Access microbiology最新文献

{"title":"Comparative genomics analysis of six Cutibacterium acnes strains isolated from contaminated platelet concentrates.","authors":"Annika Flint, Dilini Kumaran, Kelly Weedmark, Franco Pagotto, Sandra Ramirez-Arcos","doi":"10.1099/acmi.0.000938.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000938.v3","url":null,"abstract":"<p><p><i>Cutibacterium acnes</i> is a bacterial skin commensal that is often isolated during routine testing of blood products like platelet concentrates (PCs). Due to the slow-growing nature of this bacterium in culture media, <i>C. acnes</i> contaminated PCs are often transfused into vulnerable patients before retrieval of these units can be initiated. This study aimed at obtaining the whole-genome sequence of six <i>C. acnes</i> isolates derived from contaminated PCs, comparing and assessing their genetic backgrounds. Furthermore, the whole genomes of the PC isolates were compared to clinical isolates obtained from different sites and types of infection. The results indicate that these PC isolates assessed belong to four phylotypes, namely IA, IB, II and III. Whole-genome comparisons identified differences in the virulence profiles of the isolates and provide a foundation for future studies aimed at evaluating the risk to transfusion patients by determining whether the expression of virulence factors is impacted in the PC storage environment.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813351","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":"Detection of vanA genes in vancomycin-susceptible Enterococcus faecium isolates: implications for additional testing.","authors":"Victoria Jordan, Hemalatha Varadhan","doi":"10.1099/acmi.0.000959.v4","DOIUrl":"10.1099/acmi.0.000959.v4","url":null,"abstract":"<p><p>To assess the frequency of silent vancomycin resistance, phenotypically susceptible <i>Enterococcus faecium</i> isolates underwent genotypic testing using Cepheid's Xpert <i>vanA</i>/<i>vanB</i> PCR. A total of 6% of isolates had silent <i>vanA</i> genes. However, the clinical relevance of silent <i>van</i> genes and the lack of rapid, random-access genotypic methods poses an ongoing challenge to laboratories.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143775187","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 novel case of Staphylococcus pseudintermedius aortitis.","authors":"Dione Jones, Matthew Lim, Maxwell Olenski","doi":"10.1099/acmi.0.000912.v3","DOIUrl":"10.1099/acmi.0.000912.v3","url":null,"abstract":"<p><p><i>Staphylococcus pseudintermedius</i> is a common commensal and opportunistic canine pathogen with emerging pathogenicity in humans. We describe the first case of invasive <i>S. pseudintermedius</i> infection causing aortitis and mycotic aneurysm in an 83-year-old patient, treated successfully with flucloxacillin. This case highlights the potential for <i>S. pseudintermedius</i> to cause serious endovascular infection in humans.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143756881","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 rare case of Aerococcus urinae native valve endocarditis.","authors":"Sofie Goes, Kim Callebaut, Denis Pierard, Ingrid Wybo, Deborah De Geyter, Astrid Muyldermans, Jolien Geers, Laura Kerselaers, Thomas Demuyser","doi":"10.1099/acmi.0.000863.v4","DOIUrl":"10.1099/acmi.0.000863.v4","url":null,"abstract":"<p><p><b>Background.</b> <i>Aerococcus urinae</i> was initially considered a commensal of the urinary tract, but there is now increasing evidence for its involvement in urinary tract and systemic infections. <i>A</i>. urinae endocarditis has a non-negligible mortality rate and occurs mainly in patients with underlying conditions or the presence of extraneous material. <b>Case presentation.</b> This report handles the case of a 65-year-old male with cardiac antecedents, who was admitted to the cardiology department after a syncope of unknown origin and diagnosed with severe mixed aortic valve disease and mitral valve sclerosis through the means of transoesophageal echocardiography (TEE). During hospitalization, the patient progressively deteriorated with the development of shortness of breath and an inflammatory syndrome. Both the urine and blood cultures showed growth of <i>A. urinae</i>. Treatment with piperacillin/tazobactam was started empirically. Repeated TEE showed evidence of endocarditis with vegetation and perforation of the mitral valve that required an emergency surgery with mitral valve repair. After surgery, gentamicin and penicillin G were administered for 48 h, followed by combined ceftriaxone/penicillin G treatment for 6 weeks. At first, flucloxacillin was also associated as the culture of the valve was negative. Finally, the 16S rRNA gene PCR on the valve tissue confirmed the <i>A. urinae</i> endocarditis. <b>Conclusion.