Mariana Quaresma de Souza , Ana Júlia Reis , Andrea von Groll , Pedro Eduardo Almeida da Silva , Ivy Bastos Ramis
{"title":"Colorimetric methods for detecting antimicrobial resistant mycobacteria: An overview","authors":"Mariana Quaresma de Souza , Ana Júlia Reis , Andrea von Groll , Pedro Eduardo Almeida da Silva , Ivy Bastos Ramis","doi":"10.1016/j.mimet.2025.107341","DOIUrl":"10.1016/j.mimet.2025.107341","url":null,"abstract":"<div><div>Phenotypic culture-based methods continue to be recommended for identification of the susceptibility profile to antimicrobials in mycobacterial isolates. For this, in-house colorimetric methods have been developed for detection of <em>Mycobacterium tuberculosis</em> and nontuberculous mycobacteria resistant strains, associated with an easier interpretation of results. Most existing colorimetric methods are based on the use of redox colorimetric indicators, such as resazurin and tetrazolium salts. Other tests require revealing solutions to generate color, while there are also tests that target the loss of color as a way of indicating bacterial growth. This review aimed to elucidate the available colorimetric methods to detect resistant mycobacterial strains, including their evaluation and application. Despite varying in terms of the format used, the methods presented in this review are relatively simple to perform and cheaper than molecular and semi-automated phenotypic methods, and can be implemented in different scenarios, including in limited resource settings.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107341"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616032","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 microbiological method for analysis of clindamycin-based product potency and its equivalence to UV and HPLC methods","authors":"Isadora Alves Lustosa, Ana Carolina Kogawa","doi":"10.1016/j.mimet.2025.107338","DOIUrl":"10.1016/j.mimet.2025.107338","url":null,"abstract":"<div><div>Clindamycin is an antimicrobial sold in capsules, injectable solution, or gel for topical use. Despite its wide use, current official compendia and literature lack microbiological methods to assess its potency, relying mainly on physicochemical assays such as high-performance liquid chromatography (HPLC). These techniques, however, do not evaluate the biological activity of the drug. In this context, the present study proposes, for the first time, aimed to develop and validate a rapid microbiological method to determine the potency of clindamycin in capsule form and to compare its results with those obtained from UV and HPLC methods. The method employed <em>Escherichia coli</em> ATCC 8739, BHI broth as the growth medium, and a hydroalcoholic diluent (ethanol: water, 1:1 <em>v</em>/v) for solution preparation. Concentrations tested were 8, 16, and 32 μg mL<sup>−1</sup>, with incubation at 35 ± 2 °C for 4 h under agitation (70 rpm), followed by absorbance measurement at 530 nm. The method exhibited linearity (<em>r</em> > 0.99), selectivity, precision (RSD 3.16 %, 3.57 %, 3.14 %), accuracy (average recovery of 99.47 %), and robustness under most tested conditions, as percentage of inoculum, brand of BHI broth, and volume of BHI broth used in the tube. Statistical comparison confirmed the equivalence of the proposed method with UV and HPLC (F<sub>cal</sub> 0.68 < F<sub>tab</sub> 5.14). This validated microbiological method offers a fast, reliable, and biologically relevant alternative for routine potency determination of clindamycin capsules, addressing a major analytical gap in the quality control of antimicrobial products.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107338"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145587948","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}
Hossein Taiyari , Jalila Abu , Zunita Zakaria , Sharina Omar , Chan Zi Wen , Nik Mohd Faiz
{"title":"Different media affect the growth and antimicrobial minimum inhibitory concentrations of Mycoplasma gallisepticum and Mycoplasma synoviae","authors":"Hossein Taiyari , Jalila Abu , Zunita Zakaria , Sharina Omar , Chan Zi Wen , Nik Mohd Faiz","doi":"10.1016/j.mimet.2025.107350","DOIUrl":"10.1016/j.mimet.2025.107350","url":null,"abstract":"<div><div>The main pathogenic <em>Mycoplasma</em> spp. infecting chickens are <em>Mycoplasma gallisepticum</em> (MG) and <em>Mycoplasma synoviae</em> (MS). The MG and MS play an etiological role in chronic respiratory disease. One of the methods to control avian mycoplasmosis is antibiotic therapy. The microdilution minimum inhibitory concentration (MIC) assay is one of the most commonly used tests to assess the antibiotic susceptibility profile of