Microbiology spectrum最新文献

{"title":"Clinical and genomic features of <i>Chryseobacterium</i> species isolated from clinical cultures.","authors":"Eriko Muramatsu, Masahiro Suzuki, Yukino Inagaki, Tomoki Ayukawa, Jumpei Yamauchi, Ryota Hase, Takehiro Hashimoto, Naoya Itoh, Yasufumi Matsumura, Hideaki Kato, Kohei Uemura, Kayoko Hayakawa, Sho Saito, Yohei Doi, Aki Sakurai","doi":"10.1128/spectrum.01793-26","DOIUrl":"https://doi.org/10.1128/spectrum.01793-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Chryseobacterium&lt;/i&gt; species are environmental bacteria occasionally implicated in human infections; however, their clinical and genomic features are not fully characterized. This study investigated the clinical, genotypic, and phenotypic characteristics of &lt;i&gt;Chryseobacterium&lt;/i&gt; strains collected through the MultiDrug-Resistant Organisms Clinical Research Network, a multicenter prospective study of patients with carbapenem-resistant gram-negative bacilli isolated at tertiary care hospitals in Japan between April 2019 and March 2024. Among 18 patients with &lt;i&gt;Chryseobacterium&lt;/i&gt; spp. confirmed by whole-genome sequencing (WGS), 5 had infection, and 13 were colonized. Bacteremia and pneumonia were the common types of infection. The isolates comprised five species, with &lt;i&gt;Chryseobacterium indologenes&lt;/i&gt; and &lt;i&gt;Chryseobacterium culicis&lt;/i&gt; being the most frequently detected. Compared with WGS, 16S rRNA gene sequencing demonstrated the highest species-level identification accuracy (93.8%), followed by MALDI Biotyper (50.0%), VITEK-MS (31.3%), and VITEK 2 Blue (31.3%). All systems correctly identified &lt;i&gt;C. indologenes&lt;/i&gt;, but other species were frequently misidentified or remained unidentified because of limited database coverage. All isolates exhibited broad β-lactam resistance, including resistance to carbapenems, which was associated with species-specific combinations of metallo-β-lactamase and extended-spectrum β-lactamase genes. Minocycline, trimethoprim-sulfamethoxazole, and cefiderocol retained activity across all species. These findings highlight that diverse &lt;i&gt;Chryseobacterium&lt;/i&gt; species, including uncommon ones, can be associated with human infections. Incorporating genomic approaches such as WGS or 16S rRNA gene analysis can improve species-level identification, especially for rare or emerging species.IMPORTANCE&lt;i&gt;Chryseobacterium&lt;/i&gt; species are emerging opportunistic pathogens that pose a diagnostic and therapeutic challenge as they are intrinsically resistant to most β-lactams, including carbapenems, and are often misidentified by routine clinical laboratory systems. In this multicenter study, we show that clinical &lt;i&gt;Chryseobacterium&lt;/i&gt; isolates represent greater species diversity than is typically recognized, extending beyond &lt;i&gt;Chryseobacterium indologenes&lt;/i&gt; to include uncommon species associated with both infection and colonization. Whole-genome sequencing clarified species assignments, revealed species-specific β-lactamase profiles, and highlighted the limitations of commonly used identification platforms, particularly for species absent from commercial databases. Despite broad β-lactam resistance, cefiderocol, minocycline, and trimethoprim-sulfamethoxazole retained &lt;i&gt;in vitro&lt;/i&gt; activity across species. These findings emphasize the need for genomic or sequence-based identification to accurately define the clinical spectrum of &lt;i&gt;Chryseobacterium&lt;/i&gt; species, guide interpretation of antimicrobial susceptibility,","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0179326"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220543","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":"An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting, and extraction bias in sorted microbial communities.","authors":"Valerie Goethals, Nathan Vanwinsen, Fabian Mermans, Sofie De Gand, Nico Boon, Tom Van de Wiele, Kim De Paepe","doi":"10.1128/spectrum.00712-26","DOIUrl":"https://doi.org/10.1128/spectrum.00712-26","url":null,"abstract":"<p><p>Fluorescence-activated cell sorting (FACS) followed by metataxonomics is commonly used to probe the composition of microbial subpopulations with a functionality of interest. Metataxonomic analysis of sorted low-microbial-biomass samples is prone to contamination and bias introduced during sorting and DNA extraction. To improve metataxonomic accuracy, the DNA yield obtained by the DNeasy PowerSoil Pro kit was first maximized. FACS-sequencing using the optimized DNA extraction method distorted the composition of sorted microbiota by introducing sheath fluid contaminants, termed the FACSome. Since FACSome contaminants were experiment-specific, a standardized, applicable <i>in silico</i> decontamination method was developed to characterize and remove FACSome contamination in PacBio and Illumina metataxonomic sequencing data based on carefully selected controls. The optimized DNA extraction and decontamination methods were validated in soil, water, feces, saliva, gut reactor, and mock microbial communities. Metataxonomic profiles of non-selectively sorted and unsorted samples derived from these ecosystems did not perfectly match due to relic DNA depletion during FACS. Effective (97%) relic DNA depletion was confirmed with a spike-in experiment and is desirable since naturally present relic DNA can interfere with function-driven FACS-sequencing. A nuclease-based digest further enhanced relic DNA depletion. Since FACS depleted relic DNA, the preservation of intact cells prior to sorting is essential for activity- or viability-targeted FACS. Intact cells were best preserved during long-term -80°C storage of fecal samples that were not amended with glycerol-1× Tris-EDTA cryoprotectant.IMPORTANCEBulk meta-omics fail to provide sufficient resolution to gain mechanistic insights in microbial ecosystems. Function-driven microbiome research requires high-throughput profiling of active microbial subpopulations. These can be singled out through fluorescence-activated cell sorting (FACS) combined with function-, activity-, or viability-based labeling. The resulting low-biomass sorted samples present a currently overlooked challenge for accurate 16S rRNA gene profiling. We systematically identified all potential sources of interference to enable decontamination of 16S rRNA gene sequences from sorted microbiota. While this study focused on metataxonomic read-outs, our optimized extraction and decontamination workflow can advance other sequencing-based omics analyses of sorted microbial communities. Our optimized FACS-sequencing workflow is thus imperative to unlock the full potential of single-cell labeling and FACS, in turn enabling mode-of-action studies that will broaden our understanding of microbe-environment interactions.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0071226"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220550","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":"Alternative respiratory electron transport pathways drive differential aminoglycoside susceptibility.","authors":"Stuti Srivastav, L Karvannan, Amitesh Anand","doi":"10.1128/spectrum.01775-26","DOIUrl":"https://doi.org/10.1128/spectrum.01775-26","url":null,"abstract":"<p><p>Bacterial bioenergetics is increasingly recognized as a central determinant of antibiotic tolerance and resistance. Here, we define how architectural variation within the aerobic electron transport system (ETS) modulates proton motive force (PMF) and governs antibiotic susceptibility. We constructed four <i>Escherichia coli</i> strains with unbranched respiratory pathways differing in proton-translocation efficiencies. A low-PMF ETS variant exhibited selective tolerance to aminoglycosides, while susceptibility to β-lactams and tetracycline remained unchanged. Using fluorescent gentamicin, we demonstrate that reduced PMF directly limits drug uptake. Interestingly, wild-type <i>E. coli</i> was as susceptible as the high-PMF variant. These results establish respiratory energy transduction as a mechanistic bottleneck for aminoglycoside efficacy and position ETS remodeling as a bioenergetic route to antibiotic tolerance.IMPORTANCEInfectious diseases remain a major global health challenge, and the failure of antibiotics to effectively treat them is