cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29254280
title: <i>Enterobacterales</i> use capsules, transporters, mobile genetic elements, and other evolutionary adaptations to survive antibiotics exposure in the absence of resistance genes

description: Carbapenems and colistin are last-resort antibiotics used to manage difficult-to-treat infections caused by Gram-negative bacteria. However, resistance to these two antibiotics is rising globally, and there is limited knowledge on how pathogens evolve resistance when known resistance genes are absent. Whole-genome sequencing, transcriptomic profiling, and epigenomic analyses were performed. Phenotypic assays were used to evaluate the effects of various inhibitors on antibiotic susceptibility, while bioinformatic pipelines were used to characterize resistance determinants, virulence factors, and mobile genetic elements (MGEs). Phylogenetic analysis revealed widespread carriage of diverse resistance genes, particularly on plasmids of <i>K. pneumoniae</i>, while <i>Enterobacter</i> species possessed fewer known ARGs. Despite lacking known carbapenemase and <i>mcr</i> genes, several isolates demonstrated colistin or carbapenem resistance mediated by upregulation of efflux pumps, overproduction of capsular polysaccharides, mutations in outer membrane proteins, and potential lipopolysaccharide-modifying enzymes. Transcriptomic analysis revealed significant differential gene expression upon antibiotic exposure. Notably, genes encoding ABC transporter proteins were significantly downregulated (p-value &lt;0.0001, fold change &gt; 10), while genes encoding transposases were significantly upregulated (p-value &lt;0.0001, fold change &gt; 11). These changes underscore the critical role of transporters and MGEs in antibiotic resistance adaptation. In the absence of canonical carbapenemase and <i>mcr</i> genes, <i>K. pneumoniae</i> and <i>Enterobacter</i> species can deploy a spectrum of adaptive mechanisms, including efflux pumps, mobile elements, and altered outer membrane/capsule structures, to overcome colistin and carbapenem treatments. These findings support the need for ongoing surveillance of novel or underrecognized resistance mechanisms to preserve the efficacy of last-line antibiotics.
DOI: 10.6084/m9.figshare.29254280.v1
title: <i>Enterobacterales</i> use capsules, transporters, mobile genetic elements, and other evolutionary adaptations to survive antibiotics exposure in the absence of resistance genes

description: Carbapenems and colistin are last-resort antibiotics used to manage difficult-to-treat infections caused by Gram-negative bacteria. However, resistance to these two antibiotics is rising globally, and there is limited knowledge on how pathogens evolve resistance when known resistance genes are absent. Whole-genome sequencing, transcriptomic profiling, and epigenomic analyses were performed. Phenotypic assays were used to evaluate the effects of various inhibitors on antibiotic susceptibility, while bioinformatic pipelines were used to characterize resistance determinants, virulence factors, and mobile genetic elements (MGEs). Phylogenetic analysis revealed widespread carriage of diverse resistance genes, particularly on plasmids of <i>K. pneumoniae</i>, while <i>Enterobacter</i> species possessed fewer known ARGs. Despite lacking known carbapenemase and <i>mcr</i> genes, several isolates demonstrated colistin or carbapenem resistance mediated by upregulation of efflux pumps, overproduction of capsular polysaccharides, mutations in outer membrane proteins, and potential lipopolysaccharide-modifying enzymes. Transcriptomic analysis revealed significant differential gene expression upon antibiotic exposure. Notably, genes encoding ABC transporter proteins were significantly downregulated (p-value &lt;0.0001, fold change &gt; 10), while genes encoding transposases were significantly upregulated (p-value &lt;0.0001, fold change &gt; 11). These changes underscore the critical role of transporters and MGEs in antibiotic resistance adaptation. In the absence of canonical carbapenemase and <i>mcr</i> genes, <i>K. pneumoniae</i> and <i>Enterobacter</i> species can deploy a spectrum of adaptive mechanisms, including efflux pumps, mobile elements, and altered outer membrane/capsule structures, to overcome colistin and carbapenem treatments. These findings support the need for ongoing surveillance of novel or underrecognized resistance mechanisms to preserve the efficacy of last-line antibiotics.
DOI: 10.6084/m9.figshare.29818140
title: Function analysis of LIPI-4 in <i>Listeria monocytogenes</i> reveals a key role of flagella formation in the regulation of virulence

