Journal of microbiological methods最新文献

{"title":"Advancing pleural effusion diagnosis: Application of Molecular Culture ID in pathogen detection","authors":"Lauren Remijas ,&nbsp;Martine P. Bos ,&nbsp;María Miguélez Sánchez ,&nbsp;Robin van Houdt ,&nbsp;Gernot Rohde ,&nbsp;Andries E. Budding","doi":"10.1016/j.mimet.2026.107395","DOIUrl":"10.1016/j.mimet.2026.107395","url":null,"abstract":"<div><div>The diagnosis of pleural infection has traditionally relied on microbiological culture, a method often limited by slow bacterial growth and difficulties in culturing fastidious organisms. This study introduces Molecular Culture ID, a rapid and comprehensive molecular technique capable of detecting and identifying a wide range of bacteria down to the species level. By analyzing 440 pleural effusion samples derived from patients suspected of pleural infection and comparing the outcome to routine diagnostics, we demonstrate that Molecular Culture ID significantly outperforms traditional culture. Molecular Culture ID identified 133 positive samples, compared to 55 positive samples identified by traditional culture. The 78 additional positive samples detected by Molecular Culture contained important pathogens including species such as <em>Streptococcus pneumoniae, Escherichia coli</em>, and <em>Staphylococcus aureus</em>. These findings highlight Molecular Culture ID as a promising alternative for the rapid and accurate diagnosis of pleural infections, offering a substantial improvement over conventional methods.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"242 ","pages":"Article 107395"},"PeriodicalIF":1.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145994335","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":"Roadmap for emerging antimicrobial susceptibility testing and its clinical adaptation, from bench to bedside","authors":"Pradhapsingh Bharathiraja,&nbsp;Elavarasan Tamilmani","doi":"10.1016/j.mimet.2025.107386","DOIUrl":"10.1016/j.mimet.2025.107386","url":null,"abstract":"<div><div>The rapid emergence of antimicrobial resistance (AMR) underscores the urgent need for accurate and timely antimicrobial susceptibility testing (AST) to guide effective antibiotic treatment. Currently, various AST techniques have evolved, however, no single, globally adopted rapid diagnostic technology available for AST diagnosis. Disk diffusion remains a widely accepted technique around the world for AST detection, despite its limitations and ineffective antibiotic efficacy. Regardless of antimicrobial stewardship program, these delayed diagnosis lead to the overuse of broad-spectrum antibiotics to primarily treat the infections and contribute to AMR development. Although automated AST systems offer improved sensitivity and effective in rapid diagnosis, their limited accessibility in low-resource settings and expensive test cost hinders its widespread adaptation. Emerging innovative AST technologies show promise in point-of-care testing but require validation and integration into clinical workflows. Clinical AST market demands differentiated solutions like high-throughput automation for well-resourced settings and affordable semi-automated solutions for low-resource healthcare areas. Therefore, this review extensively addresses the integration of existing AST technologies with emerging techniques, the key challenges in development, regulatory compliance, and clinical implementation. Additionally, highlight the urgent need for next-generation semi-automated AST technology to balance efficacy and affordability for improving individual patient outcomes in the global fight against AMR.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107386"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145881352","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 community analyses of composts are influenced by particle size fraction and DNA extraction method","authors":"Anja Logo ,&nbsp;Tabea Koch ,&nbsp;Monika Maurhofer ,&nbsp;Thomas Oberhänsli ,&nbsp;Barbara Thürig ,&nbsp;Franco Widmer ,&nbsp;Pascale Flury ,&nbsp;Johanna Mayerhofer","doi":"10.1016/j.mimet.2025.107384","DOIUrl":"10.1016/j.mimet.2025.107384","url":null,"abstract":"<div><div>Composting plays a key role in sustainable agriculture by converting organic waste into a valuable soil conditioner. The process is driven by complex microbial communities, whose characterization is essential