mSphere最新文献

{"title":"Hsp90 and associates shaping parasite biology.","authors":"Abhilasha Gahlawat, Sunanda Bhattacharyya, Mrinal Kanti Bhattacharyya","doi":"10.1128/msphere.00329-25","DOIUrl":"https://doi.org/10.1128/msphere.00329-25","url":null,"abstract":"<p><p>Hsp90 is considered to be the master regulator of chaperone activity within the cellular context. In addition to aiding client maturation and maintaining protein homeostasis, Hsp90 serves various non-canonical functions in model eukaryotes: ranging from protein-trafficking into the nucleus to transcriptional regulation, from chromatin remodeling to assembly and disassembly of protein complexes during DNA repair and telomere maintenance. In performing all these trades, Hsp90 collaborates with its co-chaperones in a client-specific or function-specific manner. Hsp90 undergoes various conformational changes during its chaperone cycle, which is regulated via several post-translational modifications (PTM). Different combinations of such PTMs, known as the chaperone code, also play key regulatory roles for Hsp90 functions. Here, we examine various cellular functions of Hsp90 in protozoan parasites, particularly those that shuttle between insect host and human host, adapting to a temperature difference of at least 10°C. Our analyses reveal that most of the prominent co-chaperones are present in all these parasites, except for one that is essential in model eukaryotes. We reviewed the biochemical correlates of Hsp90 and its co-chaperone interactions and realized that the physiological significance of such interplay is largely unknown in the protozoan parasites. One striking observation is the lack of sequence conservation of the parasitic co-chaperones with their human counterparts, making them attractive drug targets. Our analyses revealed that in spite of the identification of few PTMs of parasitic Hsp90 proteins, the chaperone codes remain largely elusive.IMPORTANCEHsp90 is a pivotal molecular chaperone involved in maintaining proteostasis and facilitating the maturation of diverse client proteins. Beyond its canonical folding functions, Hsp90 plays non-canonical roles in nuclear trafficking, transcriptional regulation, chromatin remodeling, and DNA repair. These activities are tightly regulated through interactions with specific co-chaperones and through post-translational modifications, collectively forming the \"chaperone code.\" This study examines Hsp90's role in thermal adaptation of protozoan parasites when shuttling between the insect and human hosts. Here, we summarize the canonical and diverse non-canonical functions of Hsp90 in three protozoan parasites: <i>Plasmodium</i>, <i>Leishmania</i>, and <i>Trypanosoma</i>. We highlight all the Hsp90 isoforms found in these three parasites and also illustrate all the co-chaperones and post-translational modifications of Hsp90 found to be present in these protozoan parasites. Importantly, the divergence in co-chaperone sequences from human homologs in these parasites presents a promising avenue for targeted antiparasitic drug discovery and development.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0032925"},"PeriodicalIF":3.1,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145131632","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":"Comparative genomics of endemic <i>Staphylococcus aureus</i> ST1 in New Zealand.","authors":"Emma M Voss, Gregory M Cook, Christine Couldrey, Scott A Ferguson, Chad Harland, Ali Karkaba, Scott McDougall, Sergio E Morales, Jack Rolfe, James E Ussher, Rhys T White, Liam Williams, John Williamson","doi":"10.1128/msphere.00376-25","DOIUrl":"https://doi.org/10.1128/msphere.00376-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Staphylococcus aureus&lt;/i&gt; is a major zoonotic bacterial pathogen that causes a broad spectrum of human and animal diseases, including skin infections, sepsis, endocarditis, and bovine mastitis. In the geographically isolated setting of New Zealand, the population structure of &lt;i&gt;S. aureus&lt;/i&gt; exhibits a distinct genomic profile. Globally, bovine &lt;i&gt;S. aureus&lt;/i&gt; isolates are primarily associated with sequence types (STs), ST97 and ST151, whereas in New Zealand, ST1 predominates, accounting for approximately 70% of bovine isolates. ST1 is also a clinically significant sequence type in humans. This study employed a comparative