isolates. The effect of type of medium used in the MIC assay of MG and MS has not been evaluated. Therefore, the aim of this study is to determine the impact of two commonly used avian mycoplasmas growth media, Frey medium and Pleuropneumonia-like Organisms (PPLO) medium, on growth rate and the MIC values of MG and MS. The comparison of growth rates and MIC values between two media was conducted in three replicates, and the mean values were used for any further analysis. First, the growth rates of MG and MS were compared in both Frey and PPLO media. Then, antimicrobial MIC values were determined using the microbroth dilution method. The results show that MG and MS isolates had faster growth rates in Frey compared to PPLO (<em>p</em> ≤ 0.05). The antimicrobial MIC values of MG and MS isolates were different in Frey and PPLO media. This study indicates the significant effect of the type of medium used in the determination of antimicrobial MIC values of MG and MS, and can be used as a fundamental source for preparation of a more comprehensive MG and MS MIC protocol.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107350"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145648899","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 a rapid molecular assay for specific identification of Mycobacterium avium and Mycobacterium intracellulare","authors":"Takafumi Yoshikane , Masashi Michibuchi , Chihiro Ogawa , Takahiro Azuma , Tomomi Yamazaki , Shinji Hatakeyama , Masaki Takanashi , Kinuyo Chikamatsu , Akio Aono , Akiko Takaki , Satoshi Mitarai , Hiromichi Suzuki","doi":"10.1016/j.mimet.2025.107359","DOIUrl":"10.1016/j.mimet.2025.107359","url":null,"abstract":"<div><div>In genetic testing of non-tuberculous mycobacteria, false positives due to cross-reactions and differences in detection performance among strains are problematic. A rapid genetic testing method with high specificity to distinguish only <em>Mycobacterium avium</em> and <em>Mycobacterium intracellulare</em> and high detection performance against genetic diversity among strains is desirable. We identified completely novel genes (MAA44156_02837 for <em>M. avium</em> and KN251_15665 for <em>M. intracellulare</em>) showing strong identity with <em>M. avium</em> and <em>M. intracellulare</em> respectively. We then developed a new <em>M. avium</em>/<em>M. intracellulare</em> simultaneous detection assay targeting these genes and evaluated their specificity and sensitivity. To evaluate cross-reactivity, the newly developed assay correctly identified all <em>Mycobacterium</em> spp. type strains, except for one examination of a duplicated evaluation with a <em>Mycobacterium kyorinense</em> type strain as a false positive at McFarland 1.0. All <em>M. avium</em>-positive and <em>M. intracellulare-</em>positive clinical isolates used in this study were accurately detected using the newly developed assay. The limits of detection for the newly developed assay were estimated to be 100 CFU/mL for <em>M. avium</em> and 30 CFU/mL for <em>M. intracellulare</em>. In addition, the detection performance was maintained even in samples containing both <em>M. avium</em> and <em>M. intracellulare</em>. The <em>M. avium</em>/<em>M. intracellulare</em> simultaneous detection assay developed in this study demonstrated high specificity, detection performance, and sensitivity for detecting <em>M. avium</em> and <em>M. intracellulare</em>.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107359"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145743148","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}
Mengjie Liang , Yongxin Li , Jingyuan Yang , Chunyan Liu , Haojie Lin , Zhaohui Deng , Xin Zhang
{"title":"Construction and application of MS2 bacteriophage virus-like particles for SARS-CoV-2 detection using a single-plasmid system","authors":"Mengjie Liang , Yongxin Li , Jingyuan Yang , Chunyan Liu , Haojie Lin , Zhaohui Deng , Xin Zhang","doi":"10.1016/j.mimet.2025.107344","DOIUrl":"10.1016/j.mimet.2025.107344","url":null,"abstract":"<div><div>Research on the compatibility of MS2 bacteriophage virus-like particles (VLPs), which are used for the detection of a range of RNA viruses, with commercially available detection kits is limited. Here, we aimed to construct a positive control for RNA virus nucleic acid detection using MS2 bacteriophage VLPs and evaluate its compatibility with commercial nucleic acid detection kits to support the standardization of molecular diagnostic quality control systems. We generated recombinant plasmids expressing MS2 bacteriophage maturation enzyme, capsid proteins, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) target genes (<em>ORF1ab</em>, <em>N</em>, and <em>E</em>) using a single-plasmid dual-expression system (pACYCDuet-1). The plasmids were expressed in <em>Escherichia coli</em> BL21, and then MS2 VLPs were purified. The VLPs were characterized, and their performance as a positive control was validated for homogeneity and stability; their detection compatibility with five commercial SARS-CoV-2 nucleic acid detection kits was also examined. We successfully generated MS2 VLPs carrying SARS-CoV-2 target genes, with a uniform particle size of 23–28 nm and target gene copy number of 1.99 × 10<sup>10</sup> copies/μL. Sodium dodecyl sulfate–polyacrylamide gel electrophoresis confirmed the expression of MS2 proteins, whereas functional validation revealed excellent nuclease resistance, batch–batch homogeneity, and stability at 4 °C for ≥20 days. Importantly, the positive control exhibited consistent detection performance across all five commercial kits, confirming its practicality for routine laboratory workflows. The established positive control is readily applicable for standardizing quality control in molecular diagnostics.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107344"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616467","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}
Zhangxi Gong , Yu Zhou , Yongbing Ba , Yao Yang , Yingjie Pan , Yong Zhao , Haiquan Liu
{"title":"Single-cell RNA seq reveals heterogeneous survival strategies of Vibrio parahaemolyticus against ampicillin","authors":"Zhangxi Gong , Yu Zhou , Yongbing Ba , Yao Yang , Yingjie Pan , Yong Zhao , Haiquan Liu","doi":"10.1016/j.mimet.2025.107343","DOIUrl":"10.1016/j.mimet.2025.107343","url":null,"abstract":"<div><div>Bulk RNA-Seq only captures the average gene expression level of bacterial populations and has limitations in analysing functional differences between bacterial subpopulations. Therefore, the study innovatively applied droplet-based single-cell RNA sequencing (scRNA-seq) to resolve ampicillin resistance heterogeneity in <em>Vibrio parahaemolyticus</em> (<em>V. parahaemolyticus</em>). Findings indicate that high levels of drug resistance (MIC = 1000 μg/mL) demonstrate a significant impact on the phenotypes of interest, particularly when subinhibitory concentrations are considered. To further elucidate the phenotypic heterogeneity results, functionally specialized cellular subpopulations was identified by scRNA-seq, such as an oxidative stress defense subpopulation mediated by <em>gorA</em> upregulation, virulence modulation achieved through <em>exsD</em>-mediated repression of the type III secretion system, drug resistance conferred by MATE family efflux pumps, protein homeostasis maintained by Hsp20, metabolic reprogramming driven by NirD/YgiW/YdeI family proteins, and membrane damage repair facilitated by <em>pspA</em> upregulation. The phenotypic heterogeneity analysis results support some of the newly discovered functional annotations of resistant subpopulations, demonstrating the biological basis of bacterial heterogeneity under antibiotic pressure. The discovery of these functional drug-resistant subpopulations provides deeper insight into <em>V. parahaemolyticus</em> resistance and paves the way for developing novel antimicrobial strategies targeting key signaling proteins for population-level coordination.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107343"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145616465","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 gene manipulation methods for Enterococcus cecorum","authors":"Daisuke Takamatsu , Mariko Okamoto , Takashi Mada , Ayako Watanabe-Yanai , Koume Matsubara , Masatoshi Okura","doi":"10.1016/j.mimet.2025.107331","DOIUrl":"10.1016/j.mimet.2025.107331","url":null,"abstract":"<div><div><em>Enterococcus cecorum</em> is an emerging pathogen that causes economic losses in the poultry industry; however, our understanding of its pathogenesis remains limited. Because the lack of gene manipulation methods has hampered <em>E. cecorum</em> studies, we developed genetic manipulation methods for this organism using plasmids used in other gram-positive cocci.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107331"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145534616","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}
Yerko Lovera , Juan San Martin , Braulio Ruiz , Richard M. Bastías , Macarena Gerding , Juan Hirzel , Ernesto Moya-Elizondo
