cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.30287145
title: Immunodominant T cell responses to SARS-CoV-2 nucleocapsid protein in Omicron breakthrough infection post-inactivated vaccination

description: The widespread administration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines has not eliminated breakthrough infections due to immune evasion by viral mutations. Whether individuals with breakthrough infections can elicit effective T cell responses against the circulating Omicron JN.1 variant, and the specific immunodominant characteristics of these responses, remain to be elucidated. To address this, we recruited 93 individuals who had experienced early Omicron subvariant breakthrough infections following a three-dose regimen of inactivated SARS-CoV-2 vaccines. Intracellular cytokine staining was employed to evaluate T cell responses to the JN.1 nucleocapsid (N) protein overlapping peptide pool in peripheral blood mononuclear cells. Immunodominant epitopes were identified using a three-dimensional matrix screening approach. Human leukocyte antigen (HLA) blocking assays and truncated peptides stimulation assays were conducted to define the minimal epitope and HLA restriction. We found that breakthrough infections elicited robust CD4<sup>+</sup> and CD8<sup>+</sup> T cell responses specific to the JN.1 N protein, characterized by Th1/Tc1-skewed phenotype and preserved polyfunctionality. The immunodominant epitope profile of the N protein has undergone a significant transformation following breakthrough infection. New epitopes targeting mutated sites have emerged, while previously dominant epitopes, such as <i>N</i>-4 and <i>N</i>-66, no longer maintained their immunodominance. Instead, highly conserved epitope <i>N</i>-24 has risen as the most immunodominant target for CD4<sup>+</sup> T cells, restricted by HLA-DR, and with the minimal epitope identified as PKDHIGTRNPANNA. Our finding demonstrates that early Omicron strain breakthrough infections induce robust T cell responses targeting the circulating JN.1 subvariant and underscore the immunodominant features of these responses.
DOI: 10.6084/m9.figshare.30287145.v1
title: Immunodominant T cell responses to SARS-CoV-2 nucleocapsid protein in Omicron breakthrough infection post-inactivated vaccination

description: The widespread administration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines has not eliminated breakthrough infections due to immune evasion by viral mutations. Whether individuals with breakthrough infections can elicit effective T cell responses against the circulating Omicron JN.1 variant, and the specific immunodominant characteristics of these responses, remain to be elucidated. To address this, we recruited 93 individuals who had experienced early Omicron subvariant breakthrough infections following a three-dose regimen of inactivated SARS-CoV-2 vaccines. Intracellular cytokine staining was employed to evaluate T cell responses to the JN.1 nucleocapsid (N) protein overlapping peptide pool in peripheral blood mononuclear cells. Immunodominant epitopes were identified using a three-dimensional matrix screening approach. Human leukocyte antigen (HLA) blocking assays and truncated peptides stimulation assays were conducted to define the minimal epitope and HLA restriction. We found that breakthrough infections elicited robust CD4<sup>+</sup> and CD8<sup>+</sup> T cell responses specific to the JN.1 N protein, characterized by Th1/Tc1-skewed phenotype and preserved polyfunctionality. The immunodominant epitope profile of the N protein has undergone a significant transformation following breakthrough infection. New epitopes targeting mutated sites have emerged, while previously dominant epitopes, such as <i>N</i>-4 and <i>N</i>-66, no longer maintained their immunodominance. Instead, highly conserved epitope <i>N</i>-24 has risen as the most immunodominant target for CD4<sup>+</sup> T cells, restricted by HLA-DR, and with the minimal epitope identified as PKDHIGTRNPANNA. Our finding demonstrates that early Omicron strain breakthrough infections induce robust T cell responses targeting the circulating JN.1 subvariant and underscore the immunodominant features of these responses.
DOI: 10.6084/m9.figshare.29617818
title: Two strains of Toscana virus show different virulence and replication capacity in mice and cell culture models

