Applied and Environmental Microbiology最新文献

{"title":"A functionally selected <i>Acinetobacter</i> sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in <i>E. coli</i>.","authors":"Elizabeth Bernate, Yijun Shi, Ezabelle Franck, Terence S Crofts","doi":"10.1128/aem.02468-25","DOIUrl":"10.1128/aem.02468-25","url":null,"abstract":"<p><p>Polymyxins are last-resort antibiotics for infections caused by multidrug-resistant gram-negative bacteria such as Enterobacteriaceae, <i>Pseudomonas aeruginosa,</i> and <i>Acinetobacter baumannii</i>. This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document the potential sources of the corresponding resistance genes. This study searched for potential emerging colistin resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured <i>Acinetobacter</i> sp. DNA fragments that all contained <i>eptA</i> genes. We confirmed their ability to confer significant colistin resistance in <i>Escherichia coli</i> via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related <i>eptA</i> genes in <i>Acinetobacter</i> genomes, marking them as potential <i>mcr</i> genes or their precursors. This study highlights the potential for functional metagenomic selections for colistin resistance to capture genes from unexpected environmental sources such as the goose fecal microbiome.IMPORTANCEColistin is an important antibiotic of last resort, and increasing resistance to this drug via mobile phosphoethanolamine transferase genes, such as <i>mcr-1</i>, threatens its clinical utility. Given the discovery of <i>mcr-1</i> in pigs, the ability of animals to act as vectors in the spread of colistin resistance is alarming. We show here that functionally selected <i>Acinetobacter</i> phosphoethanolamine transferase genes from the goose microbiome have the ability to confer clinical levels of colistin resistance when transferred into <i>E. coli</i>. While the genes are annotated as <i>eptA</i> homologs, closer study of these genes suggests that they may be mobilized within the <i>Acinetobacter</i> genus, suggesting that they may be <i>mcr</i> genes of concern instead.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0246825"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599516/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148676785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental microbial community signatures associated with <i>Listeria</i> spp. detection in German meat processing facilities.","authors":"Jérôme Braun, Nicole Wildi, Jasna Kovac, Claudia Guldimann","doi":"10.1128/aem.01042-26","DOIUrl":"10.1128/aem.01042-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Listeria monocytogenes&lt;/i&gt; can persist in niches of meat processing environments despite routine cleaning and disinfection. Its persistence may depend not only on stress tolerance but also on interactions with resident microbial communities, which may promote or inhibit survival. However, these ecological relationships remain poorly understood. We combined 16S rRNA V3/V4 amplicon sequencing, culture-based detection, and multilocus sequence typing (MLST) to characterize microbial communities in six German meat processing facilities over one year. We examined associations among community structure, sampling sites, and the occurrence of &lt;i&gt;Listeria&lt;/i&gt; spp., including &lt;i&gt;L. monocytogenes&lt;/i&gt;. Microbial communities were dominated by core genera typical of food-processing environments, particularly &lt;i&gt;Pseudomonas&lt;/i&gt; spp. and &lt;i&gt;Acinetobacter&lt;/i&gt; spp., but differed significantly among facilities (PERMANOVA, &lt;i&gt;P&lt;/i&gt; = 0.001; pairwise &lt;i&gt;R&lt;/i&gt;² = 0.023-0.079), indicating facility-specific communities. Culture-based analyses detected &lt;i&gt;Listeria&lt;/i&gt; spp. in 51 of 370 environmental samples (13.8%), mainly from drains (44/51, 86.3%). &lt;i&gt;L. monocytogenes&lt;/i&gt; was detected in five of six facilities, with 19 of 21 isolates originating from drains (90.5%). MLST of 74 typeable &lt;i&gt;L. monocytogenes&lt;/i&gt; isolates revealed high diversity, comprising 21 sequence types across 15 clonal complexes, with lineage II predominating (86.5%). Overall microbial community composition was significantly associated with &lt;i&gt;Listeria&lt;/i&gt; spp. and &lt;i&gt;L. monocytogenes&lt;/i&gt; presence (PERMANOVA, &lt;i&gt;P&lt;/i&gt; = 0.001; &lt;i&gt;R&lt;/i&gt;² = 0.0137 and 0.0083). In drains, amplicon sequence variants (ASVs) assigned to the genera &lt;i&gt;Acinetobacter&lt;/i&gt;, &lt;i&gt;Rhizorhapis&lt;/i&gt;, and &lt;i&gt;Vagococcus&lt;/i&gt; showed positive associations with &lt;i&gt;Listeria&lt;/i&gt; spp.