Journal of microbiological methods最新文献

{"title":"Identification of sepsis-causing bacteria from whole blood without culture using primers with no cross-reactivity to human DNA","authors":"Yasuyuki Kawai ,&nbsp;Akifumi Nakayama ,&nbsp;Hidetada Fukushima","doi":"10.1016/j.mimet.2024.106982","DOIUrl":"10.1016/j.mimet.2024.106982","url":null,"abstract":"<div><p>Sepsis is a major health concern globally, and identification of the causative organism usually takes several days. Furthermore, molecular amplification using whole blood from patients with sepsis remains challenging because of primer cross-reactivity with human DNA, which can delay appropriate clinical intervention. To address these concerns, we designed primers that could reduce cross-reactivity. By evaluating these primers against human DNA, we confirmed that the cross-reactivity observed with conventional primers was notably absent. In silico PCR further demonstrated the specificity and efficiency of the designed primers across 23 bacterial species that are often associated with sepsis. When tested using blood samples from sepsis patients, the designed primers showed moderate sensitivity and high specificity. Surprisingly, our method identified bacteria even in samples that were detected at other sites but tested negative using conventional blood culture methods. Although we identified some challenges, such as contamination with <em>Acetobacter aceti</em> due to the saponin pretreatment of samples, the developed method demonstrates remarkable potential for rapid identification of the causative organisms of sepsis and provides a new avenue for diagnosis in clinical practice.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106982"},"PeriodicalIF":1.7,"publicationDate":"2024-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000940/pdfft?md5=068ae949409e9f6af94c40e37db689c3&pid=1-s2.0-S0167701224000940-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468692","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":"Identification of genus Deinococcus strains by PCR detection using the gyrB gene and its extension to Bacteria domain","authors":"Hyeonsik Yoon,&nbsp;Hyun Hee Lee,&nbsp;Hee Seong Noh,&nbsp;Sung-Jae Lee","doi":"10.1016/j.mimet.2024.106980","DOIUrl":"10.1016/j.mimet.2024.106980","url":null,"abstract":"<div><p>In radiation-resistant bacteria belonging to the genus <em>Deinococcus</em>, transposition events of insertion sequences (IS elements) leading to phenotypic changes from a reddish color to white were detected following exposure to gamma irradiation and hydrogen peroxide treatment. This change resulted from the integration of IS elements into the phytoene desaturase gene, a key enzyme in the carotenoid biosynthesis pathway. To facilitate species identification and distinguish among <em>Deinococcus</em> strains, the <em>gyr</em>B gene encoding the B subunit of DNA gyrase was utilized. The s gnificance of the <em>gyr</em>B gene is well recognized not only in genome replication through the regulation of supercoiling but also in phylogenetic analysis providing support for 16S rRNA-based identification. Its mutation rate surpasses that of the 16S rRNA gene, offering greater resolution between closely related species, particularly those exhibiting &gt;99% similarity. In this study, phylogenetic analysis was conducted comparing the 16S rRNA and <em>gyr</em>B gene sequences of <em>Deinococcus</em> species. Species-specific and genus-specific primers targeting <em>Deinococcus</em> species were designed and experimentally validated for selective amplification and rapid identification of the targeted species. This approach allows for the omission of 16S rRNA sequencing in the targeted <em>Deinococcus</em> species. Therefore, the <em>gyr</em>B gene is useful for identifying bacterial species and genus-level detection from individual microbes or microbial consortia using specialized primer sets for PCR amplification.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106980"},"PeriodicalIF":1.7,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000927/pdfft?md5=352267829e074c33f50c37e9160fc532&pid=1-s2.0-S0167701224000927-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468689","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":"MICA Legionella, an innovative and rapid method for enumeration of Legionella pneumophila in French sanitary water","authors":"Passot Fanny M.,&nbsp;Peslier Sabine,&nbsp;Dukan Sam,&nbsp;Dumont Audrey","doi":"10.1016/j.mimet.2024.106977","DOIUrl":"10.1016/j.mimet.2024.106977","url":null,"abstract":"<div><p>A new innovative method, MICA <em>Legionella</em>, allows for the automatic enumeration of <em>Legionella pneumophila</em> in domestic water samples in 2 days, with a detection limit of 2 CFU per test portion. Here we show that it gives equivalent results to those obtained by the French standard method NF T90–431 in 7 to 15 days.