Journal of microbiological methods最新文献

{"title":"Effect of epinephrine on growth characteristics of Actinobacillus pleuropneumoniae field isolates","authors":"Elena Schreiber ,&nbsp;Fritjof Freise ,&nbsp;Nicole de Buhr ,&nbsp;Isabel Hennig-Pauka","doi":"10.1016/j.mimet.2025.107193","DOIUrl":"10.1016/j.mimet.2025.107193","url":null,"abstract":"<div><div>Based on empirical observations, stressors in swine populations may contribute to outbreaks due to <em>Actinobacillus pleuropneumoniae</em> (<em>App</em>) in colonized pigs. Stress hormones as catecholamines were found to impact immune mechanism but also bacterial protein expression <em>in vivo</em>, so it can be hypothesized that they are key molecules in disease pathogenesis. Culturing methods to isolate <em>App</em> from tonsillar tissue of carrier pigs for further typing are mostly not successful. In this study the effect of epinephrine in culturing media on <em>App</em> growth behavior was tested. Starting cultures of different age (24-h-old or 7-day-old cultures) of three <em>App</em> field strains per serotypes 2, 5 and 12 were compared in their growth behavior in medium supplemented with various epinephrine concentrations. The response of <em>App</em> strains to epinephrine varied between strains. Highest differences in CFU/mL and in growth curve characteristics between different epinephrine concentrations were found in serotype 5 strains. Inflection points of bacterial growth curves with 24-h-old starting cultures were delayed with 100 μM epinephrine with exception of one ST5 strain. In all ST2 and ST12 as well as one ST5 strain 100 μM epinephrine led to a growth advantage in 7-day old compared to 24-h-old starting cultures. Epinephrine did not consistently enhance growth of <em>App</em>, so that it cannot be recommended as a supplement for growth media to facilitate isolation from colonized tonsils of subclinically infected pigs.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107193"},"PeriodicalIF":1.7,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144623648","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":"styMdtM gene deletion with modified λ Red recombineering approach: Implications for multidrug resistance in Salmonella Typhi","authors":"Anam Tariq ,&nbsp;Aqsa Shaheen ,&nbsp;Mazhar Iqbal ,&nbsp;Moazur Rahman","doi":"10.1016/j.mimet.2025.107191","DOIUrl":"10.1016/j.mimet.2025.107191","url":null,"abstract":"<div><div>styMdtM is a multidrug efflux transporter of <em>Salmonella Typhi</em>. In the present study, a modified λ Red recombineering approach using shorter flanking arms (ca. 50 bp) was used to generate an <em>styMdtM</em> gene deletion in the <em>S. Typhi</em> genome. This approach worked efficiently to knockout the gene and the ensuing <em>S. Typhi</em> strain was considerably more sensitive to antibiotics.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107191"},"PeriodicalIF":1.7,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144605956","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 double-antibody sandwich ELISA for detecting PEDV N protein","authors":"Yao Zhao ,&nbsp;Fang Wei ,&nbsp;Zhongyin Liu ,&nbsp;Tianai Zhang ,&nbsp;Jiamin Qin ,&nbsp;Wenke Ruan ,&nbsp;Zhen Wang ,&nbsp;Dengjin Chen ,&nbsp;Dongjie Chen ,&nbsp;Shengkui Xu","doi":"10.1016/j.mimet.2025.107186","DOIUrl":"10.1016/j.mimet.2025.107186","url":null,"abstract":"<div><div>Porcine epidemic diarrhea virus (PEDV) severely impacts piglets with high contagion and lethality, leading to significant economic losses in the swine industry. In this study, two anti-PEDV N protein monoclonal antibodies (4F2 and 2G4) were successfully prepared using the HEK-293i cell-expressed recombinant N protein as an immunogen. Functional analysis revealed that both 4F2 and 2G4 were applicable to immunofluorescence assay (IFA) and Western blot. Epitope screening showed that these mAbs recognized distinct epitopes: 4F2 bound a conserved linear epitope in the N-terminal domain, while 2G4 targeted the linear epitope “SGKNTPKKNKSRATSKE” in the C-terminal domain, which is highly conserved across different virus strains. Using the obtained antibodies, we developed a double-antibody sandwich quantitative ELISA (DAS-ELISA) for PEDV detection. The assay demonstrated remarkable sensitivity, capable of detecting the recombinant N protein at a concentration as low as 0.05 ng/mL and the virus at a titer of 10^2.59 TCID₅₀ (50 % tissue culture infectious dose). It also exhibited specificity, with no cross-reactivity to PRV, PRRSV, ASFV, or PCV2. This ELISA should enable convenient PEDV detection in piglet excreta and aid in PEDV eradication efforts.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107186"},"PeriodicalIF":1.