Microbiology spectrum最新文献

{"title":"Archaea are more hospitable hosts for mobile inteins than bacteria.","authors":"Tia M Ariagno, Jonathan D Winkelman, Marlene Belfort, Christopher W Lennon","doi":"10.1128/spectrum.02565-26","DOIUrl":"https://doi.org/10.1128/spectrum.02565-26","url":null,"abstract":"<p><p>Intervening proteins, or inteins, are mobile genetic elements characterized by their ability to rearrange peptide bonds through a post-translational, self-splicing reaction. Here, we expand the scope of a prior investigation to reexamine the distribution of inteins across archaea and bacteria. This update represents 20- and 50-fold increases in archaeal and bacterial genomes, respectively. In accordance with previous findings, inteins are enriched in DNA replication, recombination, and repair (RRR) proteins, but they are substantially more prevalent in archaea than bacteria, a difference twice that previously reported. Moreover, mini-inteins lacking homing endonucleases (HENs) are more common in bacterial inteins, suggesting bacterial inteins undergo HEN domain loss more frequently than archaeal inteins. This reduction in the prevalence of HENs, the drivers of intein mobility, offers a potential explanation for the lower density of inteins in bacteria than in archaea. Furthermore, certain classes of bacterial intein-containing proteins primarily contain mini-inteins rather than full-length inteins. The enrichment of mini-inteins within certain bacterial protein classes suggests that HEN domains may impose a greater functional cost in these proteins, creating selective pressure for HEN domain loss and resulting in reduced intein mobilityIMPORTANCEInteins are translated within host proteins and removed via a self-mediated splicing reaction. Prior comparative genomic analysis established that inteins are abundant in both bacteria and archaea, and that their distribution is strongly biased toward proteins involved in DNA transactions. Utilizing genomes made available over the last decade, this work increases the number of putative inteins by over twenty-fold. By investigating the distribution of inteins that can spread throughout/between genomes compared to those that have lost their ability to act as mobile elements, we provide a possible explanation for the higher abundance of inteins in archaea than bacteria. This work not only highlights that archaea are more hospitable intein hosts than bacteria but also serves to update the catalog of known prokaryotic inteins, which will function as a resource to the communities interested in inteins as mobile elements, tools in protein engineering, antimicrobial targets, and post-translational regulatory elements.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0256526"},"PeriodicalIF":4.1,"publicationDate":"2026-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149270661","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":"Development and preliminary validation of a CD161 immunoscore-based screening method for latent tuberculosis infection in a Chinese training cohort.","authors":"Yuanyuan Xiong, Jingyi Huang, Tao Jiang, Jin Wang, Ying Shen, Feng Shuang, Xiaobin Huang, Liping Ning, Ying Zhong, Yu Wu","doi":"10.1128/spectrum.01118-26","DOIUrl":"https://doi.org/10.1128/spectrum.01118-26","url":null,"abstract":"<p><p>Current latent tuberculosis infection (LTBI) screening is limited by tuberculin skin test (TST) cross-reactivity, return-visit requirements, and interferon-gamma release assay (IGRA) costs. We developed a flow cytometry and deep learning CD161 immunoscore screening method, evaluating it across two phases (<i>N</i> = 269) in Jiangxi, China. Phase 1 (<i>n</i> = 110; 92 males, 18 females) used healthy controls (<i>n</i> = 88) and clinically cured, post-treatment tuberculosis (TB) patients (<i>n</i> = 22) for model development. This post-treatment cohort served as a proxy and was not equivalent to untreated LTBI. Phase 2 (<i>n</i> = 159, all males) provided an independent, three-site proof-of-concept evaluation against TST, using IGRA as the reference standard. In phase 1, the optimal model achieved 100% sensitivity and 92% specificity. In phase 2, using a non-independently validated, post hoc Youden-selected cutoff (60.57), the immunoscore demonstrated 81.8% sensitivity, 80.4% specificity, and an area under the receiver operating characteristic curve (AUC) of 0.833. This performance was comparable to TST (90.9% sensitivity, 72.3% specificity, AUC = 0.816, and DeLong <i>P</i> = 0.701). The immunoscore showed significantly higher specificity than TST (<i>P</i> = 0.049) but similar sensitivity (<i>P</i> = 0.521), with an IDI of 0.077 (<i>P</i> = 0.021) and good calibration (<i>P</i> = 0.553). These exploratory, all-male