-positive samples. Together, these findings suggest that drains are key ecological niches for &lt;i&gt;Listeria&lt;/i&gt; spp. and that associated taxa may indicate drain communities linked to &lt;i&gt;Listeria&lt;/i&gt; spp. recovery.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Listeria monocytogenes&lt;/i&gt; is a major foodborne pathogen that can persist in meat processing environments despite routine cleaning and disinfection. Resident microbial communities may influence its survival, but longitudinal studies linking those communities with culture-based &lt;i&gt;Listeria&lt;/i&gt; spp. detection remain limited. Here, we characterized microbial communities in six German meat processing facilities over 1 year using 16S rRNA gene amplicon sequencing and culture-based &lt;i&gt;Listeria&lt;/i&gt; spp. detection, and MLST of &lt;i&gt;L. monocytogenes&lt;/i&gt; isolates. We identified facility-specific microbial communities, identified floor drains as key niches for &lt;i&gt;Listeria&lt;/i&gt; spp., and observed repeated recovery of different &lt;i&gt;L. monocytogenes&lt;/i&gt; sequence types across facilities. In drains, ASVs assigned to the genera &lt;i&gt;Acinetobacter&lt;/i&gt;, &lt;i&gt;Rhizorhapis&lt;/i&gt;, and &lt;i&gt;Vagococcus&lt;/i&gt; were positively associated with culture-p","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0104226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599490/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From trees to graphs: rethinking phylogeny in microbiome prediction.","authors":"Qiao Yu, Defeng Bai, Yao Wang, Yong-Xin Liu","doi":"10.1128/aem.01432-26","DOIUrl":"10.1128/aem.01432-26","url":null,"abstract":"<p><p>Microbiome prediction models overlook phylogeny or fail to preserve evolutionary structure. In a recent <i>Applied and Environmental Microbiology</i> article (B. Dong, B. Wang, J. Chen, X. Xu, and Z. Z. Xu, Appl Environ Microbiol 92:e00788-26, 2026, https://doi.org/10.1128/aem.00788-26), Dong et al. present PhyloGCNE, a graph-convolutional framework that addresses these limitations by preserving evolutionary topology and learning adaptive edge-aware signal propagation. This commentary evaluates whether and when phylogenetic information improves microbiome-based prediction and considers how biological relevance and transferability can be established across contexts.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0143226"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599496/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148863536","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soil microbial growth rate, trophic strategy, and the oligotroph-copiotroph continuum.","authors":"Chansotheary Dang, Juan Piñeiro Nevado, Ronald Schartiger, Binu M Tripathi, Jeth G Walkup, Edward Brzostek, Ember M Morrissey","doi":"10.1128/aem.01324-26","DOIUrl":"10.1128/aem.01324-26","url":null,"abstract":"<p><p>The oligotroph-copiotroph continuum is an ecological framework that describes microbial metabolic traits, habitat preferences, and growth strategies. As microbial growth rates determine soil element cycling, understanding microbial trophic strategies is critical for improving predictions of ecosystem biogeochemistry. However, accurately determining microbial trophic strategies has been challenging for soil microorganisms. Here, we examined microbial growth rates (via ¹⁸O-quantitative stable isotope probing) in rhizosphere and bulk forest soils and proposed a new approach to determine the trophic strategies of microbial taxa. Growth rates were log-normally distributed and used to classify 35% of bacterial taxa as oligotrophs (lowest growth rates), 50% as mesotrophs (intermediate growth rates), and 15% as copiotrophs (highest growth rates). The average growth rates of individual taxa exhibited phylogenetic organization, suggesting that growth rates are constrained by vertically transmitted genomic traits under varying conditions. Consistent with the expected habitat preferences, copiotrophs were more abundant and active in the rhizosphere, while bulk soil was dominated by slow-growing oligotrophs. Carbon addition positively impacted copiotroph growth rates in both the rhizosphere and bulk soil. Oligotrophic and mesotrophic