Journal of microbiological methods最新文献

{"title":"Comparative disinfectant sensitivity of methicillin-resistant and methicillin-sensitive Staphylococcus aureus cells","authors":"Ryan Karcher ,&nbsp;Lisa S. Smith ,&nbsp;Vipin K. Rastogi","doi":"10.1016/j.mimet.2025.107275","DOIUrl":"10.1016/j.mimet.2025.107275","url":null,"abstract":"<div><div>Cells of a Methicillin-resistant strain of <em>Staphylococcus aureus</em> (MRSA, ATCC 33592) were compared with a Methicillin-sensitive strain of <em>S. aureus</em> (ATCC 6358) for sensitivity to three different disinfectant active ingredient classes using the quantitative method (QM). The disinfectant active ingredient classes included reagent grade hydrogen peroxide, quaternary ammonium compound (QAC), and reagent grade sodium hypochlorite. Cells of both strains were grown in broth culture, mixed with a 3-part soil load [mucin, Bovine Serum Albumin (BSA) and yeast extract], dried briefly on small stainless-steel carriers, and exposed to different dosages of disinfectant classes, corresponding to low, intermediate, and high efficacy treatments. Results show consistent cell recovery from both strains in the range of 5.5–6.0-Log₁₀ of bacteria per carrier from control sets assessed on nine separate test days. Efficacy results measured as mean log reduction (LR) values show comparable sensitivity of the MRSA strain relative to the Methicillin-sensitive strain to the low treatment of all three disinfectant classes. The MRSA strain displayed enhanced sensitivity (an increase in LR of 1.5–2.0) to the three disinfectant classes at the intermediate treatment level relative to the Methicillin-sensitive strain. Interestingly, while the MRSA strain displayed higher sensitivity to hydrogen peroxide by 2-Log₁₀ relative to the Methicillin-sensitive strain at the high treatment level, the two strains displayed comparable sensitivity to high treatment levels of the other two disinfectant classes, i.e., sodium hypochlorite and QAC. Taken together, the results show comparable to enhanced sensitivity of the MRSA cells compared to Methicillin-sensitive cells to reagent grade hydrogen peroxide, QAC, and sodium hypochlorite. The results support the contention that antibiotic resistance in <em>S. aureus</em> is <em>not</em> correlated with higher resistance to these three classes of disinfectants.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107275"},"PeriodicalIF":1.9,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A rapid in-lab toolbox for the discrimination of Vibrio natriegens and Escherichia coli cultures","authors":"Lara S. Möller ,&nbsp;José M.M. Santos ,&nbsp;A. Rita Silva-Santos ,&nbsp;Duarte M.F. Prazeres","doi":"10.1016/j.mimet.2025.107273","DOIUrl":"10.1016/j.mimet.2025.107273","url":null,"abstract":"<div><div>We present a practical toolbox for identifying <em>Vibrio natriegens</em> in laboratory cultures, based on observable phenotypes and species-specific PCR. This workflow enables fast discrimination of <em>V. natriegens</em> from <em>Escherichia coli</em> K-12 and derivatives and microbial contaminants without sequencing or specialized equipment.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107273"},"PeriodicalIF":1.9,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization and applications of MSS pigment isolated from Streptomyces ardesiacus","authors":"Bhuvaneswari Puvarajan,&nbsp;Dharshine Susilkumar,&nbsp;Dhanushiya Dhamothara Kannan,&nbsp;Jayapradha Ramakrishnan","doi":"10.1016/j.mimet.2025.107264","DOIUrl":"10.1016/j.mimet.2025.107264","url":null,"abstract":"<div><div>Bacteria produce pigments to protect themselves from UV radiation and oxidative damage, aiding their survival and adaptation in various environments. As concerns over synthetic dyes grow, microbial pigments have gained attention for their potential benefits. They offer advantages such as high yield, cost-effectiveness, and ease of extraction. <em>Streptomyces ardesiacus,</em> isolated from <em>Moringa olifera</em> rhizophore soil produced pink/magenta colour pigment. It was characterized by UV–Vis spectrophotometry, FT-IR, HPLC, and NMR. The isolated MSS pigment showed no antimicrobial activity against tested bacterial and fungal strains, including <em>Escherichia coli, Salmonella typhi, Klebsiella pneumoniae, Candida auris and Candida albicans</em>. Moreover, it showed no haemolytic activity, indicating its potential safety for use in various applications. Importantly, the pigment demonstrated durable retention in textile dyeing (even after multiple washes) and stable incorporation in lip balm formulation, highlighting its potential as a safe and eco-friendly alternative to synthetic dyes. This study underscores the promise of microbial pigments in various industrial applications, offering a sustainable and eco-friendly solution.