsible for an outbreak of morbidity and mortality in adult ducks on a farm in Jiangsu, China. Diagnostic approaches confirmed that the outbreak was caused by the highly pathogenic DEV-JS2024 isolate. The clinical progression of the disease, characterized by lethargy, anorexia, ocular discharge, and high mortality, was accompanied by extensive hemorrhagic lesions in critical organs such as the liver, spleen, lungs, and bursa of Fabricius, consistent with known signs of DEV infection. Genomic analysis of DEV-JS2024 revealed a 45% G+C content and 76 open reading frames. BLASTn analysis revealed that the genome of DEV-JS2024 shares the highest sequence similarity with the Chinese virulent strain CV and the DEV attenuated vaccine strain C-KCE in the database. These results indicate a close genetic relationship between DEV-JS2024 and both the virulent and attenuated strains, suggesting potential similarities in their genomic architecture. Comparative genomic analysis identified 28 nucleotide mutations, including 15 non-synonymous mutations potentially related to virulence factors. The study also highlighted the first reported 528 base pairs deletion in the <i>UL2</i> gene of a virulent strain, challenging its utility as a marker for distinguishing virulent from attenuated strains. Phylogenetic analysis suggested that DEV-JS2024 may result from recombination between the vaccine and virulent strains, further complicating our understanding of DEV pathogenicity. This study provides new insights into the molecular evolution of DEV and stresses the importance of continued genomic surveillance to enhance vaccine development and control measures for duck plague.
DOI: 10.6084/m9.figshare.29900323.v1
title: Pathogenic mechanisms and molecular features of a novel UL2 gene-deficient duck enteritis virus endemic to China

description: Duck enteritis virus (DEV) was identified as the etiological agent responsible for an outbreak of morbidity and mortality in adult ducks on a farm in Jiangsu, China. Diagnostic approaches confirmed that the outbreak was caused by the highly pathogenic DEV-JS2024 isolate. The clinical progression of the disease, characterized by lethargy, anorexia, ocular discharge, and high mortality, was accompanied by extensive hemorrhagic lesions in critical organs such as the liver, spleen, lungs, and bursa of Fabricius, consistent with known signs of DEV infection. Genomic analysis of DEV-JS2024 revealed a 45% G+C content and 76 open reading frames. BLASTn analysis revealed that the genome of DEV-JS2024 shares the highest sequence similarity with the Chinese virulent strain CV and the DEV attenuated vaccine strain C-KCE in the database. These results indicate a close genetic relationship between DEV-JS2024 and both the virulent and attenuated strains, suggesting potential similarities in their genomic architecture. Comparative genomic analysis identified 28 nucleotide mutations, including 15 non-synonymous mutations potentially related to virulence factors. The study also highlighted the first reported 528 base pairs deletion in the <i>UL2</i> gene of a virulent strain, challenging its utility as a marker for distinguishing virulent from attenuated strains. Phylogenetic analysis suggested that DEV-JS2024 may result from recombination between the vaccine and virulent strains, further complicating our understanding of DEV pathogenicity. This study provides new insights into the molecular evolution of DEV and stresses the importance of continued genomic surveillance to enhance vaccine development and control measures for duck plague.
DOI: 10.6084/m9.figshare.28192352
title: A lineage 1 branch porcine reproductive and respiratory syndrome virus live vaccine candidate provides broad cross-protection against HP-like PRRSV in piglets

description: Multiple porcine reproductive and respiratory syndrome virus (PRRSV) subtypes coinfect numerous pig farms in China, and commercial PRRSV vaccines offer limited cross-protection against heterologous strains. Our previous research confirmed that a PRRSV lineage 1 branch attenuated live vaccine (SD-R) provides cross-protection against HP-PRRSV, NADC30-like PRRSV and NADC34-like PRRSV. HP-PRRSV has undergone significant genetic variation following nearly two decades of evolution and has transformed into a subtype referred to as HP-like PRRSV, which also exhibits high pathogenicity. The effectiveness of immunising piglets with the SD-R strain to provide protection against infection with HP-like PRRSV remains uncertain. In the present study, we evaluated the protective effects of SD-R vaccine strains on DLF-challenged piglets. The results revealed that piglets challenged with DLF presented clinical symptoms such as continuous high fever and an obvious decrease in daily weight gain. Importantly, the piglets immunised with SD-R exhibited notable reductions in pathological damage, especially of decreases in DLF-induced thymic atrophy. Moreover, the serum of SD-R-immunised piglets strongly neutralised DLF, and the number of SD-R-vaccinated piglets demonstrating viraemia was greatly reduced. These results suggest that the PRRSV lineage 1 branch live vaccine candidate provides broad cross-protection against HP-like PRRSV in piglets.
DOI: 10.6084/m9.figshare.28919743.v1
title: <i>Stenotrophomonas maltophilia</i> of clinical origin display higher temperature tolerance comparing with environmental isolates