One Health approach to investigate genetic differences in 520 &lt;i&gt;S. aureus&lt;/i&gt; ST1 isolated from bovine milk and human clinical samples. We aimed to explore genomic features associated with persistence and diversification across hosts, focusing on antimicrobial resistance (AMR), virulence, and mobile genetic elements. Comparative genomics revealed that human isolates carried a significantly higher burden of AMR genes, consistent with clinical selective pressure. In contrast, 83% of bovine isolates harbored a prophage (φSabovST1) similar to &lt;i&gt;S. aureus&lt;/i&gt; prophage φSaov3. This prophage encodes bovine-adapted leukocidins (LukMF'), supporting host-specific adaptation. Phylogenetic analysis revealed long branches, suggesting insufficient sampling, highlighting the need for broader genomic surveillance to resolve evolutionary relationships and transmission dynamics of &lt;i&gt;S. aureus&lt;/i&gt; ST1 in New Zealand. These findings highlight the complex history of host interactions, historical transmission events, and ongoing bacterial adaptation. Expanding sampling efforts across human, animal, and environmental reservoirs will provide deeper insights into strain diversity, elucidate transmission pathways, and inform strategies to mitigate zoonotic risks.IMPORTANCEThis study presents a comprehensive genomic analysis of &lt;i&gt;S. aureus&lt;/i&gt; ST1, a lineage that is unusually dominant in both bovine and human populations in New Zealand. Leveraging New Zealand's geographical isolation, we provide critical insights into the persistence, diversification, and adaptation of &lt;i&gt;S. aureus&lt;/i&gt;, offering valuable knowledge to advance disease prevention in both public and veterinary health and strengthening global biosecurity. The development of the first bovine ST1 reference genome serves as a valuable resource for future research, while the identification of a novel prophage (φSabovST1) carrying bovine-specific leukocidins underscores the role of mobile genetic elements in host specificity and virulence. Human isolates exhibited a higher prevalence of antimicrobial resistance genes. Phylogenetic analysis further revealed two main circulating clades of ST1 with interspersed host origins, highlighting the critical need for integrated One Health approaches to more effectively monitor and manage zoonotic pathogens across agricultural and public health","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0037625"},"PeriodicalIF":3.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125310","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":"Testing the Luedemann hypothesis: the discovery of novel antimicrobials from slow-growing microbes from nutrient-limited environments.","authors":"Brendan Lin, Sunmin Woo, Alesa Philbrick, John Bacsa, Emily Laskey, Nancy Mehra, Vijay S Gondil, Jia A Mei, George Jones, Martin S Pavelka, Michelle Dziejman, Daniel A Shutter, Christian Melander, Alexander M Perritt, Rick Jakober, Yaoyao Shen, Wei-Chen Chang, Cassandra L Quave, Paul M Dunman, George Luedemann","doi":"10.1128/msphere.00367-25","DOIUrl":"10.1128/msphere.00367-25","url":null,"abstract":"<p><p>George Luedemann is known throughout the antimicrobial community as one of the discoverers of the natural product antibiotic gentamicin. He subsequently hypothesized that slow-growing organisms inhabiting inhospitable, nutrient-limited environments may represent an enriched source of previously undescribed microbes that produce novel antimicrobials to create a competitive advantage over faster-growing rival organisms. Accordingly, 750 slow-growing microorganisms were isolated from desert rock surfaces and archived prior to Dr. Luedemann's passing in 2000. Here, we describe the characterization and antimicrobial screening of the first 147 members of the Luedemann collection. 