Journal of microbiological methods最新文献

{"title":"Composition-aware and leakage-controlled sparse log-ratio learning for mortality classification from respiratory microbiome profiles.","authors":"Linglan Hou, Xin Zhang, Keliang Huang, Weiyi Wu, Lianxiang Xing, Wei Shen, Ying Zhang, Zhiwu Dong","doi":"10.1016/j.mimet.2026.107758","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107758","url":null,"abstract":"<p><strong>Background: </strong>Respiratory microbiome profiles contain compositional information that may complement clinical variables for mortality classification in hospitalized patients with COVID-19. However, microbiome-based classifiers remain vulnerable to compositional artifacts, patient-level leakage, and cohort-specific feature construction.</p><p><strong>Objective: </strong>To develop and externally evaluate a leakage-controlled sparse log-ratio learning framework for mortality classification using respiratory microbiome profiles.</p><p><strong>Methods: </strong>This retrospective secondary analysis used three public COVID-19 respiratory microbiome cohorts. The Sparse Log-Ratio Risk Network (SLRRN) was developed using patient-level nested validation, with genus filtering, zero replacement, balance construction, model tuning, and threshold selection restricted to training partitions. The model learned 16 signed genus balances and integrated four clinical covariates available at the first eligible respiratory sampling landmark. The final specification and threshold were frozen before external evaluation.</p><p><strong>Results: </strong>The development cohort included 82 patients (20 deaths) from PRJNA678105 and PRJNA683617, and frozen external evaluation included 76 independent patients (38 fatal and 38 severe nonfatal cases) from PRJNA726205. Internal AUROC was 0.838 (95% CI, 0.765-0.911), and AUPRC was 0.674 (0.577-0.771). The paired AUROC difference versus XGBoost was 0.041 (0.009-0.073). Without refitting or threshold revision, external AUROC was 0.821 (0.738-0.904), with sensitivity of 0.816 and specificity of 0.842 at the frozen threshold of 0.37. In the outcome-enriched external cohort, the Brier score was 0.166 and the ECE was 0.065; these estimates describe the selected study sample.</p><p><strong>Conclusion: </strong>SLRRN provides a composition-aware and leakage-controlled framework for respiratory microbiome-based mortality classification. The findings support further prospective evaluation with standardized sampling and direct comparison with established clinical models before clinical translation.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107758"},"PeriodicalIF":2.5,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224310","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 generation and characterization of probiotic-derived bacterial ghosts from gram-negative and gram-positive bacteria using chemical induction.","authors":"Muneera Anwer, Krupa Bhaliya, Alan L Munn, Ming Q Wei","doi":"10.1016/j.mimet.2026.107757","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107757","url":null,"abstract":"<p><strong>Objectives: </strong>Bacterial ghost (BG) are empty bacterial cell envelopes that retain native surface architecture and antigenic structures, making them promising platforms for vaccine delivery and immunotherapy. This study aimed to develop a simple, scalable chemical method for generating probiotic BG using representative Gram-negative and Gram-positive bacterial strains.</p><p><strong>Methods: </strong>BG were produced by Tween-80-mediated lysis followed by acidic treatment. Structural and morphological integrity was assessed using scanning and transmission electron microscopy. Particle size and zeta potential were determined by physicochemical characterization, while biochemical assays were performed to confirm the release of intracellular proteins and nucleic acids.</p><p><strong>Results: </strong>Electron microscopy demonstrated evacuation of cytoplasmic contents while preserving the structural integrity of the bacterial cell envelopes. The generated BG exhibited hydrodynamic diameters of 1.18 μm and 1.14 μm, with zeta potentials of -38.4 mV and - 30.4 mV for Escherichia coli Nissle 1917 and Lactobacillus paragasseri ATCC 19992, respectively, indicating favorable colloidal stability. Biochemical analyses further supported effective ghost formation by detecting released intracellular proteins and nucleic acids.</p><p><strong>Conclusions: </strong>Tween-80-mediated chemical induction provides a simple, reproducible, and scalable strategy for generating probiotic bacterial ghosts while preserving structural integrity. Unlike gene-based lysis systems, this approach applies to both Gram-negative and Gram-positive bacteria, offering a safer alternative to pathogen-derived BG and expanding the potential of probiotic bacterial ghost platforms for vaccine delivery and other biomedical applications.