description: <i>Stenotrophomonas maltophilia</i> is a gram-negative, multidrug-resistant, opportunistic human pathogen responsible for hard-to-treat infections in immunocompromised individuals. Besides being recognized as an important clinical pathogen, <i>S. maltophilia</i> is also widespread in the natural environment, with knowledge of the pathogenic potential of the environmental <i>S. maltophilia</i> pool still lacking. In this study, we aimed to identify the differences in virulence-related traits between clinical and environmental <i>S. maltophilia</i> isolates by assessing their genotypic and phenotypic features. For this purpose, 40 <i>S. maltophilia</i> isolates from natural environment and 34 clinical isolates obtained from patients were analysed. We observed a high degree of genotypic diversity among the isolates irrespective of their origin. Although antibiotic resistance- and virulence-related genes were more prevalent in the clinical isolates, the majority of the analysed genes were also present in the environmental isolates. Most importantly, the phenotypic features, specifically the ability to form biofilms and display twitching motility at human body temperature were predominantly characteristic to the clinical isolates. Our study indicates that adaptation to endure human body temperature is a feature strongly linked to <i>S. maltophilia</i> strains of clinical origin, and is significant when differentiating harmless environmental bacteria from pathogenic <i>S. maltophilia</i> isolates.
DOI: 10.6084/m9.figshare.30294970
title: Reduction of extracellular vimentin in blood provides protection against SARS-CoV-2 infection

description: <i>In vitro</i> studies have repeatedly showed that extracellular vimentin (eVIM) promotes the penetration of viruses by acting as an adhesion factor, suggesting that reducing eVIM density in the blood could be an effective approach to treat viral infections. However, despite solid evidence, it has not been previously investigated whether eVIM plays a pathogenic role during viral infections <i>in vivo</i> experiments. Here, we provide <i>in vivo</i> evidence that eVIM plays a critical role during viral infections. The severity of COVID-19 in Roborovski SH101 hamsters was positively correlated with blood concentrations of eVIM during the infection period. The reduction of blood eVIM in the SARS-CoV-2-infected Roborovski SH101 hamster through intravenous injection of hzVSF-v13, a humanized anti-eVIM monoclonal antibody, dramatically improved disease manifestations, such as body weight reduction, body temperature, death rate, and more. It also inhibited the formation of blood clots and systemic inflammation compared to remdesivir or a SARS-CoV-2 neutralizing antibody (6D11F2). Histological examination confirmed the significantly better therapeutic efficacy of anti-eVIM compared to remdesivir or the neutralizing antibody. Quantification of SARS-CoV-2 in the hamsters’ lungs revealed that the viral titer in the anti-eVIM-treated groups was 77% to 80% lower than that in the infection group, while remdesivir and the neutralizing antibody resulted in reductions of 41.9% and 34.7% to 44.1%, respectively. We believe that this work provides a foundation for the development of hzVSF-v13 as an antiviral drug for COVID-19.
DOI: 10.6084/m9.figshare.30294970.v1
title: Reduction of extracellular vimentin in blood provides protection against SARS-CoV-2 infection