compounding the threat. This study shows that the way bacteria produce energy can strongly influence how well certain antibiotics work. By engineering bacteria with different respiratory pathways, we demonstrate that bacteria in a low-energy state became specifically more tolerant to aminoglycoside antibiotics such as gentamicin and tobramycin. Importantly, this tolerance was linked to reduced drug entry into the cell rather than resistance gained due to acquisition of adaptive genetic change. The findings reveal that bacterial energy metabolism is not simply a housekeeping process, but a major factor determining antibiotic effectiveness. This work helps explain why some bacteria survive antibiotic treatment despite lacking resistance mutations and highlights bacterial respiration as a promising target for developing strategies to restore antibiotic sensitivity and combat persistent infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0177526"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220595","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":"PASTA kinase dimerization in <i>Enterococcus faecalis</i> does not require the extracellular PASTA domains.","authors":"Dušanka Djorić, Milcah Puliyelil, Jaime L Little, Christopher J Kristich","doi":"10.1128/spectrum.02211-26","DOIUrl":"https://doi.org/10.1128/spectrum.02211-26","url":null,"abstract":"<p><p>The penicillin- and Ser/Thr-kinase-associated (PASTA) kinase family of bacterial signaling proteins encompasses a widely conserved family of transmembrane Ser/Thr kinases defined by the presence of multiple PASTA domains comprising the extracellular module. PASTA kinases are found in nearly all gram-positive bacteria and are activated in response to cell wall stress to control critical physiological processes. A thorough understanding of the mechanisms of PASTA kinase signaling is important not just for greater insight into bacterial physiology but also to target PASTA kinases for therapeutic intervention. However, many fundamental features of the proposed model for signaling by PASTA kinases have not been tested using full-length kinase in cells of its native host under physiological conditions; hence, the mechanisms of PASTA kinase signaling have remained largely obscure. In this work, we tested fundamental features of the proposed model for PASTA kinase signaling using the representative PASTA kinase of <i>Enterococcus faecalis</i>, IreK. Through a combination of genetics and biochemistry, we established that IreK participates in self-association to form dimers in <i>E. faecalis</i> cells and that the self-associated form of IreK is functionally important for signaling. However, in contrast to the proposed model for PASTA kinase signaling, IreK dimerization does not require the extracellular PASTA module, and moreover, dimerization does not correlate with IreK signaling. Additionally, dimerization of IreK is not sufficient for kinase activation. Thus, regulation of PASTA kinase signaling <i>in vivo</i> is more complex than has been proposed.IMPORTANCEMost gram-positive bacteria encode penicillin- and Ser/Thr-kinase-associated (PASTA) kinases that are activated in response to cell wall stress to control critical physiological processes, including cell division and antibiotic resistance, among others. As such, PASTA kinases have been considered potential targets for new antibiotics. A thorough understanding of the mechanisms of PASTA kinase signaling is important for effective therapeutic intervention. However, the prevailing model for signaling by PASTA kinases has not been tested using a full-length kinase in cells of its native host under physiological conditions; hence, the mechanisms of signaling remain obscure. Here, we showed that the PASTA kinase of <i>Enterococcus faecalis</i> participates in self-association to form dimers in <i>E. faecalis</i> cells and that the self-associated form is functionally important for signaling. However, some features of the prevailing model for PASTA kinase signaling are inconsistent with our results, suggesting that regulation of PASTA kinase signaling <i>in vivo</i> is more complex than has been proposed.