mSphere最新文献

{"title":"The transfer of antibiotic resistance genes between evolutionarily distant bacteria.","authors":"Marcos Parras-Moltó, David Lund, Stefan Ebmeyer, D G Joakim Larsson, Anna Johnning, Erik Kristiansson","doi":"10.1128/msphere.00114-25","DOIUrl":"10.1128/msphere.00114-25","url":null,"abstract":"<p><p>Infections from antibiotic-resistant bacteria threaten human health globally. Resistance is often caused by mobile antibiotic resistance genes (ARGs) shared horizontally between bacterial genomes. Many ARGs originate from environmental and commensal bacteria and are transferred between divergent bacterial hosts before they reach pathogens. This process remains, however, poorly understood, which complicates the development of countermeasures that reduce the spread of ARGs. In this study, we aimed to systematically analyze the ARGs transferred between the most evolutionarily distant bacteria, defined here based on their phylum. We implemented an algorithm that identified inter-phylum transfers (IPTs) by combining ARG-specific phylogenetic trees with the taxonomy of the bacterial hosts. From the analysis of almost 1 million ARGs identified in >400,000 bacterial genomes, we identified 661 IPTs, which included transfers between all major bacterial phyla. The frequency of IPTs varies substantially between ARG classes and was highest for the aminoglycoside resistance gene AAC(3), while the levels for beta-lactamases were generally lower. ARGs involved in IPTs also differed between phyla, where, for example, tetracycline ARGs were commonly transferred between Firmicutes and Proteobacteria, but rarely between Actinobacteria and Proteobacteria. The results, furthermore, show that conjugative systems are seldom shared between bacterial phyla, suggesting that other mechanisms drive the dissemination of ARGs between divergent hosts. We also show that bacterial genomes involved in IPTs of ARGs are either over- or underrepresented in specific environments. These IPTs were also found to be more recent compared to transfers associated with bacteria isolated from water, soil, and sediment. While macrolide and tetracycline ARGs involved in IPTs almost always were >95% identical between phyla, corresponding β-lactamases showed a median identity of <60%. We conclude that inter-phylum transfer is recurrent, and our results offer new insights into how ARGs are disseminated between evolutionarily distant bacteria.</p><p><strong>Importance: </strong>Antibiotic-resistant infections pose a growing threat to global health. This study reveals how genes conferring antibiotic resistance can move between bacteria that belong to different phyla lineages previously thought to be too evolutionarily distant for frequent gene exchange. By analyzing nearly 1 million resistance genes from over 400,000 bacterial genomes, the researchers uncovered hundreds of inter-phylum transfer events, exposing surprising patterns in how different classes of resistance genes spread. The findings highlight that conjugative systems are less common than expected in cross-phyla transfers and suggest that alternative mechanisms may play key roles. This new understanding of how resistance genes leap between vastly different bacterial groups can inform strategies to slow the emergence of drug-resistan","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0011425"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188727/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144208941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Altered nasal and oral microbiomes define pediatric sickle cell disease.","authors":"Audra L Crouch, Beatrice M Severance, Susan Creary, Darryl Hood, Michael Bailey, Asuncion Mejias, Octavio Ramilo, Michelle Gillespie, Stefanie Ebelt, Vivien Sheehan, Benjamin T Kopp, Matthew Z Anderson","doi":"10.1128/msphere.00137-25","DOIUrl":"10.1128/msphere.00137-25","url":null,"abstract":"<p><p>Sickle cell disease (SCD) is a chronic blood disorder that disrupts multiple organ systems and can lead to severe morbidity. Persistent and acute symptoms caused by immune system dysregulation in individuals with SCD could contribute to disease either directly or indirectly via dysbiosis of commensal microbes and increased susceptibility to infection. Here, we explored the nasal and oral microbiomes of children with SCD (cwSCD) to uncover potential dysbiotic associations with the blood disorder. Microbiota collected from nasal and oral swabs of 40 cwSCD were compared to eight healthy siblings using shotgun metagenomic sequencing. Commensal taxa were present at similar levels in the nasal and oral microbiome of both groups. However, the nasal microbiomes of cwSCD contained a higher prevalence of Pseudomonadota species, including pathobionts such as <i>Yersinia enterocolitica</i> and <i>Klebsiella pneumoniae</i>. Furthermore, the oral microbiome of cwSCD displayed lower α-diversity and fewer commensal and pathobiont species compared to the healthy siblings. Thus, subtle but notable shifts seem to exist in the nasal and oral microbiomes of cwSCD, suggesting an interaction between SCD and the microbiome that may influence health outcomes.