results do not establish discrimination between untreated LTBI, post-treatment sensitization, or active TB, necessitating diverse validation.IMPORTANCEA machine-learning-driven CD161 immunoscore using flow cytometry provides rapid latent tuberculosis infection (LTBI) screening with diagnostic performance comparable to established methods. Across this two-phase study of 269 participants, the independent all-male phase 2 cohort of 159 participants yielded a sensitivity of 81.8% and a specificity of 80.4% for the CD161 immunoscore. Performance remained consistent across colleges with sevenfold variation in LTBI prevalence (1.8%-12.2%), supporting robustness. For congregate settings such as colleges, this laboratory-based approach may offer operational advantages by providing same-day initial screening without requiring a return visit for result interpretation. A possible future application would be a staged pathway in which immunoscore-positive individuals undergo confirmatory interferon-gamma release assay testing. This implementation strategy remains conceptual and requires prospective evaluation of referral rates, laboratory capacity, acceptability, clinical outcomes, and cost-effectiveness. These proof-of-concept findings require confirmation in larger external cohorts with adequate female representation and more diverse demographic, occupational, and geographic backgrounds.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0111826"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245363","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":"Genomic diversification and modular recombination of Stx2 prophages associated with chromosomal integration sites during an STEC O111 and O157 outbreak.","authors":"Keiko Kimata, Junko Isobe, Jun-Ichi Kanatani, Tomoko Kato, Kenichi Lee, Tsuyoshi Sekizuka, Makoto Kuroda, Tetsutaro Sata, Sunao Iyoda, Masanori Watahiki","doi":"10.1128/spectrum.00870-26","DOIUrl":"https://doi.org/10.1128/spectrum.00870-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Shiga toxin 2 (Stx2) production in Shiga toxin-producing &lt;i&gt;Escherichia coli&lt;/i&gt; (STEC) is mediated by lambdoid Stx2-converting bacteriophages, which play a central role in the evolutionary and pathogenic potential of STEC lineages. However, the mechanisms through which Stx2 phages diversify and evolve during natural outbreaks remain unclear. Here, we analyzed a collection of 20 related Stx2 phage and prophage genomes recovered from STEC O111 and O157 isolates associated with a foodborne disease outbreak in Japan. These included 2 infectious, Stx2-converting phages isolated directly from bloody stool samples, 17 Stx2 prophages, and 1 &lt;i&gt;stx&lt;/i&gt;-negative prophage. Genome-wide single-nucleotide polymorphism analysis identified 282 polymorphic sites, resolving two predominant lineages associated with distinct chromosomal integration sites (&lt;i&gt;argW&lt;/i&gt; or &lt;i&gt;wrbA&lt;/i&gt;), corresponding largely to the STEC O111 and O157 backgrounds, respectively. Despite this lineage structure, the genomes exhibited extensive mosaicism, including lineage-incongruent haplotype blocks and multiple recombination junctions, indicating frequent modular exchanges among co-circulating phages. The preferential association between specific haplotypes and chromosomal integration sites further suggests that the host genomic context contributes to prophage genomic variation. Additionally, the Stx2-converting phages and &lt;i&gt;argW&lt;/i&gt;-integrated prophages encoded functionally active restriction-modification systems, indicating that prophage-encoded defense mechanisms may contribute to genome stability and diversification. Collectively, these findings highlight the genetic plasticity of Stx2 phages and prophages during a single outbreak and offer genome-based insights into the evolutionary dynamics and epidemiological significance of toxin-converting bacteriophages in STEC populations.IMPORTANCEShiga toxin-converting bacteriophages are key drivers of virulence and genomic evolution in Shiga toxin-producing &lt;i&gt;Escherichia coli&lt;/i&gt; (STEC). However, the diversity of these phages during natural disease outbreaks remains unclear. By analyzing a set of closely related Stx2 phages and prophages recovered from a single foodborne disease outbreak, this study revealed that Stx2 prophage populations are structured by their chromosomal integration sites, primarily at the &lt;i&gt;argW&lt;/i&gt; or &lt;i&gt;wrbA&lt;/i&gt; loci. Despite this lineage structure, phage genomes exhibit extensive mosaicism generated by modular recombination. We further showed that prophage-encoded restriction-modification systems are functionally active, suggesting that prophage