taxa benefited from carbon addition in the bulk soil, but not in the rhizosphere, perhaps due to intensified competition with a large population of copiotrophs. Taken together, these results demonstrate that microbial growth rates are tied to bacterial habitat preferences and carbon responses, suggesting they may be strong indicators of trophic strategy.IMPORTANCEDespite compelling culture-based evidence for the oligotroph-copiotroph framework, scientists have struggled for decades to meaningfully characterize the trophic strategies of soil microorganisms, perhaps due to methodological limitations. This work uses a growth rate approach to determine the trophic strategies of microbial taxa that is validated by testing two classic hypotheses regarding microbial trophic strategy in soil. The results support the use of growth rate-based trophic strategy classification and demonstrate that microbial growth rates are constrained by evolutionary history such that fine (e.g., families and genera) but not coarse (e.g., phyla and orders) taxonomic groups may be meaningfully described as oligotrophs or copiotrophs. These results are of broad relevance, as they suggest that growth rate measurements may be used to make a prevailing ecological theory describing all unicellular microbial life on Earth (i.e., the oligotroph-copiotroph framework) more quantitative and robust.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0132426"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148700562","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vesicle-associated exudates from <i>Alteromonas</i> enhance growth and survival of <i>Prochlorococcus</i> in batch culture.","authors":"Zhiying Lu, Sydney Plummer, James Kizziah, Steven J Biller, J Jeffrey Morris","doi":"10.1128/aem.00798-26","DOIUrl":"10.1128/aem.00798-26","url":null,"abstract":"<p><p>The cyanobacterium <i>Prochlorococcus</i> MIT9312 requires helping functions from co-existing organisms for survival under stressful conditions. Here, we show that the helper strain <i>Alteromonas macleodii</i> EZ55 also facilitates greater exploitation of medium resources by <i>Prochlorococcus</i>. The presence of <i>Alteromonas</i> allowed <i>Prochlorococcus</i> to grow to greater cell densities, delay growth cessation, and avoid cell death relative to axenic cultures, phenotypes potentially associated with <i>Alteromonas</i>-driven degradation of autotoxic substances made by <i>Prochlorococcus</i>. We found that heat-labile high-molecular-weight <i>Alteromonas</i> exudates mediated the beneficial impacts on <i>Prochlorococcus</i>, although it is unclear which specific exudate-associated activities were responsible. Both the composition and activity of the secreted material changed after 500 generations of experimental evolution, suggesting genetic control. Some exudates were located within extracellular vesicles, which were capable of physically associating with <i>Prochlorococcus</i> cells and were responsible for at least some of the growth enhancement effects. Many of the functionalities observed in <i>Alteromonas</i> exudates (e.g., increasing phosphate availability, hydrogen peroxide degradation, and siderophore capabilities) are consistent with leaky Black Queen processes (i.e., services provided by one organism that benefit the entire community) and favor the evolution of interdependencies in microbial communities. We discuss the potential ramifications of such processes being packaged into vesicles as opposed to freely diffusing through the extracellular milieu.IMPORTANCEHeterotrophic bacteria can facilitate improved growth for numerous phytoplankton, including the highly abundant cyanobacterium <i>Prochlorococcus</i>. Here, we show that for the \"helper\" interaction between <i>Alteromonas</i> and <i>Prochlorococcus</i>, this facilitation is relevant across all phases of batch culture growth and is mediated by secreted products, including proteins and membrane vesicles. We explore the composition of these exudates and show evidence that they are altered during evolutionary adaptation in a changed environment.