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107757"},"PeriodicalIF":2.5,"publicationDate":"2026-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224265","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 novel cost-effective methodology for Campylobacter isolation from human stool and chicken sample matrix containing extended-spectrum β-lactamase-producing Escherichia coli.","authors":"Mohimanul Islam, Bibi Amena, Tanvir Ahmad Nizami, Keya Ghosh, Himel Barua, Purba Biswas, Sanjoy Kanti Biswas, Paritosh Kumar Biswas","doi":"10.1016/j.mimet.2026.107756","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107756","url":null,"abstract":"<p><p>Campylobacter jejuni and C. coli are major causes of bacterial gastroenteritis, but their isolation from samples contaminated with extended-spectrum β-lactamase (ESBL)-producing Escherichia coli remains challenging. This study evaluated the performance of modified charcoal cefoperazone deoxycholate agar (mCCDA) and Preston broth, supplemented with different concentrations of a commercially available pharmaceutical-grade tazobactam-piperacillin (TP) combination for the selective isolation of Campylobacter. After determining the optimum concentration of TP to inhibit the growth of ESBL-producing E. coli while the growth of Campylobacter remained unaffected, a field evaluation was conducted for the investigation of 120 chicken caecal and 120 stool samples from pediatric diarrhea patients to compare Campylobacter recovery and background flora contamination rates in real field situations. The results demonstrated that TP-mCCDA containing 4 mg/L tazobactam flanked by 32 mg/L piperacillin effectively inhibited ESBL-producing E. coli while allowing Campylobacter growth, but TP at 4/32 mg/L in Preston broth failed to inhibit the growth of seven of the 12 ESBL E. coli isolates tested, suggesting that a unique concentration combination of TP for both mCCDA and Preston broth could not be recommended for real field situations. Based on these initial findings for determining TP concentration, TP at 4/32 mg/L in mCCDA was used for selective isolation of Campylobacter from the cecal matrix and stool samples, whereas Preston broth was used without TP supplementation for pre-enrichment of Campylobacter from the stool samples before selective isolation on TP-mCCDA. The results revealed that TP-mCCDA yielded a significantly higher Campylobacter recovery rate (59.2%) from chicken caeca compared to standard mCCDA (20.0%), with substantially reduced background flora contamination (6.7% vs. 70.0%). In stool samples from pediatric patients with diarrhea following pre-enrichment in Preston broth, TP-mCCDA also outperformed mCCDA in both Campylobacter recovery rate (4.2% vs. 0%) and competing flora contamination (19.2% vs. 80.0%). Compared with other ESBL inhibitors, TP-mCCDA was found to be highly cost-effective, achieving a higher Campylobacter isolation rate while minimizing contamination by competing ESBL-producing microflora.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107756"},"PeriodicalIF":2.5,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216426","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":"Advances in influenza A and B virus detection: molecular diagnostics, biosensors, and point-of-care applications.","authors":"Yingqi Huang, Chen Duan, Xiyan Deng, Xinlan Zhang, Meiqi Wu, Siqin Peng, Rushi Liu, Defu Hou","doi":"10.1016/j.mimet.2026.107746","DOIUrl":"10.1016/j.mimet.2026.107746","url":null,"abstract":"<p><p>Influenza A and B viruses remain major causes of seasonal epidemics and continue to pose substantial challenges for rapid clinical diagnosis and public-health surveillance. Conventional methods, including viral culture, immunological assays, and reverse-transcription real-time quantitative PCR (RT-qPCR), provide important diagnostic benchmarks but are constrained by long turnaround times, dependence on specialized equipment, or reduced sensitivity in low-viral-load specimens. This review summarizes recent advances in influenza virus detection, with emphasis on molecular diagnostics, biosensors, point-of-care testing, and high-throughput sequencing. Digital PCR offers precise absolute quantification, whereas isothermal amplification technologies such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) reduce reliance on thermal cycling and support portable testing. CRISPR-Cas systems further improve sequence specificity and are increasingly being integrated with isothermal amplification, lateral-flow readouts, and microfluidic platforms. Biosensor strategies based on optical, electrochemical, multimodal, and smartphone-assisted readouts provide promising routes for rapid, multiplexed, and point-of-care detection, although standardization and large-scale clinical validation remain key barriers. High-throughput sequencing complements rapid testing by enabling viral typing, variant monitoring, and emerging-pathogen monitoring. Overall, future influenza diagnostics are expected to move toward integrated, low-cost, \"sample-in, answer-out\" systems that combine sensitivity, speed, portability, and surveillance connectivity.