defense mechanisms may influence genome stability and diversification. Collectively, these findings elucidate how chromosomal context, recombination, and prophage-encoded functions drive the evolution of toxin-converting bacteriophages. These dynamics have important implications for STEC population structure, outbreak dynamics, and the emergence of new pathogenic st","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0087026"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245429","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":"Lineage-associated genomic features and phenotypic heterogeneity in clinical borderline oxacillin-resistant <i>Staphylococcus aureus</i>.","authors":"Qiyu Bian, Lin Xi, Shilong Li, Hantian Fang, Cong Ma, Xiao Yang, Xueli Shi, Nanyang Li, Ping Yang, Wenli Dong, Hailan Wu, Xiaoyan Wang, Jufang Wu, Beining Guo, Jing Zhang, Yaxin Fan","doi":"10.1128/spectrum.01352-26","DOIUrl":"https://doi.org/10.1128/spectrum.01352-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Borderline oxacillin-resistant &lt;i&gt;Staphylococcus aureus&lt;/i&gt; (BORSA) represents a &lt;i&gt;mecA&lt;/i&gt;/&lt;i&gt;mecC&lt;/i&gt;-negative phenotype characterized by oxacillin minimum inhibitory concentrations (MICs) of 1-8 mg/L. The molecular basis of this resistance, particularly regarding lineage-associated differences in induction profiles, remains incompletely understood. In this study, 11 clinical BORSA isolates from pneumonia and bloodstream infections were identified among 374 clinical &lt;i&gt;S. aureus&lt;/i&gt; isolates. Resistance-associated features were investigated using phenotypic profiling, whole-genome sequencing (WGS), RT-qPCR of &lt;i&gt;blaZ&lt;/i&gt; expression, and time-kill assays. All BORSA isolates were cefoxitin-susceptible, β-lactamase-positive, and distributed across six clonal backgrounds, with ST25 and ST7 each represented by three isolates. WGS identified a shared GdpP N105D substitution in all isolates, together with lineage-associated variations in &lt;i&gt;pbp1&lt;/i&gt; and &lt;i&gt;pbp4&lt;/i&gt;. Following oxacillin exposure, &lt;i&gt;blaZ&lt;/i&gt; was significantly upregulated in all three ST25 isolates (all &lt;i&gt;P&lt;/i&gt; &lt; 0.001), accompanied by accelerated nitrocefin hydrolysis, whereas the remaining isolates showed weaker or more heterogeneous responses. While oxacillin monotherapy (1× MIC) failed to prevent bacterial regrowth, oxacillin/sulbactam combinations produced sustained synergistic killing. This effect was most consistently observed among the ST25 isolates, whereas the ST7 isolates showed greater phenotypic variation. These findings suggest that the BORSA phenotype in this cohort may involve a multifactorial resistance profile, including candidate &lt;i&gt;gdpP&lt;/i&gt; variation, inducible β-lactamase activity, and alterations in penicillin-binding proteins (PBPs). The cefoxitin susceptibility of these isolates presents a diagnostic challenge that may lead to therapeutic misclassification and subsequent inappropriate therapy. β-lactam/β-lactamase inhibitor combinations demonstrated promising &lt;i&gt;in vitro&lt;/i&gt; activity and warrants further investigation for BORSA isolates exhibiting strong inducible β-lactamase activity.IMPORTANCEBorderline oxacillin-resistant &lt;i&gt;Staphylococcus aureus&lt;/i&gt; (BORSA) is difficult to detect because it lacks &lt;i&gt;mecA&lt;/i&gt;/&lt;i&gt;mecC&lt;/i&gt; and remains susceptible to cefoxitin, increasing the risk of misclassification and inappropriate β-lactam therapy. This study suggests that BORSA resistance in this cohort is multifactorial, involving candidate &lt;i&gt;gdpP&lt;/i&gt; variation, lineage-associated variations in penicillin-binding proteins, and inducible β-lactamase activity. Importantly, the ST25 isolates in this cohort exhibited rapid &lt;i&gt;blaZ&lt;/i&gt; induction and stronger responses to oxacillin/sulbactam than to oxacillin alone. These findings improve understanding of BORSA biology, highlight a significant diagnostic blind spot in routine susceptibility testing, and support further evaluation of β-lactam/β-lactamase inhibitor combinations as a promising treatment strategy for BORSA ","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0135226"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245417","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":"Biological characterization of the lytic <i>Pseudomonas aeruginosa</i> phage BUCT980 and its therapeutic efficacy in a murine lung infection model.","authors":"Xiao Yu, Jingwen Chen, Weihua Zhang, Yigang Tong, Lixin Xie, Mengzhe Li, Mengying Yao","doi":"10.1128/spectrum.01874-26","DOIUrl":"https://doi.org/10.1128/spectrum.01874-26","url":null,"abstract":"<p><p><i>Pseudomonas