description: Toscana virus (TOSV), belonging to <i>Phenuiviridae</i> family, is circulating in most Mediterranean countries and is transmitted to humans by infected female sand flies. While most infections are asymptomatic, TOSV is considered as a leading cause of meningitis and encephalitis in humans during summer. Three TOSV genotypes (named A, B, and C) have been identified, although no virus strain belonging to lineage C has been isolated so far. To date, the relationship between TOSV genetic diversity and viral pathogenicity or replication capacity remains unknown. This study aimed to compare two TOSV strains from either lineage A (TOSV-A) or B (TOSV-B) in several cell culture and two mouse models. We showed that TOSV-A replicated more efficiently in BSR and A549 cells, while TOSV-B had a replication advantage in human induced pluripotent stem cells differentiated in neural cells and LL-5 sand fly cells. <i>In vivo</i>, we were unable to detect any virus in the brains of immunocompetent C57BL/6JRj mice infected with either strain of TOSV. On the contrary, we showed that TOSV-A disseminated to the central nervous system of 129/Sv <i>ifnar</i> <sup>−/−</sup> mice unlike TOSV-B, despite higher viremia of TOSV-B and a greater dissemination of this strain in other organs. The reasons for these differences are not yet known, although we showed that the presence of TOSV neutralizing antibodies in serum was slightly delayed in TOSV-A-infected mice. Altogether, the data presented in this study provide new avenues to study TOSV-induced pathogenesis and ultimately unveil molecular viral determinants modulating TOSV replication capacity.
DOI: 10.6084/m9.figshare.29617818.v1
title: Two strains of Toscana virus show different virulence and replication capacity in mice and cell culture models

description: Toscana virus (TOSV), belonging to <i>Phenuiviridae</i> family, is circulating in most Mediterranean countries and is transmitted to humans by infected female sand flies. While most infections are asymptomatic, TOSV is considered as a leading cause of meningitis and encephalitis in humans during summer. Three TOSV genotypes (named A, B, and C) have been identified, although no virus strain belonging to lineage C has been isolated so far. To date, the relationship between TOSV genetic diversity and viral pathogenicity or replication capacity remains unknown. This study aimed to compare two TOSV strains from either lineage A (TOSV-A) or B (TOSV-B) in several cell culture and two mouse models. We showed that TOSV-A replicated more efficiently in BSR and A549 cells, while TOSV-B had a replication advantage in human induced pluripotent stem cells differentiated in neural cells and LL-5 sand fly cells. <i>In vivo</i>, we were unable to detect any virus in the brains of immunocompetent C57BL/6JRj mice infected with either strain of TOSV. On the contrary, we showed that TOSV-A disseminated to the central nervous system of 129/Sv <i>ifnar</i> <sup>−/−</sup> mice unlike TOSV-B, despite higher viremia of TOSV-B and a greater dissemination of this strain in other organs. The reasons for these differences are not yet known, although we showed that the presence of TOSV neutralizing antibodies in serum was slightly delayed in TOSV-A-infected mice. Altogether, the data presented in this study provide new avenues to study TOSV-induced pathogenesis and ultimately unveil molecular viral determinants modulating TOSV replication capacity.
DOI: 10.6084/m9.figshare.29875401
title: The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the emergency department

description: Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion of anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, <i>p</i> &lt; 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance <i>p</i> &lt; 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.
DOI: 10.6084/m9.figshare.29875401.v2
title: The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the emergency department

description: Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion of anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, <i>p</i> &lt; 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance <i>p</i> &lt; 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.
DOI: 10.6084/m9.figshare.28112042.v1
title: Roles and mechanisms of <i>gapA</i> and <i>gap</i>-encoded proteins in <i>cronobacter sakazakii</i> adhesion to and invasion of intestinal cells and neonatal rats