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106977"},"PeriodicalIF":1.7,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000897/pdfft?md5=567a382a7c83aec8fcc1d40783fa34e2&pid=1-s2.0-S0167701224000897-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468690","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":"Comparison of plate counting with flow cytometry, using four different fluorescent dye techniques, for the enumeration of Bacillus cereus in milk","authors":"Ben T. Somerton,&nbsp;Brooke L. Morgan","doi":"10.1016/j.mimet.2024.106978","DOIUrl":"10.1016/j.mimet.2024.106978","url":null,"abstract":"<div><p>This study aimed to compare the performance of flow cytometry methods with plate counting for the enumeration of bacteria, using <em>Bacillus cereus</em> as a model organism. It was found that the cFDA-propidium iodide, CellROX™ Green-propidium iodide, and DiOC₂ dye techniques had similar accuracy to plate counting, while the SYTO 24-propidium iodide dye technique was not as accurate. The four dye techniques had comparable precision to plate counting, with the CellROX™ Green-propidium iodide dye having the greatest precision. The consistency of the position and shape of the cell clusters on the flow cytometry plots, and the extent of separation of the cell from background clusters, was greatest with the DiOC₂ and CellROX™ Green-propidium iodide dyes. Furthermore, the DiOC₂ and CellROX™ Green-propidium iodide dyes performed well, even when a sample was measured containing reconstituted whole milk powder at a 10⁻¹ dilution, without the use of sample preparation to specifically remove the milk constituents prior to measurement. Given gating of only one cell cluster was required to be managed with the DiOC₂ dye, to determine the viable number of cells, it was found that the DiOC₂ dye had the greatest ease-of-use. Overall, results indicated that the DiOC₂ dye is an ideal candidate for the enumeration of viable bacteria in dairy samples on a high-throughput, routine basis.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106978"},"PeriodicalIF":1.7,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141468691","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":"Improved productivity and dye removal performance of Trametes versicolor pellets using rice husk as a co-substrate","authors":"Juan Antonio Gutiérrez-Quirós ,&nbsp;Alonso Coronado-Marchena ,&nbsp;Diego Villegas-Solano,&nbsp;Sebastián Rodríguez-Saravia,&nbsp;Víctor Castro-Gutiérrez,&nbsp;Carlos E. Rodríguez-Rodríguez","doi":"10.1016/j.mimet.2024.106976","DOIUrl":"10.1016/j.mimet.2024.106976","url":null,"abstract":"<div><p>Pellet production represents a critical step for several processes requiring fungal biomass, nevertheless, its optimization is seldom reported. The use of finely ground rice husk as a microcarrier and co-substrate permitted a marked increase (≈ 2.7×) in the productivity of fungal pellet production using <em>Trametes versicolor</em> compared to traditional production methods. The pellets show similar structure and smaller size compared to typical sole-mycelium pellets, as well as comparable laccase activity. The efficiency of the pellets for biodegradation was confirmed by the removal of the crystal violet dye, achieving significantly faster decolorization rates compared to the traditionally produced pellets. The use of these pellets during the continuous treatment of the dye in a stirred tank bioreactor resulted in 97% decolorization operating at a hydraulic residence time of 4.5 d.