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0221126"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220126","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":"Sequencing-based molecular epidemiology of mesophilic <i>Aeromonas</i> in dairy environments and water systems.","authors":"Maliha Gulzar, Mudasir Ali Rather, Syed Akram Hussain, Sabia Qureshi, Showkat Ahmad Shah, Mohammad Ruhail Gulzar, Ambreen Hamadani, Mehak Nisar Khan, Majid Shafi Kawoosa","doi":"10.1128/spectrum.01471-26","DOIUrl":"https://doi.org/10.1128/spectrum.01471-26","url":null,"abstract":"<p><p>This study investigated the prevalence, virulence gene distribution, antimicrobial resistance, and molecular epidemiology of mesophilic <i>Aeromonas</i> species from milk, dairy farm environments, and drinking water systems in Kashmir, India. <i>Aeromonas</i> prevalence varied between sample sources, with environmental samples having the highest detection rate (51.96%), followed by water sources (46.60%) and milk (36.15%). Following pasteurization and disinfection, prevalence in milk samples was significantly reduced, demonstrating the efficacy of hygiene measures in minimizing contamination. Higher detection rates were found in environmental sources like soil, cow dung, and milkers' hands, suggesting their role as potential sources of contamination. The Aeromonads exhibited a wide distribution of virulence determinants; species-associated variations were noted for the <i>ahc</i> and <i>ast</i> genes, while the <i>fla</i> gene was ubiquitous among isolates. Virulence gene distribution differed between species, with <i>Aeromonas hydrophila</i> exhibiting the most varied virulence profiles. Antimicrobial resistance patterns were generally comparable among the mesophilic <i>Aeromonas</i> species, and multidrug resistance was detected in 45.8% of the isolates. Analysis of <i>gyrA</i>, <i>gyrB</i>, and <i>rpoD</i> genes based on sequencing distinguished isolates into species-specific clades, with <i>gyrB</i> providing the highest intra-species resolution, suggesting its utility as an informative marker for molecular epidemiological investigations of <i>Aeromonas</i>. These results show that water systems and dairy environments are significant sources of genetically diverse Aeromonads carrying virulence and antimicrobial resistance determinants.IMPORTANCE<i>Aeromonas</i> species are widely distributed in aquatic environments and are increasingly recognized as emerging opportunistic pathogens, yet their role in dairy production systems remains poorly understood. The prevalence and genetic relatedness of mesophilic <i>Aeromonas</i> spp. across milk, dairy farm environments, and drinking water systems remain underexplored. By integrating prevalence data from a large and diverse collection of samples with virulence profiling, antimicrobial resistance characterization, and sequencing-based molecular epidemiology, the present study provides a comprehensive assessment of <i>Aeromonas</i> populations across these interconnected compartments. The findings underscore the importance of hygienic practices during milk production and the need for routine monitoring of environmental and water sources associated with dairy systems. Improved understanding of the genetic diversity and distribution of <i>Aeromonas</i> can support more effective surveillance strategies and help mitigate potential risks to food safety and public health.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0147126"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220198","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":"Activity of manogepix and comparator antifungal agents against uncommon filamentous fungal isolates collected in a global surveillance program.","authors":"Marisa L Winkler, Abby Klauer, Samuel Edeker, Kelley Fedler, Paul Rhomberg, Mariana Castanheira","doi":"10.1128/spectrum.02559-26","DOIUrl":"https://doi.org/10.1128/spectrum.02559-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Fosmanogepix (prodrug of manogepix) is a novel antifungal agent targeting the Gwt1 enzyme. This agent has activity against a diverse spectrum of fungal species, including species refractory to other antifungal classes or multidrug-resistant fungi. A