</b> <i>A. urinae</i> is an underestimated cause of serious infections such as endocarditis. Urinary tract infections mainly in older men can be an entry point for this type of invasive infection.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11949278/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143733852","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":"RSYD-BASIC: a bioinformatic pipeline for routine sequence analysis and data processing of bacterial isolates for clinical microbiology.","authors":"Kat Steinke, Karina Gravgaard Thomsen, Silje Vermedal Hoegh, Sanne Løkkegaard Larsen, Karina Kubel Vilhelmsen, Thøger Gorm Jensen, Marianne Nielsine Skov, Thomas Vognbjerg Sydenham","doi":"10.1099/acmi.0.000646.v6","DOIUrl":"10.1099/acmi.0.000646.v6","url":null,"abstract":"<p><p><b>Background.</b> Whole-genome sequencing of bacterial isolates is increasingly becoming routine in clinical microbiology; however, subsequent analysis often needs to be started by a bioinformatician even for comprehensive pipelines. To increase the robustness of our workflow and free up bioinformatician work hours for development and advanced analysis, we aimed to produce a robust, customizable bioinformatic pipeline for bacterial genome assembly and routine analysis results that could be initiated by non-bioinformaticians. <b>Results.</b> We introduce the RSYD-BASIC pipeline for bacterial isolate sequence analysis and provide a demonstration of its functionality with two datasets composed of publicly available sequences, in which comparable results are obtained in most cases. In some instances, the pipeline provided additional information, corresponding to <i>in vitro</i> results where these could be obtained. In routine use at our department, the pipeline has already yielded clinically relevant results, allowing us to type a variety of bacterial pathogens isolated in our clinical laboratory. We also demonstrate how RSYD-BASIC results aided in disproving a potential outbreak. <b>Conclusion.</b> With the RSYD-BASIC pipeline, we present a configurable reads-to-results analysis pipeline operated by non-expert users that greatly eases the investigation of potential outbreaks by expert end users. Results obtained with publicly available sequences show comparable performance to the original methods, while underlining the importance of standardized methods.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694990","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":"Antimicrobial effect of blue light on antibiotic-sensitive and drug-resistant Escherichia coli: a novel isotropic optical fibre.","authors":"Megan H Goh, Joseph J Connolly, Antonia F Chen, Robert A Rabiner, Santiago A Lozano-Calderon","doi":"10.1099/acmi.0.000967.v3","DOIUrl":"10.1099/acmi.0.000967.v3","url":null,"abstract":"<p><p><b>Background.</b> Orthopaedic oncological pelvic reconstructions have an elevated risk of infection with Gram-negative bacteria. This study evaluates the bactericidal ability of a novel antimicrobial blue light (ABL)-emitting optical fibre on antibiotic-sensitive <i>Escherichi coli</i> (AS-Ec) and ESBL-producing <i>E. coli</i> (ESBL-Ec). <b>Methods.</b> Time-to-kill assays used a 10 ml NaCl solution with a starting inoculum of 1×10⁵ c.f.u. ml^-1 for AS-Ec or ESBL-Ec; assays were repeated at least three times per strain. Experimental tubes had either one optical fibre [20.1 mW mm^-1; low power (LP)] or two optical fibres [40.3 mW mm^-1; high power (HP)], which delivered five wavelengths of ABL over 60 min. Control tubes had no optical fibres. Fifty microlitres of samples taken from each tube at 0, 10, 20, 30 and 60 min were streaked onto agar plates and incubated. c.f.u. ml^-1 was determined. Bactericidal reduction was defined as a 99.9% (≥3 log₁₀) reduction in c.f.u. ml^-1. One-way ANOVA was conducted. <b>Results.</b> Bactericidal effects were seen for AS-Ec under both LP-ABL and HP-ABL with a log₁₀c.f.u. ml^-1±sd difference of 3.44±0.35 (<i>P</i>=0.043) and 3.74±0.21 (<i>P</i>=0.048) at 30 and 20 min, respectively. For ESBL-Ec, while there was a significant reduction in bacterial colony formation, the bactericidal threshold was not reached with a log₁₀c.f.u. ml^-1±sd difference of only 1.02±0.41 (<i>P</i>=0.034) and 2.53±0.22 (<i>P</i>=0.037) at 60 min for LP-ABL and HP-ABL, respectively. <b>Conclusions.