description: <i>Listeria</i> pathogenicity island 4 (LIPI-4), a newly discovered virulence gene cluster, plays a critical role in the development of central nervous system infections and maternal-fetal infections caused by <i>Listeria monocytogenes</i>. This study aimed to clarify the pathogenic role of LIPI-4 in <i>L. monocytogenes</i>. Our findings revealed that LIPI-4 is involved in the invasion and intracellular proliferation of <i>L. monocytogenes</i> in Caco-2, hCMEC/D3, HTR-8/Svneo, and RAW264.7 cells and facilitates its intercellular migration. Further investigations demonstrated that the deletion of LIPI-4 significantly reduces bacterial motility and impairs flagellum formation. Transcriptomic analysis further indicated that LIPI-4 regulates flagellum formation by modulating microbial metabolic processes and carbon metabolism. Our research demonstrates that LIPI-4 promotes flagellum formation through metabolic regulation, thereby enhancing <i>L. monocytogenes</i> colonization and cellular invasion. This discovery provides novel insights into the pathogenic mechanisms of <i>L. monocytogenes</i>.
DOI: 10.6084/m9.figshare.29818140.v2
title: Function analysis of LIPI-4 in <i>Listeria monocytogenes</i> reveals a key role of flagella formation in the regulation of virulence

description: <i>Listeria</i> pathogenicity island 4 (LIPI-4), a newly discovered virulence gene cluster, plays a critical role in the development of central nervous system infections and maternal-fetal infections caused by <i>Listeria monocytogenes</i>. This study aimed to clarify the pathogenic role of LIPI-4 in <i>L. monocytogenes</i>. Our findings revealed that LIPI-4 is involved in the invasion and intracellular proliferation of <i>L. monocytogenes</i> in Caco-2, hCMEC/D3, HTR-8/Svneo, and RAW264.7 cells and facilitates its intercellular migration. Further investigations demonstrated that the deletion of LIPI-4 significantly reduces bacterial motility and impairs flagellum formation. Transcriptomic analysis further indicated that LIPI-4 regulates flagellum formation by modulating microbial metabolic processes and carbon metabolism. Our research demonstrates that LIPI-4 promotes flagellum formation through metabolic regulation, thereby enhancing <i>L. monocytogenes</i> colonization and cellular invasion. This discovery provides novel insights into the pathogenic mechanisms of <i>L. monocytogenes</i>.
DOI: 10.6084/m9.figshare.30729422
title: Glutamate dehydrogenase 2 is required for virulence by facilitating fungal growth in the host hemocoel

description: <i>Metarhizium robertsii</i>, a fungal pathogen employed in pest biocontrol, can alkalize the surrounding environment, although the biological implications remain unclear. Here, we found that <i>M. robertsii</i> glutamate dehydrogenase 2 (<i>MrGDH2</i>) was responsible for alkalization during fungal growth on insect wings or media containing cuticle powder. Loss of <i>MrGDH2</i> function resulted in significantly reduced virulence during both cuticle-passing and cuticle-bypassing infections but did not affect appressorium formation or cuticle penetration. Deletion of <i>MrGDH2</i> failed to alkalize amino acid-containing media under carbon deprivation, leading to impaired mycelia growth and conidiation. Hemolymph carbohydrates were decreased during <i>M. robertsii</i> infection, and the Δ<i>Mrgdh2</i> mutant exhibited delayed fungal growth and impaired alkalization in hemolymph cultures. Notably, expression of <i>PacC</i>, a pH-responsive transcription factor critical for virulence, was downregulated in hyphal bodies of the Δ<i>Mrgdh2</i> mutant. Contrary to the established models in plant and human fungal pathogens, we demonstrate that Gdh2 activity is dispensable for appressorium formation but essential for fungal colonization in insect hemocoel during <i>M. robertsii</i> infection.
DOI: 10.6084/m9.figshare.30729422.v1
title: Glutamate dehydrogenase 2 is required for virulence by facilitating fungal growth in the host hemocoel