16S rRNA and whole-genome sequencing revealed that the pilot isolate set is highly diverse and includes novel microbial species belonging to genera commonly associated with soil samples, including <i>Geodermatophilus</i>, <i>Streptomyces</i>, and <i>Micromonospora</i>. Antimicrobial screening and comparative genomics indicate that at least six members are likely to produce novel antimicrobials with activity toward the ESKAPE pathogens, <i>Vibrio cholerae</i> and/or <i>Mycobacterium smegmatis</i>. Indeed, we show that the library member \"9005BA\" produces a newly identified phenazine, pyocyanin A, which displays potent (0.625 µg/mL), selective bactericidal activity toward <i>Acinetobacter baumannii</i> and efficacy in animals. Genetic and biochemical assays revealed that the antimicrobial activity of pyocyanin A is likely to be mediated by oxidative stress and can be overcome by altering bacterial respiration and/or efflux. Taken together, the data suggest that slow-growing organisms inhabiting nutrient-limited environments represent a previously overlooked rich source of microbial and antimicrobial agent diversity.IMPORTANCEThe discovery and study of novel bacterial species offer an opportunity to identify new microbial biological processes, molecular mechanisms, and secondary metabolites, such as new antibiotics. Our work indicates that slow-growing organisms inhabiting nutrient-limited environments may represent an enriched source of novel microbial species. Furthermore, we find that a subset of these organisms is likely to produce corresponding novel antimicrobials, presumably as a means to outcompete faster-growing rival organisms. Indeed, we show that a putative new <i>Streptomyces</i> species is capable of producing a previously undescribed antimicrobial, pyocyanin A, with potent, selective antibacterial toward <i>Acinetobacter baumannii</i>, a prominent cause of antibiotic-resistant infections.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0036725"},"PeriodicalIF":3.1,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145125284","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":"Rapid, accurate, and reproducible <i>de novo</i> prediction of resistance to antituberculars.","authors":"Xibei Zhang, Shunzhou Wan, Agastya P Bhati, Philip W Fowler, Peter V Coveney","doi":"10.1128/msphere.00571-25","DOIUrl":"https://doi.org/10.1128/msphere.00571-25","url":null,"abstract":"<p><p>As one of the deadliest infectious diseases in the world, tuberculosis is responsible for millions of new cases and deaths reported annually. The rise of drug-resistant tuberculosis, particularly resistance to first-line treatments like rifampicin, presents a critical challenge for global health, which complicates the treatment strategies and calls for effective diagnostic and predictive tools. In this study, we apply an ensemble-based molecular dynamics computer simulation method, TIES_PM, to estimate the binding affinity through free energy calculations and predict rifampicin resistance in RNA polymerase. By analyzing 61 mutations, including those in the rifampicin resistance-determining region, TIES_PM produces reliable results in good agreement with clinical reference and identifies abnormal data points indicating alternative mechanisms of resistance. In the future, TIES_PM is capable of identifying and selecting leads with a lower risk of resistance evolution and, for smaller proteins, it may systematically predict antibiotic resistance by analyzing all possible codon permutations. Moreover, its flexibility allows for extending predictions to other first-line drugs and drug-resistant diseases. TIES_PM provides a rapid, accurate, low-cost, and scalable supplement to current diagnostic pipelines, particularly for drug resistance screening in both research and clinical domains.IMPORTANCEAntimicrobial resistance (AMR), a global threat, challenges early diagnosis and treatment of tuberculosis (TB). This study employs TIES_PM, a free-energy calculation method, to efficiently predict AMR by quantifying how mutations in bacterial RNA polymerase (RNAP) affect rifampicin (RIF) binding. On simulating 61 clinically observed mutations, the results align with WHO classifications and reveal ambiguous cases, suggesting alternative resistance mechanisms. Each mutation requires ~5 h, offering rapid, cost-effective predictions. An ensemble approach ensures statistical robustness. TIES_PM can be extended to smaller proteins for systematic codon permutation analysis, enabling comprehensive antibiotic resistance prediction, or adapted to identify low-resistance-risk drug leads. It also applies to other TB drugs and resistant pathogens, supporting personalized therapy and global AMR surveillance. This work provides novel tools to refine resistance mutation databases and phenotypic classification standards, enhancing early diagnosis while advancing translational research and infectious disease control.