</p><p><strong>Importance: </strong>The oral and nasal cavities are susceptible to environmental exposures including pathogenic microbes. In individuals with systemic disorders, antibiotic exposure, changes to the immune system, or changes to organ function could influence the composition of the microbes at these sites and the overall health of individuals. Children with sickle cell disease (SCD) commonly experience respiratory infections, such as pneumonia or sinusitis, and may have increased susceptibility to infection because of disrupted microbiota at these body sites. We found that children with SCD (cwSCD) had more pathobiont bacteria in the nasal cavity and reduced bacterial diversity in the oral cavity compared to their healthy siblings. Defining when, why, and how these changes occur in cwSCD could help identify specific microbial signatures associated with susceptibility to infection or adverse outcomes, providing insights into personalized treatment strategies and preventive measures.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0013725"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143972379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota.","authors":"Sromona D Mukherjee, Mangesh Suryavanshi, John Knight, Dirk Lange, Aaron W Miller","doi":"10.1128/msphere.00913-24","DOIUrl":"10.1128/msphere.00913-24","url":null,"abstract":"<p><p>The gut microbiota is critical for neutralizing dietary toxins. Oxalate is a toxin commonly produced by plants to deter herbivory and is widely consumed in the human diet. Excess levels of systemic or urinary oxalate increase risk of multiple urologic and cardiometabolic diseases. The current study employed multiple amplicon-based and shotgun metagenomic methodologies, alongside comparative phylogenetic analyses, to interrogate evolutionary radiation surrounding microbial oxalate degradation within the human gut microbiome. In conservative genome-based estimates, over 30% of gut microbial species harbored at least one oxalate-handling gene, with the specific pathways used dependent on bacterial phylum. Co-occurrence analyses revealed interactions between specialist genes that can metabolize oxalate or its by-products, but not multi-functional genes that can act in more than one oxalate-related pathway. Specialization was rare at the genome level. Amplicon-based metagenomic sequencing of the oxalate-degrading gene, formyl-CoA transferase (<i>frc</i>), coupled with molecular clock phylogenetic analyses are indicative of rapid evolutionary divergence, constrained by phylum. This was corroborated by paired analyses of non-synonymous to synonymous substitutions (dN/dS ratios), which pointed toward neutral to positive selection. Sequence similarity network analyses of <i>frc</i> sequences suggest extensive horizontal gene transferring has occurred with the <i>frc</i> gene, which may have facilitated rapid divergence. The <i>frc</i> gene was primarily allocated to the Pseudomonodota phylum, particularly the <i>Bradyrhizobium</i> genus, which is a species capable of utilizing oxalate as a sole carbon and energy source. Collectively evidence provides strong support that, for oxalate metabolism, evolutionary selection occurs at the gene level, through horizontal gene transfer, rather than at the species level.IMPORTANCEA critical function of the gut microbiota is to neutralize dietary toxins, such as oxalate, which is highly prevalent in plant-based foods and is not degraded by host enzymes. However, little is known about the co-evolutionary patterns of plant toxins and the mammalian gut microbiota, which are expected to exhibit features of an evolutionary arms race. In the current work, we present molecular evidence that microbial genes for oxalate degradation are highly prevalent in humans, potentially driven by extensive horizontal gene transfer events. Phylogenetic analyses reveal that oxalate-degrading genes are under a positive selection pressure and have historically undergone rapid diversification events, which has led to diverse ecological strategies for handling oxalate by gut bacteria. Collectively, data shed light on potential evolutionary relationships between the diet and the gut microbiota that occur relatively independently of the mammalian host.