description: <i>Cronobacter sakazakii</i> (<i>C. sakazakii</i>) is a foodborne pathogen whose initial process involves intestinal cell adhesion mediated by numerous virulence factors encoded in various genes. The key metabolic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, also known as GapA), is encoded by <i>gapA</i> in the glycolysis pathway and acts as an adhesin in some bacteria. In <i>C. sakazakii</i>, there is also a key enzyme in the gluconeogenesis pathway, Gap, with type I GAPDH and erythrose-4-phosphate dehydrogenase activities and encoded by <i>gap</i>. This study aimed to investigate the virulence properties of GapA and Gap of <i>C. sakazakii</i> in adhesion to and invasion of HCT-8 and HIEC-6 cells and damage to the colon and brain of neonatal rats, by gene silencing. In addition, the role of both recombinant proteins in intestinal cell adhesion and invasion was investigated, and their role in inducting inflammatory cytokine expression was assessed by ELISA and Western blot. Silencing <i>gapA</i> or <i>gap</i> decreased the viability and swimming motility of bacterial cells and reduced bacterial adhesion to and invasion of both types of intestinal cells. Both recombinant proteins contributed to <i>C. sakazakii</i> adhesion in both cells, enhanced protein phosphorylation of NF-κB, and induced inflammatory cytokine expression. Finally, silenced expression of GapA and Gap also weakened bacterial damage to the brain and colon of neonatal rats. In conclusion, we demonstrated for the first time the virulence properties of GapA and Gap in <i>C. sakazakii</i> adhesion to and invasion of intestinal cells and neonatal rats and induction of inflammatory responses.
DOI: 10.6084/m9.figshare.28623501
title: Multifaceted quorum-sensing inhibiting activity of 3-(Benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one mitigates <i>Pseudomonas aeruginosa</i> virulence

description: As antibiotic resistance escalates into a global health crisis, novel therapeutic approaches against infectious diseases are in urgent need. <i>Pseudomonas aeruginosa</i>, an adaptable opportunistic pathogen, poses substantial challenges in treating a range of infections. The quorum-sensing (QS) system plays a pivotal role in orchestrating the production of a large set of virulence factors in a cell density-dependent manner, and the anti-virulence strategy targeting QS may show huge potential. Here, we present a comprehensive investigation into the potential of the synthesized compound 3-(benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one (OZDO, C<sub>10</sub>H<sub>9</sub>NO<sub>4</sub>) as a QS inhibitor to curb the virulence of <i>P. aeruginosa</i>. By employing an integrated approach encompassing <i>in silico</i> screening, <i>in vitro</i> and <i>in vivo</i> functional identification, we elucidated the multifaceted effects of OZDO. Molecular docking predicted that OZDO interfered with three core regulatory proteins of <i>P. aeruginosa</i> QS system. Notably, OZDO exhibited significant inhibition on the production of pyocyanin, rhamnolipid and extracellular proteases, biofilm formation, and cell motilities of <i>P. aeruginosa</i>. Transcriptomic analysis and quantitative real-time PCR displayed the down-regulation of QS-controlled genes in OZDO-treated PAO1, reaffirming the QS-inhibition activity of OZDO. <i>In vivo</i> assessments using a <i>Caenorhabditis elegans</i>-infection model demonstrated OZDO mitigated <i>P. aeruginosa</i> pathogenicity, particularly against the hypervirulent strain PA14. Moreover, OZDO in combination with polymyxin B and aztreonam presented a promising avenue for innovative anti-infective therapy. Our study sheds light on the multifaceted potential of OZDO as an anti-virulence agent and its significance in combating <i>P. aeruginosa</i>-associated infections.
DOI: 10.6084/m9.figshare.28623501.v1
title: Multifaceted quorum-sensing inhibiting activity of 3-(Benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one mitigates <i>Pseudomonas aeruginosa</i> virulence

description: As antibiotic resistance escalates into a global health crisis, novel therapeutic approaches against infectious diseases are in urgent need. <i>Pseudomonas aeruginosa</i>, an adaptable opportunistic pathogen, poses substantial challenges in treating a range of infections. The quorum-sensing (QS) system plays a pivotal role in orchestrating the production of a large set of virulence factors in a cell density-dependent manner, and the anti-virulence strategy targeting QS may show huge potential. Here, we present a comprehensive investigation into the potential of the synthesized compound 3-(benzo[d][1,3]dioxol-4-yl)oxazolidin-2-one (OZDO, C<sub>10</sub>H<sub>9</sub>NO<sub>4</sub>) as a QS inhibitor to curb the virulence of <i>P. aeruginosa</i>. By employing an integrated approach encompassing <i>in silico</i> screening, <i>in vitro</i> and <i>in vivo</i> functional identification, we elucidated the multifaceted effects of OZDO. Molecular docking predicted that OZDO interfered with three core regulatory proteins of <i>P. aeruginosa</i> QS system. Notably, OZDO exhibited significant inhibition on the production of pyocyanin, rhamnolipid and extracellular proteases, biofilm formation, and cell motilities of <i>P. aeruginosa</i>. Transcriptomic analysis and quantitative real-time PCR displayed the down-regulation of QS-controlled genes in OZDO-treated PAO1, reaffirming the QS-inhibition activity of OZDO. <i>In vivo</i> assessments using a <i>Caenorhabditis elegans</i>-infection model demonstrated OZDO mitigated <i>P. aeruginosa</i> pathogenicity, particularly against the hypervirulent strain PA14. Moreover, OZDO in combination with polymyxin B and aztreonam presented a promising avenue for innovative anti-infective therapy. Our study sheds light on the multifaceted potential of OZDO as an anti-virulence agent and its significance in combating <i>P. aeruginosa</i>-associated infections.
DOI: 10.6084/m9.figshare.29875401.v1
title: The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the Emergency department