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107746"},"PeriodicalIF":2.5,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216383","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":"Comparison of RT-ddPCR and RT-qPCR for detection and quantification of SARS-CoV-2 RNA in archived skilled nursing facility wastewater.","authors":"María Burgos-Garay, Mariya Campbell, Angela Coulliette-Salmond","doi":"10.1016/j.mimet.2026.107754","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107754","url":null,"abstract":"<p><p>Wastewater RNA extracts, concentrated using nanoparticle and electronegative membrane filtration approaches, were stored at -80 °C for 14 months. Severe acute respiratory syndrome coronavirus 2 RNA was quantified using RT-ddPCR and RT-qPCR. Both assays demonstrated reliable detection in this complex matrix, supporting their use in retrospective wastewater surveillance.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107754"},"PeriodicalIF":2.5,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216412","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":"Evaluating the electrokinetic effect on microbial signaling molecules in activated sludge systems.","authors":"Asie Mahdizadeh, Hasan Amini Rad, Moslem Salehiziri, Shakiba Jafari","doi":"10.1016/j.mimet.2026.107745","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107745","url":null,"abstract":"<p><p>Quorum sensing is a communication system that plays a critical role in biofilm formation. Several studies have explored quorum-sensing inhibitors as an anti-biofouling approach. Recently, studies on the effects of an electric field on biofouling reduction have indicated that the electric field also disrupts the QS system, although the exact mechanism remains unclear. This study has investigated the effect of the electrokinetic process on QS and its possible mechanisms. The results showed that applying an electric field reduced AHL signals in both the sludge mixture and the supernatant without microbial cells, indicating a direct effect of the electric field on the signaling system. Given the high efficiency and rapid kinetics of signal removal (>90% removal within 5 min in cell-free supernatant), indirect electrochemical oxidation-potentially mediated by reactive oxygen species (ROS) such as H₂O₂-is proposed as a plausible mechanism for AHL degradation under the applied electric field. Moreover, the concentration of extracellular polymer compounds (EPS & SMP) has decreased due to the electric field, resulting from a decrease in AHL signal concentration.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107745"},"PeriodicalIF":2.5,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149216388","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":"Detection of Salmonella spp. using rapid culture method in chicken.","authors":"Syamsyul Azizan, A A Saleha, Elawad A Hussein","doi":"10.1016/j.mimet.2026.107744","DOIUrl":"10.1016/j.mimet.2026.107744","url":null,"abstract":"<p><p>The study objective was to isolate Salmonella spp. with rapid culture method. Meat samples and cloacal swabs were collected from different markets and different farms. The swabs were transported to the laboratory for further analysis. Conventional culture method and rapid culture method, lacking a non-selective enrichment step, were applied for isolation of Salmonella spp. The result was that Salmonella spp. was detected with rapid culture method from 3 out of 10 (30%) of meats samples from one market. It was not significantly different (p-value was not <0.05) from the result of conventional culture method. Furthermore, Salmonella spp. was detected with conventional culture method from 4 out of 25 cloaca swabs (16%) from one farm. It was significantly (p-value was <0.05) more sensitive than rapid culture method. It was concluded that the rapid cultural method was more concise, required media optimization, did not require sophisticated equipment. It was more sensitive but not statistically different (p-value was not <0.05) than conventional method for Salmonella spp. detection from chick meat. The conventional culture method was more statistically (p-value was <0.05) sensitive than rapid culture method for Salmonella spp. detection from cloacal swabs.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107744"},"PeriodicalIF":2.5,"publicationDate":"2026-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149182281","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":"Species-specific detection of Capnocytophaga in domestic dogs (Canis lupus familiaris) and domestic cats (Felis catus) using a two reaction end-point multiplex PCR assay.","authors":"K Sudharsanam, S Rajagunalan, M Balagangatharathilagar, K Porteen, S Sureshkannan, M Suzuki, M Jayamari","doi":"10.1016/j.mimet.2026.107742","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107742","url":null,"abstract":"<p><p>Capnocytophaga species from domestic dogs (Canis lupus familiaris; dogs hereafter) and cats (Felis catus; cats hereafter) bites poses zoonotic risks. We developed a two-reaction multiplex PCR (mPCR) assay targeting the gyrB gene for the species-specific detection of five Capnocytophaga species. Screening of 300 oral swabs from dogs and cats revealed Capnocytophaga in 51.7% of the samples. The prevalence of the species was as follows: C. cynodegmi (58.7%), C. canis (57.4%), C. canimorsus (32.9%), C. felis (9.7%), and C. stomatis (8.4%). Co-carriage was observed in 53.5% of the positive samples. This assay addresses limitations of culture-based methods and can be used as a molecular surveillance tool for Capnocytophaga detection in companion animals.