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107264"},"PeriodicalIF":1.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and in silico evaluation of a novel chimeric protein vaccine candidate against Salmonella Typhi","authors":"Mohsen Bidar Ajerloo ,&nbsp;Abbas Hajizade ,&nbsp;Shahram Nazarian ,&nbsp;Kavyan Khalili","doi":"10.1016/j.mimet.2025.107268","DOIUrl":"10.1016/j.mimet.2025.107268","url":null,"abstract":"<div><div>Typhoid fever, caused by <em>Salmonella enteritidis serovar</em> Typhi <em>(S.</em> Typhi<em>)</em>, remains a significant global health challenge, especially in regions with poor sanitation. Despite available vaccines, limitations such as short-term efficacy and variable immune responses necessitate novel strategies. Here, we designed a multi-protein chimeric protein vaccine targeting <em>S.</em> Typhi by integrating three key antigens: SteD (an immune-evasion transmembrane effector) (whole protein), flagellin (D1 domain), and STIV (<em>Salmonella</em> Typhi invasion protein) (whole protein). Proteins were linked via rigid EAAAK linkers to enhance stability. The construct exhibited high antigenicity (VaxiJen score:0. 9228) and favorable physicochemical properties (ProtParam), with non-allergenic (AlgPred) and non-toxic (ToxinPred) profiles. Structural analysis revealed a stable 3D model (I-TASSER/Phyre2/RaptorX), validated by Ramachandran plot (&gt;90 % favored regions), ProSA z-score of −5.54, and ERRAT. B-cell and T-cell epitopes predicted by IEDB, ABCPred, and Discotope 2.0 demonstrated strong binding to HLA alleles. Molecular docking confirmed robust interactions with TLR-4 (PDB:<span><span>2Z63</span><svg><path></path></svg></span><strong>)</strong> and TLR-5 (PDB:<span><span>3V44</span><svg><path></path></svg></span><strong>)</strong>, while 100-ns MD simulations (NAMD/VMD) affirmed complex stability (low RMSD/RMSF). Immune simulations (C-ImmSim) predicted potent humoral and cellular responses, including elevated IgG/IgM and Th1/Th2 cytokines. This in silico study proposes a promising vaccine candidate with high theoretical immunogenicity and structural integrity, warranting further in vitro and in vivo validation.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107268"},"PeriodicalIF":1.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of Klebsiella pneumoniae isolates between antibiotic-resistant and antibiotic-sensitive strains using polymerase chain reaction-based genotyping and protein profiling","authors":"Yadav Ranu ,&nbsp;Srajana Nayak ,&nbsp;Pallavi Bhat Ajakkala ,&nbsp;Chaitra Prabhu ,&nbsp;Caroline DSouza ,&nbsp;Biswajit Maiti","doi":"10.1016/j.mimet.2025.107265","DOIUrl":"10.1016/j.mimet.2025.107265","url":null,"abstract":"<div><div>This study explored the genetic connections between antibiotic-resistant and antibiotic-sensitive isolates using polymerase chain reaction (PCR) based genotyping methods and protein profiling of <em>Klebsiella pneumoniae</em> from clinical and environmental sources. PCR-based genotyping, such as enterobacterial repetitive intergenic consensus (ERIC) PCR and repetitive extragenic palindromic sequence-based PCR (Rep) PCR, and protein profiling using outer membrane proteins (OMPs) and whole cell proteins (WCPs) were studied. Despite their different sources, PCR-based methods revealed genetic similarity between antibiotic-resistant and sensitive isolates. The protein profile also showed varying bands around the 29–43 kDa region. The PCR-based techniques were found to be dependable and repeatable. While the OMPs and WCPs profiles limited the selectiveness of the molecular typing techniques, they could still help determine the most and least frequently occurring protein bands, which would aid in typing <em>K. pneumoniae</em> isolates. To better understand the differences between antibiotic-resistant and antibiotic-sensitive <em>K pneumoniae</em> isolates, PCR-based genotyping techniques were the most effective approach. Protein profiles and antibiogram results provided further insights into the typing process. PCR-based genotyping methods are dependable resources for examining genetic connections among <em>K. pneumoniae</em> isolates, supplemented by insights from protein profiling to improve understanding of their epidemiological relevance and antibiotic resistance mechanisms in hospital environments.