Journal of microbiological methods最新文献

{"title":"Immunofluorescence detection of Ecytonucleospora hepatopenaei (EHP) in Penaeus vannamei","authors":"Sungman Cho ,&nbsp;Deborah A. Schaefer ,&nbsp;Hung N. Mai ,&nbsp;Michael W. Riggs ,&nbsp;Arun K. Dhar","doi":"10.1016/j.mimet.2024.107039","DOIUrl":"10.1016/j.mimet.2024.107039","url":null,"abstract":"<div><p>Hepatopancreatic microsporidiosis (HPM), caused by the microsporidium <em>Ecytonucleospora hepatopenaei</em> (EHP) leads to retarded growth and enhanced susceptibility to other diseases in shrimp resulting in a major loss for the shrimp industry worldwide. It is little understood how EHP infects its host and hijacks its cellular machinery to replicate and exert clinical manifestations in infected shrimp. Since the initial record of HPM, histopathology and polymerase chain reaction (PCR)-based assays were developed for the detection of EHP to prevent spread of the disease. Availability of an antibody-based detection method would complement these existing diagnostic tools and be useful in studying EHP pathogenesis. We describe here an immunofluorescence assay (IFA) for detecting EHP using monoclonal antibodies (mAbs) that were originally developed against <em>Cryptosporidium parvum</em>, a coccidian parasite that infects calves (<em>Bos taurus</em>), other agriculturally important animals, and humans. Forty-one mAbs were screened and two mAbs, 3E2 and 3A12, were found to detect EHP successfully. The utility of these mAbs in detecting EHP was further assessed by testing 36 experimentally challenged EHP-infected shrimp (<em>Penaeus vannamei)</em>. EHP-detection data from infected shrimp were compared by Hematoxylin and Eosin (H&amp;E) histology, real-time PCR, and immunofluorescence. The data show IFA using mAbs 3E2 and 3A12 could successfully detect EHP and that the sensitivity of detection is comparable to H&amp;E histology and quantitative PCR. Availability of mAbs that can detect EHP is expected to be immensely beneficial in HPM diagnosis. Since the pathobiology of <em>C. parvum</em> has been so widely studied, these cross-reactive mAbs may also aid in gaining some insight into EHP pathogenesis and disease.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107039"},"PeriodicalIF":1.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142172625","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":"Optical detection and enumeration of Escherichia coli and Salmonella enterica using a low-magnification light microscope","authors":"Yuzhen Zhang,&nbsp;Zili Gao,&nbsp;Lili He","doi":"10.1016/j.mimet.2024.107041","DOIUrl":"10.1016/j.mimet.2024.107041","url":null,"abstract":"<div><p>A rapid and cost-effective method for detecting bacterial cells from surfaces is critical to food safety, clinical hygiene, and pharmacy quality. Herein, we established an optical detection method based on a gold chip coating with 3-mercaptophenylboronic acid (3-MPBA) to capture bacterial cells, which allows for the detection and quantification of bacterial cells with a standard light microscope under low-magnification (10×) objective lens. Then, integrate the developed optical detection method with swab sampling to detect bacterial cells loading on stainless-steel surfaces. Using <em>Salmonella enterica</em> (SE1045) and <em>Escherichia coli</em> (<em>E. coli</em> OP50) as model bacterial cells, we achieved a capture efficiency of up to 76.0 ± 2.0 % for SE1045 cells and 81.1 ± 3.3 % for <em>E. coli</em> OP50 cells at 10³ CFU/mL upon the optimized conditions, which slightly decreased with the increasing bacterial concentrations. Our assay showed good linear relationships between the concentrations of bacterial cells with the cell counting in images in the range of 10³ -10⁷ CFU/mL for SE1045, and 10³ -10⁸ CFU/mL for <em>E. coli</em> OP50 cells. The limit of detection (LOD) was 10³ CFU/mL for both SE1045 and <em>E. coli</em> OP50 cells. A further increase in sensitivity in detecting <em>E. coli</em> OP50 cells was achieved through a heat treatment, enabling the LOD to be reduced as low as 10² CFU/mL. Furthermore, a preliminary application succeeded in assessing bacterial contamination on stainless-steel surfaces following integration with the approximately 40 % recovery rate, suggesting prospects for evaluating the bacteria from surfaces. The entire process was completed within around 2 h, costing merely a few dollars per sample. Considering the low cost of standard light microscopes, our method holds significant potential for practical industrial applications in bacterial contamination control on surfaces, especially in low-resource settings.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107041"},"PeriodicalIF":1.