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107742"},"PeriodicalIF":2.5,"publicationDate":"2026-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149165548","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":"Indicator parameters of biofilm quantity in full-scale drinking water distribution system samplers identified by multivariable statistical methods.","authors":"Sharon Waller, Martina Hausner, Aaron Packman, Sally Freels","doi":"10.1016/j.mimet.2026.107725","DOIUrl":"https://doi.org/10.1016/j.mimet.2026.107725","url":null,"abstract":"<p><p>This study aims to identify indicator parameters for biofilms in drinking water distribution systems (DWDS). Biofilms grown on coupons of three pipe materials (cast iron, cement, and polyvinyl chloride) in two sampler types (pipe loops and annular reactors) installed at full scale DWDS were quantified by three analytical methods: heterotrophic plate count (HPC), total cell count by flow cytometry (FC), and in situ by confocal laser scanning microscopy (CLSM). Quantification by both biofilm HPC and CLSM biomass is recommended to avoid under-reporting of viable but non-culturable microbial populations. Multiple multivariable statistical methods were used to explore complex full-scale data sets. Principal component analysis (PCA) showed similar variability of select water parameters and biofilm quantity regardless of sampler type. Indicators of biofilm quantity were identified by taking the preponderance of results of correlation analysis, PCA, and multiple step linear regression. Indicators of biofilm quantity found here include total calcium (average range 55-108 ppm CaCO₃), total alkalinity (49-173 ppm CaCO₃), and pH (7.3-8.7). Total chlorine decay and HPC of planktonic cells were indicators of biofilms both within a single DWDS and in the aggregated data of all seven utilities sampled. Assimilable organic carbon and phosphorus appear to have secondary impacts on biofilm quantity. Oxygen reduction potential (439-644 mV measured at two utilities) may also be useful as a biofilm indicator worth further investigation.</p>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":" ","pages":"107725"},"PeriodicalIF":2.5,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149137049","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":"From clinics to the environment: A systematic review of machine learning and MALDI-TOF MS in the identification of antimicrobial-resistant bacteria","authors":"Nafyad Ibrahim Batu,&nbsp;Ilunga Kamika,&nbsp;Tshepo Joseph Malefetse","doi":"10.1016/j.mimet.2026.107414","DOIUrl":"10.1016/j.mimet.2026.107414","url":null,"abstract":"<div><div>As a result of the increasing prevalence of Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in both community and hospital settings, their identification by conventional approaches has been posing a significant issue for decades. A new approach, integrating matrix-assisted laser desorption/ionization time of-flight mass spectrometry (MALDI-TOF-MS) with machine learning (ML), has emerged as a valuable method for their identification. This review systematically evaluates the effectiveness of integrating MALDI-TOF-MS with ML for the identification of ARB. A comprehensive literature search was conducted using PubMed, Google Scholar, the Cochrane Library, Scopus, and Web of Science to identify original research articles focused on the application of MALDI-TOF-MS and ML in detecting ARB. Studies unrelated to bacteria or antibiotic resistance, as well as short communications, scientific reports, and case studies, were excluded. In accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, 401 potentially relevant articles were initially identified. Following the application of inclusion criteria and relevance assessment of titles and abstracts, 34 studies were selected for final analysis. The findings demonstrate that integrating MALDI-TOF-MS with ML models markedly improves the speed, accuracy, and reliability of ARB detection while offering valuable insights into the molecular mechanisms of resistance. Current evidence suggests that the integration of MALDI TOF MS with ML is an important approach for the identification of bacteria in clinics and environments, mainly ARB. Future research is needed to apply this approach to address the growing challenge of ARB both in clinical and environmental settings.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"243 ","pages":"Article 107414"},"PeriodicalIF":1.9,"publicationDate":"2026-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146165697","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}