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144556678","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":"Hepcidin vs Procalcitonin: Which biomarker best predicts bacteremia in the medical ICU?","authors":"Jayasree S,&nbsp;Jagan V,&nbsp;Leela K.V","doi":"10.1016/j.mimet.2025.107187","DOIUrl":"10.1016/j.mimet.2025.107187","url":null,"abstract":"<div><h3>Background</h3><div>Sepsis is a life-threatening condition caused by a dysregulated host response to infection, necessitating early diagnosis and intervention. While traditional diagnostics like blood cultures are crucial, they often delay treatment decisions. This study evaluates and compares the diagnostic and prognostic efficacy of Procalcitonin (PCT) and Hepcidin—two emerging biomarkers—in patients with bacteremia admitted to the Medical Intensive Care Unit (MICU) of a tertiary care centre.</div></div><div><h3>Methods</h3><div>A prospective, analytical study was conducted on 86 blood culture-positive MICU patients at SRM Medical College Hospital and Research Centre, Chennai. Serum PCT and Hepcidin levels were measured using Chemiluminescent Microparticle Immunoassay (CMIA) and sandwich ELISA techniques, respectively. The diagnostic value of each biomarker was assessed, and statistical analysis was performed using Chi-square tests with <em>p</em> &lt; 0.05 considered significant.</div></div><div><h3>Results</h3><div>Serum Hepcidin and PCT levels were elevated in 84.8 % and 82.6 % of sepsis patients, respectively, with statistically significant associations (<em>p</em> &lt; 0.05). Hepcidin showed a more consistent and gradual decline during recovery (96 % normalization) compared to PCT (77 % normalization). Both biomarkers correlated strongly with microbial profiles, particularly in Gram-negative infections, and demonstrated no significant variation with patient demographics or comorbidities.</div></div><div><h3>Conclusion</h3><div>Hepcidin emerges as a promising biomarker, demonstrating diagnostic and prognostic potential comparable to PCT, with a more consistent response during sepsis resolution. When used in conjunction, these markers can enhance early detection, guide treatment, and improve clinical outcomes in sepsis management.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107187"},"PeriodicalIF":1.7,"publicationDate":"2025-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560420","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":"Coconut water: A novel inducer of germ tube formation in Candida albicans - A preliminary report","authors":"Smija Kakkuth Puthenvitil,&nbsp;Surya Sokkalingam,&nbsp;Palani Perumal","doi":"10.1016/j.mimet.2025.107188","DOIUrl":"10.1016/j.mimet.2025.107188","url":null,"abstract":"<div><div>The evolving epidemiology of candidiasis necessitates accurate methods for distinguishing <em>Candida</em> species. This study explores coconut water as a substitute for fetal bovine serum in inducing germ tube formation, offering a cost-effective and ethically sound solution for diagnosing and studying <em>Candida</em> infections.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107188"},"PeriodicalIF":1.7,"publicationDate":"2025-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553776","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":"MFDF-UNet: Multiscale feature depth-enhanced fusion network for colony adhesion image segmentation","authors":"Liu Hui ,&nbsp;Wang Zhiyi ,&nbsp;Li Xue ,&nbsp;Ge Peng ,&nbsp;Tuo Yanfeng ,&nbsp;Xie Xufen","doi":"10.1016/j.mimet.2025.107185","DOIUrl":"10.1016/j.mimet.2025.107185","url":null,"abstract":"<div><div>Colony counting plays a crucial role in evaluating food quality and safety. The segmentation of colony adhesion images can significantly enhance the accuracy of food safety assessments. To achieve high-precision segmentation of colony adhesion images, this paper presents a novel multi-scale feature deep-enhanced fusion network MFDF-UNet, specifically designed for colony adhesion image segmentation. The core of the network lies in the design of a self-similar fusion fractal structure, which recursively integrates layers to enhance the network's ability to extract, integrate, and transfer multi-scale feature information. The DEC (depth-enhanced connectivity) units and PF (progressive fusion) modules in each stage progressively accumulate detailed features, thus improving the network's capacity to handle complex structures. Additionally, the design strengthens the information transfer between different layers, ensuring consistency of features across multiple layers. This reduces the imbalance in feature information transfer that can occur when certain regions of the image contain prominent edges, textures, or structural features, while other areas are relatively blurred or lack distinct features.The MFDF-UNet model achieved an average segmentation accuracy of 77.95 %, precision of 97.55 %, and a mean intersection-over-union (mIoU) of 57.94 % on the AGAR-based hybrid colony adhesion segmentation test dataset. Compared to other deep learning methods, such as PSPNet, DeepLabv3+, SegFormer, YOLOv8, U-Net, and ResNet, MFDF-UNet outperforms the highest-performing ResUNet by 7.53 % in segmentation accuracy, improves precision by 1.5 %, and surpasses ResUNet by 4.82 % in mIoU.Although our model requires slightly more parameters and training time, the improvements in segmentation accuracy and image quality sufficiently justify the additional cost, demonstrating its potential for practical applications in colony adhesion segmentation.