description: <i>In vitro</i> studies have repeatedly showed that extracellular vimentin (eVIM) promotes the penetration of viruses by acting as an adhesion factor, suggesting that reducing eVIM density in the blood could be an effective approach to treat viral infections. However, despite solid evidence, it has not been previously investigated whether eVIM plays a pathogenic role during viral infections <i>in vivo</i> experiments. Here, we provide <i>in vivo</i> evidence that eVIM plays a critical role during viral infections. The severity of COVID-19 in Roborovski SH101 hamsters was positively correlated with blood concentrations of eVIM during the infection period. The reduction of blood eVIM in the SARS-CoV-2-infected Roborovski SH101 hamster through intravenous injection of hzVSF-v13, a humanized anti-eVIM monoclonal antibody, dramatically improved disease manifestations, such as body weight reduction, body temperature, death rate, and more. It also inhibited the formation of blood clots and systemic inflammation compared to remdesivir or a SARS-CoV-2 neutralizing antibody (6D11F2). Histological examination confirmed the significantly better therapeutic efficacy of anti-eVIM compared to remdesivir or the neutralizing antibody. Quantification of SARS-CoV-2 in the hamsters’ lungs revealed that the viral titer in the anti-eVIM-treated groups was 77% to 80% lower than that in the infection group, while remdesivir and the neutralizing antibody resulted in reductions of 41.9% and 34.7% to 44.1%, respectively. We believe that this work provides a foundation for the development of hzVSF-v13 as an antiviral drug for COVID-19.
DOI: 10.6084/m9.figshare.28192352.v1
title: A lineage 1 branch porcine reproductive and respiratory syndrome virus live vaccine candidate provides broad cross-protection against HP-like PRRSV in piglets

description: Multiple porcine reproductive and respiratory syndrome virus (PRRSV) subtypes coinfect numerous pig farms in China, and commercial PRRSV vaccines offer limited cross-protection against heterologous strains. Our previous research confirmed that a PRRSV lineage 1 branch attenuated live vaccine (SD-R) provides cross-protection against HP-PRRSV, NADC30-like PRRSV and NADC34-like PRRSV. HP-PRRSV has undergone significant genetic variation following nearly two decades of evolution and has transformed into a subtype referred to as HP-like PRRSV, which also exhibits high pathogenicity. The effectiveness of immunising piglets with the SD-R strain to provide protection against infection with HP-like PRRSV remains uncertain. In the present study, we evaluated the protective effects of SD-R vaccine strains on DLF-challenged piglets. The results revealed that piglets challenged with DLF presented clinical symptoms such as continuous high fever and an obvious decrease in daily weight gain. Importantly, the piglets immunised with SD-R exhibited notable reductions in pathological damage, especially of decreases in DLF-induced thymic atrophy. Moreover, the serum of SD-R-immunised piglets strongly neutralised DLF, and the number of SD-R-vaccinated piglets demonstrating viraemia was greatly reduced. These results suggest that the PRRSV lineage 1 branch live vaccine candidate provides broad cross-protection against HP-like PRRSV in piglets.
DOI: 10.6084/m9.figshare.29986622
title: <i>Mesorhizobium huakuii</i> 7653 R regulates the endophytic bacterial communities and disease resistance pathways to promote clubroot resistance in <i>Brassica napus</i>

description: Clubroot is a global soilborne disease caused by <i>Plasmodiophora brassicae</i> that severely affects cruciferous crops. Currently, there are no effective control measures to completely eliminate pathogens in the field. Pot experiments have shown that treatment with <i>Mesorhizobium huakuii</i> 7653 R can relieve clubroot symptoms. However, whether <i>M. huakuii</i> 7653 R can be used in the field to control clubroot disease is unclear, and the mechanism of its resistance remains largely unknown. We conducted two seasons of field trials with <i>Brassica napus</i> and found that <i>M. huakuii</i> 7653 R treatment significantly reduced clubroot disease severity, and that the agronomic traits at the seedling, flowering, and harvesting stages were significantly improved compared to the control group. The average yield per hectare, thousand grain weight, and oil content increased by 83.1%, 10.4%, and 3.7%, respectively. <i>M. huakuii</i> 7653 R also enhanced the resistance and yield of the cruciferous plant <i>Brassica campestris</i> var. <i>purpuraria</i> to clubroot. We characterized the composition and structure of the endophytic microbiota using bacterial 16S sequencing, and showed that treatment with <i>M. huakuii</i> 7653 R shaped the structure of endophytic bacterial communities. The relative abundances of Actinobacteria and Bacteroidetes, which are resistant to oxidative stress, were enriched in the co-inoculation with <i>M. huakuii</i> 7653 R and <i>P. brassicae</i> on <i>B. napus</i>. Transcriptome data indicated that genes related to plant immunity, nitrogen uptake and metabolism were significantly up-regulated by co-inoculation with <i>M. huakuii</i> 7653 R and <i>P. brassicae</i>. Our findings provide a theoretical basis for the widespread application of <i>M. huakuii</i> 7653 R in clubroot biocontrol.
DOI: 10.6084/m9.figshare.29986622.v1
title: <i>Mesorhizobium huakuii</i> 7653 R regulates the endophytic bacterial communities and disease resistance pathways to promote clubroot resistance in <i>Brassica napus</i>