{"title":"A qPCR assay for the detection and quantification of Pseudomonas syringae pv. syringae in susceptible tissues of sweet cherry","authors":"Yerko Lovera , Juan San Martin , Braulio Ruiz , Richard M. Bastías , Macarena Gerding , Juan Hirzel , Ernesto Moya-Elizondo","doi":"10.1016/j.mimet.2025.107351","DOIUrl":"10.1016/j.mimet.2025.107351","url":null,"abstract":"<div><div>This study validated a qPCR assay for quantifying <em>Pseudomonas syringae</em> pv. <em>syringae</em> across three growth stages, using syrB gene as target and PVPP modification in extraction protocol, demonstrating high sensitivity and accuracy compared to the traditional drop plate method, which often overestimates bacterial loads. Results support improved disease management strategies.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107351"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145677770","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 relationship between Enterolert and ddPCR concentrations of enterococci in summer samples from beaches in Coronado, California","authors":"Matthew E. Verbyla , Rosanna Lacarra","doi":"10.1016/j.mimet.2025.107346","DOIUrl":"10.1016/j.mimet.2025.107346","url":null,"abstract":"<div><div>Enterococci, widely used as a fecal indicator in coastal recreational waters, can be quantified using different methods, including the culture-based Enterolert method and the newer, more rapid droplet digital polymerase chain reaction (ddPCR) method. Previous studies on the correlation between culture-based and PCR-based methods have shown mixed results. To address this knowledge gap, data from a study conducted at three beaches in the city of Coronado, California during the summer of 2023 were analyzed to compare ddPCR-based concentrations of <em>Enterococcus</em> with Enterolert-based concentrations of enterococci in samples collected daily for approximately two months. The concentrations using both methods were consistent with the lognormal distribution. A linear regression between ddPCR and Enterolert concentrations was statistically significant with an R<sup>2</sup> value of 0.41, but the slope was significantly lower than slopes reported in previous studies. The index of agreement between the two methods was 0.25, but it increased to 0.47 when the ddPCR concentrations were scaled to Enterolert equivalents using the regression. When comparing beach action values based on Enterolert and ddPCR, the false positive rate associated with the use of ddPCR was 56.3 %. Overall, the results of this study showed a discordance between the Enterolert and ddPCR methods at Coronado beaches during the summer of 2023, indicating that the relationship may be influenced by spatial and temporal factors.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107346"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145634628","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":"Improving the identification of pneumonia pathogens by using the real-time polymerase chain reaction (qPCR) alongside culture methods","authors":"Nurul Izzaty Najwa Zahari , Jia Ying Wong , Siti Asma’ Hassan , Rafidah Hanim Shueb , Rohimah Mohamud , Chan Yean Yean","doi":"10.1016/j.mimet.2025.107349","DOIUrl":"10.1016/j.mimet.2025.107349","url":null,"abstract":"<div><div><em>Streptococcus pneumoniae</em>, <em>Haemophilus influenzae</em>, and <em>Klebsiella pneumoniae</em> are among colonizers of the upper respiratory tract flora that can cause pneumonia upon invading the lungs. Molecular techniques have increasingly become the preferred diagnostic approach for detecting respiratory pathogens. However, sputum culture remains the standard diagnostic method for identifying respiratory pathogens in many underdeveloped and developing countries. In this cross-sectional perspective study, 94 sputum specimens were evaluated using both culture and an in-house multiplex qPCR assay. The multiplex qPCR demonstrated greater sensitivity, detecting pathogens in 79 specimens (84.04 %), compared with 32 specimens (31.37 %) identified by culture. The qPCR assay detected <em>K. pneumoniae</em> in 54 of 94 sputum samples, making it the most predominant bacterium, followed by <em>S. pneumoniae</em> (26/94), and <em>H. influenzae</em> (20/94). In contrast, culture detected <em>S. pneumoniae</em>, <em>K. pneumoniae</em>, and <em>H. influenzae</em> in 1, 14, and 3 cases, respectively. These findings support the integration of qPCR into the diagnostic routine alongside culture methods for respiratory samples, as the inclusion of qPCR methods enhances diagnostic sensitivity and accuracy, which are critical for effective patient management and treatment planning.</div></div>","PeriodicalId":16409,"journal":{"name":"Journal of microbiological methods","volume":"240 ","pages":"Article 107349"},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145634647","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}