</b> A novel ABL-emitting optical fibre exhibited bactericidal effects in AS-Ec and a clinically meaningful reduction of ESBL-Ec, providing a promising avenue for the use of ABL as a potential therapy for Gram-negative infections.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11923094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672163","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":"Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia.","authors":"Melese Yilma Zaba, Sebsib Neway, Damien Farrell, Eva Denion, Viktor Perets, Melaku Tilahun, Kidist Bobosha, Joseph P Cassidy, Asefa Asmare, Stephen V Gordon","doi":"10.1099/acmi.0.000915.v3","DOIUrl":"10.1099/acmi.0.000915.v3","url":null,"abstract":"<p><p>Bovine tuberculosis (bTB), caused by <i>Mycobacterium bovis</i> and other members of the <i>Mycobacterium tuberculosis</i> complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to isolate and genetically characterize the causative agents of bTB in cattle from four abattoirs in the Wolaita zone of Ethiopia. A total of 2,251 cattle were examined post-mortem, and suspect tuberculous lesions were identified in 122 animals. From these animals, 180 tissue samples were collected and processed for bacteriological culture and genetic analysis, including the Loopamp^™ commercial loop-mediated isothermal amplification kit, PCR targeting RD4 and RD9 loci and whole-genome sequencing (WGS). Bacteriological culture using mycobacteria growth indicator tube and Lowenstein-Jensen media ultimately identified 18 culture-positive samples, with WGS confirming <i>M. bovis</i> in lesions from four animals and <i>M. tuberculosis</i> in lesions from one animal. The <i>M. bovis</i> and <i>M. tuberculosis</i> isolates showed genetic similarity to previously identified MTBC lineages in Ethiopia. The presence of <i>M. tuberculosis</i> in cattle raises concerns about human-to-animal transmission. Additionally, non-tuberculous mycobacteria were isolated from lesions from multiple animals. Our study genetically characterized bacteria from suspect tuberculous lesions and provides the research community with new genome data for Ethiopian isolates of <i>M. bovis</i> and <i>M. tuberculosis</i>.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920072/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143665789","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":"Towards an inclusive conference experience: evaluation of the Education and Outreach Symposium at the Microbiology Society Annual Conference 2024.","authors":"Melissa M Lacey, Michael J Dillon, Sean Goodman, Victoria Easton, Alison I Graham","doi":"10.1099/acmi.0.000947.v3","DOIUrl":"10.1099/acmi.0.000947.v3","url":null,"abstract":"<p><p>The Microbiology Society Education and Outreach Symposium serves as a platform for microbiology educators to share contemporary practices with an international audience. The Symposium is held yearly during the Microbiology Society's Annual Conference and has become increasingly popular among conference attendees. In an effort to create an inclusive and engaging environment, the 2024 Symposium included contributions from participants at all career stages and from diverse global regions through a variety of presentation formats, including invited talks, offered presentations, flash talks and posters. Cabaret-style seating was used to encourage discussion amongst participants, and digital tools were used for anonymous feedback and questions after each talk to ensure all voices had an opportunity to be heard. Here, we present an analysis of qualitative and quantitative participant responses addressing two key research questions: (1) Did the Symposium foster an inclusive atmosphere for participants across all career stages? and (2) Was the content engaging and relevant to the audience? A post-Symposium questionnaire revealed strong positive feedback, with all 18 respondents agreeing or strongly agreeing that the 2024 Symposium was both an inclusive environment and covered interesting topics. Thematic content analysis of free-text responses emphasized a high appreciation for the Symposium's diversity in speakers and topics, an inclusive room layout and an overall welcoming feeling. Feedback from participants, along with the authors' own reflections, will actively feed into planning for the 2025 Symposium.