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0079826"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148668411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction for Wang et al., \"<i>Bacillus haimaensis</i> sp. nov.: a novel cold seep-adapted bacterium with unique biosynthetic potential\".","authors":"Yuanyuan Wang, Luyi Yang, Wenbo Wu, Zhengqi Feng, Jian He, Changjun Guo, Jianguo He","doi":"10.1128/aem.01157-26","DOIUrl":"10.1128/aem.01157-26","url":null,"abstract":"","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0115726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148787442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transferable <i>optrA-</i>mediated linezolid resistance in enterococci from high-altitude river sediments of Gilgit-Baltistan, Pakistan.","authors":"Serena Simoni, Andrea Brenciani, Alessandra Di Gregorio, Francesca Romana Massacci, Lucilla Cucco, Maisoor Ahmed Nafees, Saif Ud Din, Nelofar Hanif, Stefania Gorbi, Francesco Regoli, Eleonora Giovanetti, Carla Vignaroli","doi":"10.1128/aem.01129-26","DOIUrl":"10.1128/aem.01129-26","url":null,"abstract":"<p><p>Environmental dissemination of antimicrobial resistance is a growing global concern. This study investigated the occurrence, genetic context, and mobility of the oxazolidinone resistance genes in enterococci isolated from high-altitude river sediments in the Gilgit-Baltistan region of Pakistan. A total of 17 florfenicol-resistant enterococci were recovered from 3 of the 12 sampling sites analyzed. Four multidrug-resistant strains (two <i>Enterococcus faecium</i>, one <i>E. faecalis</i>, and one <i>E. hirae</i>) harboring the <i>optrA</i> gene were selected for whole-genome sequencing using Illumina and Nanopore platforms. Genomic analyses showed that <i>optrA</i> was plasmid-borne in all isolates and co-localized with additional resistance genes, including macrolide, phenicol, and tetracycline resistance determinants. The <i>optrA</i> genetic context was frequently associated with insertion sequences, suggesting their role in the mobilization of multidrug-resistance elements. Mini-translocatable units of the <i>optrA</i> genetic context were detected as circular forms in two of four strains, further supporting their mobility potential. Conjugation assays demonstrated successful horizontal transfer of the <i>optrA</i> gene mediating linezolid resistance, with transfer frequencies ranging from 2.03 × 10⁻⁶ to 6.36 × 10⁻⁴ transconjugants per recipient cell. <i>optrA</i>-carrying plasmids remained stable after serial passages without antibiotic pressure. Phylogenetic analysis showed that isolates belonged to distinct sequence types and clustered with strains of diverse geographic and ecological origins, suggesting dissemination of <i>optrA</i> across different genetic backgrounds rather than clonal expansion. The occurrence of linezolid-resistant enterococci in high-altitude river sediments suggests their widespread distribution and emphasizes the need for broader environmental surveillance programs to monitor clinically relevant resistances even in remote ecosystems.</p><p><strong>Importance: </strong>This study provides important insights into the environmental dissemination of antimicrobial resistance by demonstrating the occurrence and genetic diversity of clinically relevant resistance determinants in enterococci isolated from remote high-altitude river sediments. The findings emphasize that natural environments could serve as reservoirs and exchange hubs for antimicrobial resistance, even in ecosystems with limited direct anthropogenic impact. Therefore, integrated One Health surveillance strategies that include environmental compartments alongside human and animal populations are required to better monitor and mitigate the emergence of clinically significant resistant bacteria.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0112926"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148878865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of successive <i>ortho</i>-methyl oxidation of the priority pollutant 2,4-xylenol by a Rieske oxygenase system in <i>Pseudomonas putida</i> NCIMB 9866.","authors":"Haiqin Meng, Shun Pan, Zening Chai, Lixiang Zhou, Tianyu Zheng, Hanyu Zhang, He Fu, Lei Zou, Dongqi Liu, Jingcheng Dai, Dazhong Yan, Hong-Jun Chao","doi":"10.1128/aem.01293-26","DOIUrl":"10.1128/aem.01293-26","url":null,"abstract":"<p><p>The catabolism of the priority environmental pollutant 2,4-xylenol requires bacteria to oxidize its <i>ortho</i>-methyl group. Its exact biochemical mechanism is uncharacterized until now. In this study, we resolve key metabolic bottlenecks in <i>Pseudomonas putida</i> NCIMB 9866. We demonstrate that functionally redundant Rieske oxygenase systems ensure the robust <i>ortho</i>-methyl