for optimizing the composting process and compost quality. Molecular techniques such as amplicon sequencing are commonly used for this purpose. However, sampling procedures and DNA extraction methods, key steps in the sequencing workflow, often vary across studies, challenging comparability. We investigated two aspects of sample preparation that may influence compost microbial analyses. For DNA extraction, often fine fractions (&lt;2 mm) are used. However, compost has a heterogeneous structure, including coarse particles. To assess the effect of particle size, we separately sequenced bacterial and fungal communities of the fine (0–2 mm) and coarse (2–10 mm) fractions of three composts. In addition, DNA was extracted using a carboxyl-affinity-based magnetic method and a silanol-affinity-based filter method to evaluate the impact of the extraction technique. We found that the coarse fraction had higher bacterial richness and distinct bacterial and fungal community structures compared to the fine fraction. DNA extraction method also influenced bacterial community profiles, with the magnetic bead method improving coverage, particularly for <em>Bacillota</em>. Although the effects of particle size and extraction method were small compared to the overall diversity among composts, we recommend including coarse particles in sequencing analyses and using standardized DNA extraction protocols, especially for studies aiming at high-resolution community analyses.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107384"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145978485","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":"Developing machine learning classifiers for carbapenem resistance prediction in Klebsiella pneumoniae using Google's teachable machine","authors":"João V.O. Cruz ,&nbsp;Felipe G. Sacoda ,&nbsp;Vitor H. Moreau ,&nbsp;Luis G.C. Pacheco","doi":"10.1016/j.mimet.2025.107385","DOIUrl":"10.1016/j.mimet.2025.107385","url":null,"abstract":"<div><div>We developed neural network models trained with images from <em>Klebsiella pneumoniae</em> genomes, encoded <em>via</em> Chaos Game Representation, to predict carbapenem resistance. Both real (<em>n</em> = 168) and synthetic AI-generated (<em>n</em> = 200) images were used. The best-performing model, among the 72 developed, achieved up to 87.5 % accuracy on generalization datasets.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107385"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145881353","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":"Identification and characterization of cephalosporin-resistant Klebsiella pneumoniae by SERS: Insights into antimicrobial resistance patterns","authors":"Benish Saif ,&nbsp;Zainab Iftikhar ,&nbsp;Haq Nawaz ,&nbsp;Muhammad Irfan Majeed ,&nbsp;Mashkoor Mohsin ,&nbsp;Rabia Saleem ,&nbsp;Najah Alwadie ,&nbsp;Sundas Sakhawat ,&nbsp;Kinza Khan ,&nbsp;Aleena Ali ,&nbsp;Rimsha Khan ,&nbsp;Riha Zulfiqar ,&nbsp;Amna Sattar ,&nbsp;Muhammad Imran","doi":"10.1016/j.mimet.2025.107388","DOIUrl":"10.1016/j.mimet.2025.107388","url":null,"abstract":"<div><div>The infectious bacteria, <em>K. pneumoniae</em> has broken another defence line by showing resistance to cephalosporin antibiotics, due to presence of extended-spectrum lactamases ESBL resistance genes. Surface-enhanced Raman spectroscopy (SERS) is used to characterize third generation cephalosporin resistant and susceptible <em>K. pneumoniae</em> strains for the purpose of identification of their characteristic SERS spectral features. For this, the silver nanoparticles (Ag-NPs) are used as a SERS substrate. The SERS spectral fingerprints of <em>K. pneumoniae</em> strains, linked directly or indirectly to resistance development against third generation cephalosporins, were differentiated by analyzing their SERS spectral data with the help of support vector machines (SVM), principal component analysis (PCA), and partial least squares discriminant analysis (PLS-DA). This can result in the effective recognition, differentiation and distinction of third generation cephalosporin resistant and susceptible strains of <em>K. pneumonia</em> bacteria which is considered crucial for selecting suitable antibiotic treatment for infections<em>.