description: <i>Metarhizium robertsii</i>, a fungal pathogen employed in pest biocontrol, can alkalize the surrounding environment, although the biological implications remain unclear. Here, we found that <i>M. robertsii</i> glutamate dehydrogenase 2 (<i>MrGDH2</i>) was responsible for alkalization during fungal growth on insect wings or media containing cuticle powder. Loss of <i>MrGDH2</i> function resulted in significantly reduced virulence during both cuticle-passing and cuticle-bypassing infections but did not affect appressorium formation or cuticle penetration. Deletion of <i>MrGDH2</i> failed to alkalize amino acid-containing media under carbon deprivation, leading to impaired mycelia growth and conidiation. Hemolymph carbohydrates were decreased during <i>M. robertsii</i> infection, and the Δ<i>Mrgdh2</i> mutant exhibited delayed fungal growth and impaired alkalization in hemolymph cultures. Notably, expression of <i>PacC</i>, a pH-responsive transcription factor critical for virulence, was downregulated in hyphal bodies of the Δ<i>Mrgdh2</i> mutant. Contrary to the established models in plant and human fungal pathogens, we demonstrate that Gdh2 activity is dispensable for appressorium formation but essential for fungal colonization in insect hemocoel during <i>M. robertsii</i> infection.
DOI: 10.6084/m9.figshare.28237163
title: Restriction of mitochondrial oxidation of glutamine or fatty acids enhances intracellular growth of <i>Mycobacterium abscessus</i> in macrophages

description: <i>Mycobacterium abscessus</i> (Mab), a nontuberculous mycobacterium, is increasing in prevalence worldwide and causes treatment-refractory pulmonary diseases. However, how Mab rewires macrophage energy metabolism to facilitate its survival is poorly understood. We compared the metabolic profiles of murine bone marrow-derived macrophages (BMDMs) infected with smooth (S)- and rough (R)-type Mab using extracellular flux technology. Mab infection shifted BMDMs towards a more energetic phenotype, marked by increased oxidative phosphorylation (OXPHOS) and glycolysis, with a significantly greater enhancement in OXPHOS. This metabolic adaptation was characterized by enhanced ATP production rates, particularly in cells infected with S-type Mab, highlighting OXPHOS as a key energy source. Notably, Mab infection also modulated mitochondrial substrate preferences, increasing fatty acid oxidation capabilities while revealing significant changes in glutamine dependency and flexibility. R-type Mab infections exhibited a marked decrease in glutamine reliance but enhanced metabolic flexibility and capacity. Furthermore, targeting metabolic pathways related to glutamine and fatty acid oxidation exacerbated Mab growth within macrophages, suggesting these pathways play a protective role against infection. These insights advance our understanding of Mab’s impact on host cell metabolism and propose a novel avenue for therapeutic intervention. By manipulating host mitochondrial metabolism, we identify a potential host-directed therapeutic strategy against Mab, offering a promising alternative to conventional treatments beleaguered by drug resistance. This study underscores the importance of exploring metabolic interventions to combat Mab infection, paving the way for innovative approaches in the fight against this formidable pathogen.
DOI: 10.6084/m9.figshare.28237163.v1
title: Restriction of mitochondrial oxidation of glutamine or fatty acids enhances intracellular growth of <i>Mycobacterium abscessus</i> in macrophages

description: <i>Mycobacterium abscessus</i> (Mab), a nontuberculous mycobacterium, is increasing in prevalence worldwide and causes treatment-refractory pulmonary diseases. However, how Mab rewires macrophage energy metabolism to facilitate its survival is poorly understood. We compared the metabolic profiles of murine bone marrow-derived macrophages (BMDMs) infected with smooth (S)- and rough (R)-type Mab using extracellular flux technology. Mab infection shifted BMDMs towards a more energetic phenotype, marked by increased oxidative phosphorylation (OXPHOS) and glycolysis, with a significantly greater enhancement in OXPHOS. This metabolic adaptation was characterized by enhanced ATP production rates, particularly in cells infected with S-type Mab, highlighting OXPHOS as a key energy source. Notably, Mab infection also modulated mitochondrial substrate preferences, increasing fatty acid oxidation capabilities while revealing significant changes in glutamine dependency and flexibility. R-type Mab infections exhibited a marked decrease in glutamine reliance but enhanced metabolic flexibility and capacity. Furthermore, targeting metabolic pathways related to glutamine and fatty acid oxidation exacerbated Mab growth within macrophages, suggesting these pathways play a protective role against infection. These insights advance our understanding of Mab’s impact on host cell metabolism and propose a novel avenue for therapeutic intervention. By manipulating host mitochondrial metabolism, we identify a potential host-directed therapeutic strategy against Mab, offering a promising alternative to conventional treatments beleaguered by drug resistance. This study underscores the importance of exploring metabolic interventions to combat Mab infection, paving the way for innovative approaches in the fight against this formidable pathogen.
DOI: 10.6084/m9.figshare.29818140.v1
title: Function analysis of LIPI-4 in <i>listeria monocytogenes</i> reveals a key role of flagella formation in the regulation of virulence