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107265"},"PeriodicalIF":1.9,"publicationDate":"2025-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145102974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Routine and outbreak monitoring of Cryptosporidium using a molecular diagnostic method","authors":"Mora-Ruiz Merit,&nbsp;Torres-Martin Ana,&nbsp;Cuberos-Gomez Lucila","doi":"10.1016/j.mimet.2025.107271","DOIUrl":"10.1016/j.mimet.2025.107271","url":null,"abstract":"<div><div>Cryptosporidiosis is a significant public health disease associated with various water matrices. In response to the increase of outbreaks reported in several countries and the limitations of conventional detection methods, this study presents and validates a quantitative molecular protocol based on qPCR for the detection of <em>Cryptosporidium</em> spp. and <em>Cryptosporidium parvum</em> in different water matrices. Our method includes high-volume water filtration, thermal-mechanic-enzymatic cell disruption and an optimized qPCR assay, resulting in a highly sensitive and reproducible method. We evaluated the sensitivity, specificity, turbidity interference, and performance compared to the conventional IMS-IM method. Validation over 27 months demonstrated robust performance, with recovery rates up to 55.1 %, detection of as few as 9 oocysts per sample and a cost reduction of over 35 % compared to traditional methods. The method was successfully applied during recent outbreak investigations and offers a reliable, rapid, and scalable alternative for environmental <em>Cryptosporidium</em> monitoring, with strong potential for integration into regulatory frameworks.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107271"},"PeriodicalIF":1.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of the combinatorial dye assay for improved detection of the Salmonella Typhi biofilm","authors":"Aditya Upadhyay ,&nbsp;Dharm Pal ,&nbsp;Awanish Kumar","doi":"10.1016/j.mimet.2025.107272","DOIUrl":"10.1016/j.mimet.2025.107272","url":null,"abstract":"<div><div>Typhoidal biofilms resist antibiotics and are inadequately stained by traditional dyes. This study presents a 0.5 % combinatorial dye, prepared by mixing crystal violet and safranin in a 1:1 ratio, resulting in a final concentration of 0.25 % crystal violet and 0.25 % safranin (total 0.5 %). The formulation enhances staining intensity, quantification, and detection of typhoidal biofilms.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107272"},"PeriodicalIF":1.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbial uricase enzymes in hyperuricemia management: Sources, challenges, and technological advances","authors":"Sneha O. Pustake ,&nbsp;Prashant Bhagwat ,&nbsp;Santhosh Pillai ,&nbsp;Padma B. Dandge","doi":"10.1016/j.mimet.2025.107270","DOIUrl":"10.1016/j.mimet.2025.107270","url":null,"abstract":"<div><div>The downregulation of uric acid within the human body is intricately governed by the urate oxidase enzyme. This enzyme activity is notably present in various sources including microbial, plant, and certain animal origins. The normal concentration of uric acid in healthy individuals ranges from 3 to 6 mg/dl. However, abnormal conditions such as a high purine diet and tumor lysis syndrome can lead to elevated uric acid levels, constituting a primary etiological factor for hyperuricemia and gout. Recombinant uricases, such as rasburicase and pegloticase, have emerged as therapeutic interventions, effectively mitigating the severity of gout. Nonetheless, their utilization is constrained by immunogenicity and a relatively short half-life. Consequently, there is a compelling need for novel uricase variants characterized by lower immunogenicity and enhanced stability. This review aims to delineate alternative sources of uricase, elucidate their physico-chemical properties and clinical implications, and provide comprehensive insights into the potential of recombinant uricase. The significance of genetically modified uricase and polyethylene glycol (PEG)-conjugated uricase as highly promising treatment modalities for gout is emphasized. The application of uricase-based nanosensors, chips, biosensors, and nanocomposites for facile uric acid detection in samples is also highlighted. Given its considerable potential, uricase stands as a promising tool in the clinical realm for treating gouty and hyperuricemic conditions.