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107185"},"PeriodicalIF":1.7,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144490715","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":"Strain-level typing of Wickerhamomyces anomalus using Fourier transform infrared spectroscopy and whole-genome sequencing","authors":"Asuka Kashiwaba ,&nbsp;Asako Mitani ,&nbsp;Takumi Sonoda ,&nbsp;Naofumi Shigemune ,&nbsp;Hiroki Takahashi","doi":"10.1016/j.mimet.2025.107184","DOIUrl":"10.1016/j.mimet.2025.107184","url":null,"abstract":"<div><div>In industrial settings, identifying the source of microbial contamination is crucial for effective microbiological risk assessment. While various strain identification technologies exist, many struggle with practicality, accuracy, and reproducibility. Fourier Transform Infrared Spectroscopy (FT-IR) has emerged as a rapid method, demonstrating a strong correlation with whole-genome sequencing (WGS) for certain bacteria. However, its accuracy for identifying yeast strains has been limited.</div><div>This study focuses on improving the accuracy of FT-IR for yeast strain identification by optimizing pretreatment conditions. We conducted phylogenetic analyses on <em>Wickerhamomyces anomalus</em> using both WGS single-nucleotide polymorphisms (SNPs) and FT-IR. Although initial FT-IR results were less accurate than WGS, refining the culture and sample preparation conditions led to significant improvements. We tested 16 different conditions, using Euclidean Distances (EDs) and dendrogram comparisons to evaluate discrimination ability, including metrics like the F-measure and adjusted Rand index (ARI).</div><div>The most accurate and reproducible FT-IR results were achieved with incubation in Sabouraud dextrose (SD) broth aligning closely with WGS results. This optimized FT-IR protocol now allows for rapid and precise strain-level discrimination of <em>W. anomalus</em>, offering a practical tool for tracking contamination sources in industrial environments.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107184"},"PeriodicalIF":1.7,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144505999","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":"Rapid counting of Kazachstania humilis and Saccharomyces cerevisiae in sourdough by deep learning-based classifier","authors":"Kyoka Aiki,&nbsp;Rin Tsuchiya,&nbsp;Aiho Kushida,&nbsp;Tatsuya Tominaga","doi":"10.1016/j.mimet.2025.107183","DOIUrl":"10.1016/j.mimet.2025.107183","url":null,"abstract":"<div><div>When maintaining sourdough through backslopping, bakers must ensure that the yeast mycobiota remains stable. By introducing two-staged incubation temperatures for cultivation, we found that the colonies of <em>Kazachstania humilis</em> and <em>Saccharomyces cerevisiae</em> could be differentiated by size and color. We then developed a classifier that used the deep-learning method, YOLO, to automatically count these colonies. For sourdough isolates of <em>K. humilis</em> and <em>S. cerevisiae</em>, the classifier had accuracies of 0.99 and 0.98, respectively. This classifier also showed accuracies greater than 0.95 for <em>S. cerevisiae</em> strains used in bread, sake, and wine. To investigate the practical feasibility, the sourdough was repeatedly refreshed by backslopping at 25 °C, 30 °C, and 35 °C, with the goal of artificially fluctuating the yeast mycobiota. At 25 °C, <em>K. humilis</em> and <em>S. cerevisiae</em> accounted for proportions of approximately 25 % and 75 %, respectively, whereas at 30 °C and 35 °C, <em>K. humilis</em> comprised less than 1 % of the mycobiota. The accuracy of this classifier was 0.98 for <em>K. humilis</em> and 0.99 for <em>S. cerevisiae</em>; this was very close to the accuracy obtained with manual counting, indicating that the classifier could detect changes in the yeast mycobiota. The classifier took approximately 126 milliseconds to count colonies on one Petri dish. The use of our novel classifier can enable fast, less-laborious, and objective judgement, potentially facilitating the ability of small-scale artisan bakeries to manage fermentation on a daily basis.