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0091324"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033200","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cyanoexosortase B is essential for motility, biofilm formation, and scytonemin production in a filamentous cyanobacterium.","authors":"Gabriel A Parrett, Daniel H Haft, Maida Ruiz, Ferran Garcia-Pichel, Christopher C Ebmeier, Douglas D Risser","doi":"10.1128/msphere.01006-24","DOIUrl":"10.1128/msphere.01006-24","url":null,"abstract":"<p><p>Exosortases are involved in trafficking proteins containing PEP-CTERM domains to the exterior of gram-negative bacterial cells. The role of these proteins in cyanobacteria, where such homologs are common, has not been defined. The filamentous cyanobacterium <i>Nostoc punctiforme</i> contains a single putative exosortase, designated cyanoexosortase B (CrtB), implicated by previous work both in motility and in the production of the UV-absorbing pigment, scytonemin. To determine the role of <i>crtB</i> in <i>N. punctiforme</i>, a <i>crtB</i>-deletion strain (Δ<i>crtB</i>) was generated. Δ<i>crtB</i> presented the loss of motility, biofilm formation, and scytonemin production. In the case of motility, the Δ<i>crtB</i> mutant exhibited a specific defect in the ability of hormogonia (specialized motile filaments) to adhere to hormogonium polysaccharide (HPS), and several PEP-CTERM proteins expressed in motile hormogonia were differentially abundant in the exoproteome of the wild-type compared with the Δ<i>crtB</i> strain. These results are consistent with the hypothetical role of CrtB in the processing and export of PEP-CTERM proteins that play a critical role in stabilizing the interaction between the filament surface and HPS to facilitate motility and biofilm formation. In the case of scytonemin-the late biosynthetic steps of which occur in the periplasm and whose operon contains several putative PEP-CTERM proteins-Δ<i>crtB</i> failed to produce it. Given the abundance of putative PEP-CTERM proteins encoded in the <i>N. punctiforme</i> genome and the fact that this study only associates a fraction of them with biological functions, it seems likely that CrtB may play an important role in other biological processes in cyanobacteria.IMPORTANCEIn gram-negative bacteria, exosortases facilitate the trafficking of proteins to the exterior of the cell where they have been implicated in stabilizing the association of extracellular polymeric substances (EPS) with the cell surface to facilitate biofilm formation and flocculation, but the role of exosortases in cyanobacteria has not been explored. Here, we characterize the role of cyanoexosortase B (CrtB) in the filamentous cyanobacterium <i>Nostoc punctiforme</i>, demonstrating that <i>crtB</i> is essential for motility, biofilm formation, and the production of the sunscreen pigment scytonemin. These findings have important implications for understanding motility and biofilm formation in filamentous cyanobacteria as well as efforts toward the heterologous production of scytonemin in non-native hosts.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0100624"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188702/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144036516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Type I-E* CRISPR-Cas of <i>Klebsiella pneumoniae</i> upregulates bacterial virulence by targeting endogenous histidine utilization system.","authors":"Jieying Li, Yuxiao Liu, Jingsi Jiang, Fang Chen, Nan Zhang, Xun Kang, Lin Liu, Yingjuan Wang, Qianfeng Xia, Chuanlong Zhu, Dai Kuang","doi":"10.1128/msphere.00215-25","DOIUrl":"10.1128/msphere.00215-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; is a globally recognized microbial pathogen with significant clinical impact. The bacterium harbors the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, which provide adaptive immunity against invading foreign nucleic acids. Recent studies suggest that certain CRISPR-Cas systems can regulate endogenous genes, influencing bacterial virulence. However, their role in regulating pathogenicity in &lt;i&gt;K. pneumoniae&lt;/i&gt; remains poorly understood. This study investigates the regulatory role of the type I-E* CRISPR-Cas system in a hypervirulent &lt;i&gt;K. pneumoniae&lt;/i&gt; strain, focusing on its impact on histidine metabolism and pathogenicity. Transcriptome analyses identified differentially expressed genes (DEGs) between the &lt;i&gt;casABECD&lt;/i&gt;-deletion and wild-type strains, including significant upregulation of the histidine utilization (Hut) operon and downregulation of biofilm-related genes. These molecular changes resulted in enhanced histidine metabolic activity, reduced biofilm formation, attenuated virulence in A549 lung epithelial cells, and improved survival of &lt;i&gt;Galleria mellonella&lt;/i&gt;, as validated through phenotypic and virulence assays. Our bioinformatic analysis indicated that the CRISPR-Cas system in &lt;i&gt;K. pneumoniae&lt;/i&gt; targets the &lt;i&gt;hutT&lt;/i&gt; sequence, which is part of the Hut operon. Furthermore, the overexpression of &lt;i&gt;hutT&lt;/i&gt; mitigated CRISPR-Cas-mediated repression of the Hut operon, as observed in virulence assays, while simultaneous deletion of &lt;i&gt;hutH&lt;/i&gt; and &lt;i&gt;casABECD&lt;/i&gt; restored the reduced virulence in the Δ&lt;i&gt;casABECD&lt;/i&gt; strain. Additionally, deletion of &lt;i&gt;casABECD&lt;/i&gt; significantly enhances the growth of the strain in medium with histidine as the sole carbon source, highlighting the intricate regulatory role of the CRISPR-Cas system in metabolic adaptation. Collectively, these findings uncover a novel role for the CRISPR-Cas system in regulating metabolic pathways and virulence in hypervirulent &lt;i&gt;K. pneumoniae&lt;/i&gt;.&lt;b&gt;IMPORTANCE&lt;/b&gt;Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are primarily recognized for their roles in adaptive immunity against foreign genetic elements in bacteria. However, emerging evidence indicates that these systems can also regulate endogenous genes, thereby influencing bacterial physiology and virulence. In this study, we demonstrate that the type I-E* CRISPR-Cas system in &lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; targets the &lt;i&gt;hutT&lt;/i&gt; gene, a critical component of the histidine utilization (Hut) pathway. This targeting potentially impacts &lt;i&gt;hutT&lt;/i&gt; transcription and alters the expression of other &lt;i&gt;hut&lt;/i&gt; genes, ultimately enhancing bacterial virulence. Our findings reveal a previously unrecognized regulatory mechanism through which CRISPR-Cas systems facilitate metabolic adaptation and pathogenicity in &lt;i&gt;K. pneumoniae&lt;/i&gt;. This study broadens our understanding of the multifaceted roles of CRISPR-Cas systems in ","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0021525"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188710/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144094397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.","authors":"Catherine A Pfister, Johanna Berlinghof, Maximiliana Bogan, Ulisse Cardini, Angélique Gobet, Pauline Hamon-Giraud, Jessica Hart, Natalia Jimenez, Anne Siegel, Emma Stanfield, Marine Vallet, Catherine Leblanc, Coralie Rousseau, François Thomas, Willem Stock, Simon M Dittami","doi":"10.1128/msphere.00996-24","DOIUrl":"10.1128/msphere.00996-24","url":null,"abstract":"<p><p>Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host's unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in <i>Nereocystis luetkeana</i>-associated microbes, while only <i>Ascophyllum nodosum</i>-associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, <i>Flavobacteriia</i> showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host's metabolism and tested this inference by analyzing the genomes of both the seaweed <i>Ectocarpus subulatus</i> and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean.</p><p><strong>Importance: </strong>We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for <i>Flavobacteriia</i> in the phylum <i>Bacteroidota</i>. Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0099624"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144199671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual use and gain-of-function research: a significant endeavor with biosecurity imperatives.","authors":"James Giordano, Diane DiEuliis","doi":"10.1128/msphere.00289-25","DOIUrl":"10.1128/msphere.00289-25","url":null,"abstract":"<p><p>The current U.S. administration has recently proposed a pause on all domestic gain-of-function (GoF) research in order to fully revise existing policy. However, domestic controls on GoF research cannot mandate that other nations follow suit and thus do not prohibit non-compliant nations from engaging in such work. In fact, such national constraints may facilitate opportunities for competitor and adversarial nations (and non-state actors) to advance efforts in this space toward nefarious applications. Moreover, certain groups may argue that GoF research may be necessary for advancing biomedical science (A. Casadevall, F. C. Fang, and M. J. Imperiale, mSphere 9:e00714-23, 2024, https://doi.org/10.1128/msphere.00714-23) and global health security and, through this stance, conduct GoF research that has direct dual-use viability. In this light, we argue that all GoF research should be conducted under a robust framework of enhanced BSL controls that explicitly define its dual usability, classify any such enterprise as DURC, engage regulatory oversight, and establish ethical responsibility within the scope and tenor of international law. This essay describes the possible burdens and risks of GoF research, and in addressing the challenges posed by such work, proposes recommendations for future policy toward sustaining beneficial outcomes and preventing or mitigating threats to public health and global biosecurity.