description: Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion for anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, <i>p</i> &lt; 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance <i>p</i> &lt; 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.
DOI: 10.6084/m9.figshare.28112042
title: Roles and mechanisms of <i>gapA</i> and <i>gap</i>-encoded proteins in <i>cronobacter sakazakii</i> adhesion to and invasion of intestinal cells and neonatal rats

description: <i>Cronobacter sakazakii</i> (<i>C. sakazakii</i>) is a foodborne pathogen whose initial process involves intestinal cell adhesion mediated by numerous virulence factors encoded in various genes. The key metabolic enzyme, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, also known as GapA), is encoded by <i>gapA</i> in the glycolysis pathway and acts as an adhesin in some bacteria. In <i>C. sakazakii</i>, there is also a key enzyme in the gluconeogenesis pathway, Gap, with type I GAPDH and erythrose-4-phosphate dehydrogenase activities and encoded by <i>gap</i>. This study aimed to investigate the virulence properties of GapA and Gap of <i>C. sakazakii</i> in adhesion to and invasion of HCT-8 and HIEC-6 cells and damage to the colon and brain of neonatal rats, by gene silencing. In addition, the role of both recombinant proteins in intestinal cell adhesion and invasion was investigated, and their role in inducting inflammatory cytokine expression was assessed by ELISA and Western blot. Silencing <i>gapA</i> or <i>gap</i> decreased the viability and swimming motility of bacterial cells and reduced bacterial adhesion to and invasion of both types of intestinal cells. Both recombinant proteins contributed to <i>C. sakazakii</i> adhesion in both cells, enhanced protein phosphorylation of NF-κB, and induced inflammatory cytokine expression. Finally, silenced expression of GapA and Gap also weakened bacterial damage to the brain and colon of neonatal rats. In conclusion, we demonstrated for the first time the virulence properties of GapA and Gap in <i>C. sakazakii</i> adhesion to and invasion of intestinal cells and neonatal rats and induction of inflammatory responses.
DOI: 10.6084/m9.figshare.29567345
title: Carnosol attenuates <i>Acinetobacter baumannii</i> virulence by interfering with indole-mediated quorum sensing

description: Many bacterial pathogens utilize quorum sensing (QS) signals to modulate the biological functions in a cell density-dependent manner. <i>Acinetobacter baumannii</i> is a harmful pathogen and a major cause of hospital-acquired infections due to its severe drug-resistance and pathogenic nature. Therefore, the development of innovative antibacterial strategies for <i>A. baumannii</i> infections is important. Earlier studies have proved that <i>A. baumannii</i> utilizes N-acyl-L-homoserine lactones (AHLs) and indole signalling systems to modulate its biological functions and virulence. Here, we report that carnosol, which is isolated from <i>Salvia officinalis</i> L. (<i>S. officinalis</i>), inhibited the pathogenicity of <i>A. baumannii</i> by interfering with indole-mediated quorum sensing. Phenotypic and virulence experiments have revealed that carnosol decreased the formation of biofilms, motility, and cytotoxicity of <i>A. baumannii</i>, without affecting its growth rate. Genetic and biochemical analysis results showed that carnosol reduced the regulatory effect of AbiR on the transcription of target genes by inhibiting the binding of AbiR to the promoters of these genes. Our results suggest that the indole QS system of <i>A. baumannii</i> could be used as a new target and that carnosol might be developed as a new anti-virulence agent against <i>A. baumannii</i> infections.