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0057125"},"PeriodicalIF":3.1,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113887","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":"Intra-host variation and transmission dynamics of SARS-CoV-2 Omicron outbreaks in Shandong, China.","authors":"Xuemin Wei, Qi Gao, Yuhao Wang, Xinyi Gao, Zengqiang Kou, Xiujun Li, Yifei Xu","doi":"10.1128/msphere.00355-25","DOIUrl":"https://doi.org/10.1128/msphere.00355-25","url":null,"abstract":"<p><p>Investigating the intra-host diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for understanding its transmission and the emergence of new variants. However, there is limited insight into SARS-CoV-2 intra-host diversity and the extent to which shared intra-host single nucleotide variants (iSNVs) occur among samples without epidemiological links. To characterize intra-host diversity, we analyzed sequencing data from 803 samples across four Omicron transmission clusters. The potential co-mutation patterns formed by shared iSNVs contributed to regions in the genome with elevated iSNV density. Most samples did not share iSNVs. Even among the sample pairs that did share at least one iSNV, 24.4% originated from different transmission clusters. For shared iSNV sites that can become fixed as single nucleotide polymorphisms (SNPs), iSNVs cluster within the phylogenetic tree, with branches supporting the same variants as SNPs. This observation suggests that iSNVs likely serve as reservoirs for SNPs. Additionally, the BA.1.1 samples carried iSNVs identical to the characteristic mutations of BA.2 and BA.2.3. These findings provide important insights into the evolution and transmission inference of SARS-CoV-2.</p><p><strong>Importance: </strong>Understanding the mechanisms behind viral evolution and transmission is crucial, as novel SARS-CoV-2 variants continue to emerge and spread worldwide. Viral evolution is driven not only by variants that circulate globally but also by mutations arising within individual hosts, resulting in the emergence of iSNVs. The role of iSNVs in shaping SARS-CoV-2 evolution and transmission remains poorly characterized. Our results showed a significant enrichment of shared iSNVs in high-density genomic regions, potentially contributing to the formation of co-mutation patterns. However, the presence of shared iSNVs in samples lacking epidemiological links indicates that they alone are insufficient for accurately reconstructing transmission routes. Instead, iSNVs may act as a reservoir for the emergence of single nucleotide polymorphisms. Our study offers new insights into the evolution of SARS-CoV-2 and the interpretation of transmission from sequencing data.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0035525"},"PeriodicalIF":3.1,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113864","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":"CRISPR adaptation in <i>Streptococcus thermophilus</i> benefits from phage environmental DNA.","authors":"F R Croteau, J Tran, A P Hynes","doi":"10.1128/msphere.00453-25","DOIUrl":"https://doi.org/10.1128/msphere.00453-25","url":null,"abstract":"<p><p>The CRISPR-Cas system is a bacterial adaptive immune system that protects against infection by phages: viruses that infect bacteria. To develop immunity, bacteria integrate spacers-fragments of the invading nucleic acids-into their CRISPR array to serve as the basis for sequence-targeted DNA cleavage. However, upon infection, a phage quickly takes over the metabolism of the bacterium, leaving little time for the bacterium to acquire new spacers, transcribe them, and use them to cut the invading DNA. To develop CRISPR immunity, bacteria must be safely exposed to phage DNA. Phage infection releases environmental DNA (eDNA) which could be involved in the development of CRISPR immunity. Using <i>Streptococcus thermophilus</i> and phages 2972 and 858 as a model for CRISPR immunity, we show that eDNA is involved in CRISPR immunity, as generation of phage-immune bacterial colonies decreases with eDNA digestion. Furthermore, it is phage eDNA specifically that impacts CRISPR immunity since only its addition increases the generation of phage-immune colonies. We also show that the effect of eDNA is phage-specific, sequence-specific, and can even be traced to a region of the genome covering the early-expressed genes, which differ between phages 2972 and 858. However, we also show that eDNA is not used as a source of genetic information for spacer acquisition. These results link eDNA to the CRISPR-Cas system, providing a better understanding of the context of the emergence of CRISPR immunity and could inform our understanding of the mechanisms through which bacteria detect phage infection.IMPORTANCEHow can a bacterial adaptive immune system (the CRISPR-Cas system) exist at all, when exposure to a virulent phage is so consistently lethal? We proposed that bacteria might actively sample their genetic environment for phage DNA through natural competence. In testing this hypothesis, we revealed that free phage DNA is important to CRISPR immunity-but not as the source of the immunological memory.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0045325"},"PeriodicalIF":3.1,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113929","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":"TAK1 phosphorylation mediates macozinone (PBTZ169) induced innate immune activation against tuberculosis.","authors":"Xinda Li, Xiaoyi Luo, Bin Wang, Lei Fu, Xi Chen, Yu Lu","doi":"10.1128/msphere.00513-25","DOIUrl":"https://doi.org/10.1128/msphere.00513-25","url":null,"abstract":"<p><p>The management of tuberculosis (TB), particularly drug-resistant variants, presents enduring clinical challenges characterized by complex therapeutic regimens, prolonged treatment durations, suboptimal success rates, and significant adverse effects, issues that have persisted as critical concerns in global healthcare. Current TB drug development predominantly focuses on novel compounds and combination therapies targeting pathogen-specific pathways while overlooking the influence of different drugs on host immunity, which is indeed a key factor affecting treatment-related tissue damage and treatment time. In this study, we evaluated the effects of important anti-TB drugs and candidate drugs on host innate immunity and found that PBTZ169 showed potent innate immunity activator, which is a promising drug for the treatment of drug-sensitive and -resistant TB. The expression of cytokines and type I interferon was strongly upregulated by PBTZ169 under lipopolysaccharide (LPS) stimulation and PBTZ169-resistant strain infection, and the innate immune activation enhanced antibacterial activity in macrophages. Mechanistically, PBTZ169 upregulated the NF-kB and MAPK signaling pathways by activating the phosphorylation of TAK1. TAK1 knockdown abrogated PBTZ169-mediated immune activation and antibacterial effects. We thus demonstrate for the first time that PBTZ169 up-regulates NF-κB and MAPK innate immune signaling pathways via activating TAK1 phosphorylation, which may inform clinical deployment strategies and patient selection.IMPORTANCEMaintaining immune homeostasis is paramount for efficient <i>Mycobacterium tuberculosis</i> (Mtb) clearance and tissue repair. Current therapeutic strategies, however, predominantly focus on achieving maximal bacterial suppression within compressed timelines while overlooking the immunomodulatory consequences of anti-tuberculosis agents. This critical knowledge gap underscores the urgent need for mechanistic investigations to establish evidence-based frameworks for optimizing drug combinations and integrating therapies with host-directed approaches.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0051325"},"PeriodicalIF":3.1,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113847","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":"Mixed-biofilm natural transformation assay reveals the presence of staphylococci in human environments that can transfer SCC<i>mec</i> to <i>Staphylococcus aureus</i>.","authors":"Mais Maree, Yuri Ushijima, Annisa Krama, Maaya Sasaki, Terumi Miyata, Masato Higashide, Le Thuy Thi Nguyen, Kazuya Morikawa","doi":"10.1128/msphere.00442-25","DOIUrl":"https://doi.org/10.1128/msphere.00442-25","url":null,"abstract":"<p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) is an important pathogen that causes healthcare-, community-, and livestock-associated infections. The methicillin resistance gene <i>mecA</i> is embedded in the mobile genetic element termed Staphylococcal Cassette Chromosome (SCC<i>mec</i>). SCC<i>mec</i> is shared among staphylococci inhabiting human and animal hosts, which are recognized epidemiologically as the genetic