oxidation of 2,4-xylenol. On the <i>para</i>-methyl oxidation branch, PchA2 acts as the main aldehyde dehydrogenase. It shows significantly higher catalytic efficiency than the previously reported PchA. Additionally, we characterized PmmA1B1, a newly identified three-component Rieske oxygenase system responsible for <i>ortho</i>-methyl oxidation, which is supported by two redundant isoenzymes (PmmA2B2 and PmmA3B3), by recruiting the shared endogenous ferredoxin Orf05169. The PmmA1B1-Orf05169 system catalyzes the successive oxidation of the <i>ortho</i>-methyl group of 4-hydroxy-3-methylbenzoate to a carboxyl group, yielding the high-value pharmaceutical precursor 4-hydroxyisophthalate. Structural and kinetic data revealed that the active site architecture of PmmA1 enables efficient successive oxidation, distinguishing it from isoenzymes PmmA2B2 and PmmA3B3 that, when coupled with Orf05169, catalyze only incomplete oxidation. Overall, these results complete the 2,4-xylenol catabolic pathway by defining the enzymes required for both <i>para</i>- and <i>ortho</i>-methyl oxidation. They also reveal functional redundancy as an adaptive feature of microbial aromatic degradation and establish Rieske oxygenases as biocatalysts for converting methylated aromatic pollutants into value-added chemicals.IMPORTANCEMethylated aromatics like 2,4-xylenol pose ongoing environmental risks and are primary targets for bioremediation. We know how bacteria break down many simple aromatics, but the precise ways that enzymes bypass the steric and electronic hurdles of hindered methyl groups remain unclear. In this study, we characterized a novel three-component Rieske oxygenase, PmmA1B1-Orf05169, capable of a rare successive oxidation that turns an <i>ortho</i>-methyl group directly into a carboxyl group. We also found parallel, redundant oxygenase pathways that protect the bacterium's ability to degrade 2,4-xylenol during environmental stress or genetic loss. This discovery not only completes the metabolic map of 2,4-xylenol but also provides a robust biocatalytic tool for the green synthesis of 4-hydroxyisophthalate, a high-value pharmaceutical precursor.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0129326"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599478/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148672946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Klebsiella pneumoniae</i> from fuchka: insights into the genetic diversity, virulence, and antibiogram profile.","authors":"Bushra Benta Rahman Prapti, Md Tanjir Ahmmed, Chinmoy Dev Nath, Aminur Rahman, Sakhyajit Saha Parijat, Partho Protim Acharjee, Jayedul Hassan, Md Shafiqul Islam, Mahbubul Pratik Siddique","doi":"10.1128/aem.00996-26","DOIUrl":"10.1128/aem.00996-26","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; is an emerging pathogen of global concern due to its capacity to acquire antimicrobial resistance and virulence determinants, yet its presence in the food environment remains unexplored. This study investigated the prevalence, antimicrobial resistance, virulence genes, biofilm formation, and genomic characteristics of &lt;i&gt;K. pneumoniae&lt;/i&gt; isolated from a widely consumed street food in Bangladesh. A total of 90 fuchka and related samples from different sources were collected and analyzed using culture-based methods, PCR confirmation, matrix-assisted laser desorption ionization time-of-flight assay, and 16S rRNA sequencing. Antibiotic sensitivity was determined using the disk diffusion method, and resistance- and virulence-associated genes were detected by PCR. Biofilm formation was quantified using a 96-well microtiter plate assay, and genetic diversity was assessed by enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR) fingerprinting. Whole-genome sequencing (WGS) was performed on four representative isolates for in-depth genomic characterization. &lt;i&gt;K. pneumoniae&lt;/i&gt; was recovered from 46.7% of samples. Among the isolates, 37.5% exhibited a multidrug-resistant (MDR) phenotype, with universal resistance to ampicillin. Virulence genes including &lt;i&gt;wab&lt;/i&gt;G (90.5%) and &lt;i&gt;uge&lt;/i&gt; (95.2%) were highly prevalent, whereas &lt;i&gt;rmp&lt;/i&gt;A and &lt;i&gt;bfp&lt;/i&gt; were absent. Capsular serotypes K3 and K5 were detected in 16.7% of isolates. The class 1 integron (&lt;i&gt;int&lt;/i&gt;1) (83.3%) and &lt;i&gt;tet&lt;/i&gt;A (56.7%) were the most frequently detected resistance determinants. Biofilm formation was observed in 31% of isolates and significantly associated with the MDR phenotype. WGS revealed clinically relevant sequence types (ST2262) phylogenomically related to human clinical strains. These findings indicate that fuchka may act as a reservoir for virulent and MDR &lt;i&gt;K. pneumoniae,&lt;/i&gt; highlighting the urgent need for improved hygiene practices and integration of street food into the One Health antimicrobial surveillance framework.