description: <i>Listeria</i> Pathogenicity Island 4 (LIPI-4), a newly discovered virulence gene cluster, plays a critical role in the development of central nervous system infections and maternal-foetal infections caused by <i>Listeria monocytogenes</i>. This study aimed to clarify the pathogenic role of LIPI-4 in <i>L. monocytogenes</i>. Our findings revealed that LIPI-4 is involved in the invasion and intracellular proliferation of <i>L. monocytogenes</i> in Caco-2, hCMEC/D3, HTR-8/Svneo, and RAW264.7 cells, and facilitates its intercellular migration. Further investigations demonstrated that the deletion of LIPI-4 significantly reduces bacterial motility and impairs flagellum formation. Transcriptomic analysis further indicated that LIPI-4 regulates flagellum formation by modulating microbial metabolic processes and carbon metabolism. Our research demonstrates that LIPI-4 promotes flagellum formation through metabolic regulation, thereby enhancing <i>L. monocytogenes</i> colonization and cellular invasion. This discovery provides novel insights into the pathogenic mechanisms of <i>L. monocytogenes</i>.
DOI: 10.6084/m9.figshare.29041344
title: Multi-omics profiling of acute <i>Pseudomonas aeruginosa</i> pneumonia unmasks conventional NK cell depletion and stage-specific therapeutic targets

description: <i>Pseudomonas aeruginosa</i> (PA) is a key pathogen in hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), challenging clinical medicine. This study aims to elucidate the characteristics of the host’s innate immune response following inhalational PA infection. We developed a mouse model by aerosolized intratracheal inoculation with PA and conducted a comprehensive analysis at the protein, cellular, and gene expression levels. Protein analysis revealed a substantial increase in inflammatory proteins in the bronchoalveolar lavage fluid and serum, indicating a robust inflammatory response in the lungs and systemic circulation. Cellular investigations showed an increase in neutrophils, monocytes, and alveolar macrophages during infection, whereas NK cells showed a marked reduction from 5.88% pre-infection to 2.41% at 24 h (<i>p</i> = 0.0102) and 1.55% by 48 h (<i>p</i> = 0.0023). To assess gene expression changes, RNA-sequencing technology was employed to map the temporal shifts in the transcriptional profile of the host lung post-infection. We analysed the expression patterns and dynamic transcriptional characteristics of differentially expressed genes (DEGs), describing the inflammation progression. Importantly, Through the analysis of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, we observed the reduction in conventional natural killer (cNK) cells, rather than tissue-resident natural killer (trNK) cells in the early stages of PA infection. Sequential scRNA-seq analysis resolved NK-subset heterogeneity, revealing that cNK dominance (77.8% of total NK cells) under homeostasis collapsed to 9.2% within 24 h post-infection. Our findings establish cNK attrition as the earliest immune checkpoint failure in PA pneumonia and provide proof-of-concept for cNK-targeted immunotherapies to counteract lethal pulmonary infections. Keywords: <i>Pseudomonas aeruginosa</i>, aerosolized intratracheal inoculation, conventional NK cells, innate immunity, RNA-sequencing
DOI: 10.6084/m9.figshare.29041344.v1
title: Multi-omics profiling of acute <i>Pseudomonas aeruginosa</i> pneumonia unmasks conventional NK cell depletion and stage-specific therapeutic targets

description: <i>Pseudomonas aeruginosa</i> (PA) is a key pathogen in hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), challenging clinical medicine. This study aims to elucidate the characteristics of the host’s innate immune response following inhalational PA infection. We developed a mouse model by aerosolized intratracheal inoculation with PA and conducted a comprehensive analysis at the protein, cellular, and gene expression levels. Protein analysis revealed a substantial increase in inflammatory proteins in the bronchoalveolar lavage fluid and serum, indicating a robust inflammatory response in the lungs and systemic circulation. Cellular investigations showed an increase in neutrophils, monocytes, and alveolar macrophages during infection, whereas NK cells showed a marked reduction from 5.88% pre-infection to 2.41% at 24 h (<i>p</i> = 0.0102) and 1.55% by 48 h (<i>p</i> = 0.0023). To assess gene expression changes, RNA-sequencing technology was employed to map the temporal shifts in the transcriptional profile of the host lung post-infection. We analysed the expression patterns and dynamic transcriptional characteristics of differentially expressed genes (DEGs), describing the inflammation progression. Importantly, Through the analysis of single-cell RNA sequencing (scRNA-seq) datasets in public repositories, we observed the reduction in conventional natural killer (cNK) cells, rather than tissue-resident natural killer (trNK) cells in the early stages of PA infection. Sequential scRNA-seq analysis resolved NK-subset heterogeneity, revealing that cNK dominance (77.8% of total NK cells) under homeostasis collapsed to 9.2% within 24 h post-infection. Our findings establish cNK attrition as the earliest immune checkpoint failure in PA pneumonia and provide proof-of-concept for cNK-targeted immunotherapies to counteract lethal pulmonary infections. Keywords: <i>Pseudomonas aeruginosa</i>, aerosolized intratracheal inoculation, conventional NK cells, innate immunity, RNA-sequencing
DOI: 10.6084/m9.figshare.29597774
title: STA regulates succinylated AflM triggered by SCS to contribute to aflatoxin biosynthesis through the Ach1