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106976"},"PeriodicalIF":1.7,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141457436","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":"LC-HRMS-based metabolomics and lipidomics analyses of a novel probiotic Akkermansia Muciniphila in response to different nutritional stimulations","authors":"Huan Zhang,&nbsp;Shiqi Zhang,&nbsp;Li Chen,&nbsp;Rui Xu,&nbsp;Jiangjiang Zhu","doi":"10.1016/j.mimet.2024.106975","DOIUrl":"10.1016/j.mimet.2024.106975","url":null,"abstract":"<div><p>The mucin-degrading gut commensal <em>Akkermansia muciniphila</em> (<em>A. muciniphila</em>) negatively correlates with various diseases, including metabolic disorders, neurodegenerative disorders, and cancers, through interacting with host receptors by diverse molecules. Still, their exact metabolic capability within the nutrient-rich environment (such as in the human gut) is not fully characterized. Therefore, in the present study, we investigated the comprehensive metabolome and lipidome of <em>A. muciniphila</em> after supplementation of four major gut microbial nutrients: mucin, inorganic salts, bile salts, and short-chain fatty acids (SCFAs). Our results showed that mucin is the predominant driver of the different lipidomic and metabolomic profiles of <em>A. muciniphila</em>, and it promotes the overall growth of this bacteria. While the addition of inorganic salts, bile salts, and SCFAs was found to inhibit the growth of <em>A. muciniphila</em>. Interestingly, inorganic salts affected the purine metabolism in <em>A. muciniphila</em> cultures, while adding bile salts significantly increased the production of other bile acids and N-acyl amides. Lastly, SCFAs were identified to alter the <em>A. muciniphila</em> energy utilization of triglycerides, fatty acyls, and phosphatidylethanolamines. To our knowledge, this is the first study to examine the comprehensive lipidome and metabolome of <em>A. muciniphila</em>, which highlights the importance of nutritional impacts on the lipidome and metabolome of <em>A. muciniphila</em> and hence providing foundational knowledge to unveil the potential effects of <em>A. muciniphila</em> on host health.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106975"},"PeriodicalIF":1.7,"publicationDate":"2024-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000873/pdfft?md5=e86072d8421b2af973c960e6ce2459ef&pid=1-s2.0-S0167701224000873-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141419569","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":"Adaptation and validation of a light microscope for use in energy insecure settings: a proof-of-concept study","authors":"Nina Bühler ,&nbsp;Diana Velten ,&nbsp;Philipp Jung ,&nbsp;Sophie E. Müller ,&nbsp;Sören L. Becker ,&nbsp;Sakib Burza ,&nbsp;Sophie Schneitler","doi":"10.1016/j.mimet.2024.106974","DOIUrl":"10.1016/j.mimet.2024.106974","url":null,"abstract":"<div><p>Microscopy as a basic diagnostic method cannot be used everywhere globally. Validity of slide reading was tested on torch-modified microscopes. Experienced microscopists handled the modification without prior standard-adaptation. In contrast, microscopist-trainees required more detailed instructions to get acquainted with this new technique. The overall results encourage further, setting-specific validation.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106974"},"PeriodicalIF":1.7,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000861/pdfft?md5=371e7f3d5f9f26a4d738ccaeede7ad56&pid=1-s2.0-S0167701224000861-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141331132","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":"Integrated decentralized blood culture incubation: A step towards a 24/7 microbiology service?","authors":"Frieder Schaumburg ,&nbsp;Franziska Schuler ,&nbsp;Manfred Fobker ,&nbsp;Jutta Esser","doi":"10.1016/j.mimet.2024.106973","DOIUrl":"https://doi.org/10.1016/j.mimet.2024.106973","url":null,"abstract":"<div><p>To have an impact on the mortality of bloodstream infections, microbiological diagnostics of blood cultures (BC) should provide first results within 12 h. Here, we show how a decentralized BC incubation connected to the central BC incubators via a browser-based application significantly reduces turnaround times.