Access microbiology最新文献

{"title":"An unusual case of Clostridium tetani bacteraemia likely arising from a skin and soft tissue infection.","authors":"Jun Yu Tay, Ibakkanavar Rajiva Guddappa, Alicia X Y Ang, Angie Natalie Pinto","doi":"10.1099/acmi.0.001177.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.001177.v3","url":null,"abstract":"<p><p><i>Clostridium tetani</i>, the causative organism of tetanus, is unusual in developed countries, including Singapore, and to our knowledge, only three known cases of <i>C. tetani</i> bacteraemia have been reported worldwide. This case report describes a case of <i>C. tetani</i> bacteraemia in a Singaporean patient without clinical manifestations of tetanus, likely arising from a sacral sore, highlighting the need for early recognition and targeted antimicrobial treatment for the condition and its complications.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492703/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148804256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clade-specific multiplex digital PCR assay for monkeypox virus detection in spike-in wastewater samples.","authors":"Melissa Pitton, Charles Gan, Patrick Schmidhalter, Christoph Ort, Timothy R Julian","doi":"10.1099/acmi.0.001041.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.001041.v3","url":null,"abstract":"<p><p>Monkeypox virus (MPXV) is a zoonotic pathogen that has recently caused outbreaks in non-endemic areas. Wastewater-based surveillance is independent of individual testing and offers substantial potential for monitoring population-level disease dynamics of MPXV at the clade level, as clades differ in transmissibility and mortality rate. Here, we report the validation of a four-plex digital PCR assay to detect and quantify the major clades and subclades of MPXV. The assay demonstrated strong linearity, analytical sensitivity (limits of detection ranged from 6.7 to 9.6 copies per reaction across targets) and specificity in distinguishing and quantifying MPXV by clade, which is advantageous for both clinical and wastewater applications.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13492878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148804267","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PacBio HiFi reads data sets for the ATCC-authenticated isolate of Candida albicans SC5314 (ATCC MYA-2876).","authors":"Lois L Hoyer, Elizabeth K Hogan, Alvaro G Hernandez","doi":"10.1099/acmi.0.001142.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.001142.v3","url":null,"abstract":"<p><p><i>Candida albicans</i> is a yeast of major medical importance. The genome sequence for the reference isolate SC5314 has been available for many years and is displayed as a phased diploid assembly through a public community resource. As DNA sequencing technologies continue to advance, new high-quality data sets can be generated to augment existing genome resources. Here, we present Pacific Biosciences (PacBio) HiFi data sets with exceptional read length and sequencing depth. The data sets were generated from <i>C. albicans</i> SC5314 newly obtained from the American Type Culture Collection, thereby authenticating the isolate to a community-accessible source. The PacBio HiFi data set with a mean read length greater than 14 kb was assessed for its potential to support construction of a phased diploid genome assembly. Most chromosomes were effortlessly resolved as gapless, phased haplotypes with telomeres at both ends; however, challenging regions including the rDNA locus on one copy of chromosome R remained longer than could be fully resolved using these high-quality, state-of-the-art data. The PacBio HiFi reads data sets are available through GenBank and provide a valuable resource for exploring diploid loci in this important reference strain.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13472535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148765645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A conserved residue in the histidine kinase BceS tunes bacitracin stress responses in Bacillus subtilis.","authors":"Kate Gridley, Alan Koh","doi":"10.1099/acmi.0.001145.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.001145.v3","url":null,"abstract":"<p><p>Two-component systems regulate bacterial responses through histidine kinases (HKs), where the majority act as both a kinase and a phosphatase. In <i>Bacillus subtilis</i>, the BceRS-BceAB system mediates bacitracin resistance, but it is unknown whether its HK, BceS, also functions as a phosphatase. Here, we identify the conserved motif within the BceS DHp domain and show that Thr-128 contributes to maintaining kinase-phosphatase balance. Substitutions at this site impaired BceS signalling and bacitracin resistance. Our findings demonstrate that in BceS, Thr-128 is important for proper BceAB regulation.