aeruginosa</i> is an important opportunistic pathogen whose increasing multidrug resistance limits conventional antimicrobial treatment options and underscores the need for alternative antibacterial strategies. In this study, we isolated and systematically characterized a novel lytic phage, BUCT980, and evaluated its antibacterial activity and therapeutic potential. Transmission electron microscopy showed that BUCT980 is a myovirus. One-step growth analysis indicated an apparent latent period of approximately 60 min and a burst size of approximately 173 PFU per infected cell. The BUCT980 genome is 60,697 bp in length, and comparative genomic and phylogenetic analyses support its placement within the class <i>Caudoviricetes</i>. No known lysogeny-associated genes, virulence factors, or antibiotic resistance genes were identified by genomic analysis. <i>In vitro</i>, BUCT980 markedly suppressed the growth of <i>P. aeruginosa</i> PAO1 across the tested multiplicities of infections (MOIs) and inhibited biofilm formation. In 10-fold serial-dilution spot assays, BUCT980 formed clear plaques on 4 of 29 clinical isolates and produced visible inhibition in 13 additional isolates representing multiple sequence types. In a murine model of acute <i>P. aeruginosa</i> pneumonia, intranasal administration of BUCT980 significantly improved survival, reduced pulmonary bacterial burden, and alleviated lung injury. No overt histopathological abnormalities were observed in the liver or kidney during short-term observation. These findings support further evaluation of BUCT980 as a candidate therapeutic phage for acute <i>P. aeruginosa</i> lung infection.IMPORTANCE<i>Pseudomonas aeruginosa</i> is a major cause of difficult-to-treat respiratory infections because of its antibiotic resistance and biofilm-forming capacity. Here, we characterized BUCT980, a lytic phage that suppressed <i>P. aeruginosa</i> growth, inhibited early biofilm formation, and showed activity against clinical isolates from multiple sequence-type backgrounds. Genomic screening identified no known lysogeny-associated genes, virulence factors, or antibiotic resistance genes. In a murine acute pneumonia model, intranasal BUCT980 treatment improved survival, reduced pulmonary bacterial burden, and alleviated lung injury. Bacterial regrowth during prolonged exposure and limited activity against established biofilms indicate that combination strategies may be needed for sustained treatment. These findings support further preclinical evaluation of BUCT980 for acute <i>P. aeruginosa</i> lung infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0187426"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245327","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":"Core bacterial and host fruit-specific yeast microbiota in a polyphagous fly pest.","authors":"Sido Dunis, Marie Lapègue, Candice Deschamps, Lily Cesari, Anne Loiseau, Benoit Facon, Nicolas O Rode","doi":"10.1128/spectrum.01607-26","DOIUrl":"https://doi.org/10.1128/spectrum.01607-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Holometabolous polyphagous insects undergo metamorphosis and exploit multiple host plants, exposing them to highly variable ecological conditions across both life stages and host plants. Whether these insects harbor a stable core microbiota, a life stage- or a host plant-specific microbiota remains open questions. Here, we characterized fungal and bacterial communities associated with &lt;i&gt;Drosophila suzukii&lt;/i&gt; across life stages (larvae, pupae, and emerging flies) and host fruits (cherry, blackberry, and strawberry) using 16S and ITS metabarcoding. We tested the relative influence of life stage and host fruit on microbiota composition using community and network-based analyses. First, we identified that yeasts, but not bacteria, were strongly structured among host fruits. Bacteria and filamentous fungi were shared across fruits, constituting a fruit core microbiota dominated by &lt;i&gt;Gluconobacter cerinus&lt;/i&gt;, &lt;i&gt;Tatumella&lt;/i&gt; sp., and &lt;i&gt;Cladosporium&lt;/i&gt; spp. In contrast, yeast were rather fruit-specific: the genera &lt;i&gt;Hanseniaspora&lt;/i&gt; and &lt;i&gt;Pichia&lt;/i&gt; were mostly associated with cherries and strawberries, contrary to &lt;i&gt;Metschnikowia&lt;/i&gt; with blackberries. Second, we found that fungal, but not bacterial, communities of &lt;i&gt;D. suzukii&lt;/i&gt; were structured among host fruits. &lt;i&gt;D. suzukii&lt;/i&gt; harbored a core bacterial microbiota composed of &lt;i&gt;G. cerinus&lt;/i&gt; and a niche-specific (host plant-specific) microbiota composed of yeasts: &lt;i&gt;Hanseniaspora&lt;/i&gt; was typical in individuals related to cherry and