reservoir of SCC<i>mec</i>. However, the ability of diverse methicillin-resistant staphylococci (MRS) to serve as SCC<i>mec</i> donors for <i>S. aureus</i> has not been tested experimentally. Here, we investigated the ability of 157 MRS isolates from pets, meat, livestock, and humans to transfer SCC<i>mec</i> to methicillin-sensitive <i>S. aureus</i> strains using a recently developed natural transformation protocol in mixed biofilms. We found that 25 out of 157 isolates were able to transfer SCC<i>mec</i> to <i>S. aureus</i>. The most effective donor species were <i>S. epidermidis</i> (~33% of the tested isolates), <i>S. felis</i> (40%), and <i>S. capitis</i> (30%). Isolates from meat and livestock (collected in Vietnam and Thailand) had lower transfer rates of SCC<i>mec</i> (5% and 3%, respectively), compared to human and pet isolates from Japan (35% and 25%, respectively). The SCC<i>mec</i> transfer depended on site-specific integration/excision mediated by an intact <i>attB</i> site, which is recognized by the SCC recombinase Ccr. Our study experimentally demonstrates the presence of SCC<i>mec</i> donors in our living environments, highlighting the importance of specific staphylococcal species.IMPORTANCEHow MRSA emerges has long been the pivotal question regarding the ever-increasing burden of antimicrobial resistance (AMR) issues for over half a century. Extensive research efforts in bacteriology, epidemiology, genome biology, and healthcare fields have led to the common understanding that SCC<i>mec</i> is transmitted among distinct staphylococcal species. However, global efforts to provide empirical evidence for intercellular SCC<i>mec</i> transmission have yielded limited results. We recently established the mixed-biofilm transformation assay to evaluate intercellular and interspecies SCC<i>mec</i> transmission. This novel assay system allows us to gain insight into the question \"How MRSA emerges,\" and here, we provide the first experimental results about the potential donor species and habitats. This is the first report to show the ability of staphylococci from distinct sources to transfer SCC to <i>S. aureus</i>. Moreover, the new finding of <i>S. felis</i> as an effective donor that is not commensal to humans reinforces the importance of the One Health concept.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0044225"},"PeriodicalIF":3.1,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113860","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":"A nitric oxide-sensing two-component system regulates a range of infection-related phenotypes in <i>Burkholderia pseudomallei</i>.","authors":"Matthew W Scurlock, Stephen L Michell, Steven L Porter","doi":"10.1128/msphere.00423-25","DOIUrl":"https://doi.org/10.1128/msphere.00423-25","url":null,"abstract":"<p><p>The tier 1 bioterrorism agent <i>Burkholderia pseudomallei</i> causes melioidosis, a tropical disease with fatality rates that can exceed 40% despite antibiotic therapy. Antibiotic failure is likely to be, at least in part, due to biofilm-dwelling <i>B. pseudomallei,</i> and therefore, an improved understanding of how this pathogen regulates biofilm formation could reveal new opportunities for clinical intervention. The antimicrobial radical nitric oxide (NO) plays a key role in host immune defenses against bacteria, and the ability of <i>B. pseudomallei</i> to sense and mitigate NO toxicity is vital for establishing infection. NO-sensing proteins (NosPs), which have recently emerged as key regulators of biofilm formation in many bacterial species, use a FIST domain to sense NO via a bound heme. We hypothesized that the NosP homolog in <i>B. pseudomallei</i> would regulate biofilm formation and mediate NO-protective responses. We used [γ-³²P]ATP autophosphorylation assays to show that NosP of <i>B. pseudomallei</i> controls the autophosphorylation rate of an associated histidine kinase protein (NosK) in an NO-dependent manner. NosK was found to phosphorylate a response regulator protein (NosR) with an HD-GYP output domain, which is associated with c-di-GMP signaling, therefore implicating NosP in modulating c-di-GMP-regulated phenotypes. Unmarked, in-frame deletion of either <i>nosP</i> or <i>nosK</i> caused significant changes in <i>B. pseudomallei</i> biofilm formation and increased sensitivity to nitrosative stress, in addition to affecting other virulence