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13473831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148763265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the antifungal efficacy and bioactive metabolites of a traditional polyherbal aqueous formulation BioCC+ against Fusarium graminearum and Fusarium verticillioides.","authors":"Elisee Kouassi Kporou, Zilfa Irakoze, Nataliia Voloshchuk, Joshua D Lambert, Joshua J Kellogg, Josephine Wee","doi":"10.1099/acmi.0.001173.v3","DOIUrl":"10.1099/acmi.0.001173.v3","url":null,"abstract":"<p><p>Fungal contamination of cereal crops threatens global food security by compromising grain quality and introducing harmful mycotoxins that endanger human and animal health. In West Africa, the long-standing ancestral use of native plant extracts to manage fungal contamination provides sustainable and locally adaptable solutions. Building on this knowledge, BioCC+, a polyherbal aqueous formulation containing <i>Azadirachta indica</i>, <i>Cymbopogon citratus</i>, <i>Allium sativum</i> and <i>Capsicum frutescens</i>, was developed to control maize contamination during storage in Côte d'Ivoire. This study evaluated the antifungal activity of BioCC+ against <i>Fusarium graminearum</i> and <i>Fusarium verticillioides</i> followed by bioactivity-guided untargeted metabolomics to explain observed effects. Crude BioCC+ extracts inhibited <i>F. graminearum</i> at 12.5 mg ml^-1 and <i>F. verticillioides</i> at 25.0 mg ml^-1, with the dichloromethane extract (DCMe) showing greater antifungal activity than methanol or water extracts. Based on the observed growth inhibition, DCMe was selected for fractionation using silica gel column chromatography with the following mixtures of hexane:ethyl acetate as the mobile phase: 100 : 0 for F1, 75 : 25 for F2, 50 : 50 for F3, 25 : 75 for F4 and 0 : 100 for F5, as well as 100% methanol for F6. Fractionation of DCMe resulted in three active fractions (F3, F4 and F6), with F4 showing the strongest inhibition (MIC=0.4 mg ml^-1) against <i>F. graminearum</i>. Integration of antifungal activity assays with chemometric data through multivariate, univariate and correlation-based analysis identified six putative antifungal candidates, two known and four uncharacterized metabolites. These results provide a first step for integrating bioactivity assays with metabolomics to validate ancestral knowledge and develop community-driven practices for mitigating fungal contamination in staple crops.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13463721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148727655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Risk factors for mortality in Stenotrophomonas maltophilia bacteraemia: a 22-year retrospective study in a Japanese acute care hospital.","authors":"Michiya Tanuma, Takayuki Sakurai, Hidemasa Nakaminami, Masayo Tanaka","doi":"10.1099/acmi.0.001194.v3","DOIUrl":"10.1099/acmi.0.001194.v3","url":null,"abstract":"<p><p><i>Stenotrophomonas maltophilia</i> is a Gram-negative bacterium associated with nosocomial infections and high mortality, although reported risk factors vary. We retrospectively analysed 43 cases of <i>S. maltophilia</i> bacteraemia at NTT Medical Center Tokyo (2002-2024). The overall mortality rate was 44.2%. Univariate analysis revealed that higher Sequential Organ Failure Assessment (SOFA) scores (<i>P</i>=0.010), central venous catheterization (CVC) (<i>P</i>=0.028), total parenteral nutrition (<i>P</i>=0.003) and diabetes mellitus (<i>P</i>=0.033) were significantly associated with mortality. Multivariate analysis suggested SOFA score (<i>P</i>=0.048) and CVC presence (<i>P</i>=0.039) as independent risk factors. Appropriate antimicrobial therapy was not significantly associated with reduced overall mortality. However, it was associated with improved survival in patients with SOFA scores ≥5 (<i>P</i>=0.029). Additionally, among patients with CVC, catheter removal was associated with improved survival (<i>P</i>=0.005). These findings suggest that the SOFA score and CVC were associated with mortality in <i>S. maltophilia</i> bacteraemia and indicate that the effectiveness of antimicrobial therapy may depend on disease severity. The study underscores the potential need to implement diverse infection-control strategies to prevent <i>S. maltophilia</i> transmission and to tailor antimicrobial therapy to disease severity.