strawberry, whereas &lt;i&gt;Metschnikowia&lt;/i&gt; to blackberry. We also verified that individuals from artificial laboratory infestations and natural field infestations harbored similar microbial communities when they developed under the same laboratory conditions. Components of both core and niche-specific microbiota were most likely horizontally acquired by &lt;i&gt;D. suzukii&lt;/i&gt; from host fruits. Taken together, our results underline the importance of metacommunity approaches to investigate tripartite interactions among insects, host plants, and microbiota.IMPORTANCEThe role of microbiota in mediating interactions between phytophagous insects and their host plants has been well illustrated in specialist species. However, it has been less comprehensively studied in polyphagous species, which infest multiple host plants, and across life stages in holometabolous species that experience separate ecological niches through development. We tested the existence of a core, a niche-specific, and a stage-specific microbiota in a polyphagous holometabolous species, &lt;i&gt;D. suzukii&lt;/i&gt;. We examined both fungal and bacterial communities in larvae, pupae, and emerging flies infesting three host fruits. Our results showed, first, that the assembly of bacteria, filamentous fungi, and yeasts on fruits is driven by different ecological processes. Second, &lt;i&gt;D. suzukii&lt;/i&gt; harbors a core bacterial microbiota, a niche-specific microbiota constituted by yeasts and no stage-specific","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0160726"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245386","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 microscopy-free approach for detection of fungal elements in tissue using mannan immunoassay.","authors":"Audrey M Rank, Amanda R Burnham-Marusich, Kathleen R Zayac, Menen G Ashagrie, Lawrence Mariano, Sheelagh Duncan, Bethany Mills, Thomas R Kozel","doi":"10.1128/spectrum.02253-26","DOIUrl":"https://doi.org/10.1128/spectrum.02253-26","url":null,"abstract":"<p><p>KOH microscopy is a routine method to determine the presence of fungal elements in infected tissue. Although widely used, the procedure requires trained personnel and the infrastructure needed for microscopy. An alternative approach is the extraction of fungal antigens and detection by immunoassay. In this study, we used oxidative release with sodium hypochlorite to extract mannan from fungal cells. Quenching of free sodium hypochlorite was done using an excess of bovine serum albumin or sodium thiosulfate. Quenching reagents were incorporated into sample pads of lateral flow immunoassays (LFIAs), followed by detection of released mannan using mannan-specific monoclonal antibodies coupled to colloidal gold on the LFIA platform. Cells of <i>Candida</i> spp. or <i>Aspergillus</i> spp. were used to evaluate the extraction/quenching steps. The results showed that sodium thiosulfate was particularly well suited for hands-free, in-strip neutralization. The analytical sensitivity (minimum limit of detection, LOD) of the <i>Candida</i> LFIA was 67 ng/mL of formaldehyde-inactivated, whole <i>Candida albicans</i> cells. The LOD of the <i>Aspergillus</i> LFIA was 250 ng/mL of formaldehyde-inactivated, whole <i>Aspergillus fumigatus</i> cells. Proof-of-concept for oxidative release of mannan followed by detection of antigen by LFIA was provided using an <i>ex vivo</i> porcine corneal model of fungal keratitis. The results demonstrated that the test is a rapid two-step, specimen-to-result protocol suitable for point-of-care use. Such a diagnostic would be particularly valuable in settings that lack access to the trained personnel or infrastructure needed for KOH microscopy.IMPORTANCEKOH microscopy is widely used to detect fungal infection, but it requires trained personnel and microscopy infrastructure. An alternative approach is extraction of antigens from fungal cells within infected tissue and detection by lateral flow immunoassay. In this study, we developed a <20 min, specimen-to-result protocol suitable for point-of-care use that combines (i) oxidative release via sodium hypochlorite to rapidly extract fungal mannan from specimens, (ii) on-strip (hands-free) quenching of sodium hypochlorite with sodium thiosulfate or bovine serum albumin, and (iii) visual detection of positive signal via novel, mannan-specific monoclonal antibodies coupled to colloidal gold. Analytical performance of the <i>Candida</i> and <i>Aspergillus</i> tests was evaluated with cultured fungal cells. Clinical proof-of-concept for each assay was provided using an <i>ex vivo</i> porcine corneal model of fungal keratitis. This diagnostic strategy would be particularly valuable in settings that lack access to trained personnel or the infrastructure needed for KOH microscopy.