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;The presence of multidrug-resistant (MDR) &lt;i&gt;Klebsiella pneumoniae&lt;/i&gt; in ready-to-eat street foods poses a significant public health concern, particularly in low- and middle-income countries where informal food vending is widespread. Fuchka is consumed daily by diverse population groups in Bangladesh, including children and young adults, making it a potential route for silent transmission of clinically important pathogens. The detection of MDR strains harboring virulence factors, integrons, and biofilm-forming ability suggests an elevated risk of persistence, spread, and limited treatment options in case of infection. This study highlights street food as an overlooked reservoir in the One Health framework, bridging community environments and clinical settings. Improved surveillance, vendor hygiene training, and enforcement of food safety regulations are crucial to reduce th","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0099626"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148676789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The PucR-type activator IppR regulates 2-isopropylphenol hydroxylation in strain <i>Rhodococcus</i> sp. D-6.","authors":"Qian Zhu, Kangning Wei, Yike Lyu, Qi Xie, Kaihua Pan, Qian Li, Weihao Zhu, Zhijian Ke, Jiguo Qiu, Mingliang Zhang, Junqiang Hu, Shang Dai, Qing Hong","doi":"10.1128/aem.01277-26","DOIUrl":"10.1128/aem.01277-26","url":null,"abstract":"<p><p>Although genes involved in isoprocarb (IPC) degradation, including the IPC hydrolase gene <i>ipcH</i> and the 2-isopropylphenol (IPP) hydroxylation gene cluster <i>ippA1A2</i>, have been identified in <i>Rhodococcus</i> sp. D-6, the transcriptional regulatory mechanism remains unclear. In this study, we characterized a PucR-type transcriptional regulator, IppR, which controls the inducible expression of the <i>ippA1A2</i> cluster. Gene disruption and complementation analyses revealed that <i>ippR</i> was essential for activation of <i>ippA1A2</i> expression in response to IPP in strain D-6. Quantitative reverse transcription-PCR (qRT-PCR) and promoter activity assays demonstrated that IPP was the effector molecule of IppR. Electrophoretic mobility shift assay (EMSA) showed that IppR bound to a 24-bp motif in the promoter region, with the CC/CG box within this motif identified as the critical site for IppR binding. Moreover, IppR residues likely involved in IPP binding include Val188, Leu192, Val218, Trp257, Trp259, His297, and Ala300, along with Lys382 and Thr384, which are predicted to be essential for DNA recognition. This study elucidates the regulatory mechanism of IPC degradation in strain D-6, and the identification of IppR expands the diversity of regulatory models within the PucR-type regulator.IMPORTANCECarbamate insecticides pose a potential threat to the environment and human health. Bacteria play an important role in the biodegradation of these compounds. <i>Rhodococcus</i> sp. D-6, which is capable of degrading isoprocarb (IPC), a representative carbamate insecticide, was isolated in our previous study. The expression of the IPC hydrolase gene <i>ipcH</i> was constitutive, while the expression of the <i>ippA1A2</i> cluster responsible for hydroxylation of 2-isopropylphenol (IPP), the hydrolysis product of IPC, was inducible. The present study functionally characterized the PucR-type transcriptional regulator IppR, which activates the transcription of the <i>ippA1A2</i> cluster to mediate IPP hydroxylation in strain D-6. This study advances our understanding of the regulatory mechanisms underlying IPC degradation.</p>","PeriodicalId":8002,"journal":{"name":"Applied and Environmental Microbiology","volume":" ","pages":"e0127726"},"PeriodicalIF":4.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13599513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148676903","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}