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13456690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An open-source, configurable machine learning pipeline for predicting blood culture outcomes from routine haematology parameters.","authors":"Benjamin R McFadden, Timothy J J Inglis, Mark Reynolds","doi":"10.1099/acmi.0.001212.v3","DOIUrl":"10.1099/acmi.0.001212.v3","url":null,"abstract":"<p><p><b>Background.</b> Bloodstream infections remain a major cause of morbidity and mortality worldwide, yet blood culture (BC) positivity rates are typically low, highlighting a need to optimize test use. Machine learning models trained on routinely available haematology parameters have shown promise for predicting BC outcomes. However, there is a lack of open-source software to implement methods described in the peer-reviewed literature. <b>Results.</b> We present an open-source pipeline for training, evaluation, and reporting of binary classification models that predict BC outcomes from complete blood count (CBC), white blood cell differential (DIFF) and cell population data (CPD) generated by Sysmex XN-series haematology analysers. This pipeline implements four classifier types (LR: logistic regression, DT: decision tree, RF: random forest and XG: XGBoost), two default feature spaces (19-feature CBC/DIFF and 50-feature CBC/DIFF/CPD) and feature selection methods (Boruta all-relevant selection and recursive feature elimination), along with nested cross-validation (CV) to prevent data leakage during feature selection. Trained LR coefficients and DT rules were exported in portable formats suited to deployment in spreadsheet-based or laboratory information management system environments without requiring the Python programming language runtime. RF and XG models were also exported. The pipeline was fully configurable via a single JSON file and allowed adaptation to any binary classification problem without source code modification. Automated HTML reports with embedded area under the receiver operating characteristic curves and confusion matrices were generated for both training and inference runs. <b>Conclusions.</b> This open-source repository addresses key limitations in existing BC outcome prediction workflows by providing a reproducible, transparent method and clinically deployable pipeline. Its configurable architecture, nested CV strategy, multiple feature selection methods and export of interpretable model artefacts make it suitable for both research and clinical decision support applications.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13456689/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"When 'Clean' is not clean: a diagnostic pitfall in Gram staining leading to pseudobacterial meningitis.","authors":"Takayuki Kawamura, Sachie Koyama, Haruka Karaushi, Yasuhiro Ebihara, Kotaro Mitsutake","doi":"10.1099/acmi.0.001219.v3","DOIUrl":"10.1099/acmi.0.001219.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Gram staining is a fundamental and widely used technique in clinical microbiology because of its simplicity and diagnostic value, particularly in the diagnosis of bacterial meningitis. However, its reliability may be compromised by contamination and staining artefacts. <b>Case Presentation.</b> This report describes a case of pseudobacterial meningitis in a previously healthy 25-year-old woman who presented with fever, headache and nuchal rigidity. Cerebrospinal fluid (CSF) analysis revealed pleocytosis with a predominance of mononuclear cells. Gram staining revealed findings consistent with Gram-negative bacilli, prompting empiric antibacterial therapy with concurrent antiviral treatment. Comprehensive microbiological investigations, including CSF culture and broad-range 16S rRNA PCR testing, yielded negative results. Residual material or microscopic debris on supposedly 'clean' slides was suspected to produce artefact-like appearances that mimicked micro-organisms, leading to false-positive interpretations. <b>Conclusion.</b> This case highlights a potential laboratory pitfall in the interpretation of CSF Gram stains and underscores the importance of considering staining artefacts, particularly when Gram stain findings are discordant with the overall clinical and laboratory findings.