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0225326"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245334","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":"Antibacterial mechanism of hypocrellin against <i>Ralstonia solanacearum</i> in tobacco and its modulation of the endophytic microbiome.","authors":"Wen Du, Chunlong Sun, Jun Wang, Jingtao Liu, Yanmei Wang, Wenwen Huang, Guolan Liu, Jian Li, Ran Wang, Zhiwei Su, Wenjuan Zhao, Chenzhao Wang","doi":"10.1128/spectrum.02941-25","DOIUrl":"https://doi.org/10.1128/spectrum.02941-25","url":null,"abstract":"<p><p>The photosensitive compound hypocrellin, derived from the traditional Chinese medicinal fungus <i>Shiraia bambusicola</i> Henn., shows potential as a novel pesticide. To evaluate its efficacy against bacterial wilt disease caused by <i>Ralstonia solanacearum</i> in tobacco, this study examined its antibacterial mechanisms through <i>in vitro</i> experiments and analyzed their impact on tobacco endophytic microbiota. An optimized hypocrellin offering a promising sustainable formulation-with a 2:3 ratio of hypocrellin A to hypocrellin B-was developed for enhanced antibacterial activity, and its interaction with bacterial DNA, intracellular components, and membrane integrity was systematically investigated. Hypocrellins exhibited strong antibacterial effects by disrupting the cell wall and membrane integrity of <i>R. solanacearum</i>, increasing membrane permeability, and inducing the leakage of intracellular K⁺, soluble proteins, and reducing sugars. Dual DNA-binding mechanisms were suggested: electrostatic adsorption to phosphate groups, followed by groove insertion, and intercalation between base pairs. In tobacco plants, hypocrellin treatment significantly altered the endophytic microbial community, increasing microbial richness and diversity, increasing the proportion of Bacillota and Pseudomonadota, and significantly reducing pathogen abundance. Predictive functional analysis based on PICRUSt2 suggested that hypocrellin may have influenced metabolic pathways associated with microbial basal metabolic activity and proliferation potential. Hypocrellins mitigate <i>R. solanacearum</i> infection through multi-target mechanisms: physical disruption of bacterial membranes and DNA, restoration of beneficial endophytic microbiota, and activation of metabolic pathways critical for plant defense.IMPORTANCEThis study highlights the multi-target antibacterial mechanisms and microbiome-modulating effects of hypocrellin, offering a promising candidate for a sustainable strategy for controlling soil-borne diseases. Unlike conventional chemical pesticides, hypocrellin acts through physical disruption of bacterial membranes and DNA interaction, while simultaneously restoring beneficial endophytic microbiota and activating metabolic pathways critical for plant defense in tobacco. Its ability to suppress <i>Ralstonia solanacearum</i> and enhance microbial ecological balance positions hypocrellin as both an effective antibacterial agent and a microbiome regulator. These findings provide a scientific basis for developing hypocrellin-based bio-pesticides and support further research into its application in eco-friendly agricultural practices.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0294125"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245309","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":"Isolation and genomic characterization of a novel <i>Pseudomonas</i> jumbo phage ΦBRkr.","authors":"Yoshiaki Sakata, Tomohiro Nakamura, Jumpei Fujiki, Kohana Tamamura, Natsuko Ichikawa, Keisuke Nakamura, Tomohito Iwasaki, Hidetomo Iwano","doi":"10.1128/spectrum.02068-26","DOIUrl":"https://doi.org/10.1128/spectrum.02068-26","url":null,"abstract":"<p><p>Jumbo phages generally have large viral genomes packaged in large virions and exhibit a broad host spectrum. However, the detailed variation in host spectrum among jumbo phages, particularly in the context of bacterial phage defense systems, is not fully understood yet. In the present study, we isolated a novel <i>Pseudomonas</i> virus, ΦBRkr, from sewage water in Japan. Transmission electron microscopic analysis and whole-genome sequencing revealed that ΦBRkr is a jumbo phage with a total DNA length of 306,291 bp, and suggested a novel <i>Pawinskivirus</i>-like phage. Furthermore, ΦBRkr showed broader infectivity against 100 genetically diverse <i>Pseudomonas aeruginosa</i> clinical isolates (62.0% of host spectrum) compared with <i>Phikzvirus</i> ΦNK1 (40.0% of host spectrum). By examining the correlation between phage infectivity and the presence of predicted phage defense