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106973"},"PeriodicalIF":2.2,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S016770122400085X/pdfft?md5=154e9ff09e1669dfb263c261b0a3a093&pid=1-s2.0-S016770122400085X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141328880","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":"Comparison of available methods to evaluate cefiderocol susceptibility in Acinetobacter spp","authors":"Fernando Pasteran ,&nbsp;Olivia Wong ,&nbsp;Vyanka Mezcord ,&nbsp;Christina Lopez ,&nbsp;Nardin Georgeos ,&nbsp;Venjaminne Fua ,&nbsp;Alonzo Ozuna ,&nbsp;Dema Ramlaoui ,&nbsp;Cristian Sánchez ,&nbsp;Paulina Marchetti ,&nbsp;Alejandra Corso ,&nbsp;Marcelo E. Tolmasky ,&nbsp;Robert A. Bonomo ,&nbsp;María Soledad Ramirez","doi":"10.1016/j.mimet.2024.106972","DOIUrl":"10.1016/j.mimet.2024.106972","url":null,"abstract":"<div><p>Recently, considerable uncertainty has arisen concerning the appropriate susceptibility testing for cefiderocol in gram-negative bacilli, particularly in the context of its application to <em>Acinetobacter</em> spp. The optimal method for assessing the susceptibility levels of <em>Acinetobacter</em> spp. to cefiderocol remains a subject of debate due to substantial disparities observed in the values obtained through various testing procedures. This study employed four minimum inhibitory concentration (MIC) methodologies and the disk diffusion to assess the susceptibility of twenty-seven carbapenem resistant (CR)-<em>Acinetobacter</em> strains to cefiderocol. The results from our study reveal significant variations in the minimum inhibitory concentration (MIC) values obtained with the different methods and in the level of agreement in interpretation categories between the different MIC methods and the disk diffusion test. Among the MIC methods, there was relatively more consistency in reporting the interpretation categories. For European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints, the categorical agreement (CA) for MIC methods ranged between 66.7 and 81.5%. On the other hand, the essential agreement (EA) values were as low as 18.5–29.6%. The CA between MIC methods and disk diffusion was 81.5%. These results emphasize the need for a reliable, accurate, and clinically validated methodology to effectively assess the susceptibility of <em>Acinetobacter</em> spp. to cefiderocol. The wide variability observed in our study highlights the importance of standardizing the susceptibility testing process for cefiderocol to ensure consistent and reliable results for clinical decision-making.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106972"},"PeriodicalIF":1.7,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0167701224000848/pdfft?md5=e6dbec05291796b917b5e740df07c133&pid=1-s2.0-S0167701224000848-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141317557","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":"Detection of KPC enzyme by MALDI-TOF MS from bacteria impregnated in filter paper","authors":"Camila M. Wilhelm ,&nbsp;Natália K. Moreira ,&nbsp;Maiara S. Carneiro ,&nbsp;Priscila L. Wink ,&nbsp;Juliana Caierão ,&nbsp;Afonso L. Barth","doi":"10.1016/j.mimet.2024.106962","DOIUrl":"10.1016/j.mimet.2024.106962","url":null,"abstract":"<div><p>The main mechanism that causes resistance to carbapenem, one of the most potent antibiotic available, in <em>Enterobacterales</em> bacterial isolates, is due to <em>Klebsiella pneumoniae</em> carbapenemase (KPC) production by the bacterium. KPC is spread worldwide, requiring laboratories to be capable of identifying this enzyme, however some methods can be expensive for small laboratories, especially in developing countries. Therefore, the development of methods with low cost of reagents for the detection of KPC enzyme is necessary. The objective of this study was to evaluate the detection of KPC enzyme by MALDI-TOF MS from inactivated bacteria impregnated in filter paper. A total of 129 <em>Enterobacterales</em> isolates were impregnated in filter paper, and after 7 days at room temperature, they were subjected to a protein extraction protocol and spectra acquisition, in triplicates, by MALDI-TOF MS. The spectra were evaluated and KPC was identified according to the presence of a peak of 28,712.62 ± 27.80 <em>m</em>/<em>z</em>. Considering the presence of the KPC peak in at least one spectrum of the triplicates, this method presented 60.8% sensitivity and 96.4% specificity. However, considering the presence of KPC peak in at least two spectra of the triplicate, a specificity of 100% was achieved. The detection of KPC enzyme from inactivated bacteria impregnated in filter paper can be used as a method to confirm the presence of KPC, which could be very significant for small laboratories with limited resources.</p></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"223 ","pages":"Article 106962"},"PeriodicalIF":2.2,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141135420","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}