</em></div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107388"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145892591","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":"Real-time PCR-based method for measuring the phase variation frequency of flagellin in Salmonella enterica serovar Typhimurium","authors":"Momoko Nakayama ,&nbsp;Nobuo Arai ,&nbsp;Yohsuke Ogawa ,&nbsp;Masahiro Kusumoto ,&nbsp;Masahiro Eguchi","doi":"10.1016/j.mimet.2025.107362","DOIUrl":"10.1016/j.mimet.2025.107362","url":null,"abstract":"<div><div>Some <em>Salmonella</em> serovars possess two antigenic phases of the H antigen, known as phase 1 and phase 2. These phases reversibly switch between each other at a constant frequency; phase variation frequency. Previously, we focused on the inversion of <em>hin</em> and developed a real-time PCR system, H-qPCR, to quantitatively measure the proportion of bacterial cells expressing each phase of flagellin for <em>Salmonella enterica</em> serovar Typhimurium (<em>S.</em> Typhimurium). In this study, we developed a novel method to analyze the phase variation frequency of H antigen of <em>S.</em> Typhimurium, based on the H-qPCR approach. It was shown that our method offered equivalent accuracy but superior sensitivity compared with the conventional method for measuring the phase variation frequency. Our real-time PCR-based method is expected to contribute to the analysis of phase variation frequency as a useful tool.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107362"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145756807","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":"Fungal false positive in BioFire® FilmArray® analysis for bloodstream infection","authors":"Osamu Imataki ,&nbsp;Ryoko Masumoto ,&nbsp;Masahiro Hamano ,&nbsp;Masaki Ishimatsu ,&nbsp;Shin-ichiro Suemori ,&nbsp;Takayuki Tsujioka ,&nbsp;Masayo Tamura ,&nbsp;Akira Kitanaka","doi":"10.1016/j.mimet.2025.107380","DOIUrl":"10.1016/j.mimet.2025.107380","url":null,"abstract":"<div><h3>Background</h3><div>The BioFire FilmArray® system is an automated multiplex PCR tool for detecting pathogens in clinical samples. False positives occasionally occur due to cross-reactivity, contamination, or assay specificity issues. This study investigated false-positive fungal results in FilmArray® blood culture identification panel 2 (BCID2) detection system.</div></div><div><h3>Method</h3><div>We collected the continuous cases in which bloodstream infection (BSI) was suspected in our institute for 12 months, from April in 2024 to March in 2025. We routinely used Bactec FX culture system (Beckton Dickinson) with BD BACTEC culture bottles. Alongside, we identified fungus using standard culture method and matrix-assisted laser desorption ionization-time of flight mass spectrometry (biomerieux, VITEK MS PRIME).</div></div><div><h3>Results</h3><div>We evaluated continuous 454 blood culture positive sample. Average blood culture sampling were totally 5357 samples per year (44.3/1000 patients days) of blood cultures during our study period. We collected 28 cases of fungemia among totally recruited 454 samples (6.2 %, 28/454). Accordance of blood culture and FilmArray® were 50.0 % (14 samples). We observed eight false positive samples (1.8 %. 8/454) as fungemia out of total 454 samples, in where one false organism was <em>Candida albicans</em> and seven were <em>Candida tropicalis</em>. In the cases of four false <em>Candida tropicalis</em> samples, the FilmArray® reported the two fungal combination, <em>Candida parapsilosis</em> and <em>Candida tropicalis</em>.</div></div><div><h3>Conclusion</h3><div>Our investigation revealed a substantial incident of false positive of <em>Candida</em>. The study highlights recurrent false positives of <em>Candida tropicalis</em>, often detected alongside <em>Candida parapsilosis</em>. The main cause of the detection of false positive organism in BCID2 including <em>Candida</em> spp. has been reported as contamination or technical errors. We speculated that our observation could be derived from the non-viable DNA fragments (<em>Candida albicans</em>) contained in the blood culture media and cross-reaction of <em>Candida parapsilosis</em> with <em>Candida tropicalis</em>. We should remember these FilmArray® assay limitations linked to non-viable DNA contamination and high reactivity of sensitive PCR analysis. False positive results for <em>Candida</em> spp. in BCID2 assays require careful interpretation with microbiological expertise. Clinical decisions should be guided by the patient's overall context. Further research is necessary to assess the accuracy of fungal BSI. (341/500 words).