systems across these 100 strains in an exploratory screening, we found that among the 50 predicted defense systems evaluated, the Jumbo phage killer (Juk) AB system emerged as the potential candidate showing a distinct differential restriction between the two phages. While ΦNK1 completely failed to infect any strains harboring the predicted JukAB, ΦBRkr may evade this defense mechanism in some strains. Genomic comparisons revealed that, unlike ΦKZ and ΦNK1, ΦBRkr lacks a homolog of the KZ241 gene, which is known to trigger the JukAB system. It has been suggested that this absence likely confers a stealth advantage to ΦBRkr during <i>P. aeruginosa</i> infection. These results contribute to a deeper understanding of the diversity of <i>Pseudomonas</i> jumbo phages and provide insights into their advantageous properties for future applications.IMPORTANCE<i>Pseudomonas aeruginosa</i> is an opportunistic pathogen causing severe multidrug-resistant infections, making phage therapy a promising alternative treatment. Jumbo phages are attractive candidates because they typically infect a wide range of bacterial strains. However, bacteria constantly deploy diverse defense systems to block viral infections, which can limit therapeutic efficacy. In this study, we isolated a novel jumbo phage, ΦBRkr, which exhibits a broad intra-species host range, infecting 62.0% of 100 diverse clinical <i>P. aeruginosa</i> isolates tested. Our results suggest that its ability to effectively evade the predicted Jumbo phage killer (Juk) defense system, a robust barrier restricting other well-known jumbo phages, contributed to its broader host range. Viral genomic evidence implies this phage employs a natural stealth strategy by lacking the specific protein targeted by the putative Juk system. Uncovering how certain phages naturally bypass robust bacterial immunities provides critical insights for selecting and developing highly effective phages for future applications.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0206826"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245456","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":"SARS-CoV-2 spike protein enhances HBV replication via autophagy and aggravates inflammation in CHB patients with liver dysfunction.","authors":"Liangjuan Chen, Yufen Jiang, Xingzhong Miao, Hanying Wang, Honglin Shi, Linle Xu, Shiqing Li, Yu Chen, Hongbo Shi","doi":"10.1128/spectrum.01970-26","DOIUrl":"https://doi.org/10.1128/spectrum.01970-26","url":null,"abstract":"<p><p>This study investigated the effects of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S protein) on hepatitis B virus (HBV) replication and immune function in patients with chronic hepatitis B (CHB), aiming to elucidate the underlying mechanisms of S protein-HBV interaction. Through <i>in vitro</i> cell experiments and clinical sample analyses, S protein expression was induced in HepG2.2.15 cells, leading to enhanced HBV replication; this effect was reduced by autophagy inhibitors, confirming the critical mediating role of autophagy. Furthermore, peripheral blood mononuclear cells (PBMCs) from CHB patients were co-cultured with the S protein, resulting in increased inflammatory responses in T cells and monocytes, particularly in patients with concurrent abnormal liver function and lipid metabolism disorders. In summary, the S protein promotes HBV replication by activating autophagy and exacerbates immune inflammation in CHB patients. Autophagy inhibitors block its effect on HBV replication, suggesting autophagy as a key regulatory target. The immune-activating effects of the S protein are more pronounced in patients with liver dysfunction and metabolic abnormalities. These findings provide a basis for further investigation into the interplay between the S protein and autophagy in HBV infection.IMPORTANCEThis study reveals that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein promotes hepatitis B virus (HBV) replication by activating the autophagy pathway and elucidates its role in exacerbating immune inflammation in patients with chronic hepatitis B, particularly showing more pronounced responses in patients with liver dysfunction and lipid metabolism disorders. These findings provide critical molecular insights into the viral interaction and immunopathological mechanisms during SARS-CoV-2 and HBV co-infection. They also improve our understanding of the interplay between SARS-CoV-2 and HBV in the context of co-infection and provide a basis for future studies.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0197026"},"PeriodicalIF":4.1,"publicationDate":"2026-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149245373","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}