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232664","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":"Evaluation of cobas® Liat® Cdiff, STANDARD™ M10 C. difficile and Xpert® C. difficile BT assays for rapid detection of toxigenic Clostridioides difficile","authors":"Juulia Suominen ,&nbsp;Suvi Korhonen ,&nbsp;Heini Kutvonen ,&nbsp;Hanna Jarva ,&nbsp;Anu Pätäri-Sampo ,&nbsp;Raisa Loginov","doi":"10.1016/j.mimet.2024.107043","DOIUrl":"10.1016/j.mimet.2024.107043","url":null,"abstract":"<div><p>We evaluated the analytical performance of three commercial molecular assays for rapid detection of <em>Clostridioides difficile</em> toxin B in stool samples. The results were compared with results from the BD MAX™ Cdiff assay. We analyzed forty negative and thirty-two positive stool samples with three rapid assays: Roche cobas® Liat® Cdiff, SD Biosensor STANDARD™ M10 <em>C. difficile</em> and Cepheid Xpert® <em>C. difficile</em> BT. The assays demonstrated a sensitivity of 96.9 %, 96.9 % and 100.0 % and a specificity of 100 %, 97.5 % and 97.5 %, respectively. There is limited data available on the analytical performance of the newly introduced STANDARD™ M10 <em>C. difficile</em> assay. In this study, all three rapid assays demonstrated similarly high analytical performance and can be used for detection of toxigenic <em>C. difficile</em>.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107043"},"PeriodicalIF":1.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224001556/pdfft?md5=00756b5b8da14dc99fad7302cefecc61&pid=1-s2.0-S0167701224001556-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142240765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of a synthetic oligonucleotide to detect false positives caused by cross-contamination in nested PCR","authors":"Alexandre S. Maekawa ,&nbsp;Luciene S. Santos ,&nbsp;Paulo E.N.F. Velho ,&nbsp;Marina R. Drummond","doi":"10.1016/j.mimet.2024.107040","DOIUrl":"10.1016/j.mimet.2024.107040","url":null,"abstract":"<div><p>Nested PCR is a useful tool for identifying low-abundance target sequences of pathogens and avoiding false negatives. However, it carries an increased risk of cross-contamination, especially with its positive control. Here, we propose using customized synthetic oligonucleotides to detect false positives due to cross-contamination.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107040"},"PeriodicalIF":1.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142172626","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":"Prediction strategy for screening functional Haloarchaea strains with qPCR assays","authors":"Xinyu Hu ,&nbsp;Wenxiang Sun ,&nbsp;Meng Zhang ,&nbsp;Wenjun Guo ,&nbsp;Shujing Yang ,&nbsp;Lin Zhu ,&nbsp;Xiang Xiao ,&nbsp;Xiangru Xu ,&nbsp;Wei Wei","doi":"10.1016/j.mimet.2024.107029","DOIUrl":"10.1016/j.mimet.2024.107029","url":null,"abstract":"<div><p>As an extremophile resource, functional Haloarchaea strains are extremely time-consuming to screen. Here, taking the screening of low-salt-tolerant strains as an example, based on the qPCR assays that shortened time by 4–7 times and achieved 100 % accuracy, a universal strategy for rapid and accurate screening of functional Haloarchaea strains was established.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107029"},"PeriodicalIF":1.7,"publicationDate":"2024-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154390","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 short-chain organic acids (SCOAs) obtained from anaerobic fermentation process","authors":"M. Ghalibaf,&nbsp;N. Pap,&nbsp;M. Vainio,&nbsp;N. Honkala,&nbsp;S. Rasi","doi":"10.1016/j.mimet.2024.107031","DOIUrl":"10.1016/j.mimet.2024.107031","url":null,"abstract":"<div><p>Short-chain organic acids (SCOAs) are the intermediates in the anaerobic fermentation process, and can be used in food, textile, and pharmaceutical industries to produce different end use products. SCOAs can be separated, purified, and concentrated by different processes, such as distillation, extraction or membrane-based systems. SCOAs production adds more profitable possibilities to an acidic fermentation process by integration these marketable acids as highly concentrated mixtures with other refinery processes. The present study investigated two approaches for recovering of SCOAs: i) the production of clarified SCOAs liquid by microfiltration (MF) and then performing their concentration by reverse osmosis (RO) and ii) the recovery and concentration by the so-called integrated neutralization and acidified reaction method. The results of MF showed that some SCOAs were retained in the retentate together with the solids. However, in the following RO treatment, SCOAs could be successfully concentrated with a yield retention of over 90 % from the SCOAs liquid. In the latter method, a color-free SCOAs liquid was obtained with an increase in the total SCOAs concentration from 23 g/L to 146 g/L.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107031"},"PeriodicalIF":1.