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0028925"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188730/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144216331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pan-variant potential of light: 425 nm light inactivates SARS-CoV-2 variants of concern and non-cytotoxic doses reduce viral titers in human airway epithelial cells.","authors":"Nathan Stasko, Leslee Arwood, Nicole Jandick, Derry Spragion, Rachel C Roberts, Mónica Setién, Ibrahim Henson, Abigail Annas, M Leslie Fulcher, Marisa Brotton, Larry Kummer, Frank Szaba, Matt Reagan, Kathleen Lanzer, Tres Cookenham, Sean Casey, Nagarama Kothapalli, Tricia Hart, Shelton S Bradrick, David Emerson, Adam S Cockrell, Scott H Randell, Jacob F Kocher","doi":"10.1128/msphere.00230-25","DOIUrl":"10.1128/msphere.00230-25","url":null,"abstract":"<p><p>Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) prolonged the coronavirus disease 2019 (COVID-19) pandemic. The continued development of novel pan-variant therapeutics to treat currently circulating and future VOCs is critically important. Photomedicine may offer broadly applicable, pan-variant treatments. In this study, we show that visible light centered around 425 nm inactivates each of the five SARS-CoV-2 VOC lineages that have been identified by the World Health Organization (Alpha, Beta, Delta, Gamma, and Omicron) in cell-free suspensions in a dose-dependent manner, including bamlanivimab-resistant variants. Specifically, 60 J/cm² of 425 nm light reduced SARS-CoV-2 titers by >4 log₁₀ relative to unilluminated controls. We observed that 425 nm light inactivates SARS-CoV-2 through restricted entry to host cells. In addition, a non-cytotoxic dosing regimen of 32 J/cm² of 425 nm light reduced infectious virus titers in well-differentiated air-liquid interface (ALI) human airway epithelial (HAE) cells infected with the Beta, Delta, and Omicron variants that incorporate mutations associated with immune evasion and/or increased transmissibility. Infectious SARS-CoV-2 titers were reduced when dosing began during the early stages of infection or in more established infections. Finally, we translated these findings to the RD-X19, a novel medical device that emits 425 nm light; our results showed that the RD-X19 restricted spike binding to ACE-2 and reduced SARS-CoV-2 titers in cell-free suspensions (by >2 log₁₀) and in the ALI HAE model (by >1 log₁₀). These findings indicate that photomedicine utilizing 425 nm visible light may serve as a novel, pan-variant treatment modality for COVID-19.<b>IMPORTANCE</b>The continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of variants that can evade public health measures, including vaccines and therapeutics. Thus, the continued development of broadly applicable measures to supplement current public health measures and standards of care remains critical. Photomedicine is one such approach. In this study, we show that non-ultraviolet visible light can inactivate each SARS-CoV-2 variant of concern (VOC) by preventing entry to host cells. Furthermore, visible light reduced the amount of virus produced in an infection model of the human airway at multiple stages of infection, demonstrating the antiviral capability of visible light. This study provides preclinical support for the development of visible light to serve as a SARS-CoV-2 countermeasure and warrants further investigation.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0023025"},"PeriodicalIF":3.7,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12188739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144160693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pre-mRNA splicing modulator pladienolide B inhibits <i>Cryptococcus neoformans</i> germination and growth.","authors":"Sierra L Love, Megan C McKeon, Henrik Vollmer, Joshua C Paulson, Nanami Oshimura, Olivia Valentine, Sébastien C Ortiz, Christina M Hull, Aaron A Hoskins","doi":"10.1128/msphere.00248-25","DOIUrl":"https://doi.org/10.1128/msphere.00248-25","url":null,"abstract":"<p><p><i>Cryptococcus neoformans</i> is an opportunistic fungal pathogen responsible for life-threatening infections, particularly in immunocompromised individuals. The limitations of current antifungal therapies due to toxicity and the emergence of resistance highlight the need for novel treatment strategies and targets. <i>C. neoformans</i> has an intron-rich genome, and pre-mRNA splicing is required for expression of the vast majority of its genes. In this study, we investigated the efficacy of a human splicing inhibitor, pladienolide B (PladB), as an antifungal against <i>C. neoformans</i>. PladB inhibited the growth of <i>C. neoformans</i> in liquid culture and spore germination. The potency of PladB could be increased by simultaneous treatment with either FK506 or clorgyline. This combination treatment resulted in significant reductions in fungal growth and prevented spore germination. Transcriptomic analysis revealed that PladB inhibits splicing in <i>C. neoformans</i> and results in widespread intron retention. In combination with FK506, this resulted in downregulation of or intron retention in transcripts from processes vital for cellular growth, including translation, transcription, and RNA processing. Together, these results suggest that targeting RNA splicing pathways could be a promising antifungal strategy and that the effectiveness of splicing inhibitors as antifungals can be increased by co-administering drugs such as FK506.IMPORTANCEFungal infections, like those caused by <i>Cryptococcus neoformans</i>, can turn deadly for many patients. New treatments and therapeutic targets are needed to combat these pathogens. One potential target is the pre-mRNA processing pathway, which is required for expression of nearly all protein-coding genes in <i>C. neoformans</i>. We have determined that a pre-mRNA splicing inhibitor can inhibit both <i>C. neoformans</i> growth and germination and that the potency of this drug can be increased when used in combination with other molecules. This work provides evidence that targeting steps in pre-mRNA processing may be an effective antifungal strategy and avenue for the development of new medicines.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0024825"},"PeriodicalIF":3.7,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144476112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Refinement of the Reference Viral Database (RVDB) for improving bioinformatics analysis of virus detection by high-throughput sequencing (HTS).","authors":"Pei-Ju Chin, Jaysheel D Bhavsar, Trent J Bosma, Madolyn L MacDonald, Shawn W Polson, Arifa S Khan","doi":"10.1128/msphere.00286-25","DOIUrl":"https://doi.org/10.1128/msphere.00286-25","url":null,"abstract":"<p><p>All biological products are required to demonstrate the absence of adventitious viruses (AVs), which may be inadvertently introduced at different steps involved in the manufacturing process. The currently recommended <i>in vitro</i> and <i>in vivo</i> virus detection assays have limitations for broad detection and are lengthy and laborious. Additionally, the use of animals is discouraged by the global 3 R's initiative for replacement, reduction, and refinement. High-throughput or next-generation sequencing (HTS/NGS) technologies can rapidly detect known and novel viruses in biological materials. There are, however, challenges for HTS detection of AVs due to differential abundance of viral sequences in public databases, which led to the creation of a non-redundant, Reference Viral Database (RVDB) containing all viral, viral-like, and viral-related sequences, with a reduced cellular sequence content. In this paper, we describe improvements in RVDB, which include the transition of RVDB production scripts from the original Python 2 to Python 3 codebase, updating the semantic pipeline to remove misannotated non-viral sequences and irrelevant viral sequences, use of taxonomy for the removal of phages, and inclusion of a quality-check step for SARS-CoV-2 genomes to exclude low-quality sequences. Additionally, RVDB website updates include search tools for exploring the database sequences and implementation of an automatic pipeline for providing annotation information to distinguish non-viral and viral sequences in the database. These updates for refining RVDB are expected to enhance HTS bioinformatics by reducing the computational time and increasing the accuracy for virus detection.IMPORTANCEHigh-throughput sequencing (HTS) has emerged as an advanced technology for demonstrating the safety of biological products. HTS can be used as an alternative adventitious virus detection method for replacing the currently recommended <i>in vivo</i> and PCR assays and supplementing or replacing the <i>in vitro</i> cell culture assays. However, HTS bioinformatics analysis for broad virus detection, including both known and novel viruses, depends on using a comprehensive and accurately annotated database. In this study, we have refined our original comprehensive Reference Virus Database (RVDB) for greater accuracy of virus detection with a reduced computational burden. Additionally, the production script for automating the generation of RVDB was updated to facilitate reliable database production and timely availability.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0028625"},"PeriodicalIF":3.7,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144476111","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}