total of 332 molds from a worldwide surveillance study were susceptibility tested for manogepix and comparator antifungal agents by the Clinical and Laboratory Standards Institute (CLSI) reference broth microdilution method. Wild-type upper limit (WT-UL) values were determined for manogepix against organism groups using cumulative surveillance data. Isolates were collected from 20 countries, 41 hospitals, and 7 different infection sources. Eighteen genera were represented. Isolates included 208 non-&lt;i&gt;fumigatus Aspergillus&lt;/i&gt; spp.; 37.3% (124 isolates) were non-&lt;i&gt;Aspergillus&lt;/i&gt; molds. The manogepix minimum effective concentration (MEC&lt;sub&gt;50/90&lt;/sub&gt;) was lower than the MIC&lt;sub&gt;50/90&lt;/sub&gt; for azole comparators or amphotericin B against all &lt;i&gt;Aspergillus&lt;/i&gt; spp., &lt;i&gt;Fusarium&lt;/i&gt; spp., &lt;i&gt;Scedosporium&lt;/i&gt; spp., &lt;i&gt;Lomentospora&lt;/i&gt; spp., &lt;i&gt;Mucor&lt;/i&gt; spp., and &lt;i&gt;Penicillium&lt;/i&gt; spp. Only &lt;i&gt;Rhizopus&lt;/i&gt; spp. had higher MEC&lt;sub&gt;50/90&lt;/sub&gt; values for manogepix than the MIC&lt;sub&gt;50/90&lt;/sub&gt; values of the comparators. The WT-UL values reflected this, with the highest values for &lt;i&gt;Rhizopus&lt;/i&gt; spp. at 16 mg/L and &lt;i&gt;Mucor&lt;/i&gt; spp. at 4 mg/L, while they were ≤0.12 mg/L for all other organisms. Between 2023 and 2024, there were no organisms with MECs for manogepix above the WT-UL value. Manogepix displayed robust &lt;i&gt;in vitro&lt;/i&gt; activity against contemporary non-&lt;i&gt;Aspergillus fumigatus&lt;/i&gt; mold isolates. This agent was more potent than azole comparators or amphotericin B against most organism groups. Historically, less than 5% of isolates tested (&lt;i&gt;n&lt;/i&gt; = 19) had MECs above the WT-UL cutoff values. These data support the continued development of manogepix for the treatment of mold infections.IMPORTANCEFosmanogepix (prodrug of manogepix) is a novel antifungal agent with a new mechanism of action and broad-spectrum activity, including against yeasts and molds. It is currently in two Phase 3 clinical trials for the treatment of invasive candidiasis and invasive mold infections and has previously been used for the treatment of &lt;i&gt;Fusarium&lt;/i&gt; spp. infections during an outbreak. There are three main antifungal classes (echinocandins, azoles, and polyenes), but only azoles and amphotericin B have activity against non-&lt;i&gt;Aspergillus&lt;/i&gt; molds; therefore, novel antifungal agents are urgently needed because invasive fungal infections have high morbidity and mortality rates. Here, we look at the &lt;i&gt;in vitro&lt;/i&gt; activity of manogepix and comparator antifungal agents against non-&lt;i&gt;Aspergillus fumigatus&lt;/i&gt; mold isolates collected from patient infections in 2023 and 2024. Manogepix showed potent &lt;i&gt;in vitro&lt;/i&gt; activity against these organisms, with similar to or better activity than that of the comparator","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0255926"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220559","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":"High Canadian Arctic <i>Pseudomonas</i> spp. and their potential as biostimulants in cold growth conditions.","authors":"Louis-Philippe Thériault, Adrien Biessy, Martine Dorais, Martin Filion","doi":"10.1128/spectrum.02837-26","DOIUrl":"https://doi.org/10.1128/spectrum.02837-26","url":null,"abstract":"<p><p>This study investigated the potential of <i>Pseudomonas</i> strains isolated from the Canadian Arctic environment to be used as plant growth-promoting rhizobacteria (PGPR) in cold and temperate conditions. Forty bacterial strains were isolated from soil samples collected in the Cambridge Bay area, Nunavut. Their genomes were sequenced and annotated, their taxonomical affiliation determined, and genes/clusters associated with selected phytobeneficial traits were identified. In parallel, some of these traits, including atmospheric nitrogen fixation, siderophore production, auxin production, and phosphate solubilization, were evaluated <i>in vitro</i>. Based on these findings, the most promising strains were