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S016770122400143X/pdfft?md5=2943388e82132b3204ea52ff92316efb&pid=1-s2.0-S016770122400143X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid and visual detection of Mycoplasma genitalium using recombinase polymerase amplification combined with lateral flow strips","authors":"Pufang Ren ,&nbsp;Yingmin Zeng ,&nbsp;Yao Feng ,&nbsp;Honghai Hong,&nbsp;Yong Xia","doi":"10.1016/j.mimet.2024.107030","DOIUrl":"10.1016/j.mimet.2024.107030","url":null,"abstract":"<div><p><em>Mycoplasma genitalium</em> (MG) is an important sexually transmitted pathogen that can cause urethritis in males and pelvic inflammatory disease in females. Due to its complex growth requirements and lengthy incubation times, culturing MG in clinical laboratories is impractical. Here we describe a rapid and visual assay combining recombinase polymerase amplification (RPA) with lateral flow (LF) strips to detect MG (MG-RPA-LF). The limit of detection (LoD) of this method was 33.6 genome equivalents (GE) per reaction, using a dilution series of purified genomic DNA. Clinical performance was evaluated by testing 100 urogenital swabs. Compared to the Simultaneous Amplification and Testing assay, our MG-RPA-LF assay showed a sensitivity of 94 % (95 % CI, 82 %–98 %) and a specificity of 100 % (95 % CI, 91 %–100 %). The overall concordance between the two methods was 97 % (95 % CI, 91 %–99 %) with a κ coefficient of 0.94 (<em>P</em> &lt; 0.001). Without cumbersome and expensive instruments, this method is anticipated to be a promising alternative to diagnose MG infection, especially in resource-poor settings.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107030"},"PeriodicalIF":1.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154391","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":"The effect of Tyloxapol on the metabolome of Mycobacterium tuberculosis","authors":"Monique Opperman ,&nbsp;Ray-Dean Pietersen ,&nbsp;Du Toit Loots ,&nbsp;Mari van Reenen ,&nbsp;Derylize Beukes ,&nbsp;Bienyameen Baker ,&nbsp;Ilse du Preez","doi":"10.1016/j.mimet.2024.107028","DOIUrl":"10.1016/j.mimet.2024.107028","url":null,"abstract":"<div><p>The use of detergents when culturing <em>Mycobacterium tuberculosis</em> (<em>M. tuberculosis</em>) are essential to prevent clumping. However, these detergents may influence research outcomes by impacting bacterial morphology and metabolism. This study aimed to assess the metabolome of a <em>M. tuberculosis</em> H37Rv strain cultured with Tyloxapol (H37Rv^Tyloxapol), compared to a control group of H37Rv strain cultured without detergent (H37Rv^Control) to evaluate Tyloxapol's suitability for metabolomic studies. Distinct metabolic alterations were observed in H37Rv^Tyloxapol compared to H37Rv^Control, primarily associated with fatty acid, sugar and pentose phosphate metabolic pathways. These changes are associated with the surface stress exerted by Tyloxapol on the bacteria, prompting an adaptation of <em>M. tuberculosis</em> metabolism to that usually observed in stress environments. Nevertheless, the effect of Tyloxapol is less pronounced than that of a previous investigation using Tween 80, indicating its potential as the more favourable choice for culturing <em>M. tuberculosis</em> for metabolomic analysis, with due consideration to dosage and result interpretation.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"226 ","pages":"Article 107028"},"PeriodicalIF":1.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142154393","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":"Physical radiation induced the yield of triterpenoids in hypha of Inonotus obliquus to increase","authors":"Yan Wang ,&nbsp;Xin Liu ,&nbsp;Lirui Sun ,&nbsp;Boxin Dou ,&nbsp;Jiaying Xin ,&nbsp;Na Zhang ,&nbsp;Lanwei Zhang","doi":"10.1016/j.mimet.2024.107025","DOIUrl":"10.1016/j.mimet.2024.107025","url":null,"abstract":"<div><p>HSD-IO01, a new pure strain of <em>I. obliquus</em>, was isolated and purified from the sclerotium of <em>I. obliquus</em> of Daxing'an Mountains. Physical radiation-assisted liquid fermentation technology was explored to increase the triterpenoids yield of HSD-IO01. In the 100 mL optimized liquid fermentation system, the hypha dry weight of HSD-IO01 was 1.7734 g, and the triterpenoids yield was 43.43 mg. Yields of triterpenoids increased after induction with ultrasound, microwave, or UV light, respectively. Among them, ultrasonic treatment had the most remarkable induction effect. The yield of triterpenoids would be increased to 68.35 mg (57.38 %) when the HSD-IO01 was treated by 100 W ultrasonic for 45 min. Establishing ultrasonic-assisted liquid fermentation technology could further promote the detailed development and comprehensive utilization of <em>I. obliquus</em> resources.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107025"},"PeriodicalIF":1.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108283","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":"Corrigendum to “Visualisation of Mycobacterium avium subsp. paratuberculosis in cultured cells, infected sheep and human tissue sections using fluorescent in situ hybridization (FISH)” [Journal of Microbiological Methods 224 (2024) 107001]","authors":"Neil Rayment ,&nbsp;Glenn Rhodes ,&nbsp;Barry Hudspith ,&nbsp;Valerie Hughes ,&nbsp;Francesca Chianini ,&nbsp;Gaurav Agrawal ,&nbsp;Tim J. Bull ,&nbsp;Roger Pickup ,&nbsp;Jeremy Sanderson","doi":"10.1016/j.mimet.2024.107024","DOIUrl":"10.1016/j.mimet.2024.107024","url":null,"abstract":"","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"225 ","pages":"Article 107024"},"PeriodicalIF":1.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224001362/pdfft?md5=5666f32d0def5b16e3f9ae5e390ae78a&pid=1-s2.0-S0167701224001362-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142108275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}