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107183"},"PeriodicalIF":1.7,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144491289","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":"Exploring the multifaceted probiotic potential of Lactiplantibacillus plantarum NMGL2, investigating its antimicrobial resistance profiles and bacteriocin production","authors":"Tariq Aziz ,&nbsp;Muhammad Aqib Shabbir ,&nbsp;Abid Sarwar ,&nbsp;Ayaz Ali Khan ,&nbsp;Liqing Zhao ,&nbsp;Zhennai Yang ,&nbsp;Ashwag Shami ,&nbsp;Maher S. Alwethaynani ,&nbsp;Fahad Al-Asmari ,&nbsp;Abeer M. Alghamdi ,&nbsp;Fakhria A. Al-Joufi","doi":"10.1016/j.mimet.2025.107178","DOIUrl":"10.1016/j.mimet.2025.107178","url":null,"abstract":"<div><h3>Background</h3><div><em>Lactiplantibacillus plantarum</em> is widely recognized for its probiotic and antimicrobial properties, making it a valuable candidate for food and clinical applications. Genomic characterization provides deeper insight into its potential health benefits and safety profile.</div></div><div><h3>Aim</h3><div>This study aimed to sequence and analyze the genome of <em>L. plantarum</em> NMGL2 to evaluate its antimicrobial resistance, probiotic potential, and genetic suitability for biotechnological applications.</div></div><div><h3>Methods</h3><div>The genomic DNA of L. <em>plantarum</em> NMGL2 was extracted and sequenced using Illumina technology. Genome assembly and annotation were performed, followed by gene prediction using Prokka and identification of antimicrobial resistance genes, virulence factors, and probiotic markers via BLAST. Metagenomic analysis of gut microbiota samples and phylogenetic analysis were conducted to assess strain relationships with other L. <em>plantarum</em> isolates.</div></div><div><h3>Results</h3><div>The genome analysis revealed approximately 3000 protein-coding genes, including those encoding bile salt hydrolase, antimicrobial peptides, and antibiotic resistance determinants. Phylogenetic analysis showed that NMGL2 is closely related to other probiotic L. <em>plantarum</em> strains, supporting its probiotic characteristics and its potential role in combating pathogens.</div></div><div><h3>Conclusion</h3><div><em>L. plantarum</em> NMGL2 demonstrates promising probiotic traits and carries genes that support its application in food safety and clinical contexts. Further, in vivo studies are needed to validate its health benefits and ensure safety, particularly in treating gastrointestinal disorders.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107178"},"PeriodicalIF":1.7,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144321716","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":"Combination of slightly electrolyzed water and ultraviolet light for the treatment of Staphylococcus aureus-induced skin abscesses in mice by effective inactivation of Staphylococcus aureus","authors":"Jiahong Han ,&nbsp;Yao Zang ,&nbsp;Haojie Zhu,&nbsp;Yingjie Feng,&nbsp;Yitian Zang,&nbsp;Huaping Zheng,&nbsp;Tao Zha,&nbsp;Xinyi Yin,&nbsp;Juncheng Luo,&nbsp;Changming Wang,&nbsp;Jiarong Hu","doi":"10.1016/j.mimet.2025.107181","DOIUrl":"10.1016/j.mimet.2025.107181","url":null,"abstract":"<div><div>In this study, the combined effectiveness of slightly acidic electrolyzed water (SAEW) and ultraviolet light-C (UV) (SAEW + UV) against infections caused by <em>Staphylococcus aureus</em> (<em>S. aureus</em>) was evaluated, both in vivo and in vitro, with a specific focus on skin abscess in mice. The superior effectiveness of the SAEW + UV combination compared to individual treatments with SAEW or UV alone was observed (<em>P</em> &lt; 0.05). Notably, a significant nonlinear increase in <em>S. aureus</em> inactivation over time and effective chlorine concentrations was observed with the synergistic action of SAEW + UV (<em>P</em> &lt; 0.05). Even in the presence of organic interference, remarkable efficacy in <em>S. aureus</em> eradication was demonstrated by SAEW + UV. Significantly, SAEW + UV efficiently removes <em>S. aureus</em> from mouse skin abscesses, leading to a reduction in bacterial load of visceral tissues, oxidative stress levels and inflammatory factors (<em>P</em> &lt; 0.05). Consequently, facilitated regression of abscesses and accelerated wound healing in mice were observed. Notably, after 9 days of SAEW + UV treatment, 93.97 % wound healing rate was observed in mice, compared to the untreated model group with only 48.66 % healing achieved. These findings underscore the promising potential of SAEW + UV therapy in mitigating oxidative stress and expediting skin wound healing, owing to its effective bactericidal activity. However, to comprehensively elucidate the specific cellular signaling mechanisms involved in reducing oxidative stress, further research is imperative. In conclusion, SAEW + UV emerges as a highly promising therapeutic approach for treating skin diseases.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"236 ","pages":"Article 107181"},"PeriodicalIF":1.7,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144365889","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}