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13456105/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148709031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The metal-uptake-deficient Escherichia coli strain GR536 contains the ϕ80 prophage.","authors":"Ayuki Shimpo, Jerry Augustine, Luke J Acton, Lindsay J Hall, Peter Chivers","doi":"10.1099/acmi.0.001204.v3","DOIUrl":"10.1099/acmi.0.001204.v3","url":null,"abstract":"<p><p>We report the genome sequence of <i>Escherichia coli</i> GR536, a previously constructed metal-uptake-deficient strain derived from <i>E. coli</i> W3110. Growth of GR536 in an iron-restricted liquid medium resulted in apparent lysis during the early exponential growth phase. This effect was exacerbated in cells transformed with pBAD30, a commonly used arabinose-inducible expression vector. Whole-genome sequencing confirmed the expected gene disruptions (<i>entC</i>, <i>feoABC</i>, <i>mntH</i>, <i>zupT::cat</i> and <i>fecABCDE::kan</i>). However, comparison to <i>E. coli</i> W3110 identified the presence of the ϕ80 prophage (46.16 kbp) and cryptic prophage CPZ-55 (6.763 kbp), as well as the absence of cryptic prophage e14 (15.193 kbp). We also identified 9 IS-element deletions, 3 IS-element insertions, 7 other deletions or insertions and 74 candidate individual nucleotide changes. The growth defect in GR536 correlated with lysis due to the production of ϕ80 virions as determined by the inability of isolated phage to infect an <i>E. coli</i> strain lacking the phage receptor (∆<i>fhuA</i>) and the <i>Bam</i>HI digestion pattern of the purified phage DNA. We further determined that the ϕ80-dependent lysis in GR536 is exacerbated by the presence of the chloramphenicol- and kanamycin-resistance markers introduced during construction of GR536 and the pBAD30 plasmid multiple cloning site. Removal of the markers (<i>E. coli</i> GR536*) and disruption of the pBAD30 multiple cloning site generated a strain that showed a 10⁴-fold reduction in ϕ80 production. Furthermore, construction of a W3110 lysogen containing the ϕ80 prophage and comparison with GR536* grown under the same conditions showed a ~10⁴-fold higher level of phage production by the parent strain, indicating that phage-dependent lysis was not increased by the deletion of the metal-uptake genes and thus independent of iron availability. These observations clarify growth conditions that limit the effects of ϕ80-dependent lysis when using GR536 to identify metal-uptake genes by complementation, specifically, removal of the antibiotic resistance markers and the avoidance of using intact pBAD30 as a negative control.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13449921/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698706","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Game-based learning in microbiology education: design and classroom use of MicroBioCombat.","authors":"Raul Vinicius Salata Souto, Edmara Rocha Dos Santos Moreira, Leandro Marcio Moreira","doi":"10.1099/acmi.0.001238.v3","DOIUrl":"10.1099/acmi.0.001238.v3","url":null,"abstract":"<p><p>Microbiology is often perceived by students as a challenging subject, particularly when addressing pathogenic mechanisms and disease transmission. Active learning approaches, including educational games, have been shown to enhance student engagement and conceptual understanding by integrating playful elements with scientific content. In this study, we present <i>MicroBioCombat</i>, a card-based educational game developed for use in secondary school microbiology education. The game comprises 81 cards representing pathogenic bacteria, transmission routes and prophylactic or therapeutic strategies. During gameplay, students combine cards to simulate infection scenarios and corresponding defence mechanisms, with the aim of reducing their opponent's score to zero. Beyond reinforcing microbiological concepts, <i>MicroBioCombat</i> promotes peer interaction, communication and decision-making, contributing to a more dynamic and inclusive classroom environment. The game is adaptable to different educational levels and curricular contexts, and an accompanying online forum enables educators and students to share experiences and gameplay strategies, supporting collaborative and reflective learning.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"8 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2026-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13450638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148698690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}