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897172/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143627324","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":"Isolated Neisseria meningitidis-associated endophthalmitis in an immunocompetent host: case report and literature review.","authors":"Calvin Ka-Fung Lo, Lauren Hughes, Cole Schonhofer, William R Bowie, Iain McCormick, Andrew Kirker","doi":"10.1099/acmi.0.000901.v3","DOIUrl":"10.1099/acmi.0.000901.v3","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Neisseria meningitidis</i> is a Gram-negative diplococcus with significant infectious sequelae, including meningitis and disseminated meningococcal bloodstream infection. Rarely has it been reported in the context of endophthalmitis without central nervous system involvement. We report a clinical case of isolated meningococcal endophthalmitis in an immunocompetent patient and present a literature review on published cases, including treatment regimens and clinical outcomes. <b>Case Presentation.</b> A 51-year-old male with no significant medical history presented to the emergency department with acute vision loss in the right eye after returning from Mexico. Ophthalmic examination was consistent with endophthalmitis, presumed to be endogenous in the absence of recent ocular trauma or surgery. Vitreous culture was positive for growth of Gram-negative diplococci, subsequently identified as <i>N. meningitidis</i>. Blood and cerebrospinal fluid cultures were negative for growth of similar or implicative pathogens. There was no evidence of disseminated meningococcal infection; imaging did not demonstrate any drainable collections or sequelae of extension into the central nervous system. The patient was treated with intravitreal antibiotics as well as topical steroids and antibiotics. In addition, he completed a 2-week course of systemic antibiotics. Visual outcome was unfortunately poor. <b>Conclusion.</b> This case illustrates a rare case of isolated endophthalmitis secondary to meningococcus, presumably from a nasopharyngeal source. In these clinical scenarios, clinicians should perform a thorough evaluation for predisposing immunodeficiencies.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936350/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712573","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":"Ubiquitous microbial contaminants associated with scientific ocean drilling.","authors":"Jessica M Labonté, Kathryn L Campbell, Jordan R Walker, Milena A Rodriguez-Pilco","doi":"10.1099/acmi.0.000865.v3","DOIUrl":"10.1099/acmi.0.000865.v3","url":null,"abstract":"<p><p>Deep-sea subsurface samples typically have low microbial biomass, making them more susceptible to contamination. Potential contaminants can be introduced during any step of the scientific process, including drilling (contamination from the drilling fluid and lubricants and seawater); sample preparation (contamination from air and human handling); and DNA extraction, amplification and sequencing (contamination from reagents). The International Ocean Discovery Program (IODP) samples that are dedicated to microbiological analyses (known as MBIO samples) are routinely tested for contamination by injecting known concentrations of fluorescent microspheres or tracers directly into the drilling fluids. These tracers are a great tool to determine the level of drilling fluid contamination on board, but they are not consistently used, and contamination of the samples could occur during other steps of sample processing and analysis. Moreover, there is an increased risk of contamination dominating the results of microbial surveys using PCR amplification of marker genes. Here, we built a database of common contaminants through the screening of contamination controls from available 16S rRNA gene amplicon datasets from past IODP expeditions. These controls included various lubricants used on board, drilling fluids, seawater, DNA extraction blanks and PCR blanks. The order <i>Burkholderiales</i> dominated most of the very low biomass samples, including negative controls, indicating the order's ubiquity and its potential to be overamplified with common 16S rRNA amplification protocols. We amplified the 16S rRNA gene from preserved IODP legacy microbiological core samples and tested their level of contamination using the database. We also looked at published studies that did not sequence negative controls. Our results demonstrate that the type of drilling, amount of manipulation of the sample prior to preservation and sample depth, often associated with biomass, can influence the level of contamination within subsurface samples. This work provides an analysis framework for microbial taxonomic survey studies from low biomass subsurface samples for future scientific ocean drilling expeditions.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11936376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143712575","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}