then tested for their ability to promote lettuce plant growth under cold (10°C) and temperate (20°C) conditions. The results revealed that most of the strains under study do not belong to species with validly published and correct names, representing 28 potential new species within the genus <i>Pseudomonas</i>. Substantial functional and taxonomic diversity among isolates was observed, highlighting the ecological complexity of Northern microbial communities. Interestingly, strains displaying higher phytobeneficial trait performance under <i>in vitro</i> assays did not consistently enhance plant growth. Yet, different strains significantly increased lettuce fresh and/or dry weight under cold and temperate conditions. The most efficient strains (LBUM1647, LBUM1648, LBUM1661, LBUM1666, and LBUM1675) do not share high taxonomical similarities, suggesting strain-specific rather than species-specific effects. These findings underscore the importance of considering PGPR trait expression in soil, strain-specific effects, and plant and microbe compatibility when selecting candidate <i>Pseudomonas</i> spp. More integrative screening strategies that better reflect rhizosphere conditions should therefore be developed.IMPORTANCEThis study explored the potential of using plant-beneficial bacteria isolated from Canadian Arctic soils to promote plant growth at low temperatures. It addresses a gap in knowledge as only very limited information on <i>Pseudomonas</i> strains from the Canadian Arctic is available and their potential role in supporting plant growth under cold conditions has not yet been well demonstrated. In addition, the functional traits these microorganisms harbor and their actual effects on plant growth at low temperatures remain poorly understood. Here, we identified and characterized promising plant growth promoters isolated from Canadian Arctic soils and belonging to the genus <i>Pseudomonas</i>. The identification of cold-adapted <i>Pseudomonas</i> spp. capable of promoting plant growth under low temperature conditions has important implications for agriculture in cold climates and shows great potential to support the development of sustainable biological solutions adapted to cold agricultural systems.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0283726"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220601","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":"Coevolution of carbohydrate-binding and catalytic modules revealed by a novel distant subgroup of CBM22 in a highly efficient GH10 xylanase PphXyn10B.","authors":"Yuan Yuan Yang, Shuai Li Pang, Zhi Ling Chen, Yan Hong Li","doi":"10.1128/spectrum.00825-26","DOIUrl":"https://doi.org/10.1128/spectrum.00825-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;GH10 endoxylanases exhibit significant structural and modular diversity, with many members containing carbohydrate-binding modules (CBMs) whose functions remain to be elucidated. In this study, we identified a GH10 endoxylanase PphXyn10B from the xylanolytic bacterium &lt;i&gt;Paenibacillus physcomitrellae&lt;/i&gt; XB. Predictions by AlphaFold3 and modeling by SWISS-MODEL suggested that its N-terminus contains two novel CBM22 modules (nCBM22s). To investigate the functions of this enzyme and its nCBM22s, we heterologously expressed the full-length recombinant enzyme (rnCBM22s-Xyn10B), truncated variants containing only a single nCBM22, both two nCBM22s (rnCBM22s), and retaining only the intact GH10 catalytic domain (CD, rXyn10B). The full-length recombinant efficiently hydrolyzed beechwood xylan (BWX) and arabinoxylan (AX), with xylobiose as the main oligosaccharide end product. Deletion of the two nCBM22s did not significantly alter the product profile or hydrolysis characteristics, except for an increase in the initial reaction rate. Notably, the two nCBM22s exhibited broad carbohydrate-binding capacity, recognizing not only insoluble BWX but also soluble AX and glucuronoxylan. Combined phylogenetic and domain analyses revealed that CBM22s in GH10 xylanases from different strains are highly diverse, with CBM22s from different subgroups being linked to the corresponding subgroups of GH10 CDs. The majority of nCBM22s clustered into a branch and were exclusively associated with the GH10_e130 CDs, suggesting that they may represent an evolutionary type among the various annotated CBM22 subgroups. This study is of great significance for understanding the diversity of the CBM22 family and its co-evolution with GH10 CDs, as well as for deepening our knowledge of the action mechanisms of efficient hydrolases.