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107270"},"PeriodicalIF":1.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating multi-compartment microbiome data with clinical parameters enhances mortality prediction using autoencoder","authors":"Binaya Dhakal,&nbsp;Lakshmi Sai Kishore Savarapu,&nbsp;Khaled Sayed","doi":"10.1016/j.mimet.2025.107267","DOIUrl":"10.1016/j.mimet.2025.107267","url":null,"abstract":"<div><div>The human microbiome, a complex ecosystem of microorganisms residing in different body compartments, significantly influences health outcomes and disease progression, however, leveraging this data for developing clinical prediction models remains challenging due to its high dimensionality, sparsity, and compositional nature. Traditional machine learning approaches often struggle to capture the intricate microbial interactions that contribute to mortality risk, particularly when analyzing data across multiple compartments with distinct microbial compositions. To address these limitations, we introduce a novel framework utilizing an autoencoder-based model trained on high-dimensional microbiome data collected from oral, lung, and gut compartments. Our approach encodes microbiome data into a low-dimensional latent space while preserving essential microbial community characteristics, enabling more effective feature extraction and pattern recognition than conventional dimensionality reduction techniques. Through systematic evaluation of three data configurations—microbiome taxa only, clinical data only, and an integrated model combining both—we demonstrated that the integrated approach consistently achieved superior prediction accuracy (98 % in lung microbiome) compared to using either data source independently. Clinical data alone provided reasonable but inconsistent performance (70–90 %), while microbiome taxa alone yielded the weakest results (53–65 %). Furthermore, our investigation of preprocessing techniques revealed that applying z-score normalization to the taxa data significantly enhanced performance and substantially improved recall metrics across all compartments. By analyzing compartment-specific microbial contributions, our study reveals distinct predictive roles of the oral and lung microbiomes compared to the gut microbiome, underscoring of body-site specificity in microbiome-based predictive modeling.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107267"},"PeriodicalIF":1.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091832","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of integrated in vitro fecal cultivation and 16S rRNA gene sequencing for optimizing beneficial gut microbiota combinations","authors":"Emmanuel Hitayezu ,&nbsp;Intan Rizki Mauliasari ,&nbsp;Seonmi Yu ,&nbsp;Sung Hyun Moon ,&nbsp;Bo-Ram Cho ,&nbsp;Yoon-Han Kang ,&nbsp;Sang Kyun Lim ,&nbsp;Kwang Hyun Cha","doi":"10.1016/j.mimet.2025.107269","DOIUrl":"10.1016/j.mimet.2025.107269","url":null,"abstract":"<div><div>Obesity is a global health concern closely linked to changes in gut microbiota and other metabolic disorders. In this study, we used 16S rRNA gene amplicon sequencing to analyze the gut microbiota composition of normal and obese fecal samples. We further investigated the influence of a beneficial gut microbiota combination, consisting of <em>Phocaeicola vulgatus</em> KBL981, <em>Roseburia intestinalis</em> KBL982, and <em>Akkermansia muciniphila</em> KBL983, strains considered beneficial for obesity management, using <em>in vitro</em> feces cultivation. Results showed a significant difference between the microbiota composition of normal and obesity fecal samples, with the obesity group displaying lower diversity and higher levels of pathogenic <em>Shigella boydii</em> and inflammation-related <em>Bacteroides fragilis</em>. The ideal beneficial gut microbiota mixture (1:1:100) significantly enhanced microbial diversity, balanced the short-chain fatty acid ratio, promoted the growth of beneficial bacteria, and inhibited the growth of harmful obesity-related species. However, oversupplementation of beneficial microbiota reduced the microbial diversity and disrupted the microbial ecosystem. The current study demonstrates that a combined beneficial gut microbiota treatment can help manage obesity-related dysbiosis.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"238 ","pages":"Article 107269"},"PeriodicalIF":1.9,"publicationDate":"2025-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145091897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}