description: <i>Aspergillus flavus</i> and its secondary metabolites, aflatoxins (AFs), especially aflatoxin B1 (AFB1), seriously affect agricultural production, food storage, and human health. Succinyl-CoA synthase ADP-forming subunit β (SCS) is involved in the synthesis of succinate from succinyl-CoA in the tricarboxylic acid cycle. In this study, we demonstrated that SCS led to decreased aflatoxin production. Bioassay results showed that deletion of <i>sucB</i> (the gene coding for SCS) led to increased succinyl-CoA accumulation. Catalyzed by succinyl transferase (STA), the increased amount of succinyl-CoA in Δ<i>sucB</i> leads to increased levels of global protein succinylation, which causes upregulation of AFB1 accumulation in Δ<i>sucB</i>. To elucidate the mechanism of increased AFB1 accumulation in Δ<i>sucB</i>, the relevant enzymes and metabolites involved in the aflatoxin biosynthesis pathway were examined through proteome and metabolome analyses. These data illustrate that the deletion of <i>sucB</i> results in an increase in (1’S, 5’S) – averufin catalyzed by AflK, (1’S)-averantin catalyzed by AflD, and aflatoxin G2/O- methylsterigmatocystin catalyzed by AflP. We also found that AflM is not only upregulated but also succinylated in Δ<i>sucB</i>; Ach1 (acetyl-CoA hydrolase, Ach1) is downregulated in Δ<i>sucB</i> and interacts with SCS. Therefore, we deduce a pathway of Ach1/STA-SCS-succinylated AflM for AFB1 biosynthesis, which provides knowledge for the control of <i>A. flavus</i> and AFs.
DOI: 10.6084/m9.figshare.29597774.v1
title: STA regulates succinylated AflM triggered by SCS to contribute to aflatoxin biosynthesis through the Ach1

description: <i>Aspergillus flavus</i> and its secondary metabolites, aflatoxins (AFs), especially aflatoxin B1 (AFB1), seriously affect agricultural production, food storage, and human health. Succinyl-CoA synthase ADP-forming subunit β (SCS) is involved in the synthesis of succinate from succinyl-CoA in the tricarboxylic acid cycle. In this study, we demonstrated that SCS led to decreased aflatoxin production. Bioassay results showed that deletion of <i>sucB</i> (the gene coding for SCS) led to increased succinyl-CoA accumulation. Catalyzed by succinyl transferase (STA), the increased amount of succinyl-CoA in Δ<i>sucB</i> leads to increased levels of global protein succinylation, which causes upregulation of AFB1 accumulation in Δ<i>sucB</i>. To elucidate the mechanism of increased AFB1 accumulation in Δ<i>sucB</i>, the relevant enzymes and metabolites involved in the aflatoxin biosynthesis pathway were examined through proteome and metabolome analyses. These data illustrate that the deletion of <i>sucB</i> results in an increase in (1’S, 5’S) – averufin catalyzed by AflK, (1’S)-averantin catalyzed by AflD, and aflatoxin G2/O- methylsterigmatocystin catalyzed by AflP. We also found that AflM is not only upregulated but also succinylated in Δ<i>sucB</i>; Ach1 (acetyl-CoA hydrolase, Ach1) is downregulated in Δ<i>sucB</i> and interacts with SCS. Therefore, we deduce a pathway of Ach1/STA-SCS-succinylated AflM for AFB1 biosynthesis, which provides knowledge for the control of <i>A. flavus</i> and AFs.