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;GH10 endoxylanases are ubiquitously distributed across microbial taxa and play essential roles in depolymerizing structurally heterogeneous xylans in plant cell walls. The discovery and systematic characterization of GH10 enzymes with potent activity against recalcitrant xylans are critical for advancing their application in lignocellulosic biomass conversion and sustainable bioenergy production. In this study, a GH10 endoxylanase, PphXyn10B, from &lt;i&gt;Paenibacillus physcomitrellae&lt;/i&gt; strain XB, exhibited broad substrate specificity and high catalytic efficiency toward various xylans, including beechwood xylan, wheat arabinoxylan, and xylooligosaccharides, yielding xylobiose as the predominant hydrolysis product. Furthermore, this enzyme contains two novel CBM22 modules and forms a phylogenetically distinct and well-supported lineage within the GH10_e130 catalytic domain (CD), evolutionarily separate from the known CBM22-associated GH10 CD. Collectively, these findings enhance our understanding of modular coevolution in GH10 xylanases and provide a mechanistic foundation for the rational engineering of multi-domain xyl","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0082526"},"PeriodicalIF":4.1,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149220538","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":"Whole-genome sequencing and antibiotic resistance analysis of a clinical carbapenem-resistant <i>Enterobacter chuandaensis</i>.","authors":"Ru Li, Yunxia Zhu, Weiting Zhang, Yue Zhang, Haifang Zhang, Junfeng Wang","doi":"10.1128/spectrum.02713-26","DOIUrl":"https://doi.org/10.1128/spectrum.02713-26","url":null,"abstract":"<p><p>This study aimed to characterize a rare clinical isolate, <i>Enterobacter chuandaensis</i>, carrying the carbapenem resistance gene <i>bla</i>_NDM-1. The antimicrobial susceptibility analysis revealed that <i>E. chuandaensis</i> EC001 was resistant to the majority of commonly used antimicrobial agents, except for amikacin, chloramphenicol, and minocycline. The results of the modified carbapenem inactivation method and EDTA-modified carbapenem inactivation method confirmed that <i>E. chuandaensis</i> EC001 produces metallo-β-lactamase. <i>E. chuandaensis</i> EC001 was typed as sequence type 2493 and presented an extensive drug-resistant profile. Whole-genome sequencing analysis demonstrated that the strain harbors two plasmids (p1_EC001 and p2_EC001), among which <i>bla</i>_NDM-1 is located on the conjugative plasmid p1_EC001 of IncFIB/IncFII-type. Plasmid p1_EC001 could be transferred into <i>Escherichia coli</i>, indicating its interbacterial horizontal transmission potential. The majority of plasmid-mediated resistance genes reside within or adjacent to various mobile genetic elements in p1_EC001. In addition, an <i>IS</i>3000 element (3,018 bp) was detected upstream of <i>bla</i>_NDM-1, while the bleomycin resistance-related gene <i>ble</i>_MBL was located downstream of <i>bla</i>_NDM-1, followed by <i>trpF</i>, <i>dsbD</i>, <i>cutA</i>, <i>groS</i>, <i>groL</i>, and <i>IS</i>Kpn19. Moreover, one class 1 integron harboring the genetic array <i>intI1-dfrA12-aadA2-qacEdeltal-sul1</i> was identified on p1_EC001. The plasmid p2_EC001 was characterized as a mobilizable plasmid, and two key genes, <i>mbeA</i> and <i>mbeC</i>, were detected, which encode the plasmid mobilization relaxase MbeA and the accessory protein MbeC, respectively. In summary, this study demonstrated the antimicrobial susceptibility, plasmid features, and potential transmission mechanisms of <i>E. chuandaensis</i> EC001, which serve as evidence for controlling and prevention of clinical <i>E. chuandaensis</i>.IMPORTANCECurrent research on carbapenem resistance in <i>E. chuandaensis</i> remains relatively limited. This study performed detailed genome characterization of the two plasmids (p1_EC001 and p2_EC001) carried by <i>E. chuandaensis</i> EC001 and analyzed their resistance gene profiles, plasmid features, and potential transmission mechanisms. The findings provide a theoretical foundation for the formulation of hospital infection control strategies, improve the capability for early warning and prevention of carbapenem-resistant <i>Enterobacterales</i>, and exhibit substantial scientific significance, as well as promise clinical application value.