</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107380"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145846728","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":"Promising diagnostic performance of a commercial qPCR assay for Plasmodium vivax detection: Contributing to malaria control and elimination","authors":"Marcelo Cerilo-Filho ,&nbsp;Marrara P. Sampaio ,&nbsp;Maria Naely G. Almeida ,&nbsp;Amanda A. Silva ,&nbsp;Gabriel Montoia ,&nbsp;Luciane M. Storti-Melo ,&nbsp;Andréa Regina S. Baptista ,&nbsp;Silvia Maria Di Santi ,&nbsp;Ricardo Luiz D. Machado","doi":"10.1016/j.mimet.2026.107391","DOIUrl":"10.1016/j.mimet.2026.107391","url":null,"abstract":"<div><div>This study evaluated a commercial qPCR assay for <em>P. vivax</em> detection. Among 167 samples, the assay showed greater sensitivity than microscopy, detecting three additional positives. It also demonstrated high specificity and no cross-reactivity. Our results support its value as a reliable tool for malaria diagnosis and surveillance.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107391"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145939751","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 strategy to enhance detection of Corynebacterium in pus from human non-puerperal mastitis via pre-culture and extended incubation","authors":"Nan Zheng,&nbsp;Xidong Gu,&nbsp;Jiangting Yu,&nbsp;Jiaying Chen,&nbsp;Tianjian Huang,&nbsp;Yiming Zhou,&nbsp;Bei Yang,&nbsp;Aimei Shi,&nbsp;Zhejiong Wang","doi":"10.1016/j.mimet.2025.107381","DOIUrl":"10.1016/j.mimet.2025.107381","url":null,"abstract":"<div><div>This study aimed to optimize the detection method for <em>Corynebacterium</em> in pus from patients with non-puerperal mastitis (NPM) to enhance diagnostic accuracy and provide guidance for clinical treatment. A total of 216 pus samples from NPM patients were retrospectively included and randomly divided into a control group and an experimental group, with 108 cases in each group. The control group was subjected to the traditional direct plate culture method, while the experimental group was treated with an improved method involving pre-cultivation in blood culture bottles followed by extended incubation for up to 5 days. The results showed that the improved method significantly increased the overall detection rate of <em>Corynebacterium</em> from 36.1 % (39/108) to 60.2 % (65/108), with the difference between the groups being statistically significant (χ² = 12.5, <em>P</em> &lt; 0.001, 95 % CI: 11.0–37.1, Cramér's V = 0.24). These findings indicate that optimizing culture conditions and extending incubation time can effectively enhance the detection sensitivity of <em>Corynebacterium</em> in NPM pus. The proposed method demonstrates good clinical applicability and can provide laboratory support for the etiological diagnosis and subsequent individualized treatment of NPM.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107381"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145843712","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":"Recovery of Escherichia coli and Salmonella enterica from long frozen rectal swabs using enrichment methods in a low-resource setting","authors":"Hafeez A. Adekola,&nbsp;Jacob I. Yisau,&nbsp;Ajoke O. Adagbada,&nbsp;Oluwatoyin B. Awoderu,&nbsp;Samson A. Luka,&nbsp;Adenike Aiyedogbon,&nbsp;Olusola Ajibaye,&nbsp;Toyosi Y. Raheem,&nbsp;Muinah A. Fowora,&nbsp;Emelda E. Chukwu,&nbsp;Tajudeen A. Bamidele,&nbsp;Abideen O. Salako,&nbsp;Oliver C. Ezechi","doi":"10.1016/j.mimet.2025.107382","DOIUrl":"10.1016/j.mimet.2025.107382","url":null,"abstract":"<div><div>This study evaluated bacterial recovery from rectal swabs stored at −20 °C for one month in Cary Blair medium. Enrichment methods markedly improved detection of <em>Escherichia coli</em> and <em>Salmonella enterica</em> compared to direct plating. Tryptone Soy Broth best recovered <em>E. coli</em>, while Peptone Water enhanced <em>S. enterica</em> recovery, strengthening surveillance reliability in low-resource settings.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"241 ","pages":"Article 107382"},"PeriodicalIF":1.9,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145856580","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}