traits such as growth and swimming motility. These results indicate that NosP and NosK signaling control a range of infection-relevant phenotypes and may serve as targets for novel therapeutic intervention.IMPORTANCEMelioidosis is an emerging, potentially life-threatening infection caused by the bacterium <i>Burkholderia pseudomallei</i>, killing ~89,000 people per year globally. Antibiotic therapy fails in ~10%-40% of cases, and hence, an improved understanding of the molecular mechanisms that control <i>B. pseudomallei</i> virulence could reveal new approaches for improving melioidosis treatment. Biofilm formation and resistance to the antimicrobial radical NO are virulence traits that help bacteria establish infections. Here, we show that two proteins in <i>B. pseudomallei</i>, NosP and NosK, work together to detect NO and regulate a suite of virulence traits, including NO resistance, biofilm formation, growth, and swimming motility. This work, therefore, improves our understanding of the molecular mechanisms that control infection-related phenotypes in <i>B. pseudomallei</i>.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0042325"},"PeriodicalIF":3.1,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075727","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":"Identification and predictive machine learning model construction of gut microbiota associated with carcinoembryonic antigens in colorectal cancer.","authors":"Yongzhi Wu, Zigui Huang, Yongqi Huang, Chuanbin Chen, Mingjian Qin, Zhen Wang, Fuhai He, Shenghai Liu, Rumao Zhong, Jun Liu, Chenyan Long, Jungang Liu, Xiaoliang Huang","doi":"10.1128/msphere.00454-25","DOIUrl":"https://doi.org/10.1128/msphere.00454-25","url":null,"abstract":"<p><p>Carcinoembryonic antigen (CEA) is a critical colorectal cancer (CRC) biomarker, but its mechanistic link to gut microbiota remains unclear. This study characterized gut microbiota differences between high-CEA (H-CEA) and low-CEA (L-CEA) CRC patients and explored their associations with host immunity and tumor progression mechanisms. Stool samples from 187 CRC patients were subjected to 16S rRNA sequencing, identifying 30 differentially abundant bacteria using LEfSe analysis. <i>Ruminococcus callidus</i> was significantly enriched in H-CEA patients. Transcriptome sequencing of tumor tissues from 25 patients revealed distinct immune micro-environments: H-CEA patients showed elevated resting memory CD4⁺ T cells, while L-CEA patients showed increased T follicular helper cells. Functional enrichment analysis identified differential GO terms (26 in L-CEA; 31 in H-CEA) and KEGG pathways (three in H-CEA). <i>R. callidus</i> correlated positively with mast cell infiltration, CXCL1 chemokine, and long-chain fatty acid upregulation. The area under the curve (AUC) values of the subjects in the training set for the RF and XGBoost models constructed based on differential gut microbiota for predicting high and low CEA levels were 0.969 and 0.815, respectively, and the AUC for the test set were 0.715 and 0.639. These findings demonstrate that CEA-level-specific gut microbiota dysbiosis modulates CRC progression through immune micro-environment alterations and related biological pathway regulation. Gut microbiota, as a noninvasive biomarker, can be used to construct an effective machine learning (ML) model for predicting blood CEA levels.</p><p><strong>Importance: </strong>This study reveals <i>R. callidus</i> as a key gut microbiota species enriched in CRC patients with high CEA levels, demonstrating its novel pro-tumor associations through positive correlations with mast cell infiltration and CXCL1 chemokine and upregulation of long-chain fatty acid metabolism. Concurrently, we identify distinct immune micro-environments: elevated resting memory CD4+ T cells in high-CEA patients versus increased T follicular helper cells in low-CEA cohorts. Critically, by leveraging 30 differential microbial features, we develop ML models for noninvasive prediction of CEA levels. These findings establish gut microbiota as both a mechanistic mediator of CEA-driven CRC progression and a foundation for microbiome-based diagnostic tools.</p>","PeriodicalId":19052,"journal":{"name":"mSphere","volume":" ","pages":"e0045425"},"PeriodicalIF":3.1,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145075765","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}