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0271326"},"PeriodicalIF":4.1,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149195370","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":"Diagnostic accuracy of TB-LAMP assay on tongue swabs for pulmonary tuberculosis.","authors":"Qingtao Liang, Ruiqi Han, Yuanyuan Shang, Yu Dong, Weicong Ren, Yilin Wang, Hongfei Duan, Yu Pang","doi":"10.1128/spectrum.02391-26","DOIUrl":"https://doi.org/10.1128/spectrum.02391-26","url":null,"abstract":"<p><p>Tuberculosis (TB) remains a leading cause of infectious disease mortality worldwide. However, underdiagnosis and delayed diagnosis continue to facilitate disease transmission. Tongue swab sampling has emerged as a promising non-invasive alternative for the diagnosis of pulmonary TB. This study evaluated the diagnostic performance of the Eiken TB-LAMP assay when utilizing tongue swab specimens and refined the processing protocols following tongue swab collection. In this prospective study, consecutive outpatients with suspected pulmonary tuberculosis who were able to provide sputum specimens were enrolled. Tongue swab specimens were tested using the WHO-endorsed Eiken TB-LAMP platform (EIKEN CHEMICAL CO., LTD., Tokyo, Japan). Sputum samples were analyzed by Xpert MTB/RIF and culture tests. The microbiological reference standard (MRS) was defined as positivity by either sputum culture or Xpert MTB/RIF. Diagnostic performance was compared to both MRS and Xpert MTB/RIF assay. Among the 243 enrolled participants, 136 (56.0%) were MRS-positive, and 107 (44.0%) were MRS-negative. The tongue swab Eiken TB-LAMP assay achieved a sensitivity of 80.2% (95% CI: 72.5%-86.1%) and a specificity of 94.6% (95% CI: 88.8%-97.5%) compared to sputum Xpert MTB/RIF, and 80.1% sensitivity (95% CI: 72.7%-86.0%) and 98.1% specificity (95% CI: 93.4%-99.7%) compared to the MRS. Sensitivity varied by bacterial load, ranging from 100% (95% CI: 77.2%-100.0%) in high-load cases to 62.5% (95% CI: 45.3%-77.1%) in very-low-load cases. The Eiken TB-LAMP assay using tongue swabs offers a rapid, reliable, and non-invasive diagnostic alternative for TB diagnosis with high specificity and favorable sensitivity. It could significantly reduce the current diagnostic gap, facilitating earlier intervention and helping to curb the ongoing transmission of tuberculosis in high-burden regions.</p><p><strong>Importance: </strong>Effective control of the disease caused by the bacterium <i>Mycobacterium tuberculosis</i> is often hindered by the challenges of collecting sputum samples and the high costs associated with specialized laboratory equipment. This study examines a new diagnostic approach using tongue swabs combined with loop-mediated isothermal amplification (LAMP). Unlike traditional methods that can be difficult for patients to perform and risky for healthcare workers to manage, tongue swabs are non-invasive, safe, and easy to collect. Because LAMP amplifies DNA under isothermal conditions without requiring thermal cycling, it is more affordable and requires minimal infrastructure, making it particularly suitable for clinics in remote or resource-limited areas. By demonstrating that this approach is effective, the research provides a foundation for faster and more accessible diagnosis. This shift could significantly improve patient care and help bridge the global gap in detecting this infectious disease.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0239126"},"PeriodicalIF":4.1,"publicationDate":"2026-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149195267","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}