description: Clubroot is a global soilborne disease caused by <i>Plasmodiophora brassicae</i> that severely affects cruciferous crops. Currently, there are no effective control measures to completely eliminate pathogens in the field. Pot experiments have shown that treatment with <i>Mesorhizobium huakuii</i> 7653 R can relieve clubroot symptoms. However, whether <i>M. huakuii</i> 7653 R can be used in the field to control clubroot disease is unclear, and the mechanism of its resistance remains largely unknown. We conducted two seasons of field trials with <i>Brassica napus</i> and found that <i>M. huakuii</i> 7653 R treatment significantly reduced clubroot disease severity, and that the agronomic traits at the seedling, flowering, and harvesting stages were significantly improved compared to the control group. The average yield per hectare, thousand grain weight, and oil content increased by 83.1%, 10.4%, and 3.7%, respectively. <i>M. huakuii</i> 7653 R also enhanced the resistance and yield of the cruciferous plant <i>Brassica campestris</i> var. <i>purpuraria</i> to clubroot. We characterized the composition and structure of the endophytic microbiota using bacterial 16S sequencing, and showed that treatment with <i>M. huakuii</i> 7653 R shaped the structure of endophytic bacterial communities. The relative abundances of Actinobacteria and Bacteroidetes, which are resistant to oxidative stress, were enriched in the co-inoculation with <i>M. huakuii</i> 7653 R and <i>P. brassicae</i> on <i>B. napus</i>. Transcriptome data indicated that genes related to plant immunity, nitrogen uptake and metabolism were significantly up-regulated by co-inoculation with <i>M. huakuii</i> 7653 R and <i>P. brassicae</i>. Our findings provide a theoretical basis for the widespread application of <i>M. huakuii</i> 7653 R in clubroot biocontrol.
DOI: 10.6084/m9.figshare.29499282
title: Impact of virus-mediated bacterial interactions on acute gastroenteritis symptoms: A new scoring system for clinical assessment

description: Acute gastroenteritis (AGE) exerts a substantial healthcare burden and economic loss annually, mainly due to viral infections. The objective of the study was to elucidate the impact of the interactions between the AGE virus and gut microbiota on patient clinical symptoms, thereby facilitating the early diagnosis and treatment of AGE. Clinical information and fecal samples were collected from 289 AGE patients (exclude fungal, parasitic, and bacterial infections), of whom 23.5% were infected with AGE viruses. A scoring method was developed to assess the severity of virus-induced AGE in patients. The results indicate significant differences (<i>p</i> &lt; 0.05 indicates a significant difference, as determined by Kruskal–Wallis test, <i>p</i> = 0.03) in clinical symptom scores among the None-virus, Single-virus, and Dual-virus group. The Single-virus (14.82) and Dual-virus (15.33) groups exhibited more severe clinical symptom, with scoring values higher than None-virus group (12.40). Although significant differences in microbial community composition were observed between the Single-virus and Dual-virus groups (as determined by Adonis analysis, Variation = 0.11, <i>p</i> = 0.034), the diversity index (e.g. Chao1) did not significantly differ among the None-virus (288.14), Single-virus (345.74), and Dual-virus (282.70) groups. Notably, the patients with a higher <i>Prevotella</i>/<i>Bacteroide</i>s index displayed more severe clinical symptom, as the index in the Single-virus and Dual-virus groups was over 10-times greater than in the None-virus group. In summary, this study shows that clinical symptoms of patients with viral AGE could be exacerbated through promoting bacterial competitions, and this understanding would facilitate the early diagnosis and treatment of viral AGE.