Access microbiology最新文献

{"title":"Genome sequence of antibiotic-resistant Klebsiella quasipneumoniae FSFC0558: a novel sequence type (ST8212).","authors":"Daniel Robins, Richard N Goodman, Ralfh Pulmones, Upendo O Kibwana, Joel Manyahi, Bjørn Blomberg, Nina Langeland, Sabrina Moyo, Adam P Roberts","doi":"10.1099/acmi.0.000944.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000944.v3","url":null,"abstract":"<p><p><i>Klebsiella quasipneumoniae</i> are Gram-negative bacteria of the family <i>Enterobacteriaceae</i>, distinguished from other members of the <i>Klebsiella</i> genus through a chromosomally encoded extended spectrum β-lactamase, <i>bla_OKP</i> . Here, we report a hybrid assembled genome of a novel sequence type of <i>K. quasipneumoniae</i> subspecies <i>similipneumoniae</i> isolated from a faecal sample of a patient with sepsis.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12032403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045025","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":"Opportunities for microbiology citizen science: lessons learnt from three pilot projects.","authors":"Rachel M Pateman, Joyce Bennett, Anthony C Hilton, Isabella Romeo-Melody, Anton Rosenfeld, Sarah J Routledge, Caroline Rymer, Benjamin M C Swift, Lucy Way, Louise Whatford, Naomi C Wilkinson, Tony Worthington, Lewis Yandle, Ayesha S Younis, Sarah E West, Alan D Goddard","doi":"10.1099/acmi.0.000899.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000899.v3","url":null,"abstract":"<p><p>Citizen science (CS) is the partnering of professional scientists and members of the public to answer real-world scientific questions. There has been huge growth in CS over the past two decades, but uptake in microbiology research has, thus far, been relatively limited. In the first part of this article, we discuss how CS is well aligned with microbiology research: sample collection methods can be simplified and used in a variety of environments; projects are expected to appeal to participants as topics are likely to be of relevance to people's lives and interests, including the health of people and the environment; and projects can also lead to real-world impact, including the identification of new drugs or biotechnological solutions. In the second part of this article, we present our reflections on three pilot projects we have recently completed. In order for the field to grow, people need to share both their successes as well as the challenges they have faced, so that others wanting to use the method can learn from these experiences. We share simplified sampling methods for yeast strains from home brewing and baking, antimicrobial-resistant bacteria on home-grown produce and microbes on chopping boards. However, participation in our projects was limited by a range of factors, including time available and resourcing, which impacted on our ability to generate new knowledge and wider impacts. We provide recommendations for others wishing to run microbiology CS projects, including ensuring appropriate resourcing and considering the ethical implications of projects.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12003925/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065543","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":"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":"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":"Selection and maintenance of mobile linezolid-resistance genes and plasmids carrying them in the presence of florfenicol, an animal-specific antimicrobial.","authors":"Akira Fukuda, Masaru Usui","doi":"10.1099/acmi.0.000997.v3","DOIUrl":"10.1099/acmi.0.000997.v3","url":null,"abstract":"<p><p>Mobile linezolid-resistance genes (<i>optrA</i>, <i>poxtA</i> and <i>cfr</i>) that confer resistance to linezolid and florfenicol have been detected globally in various sources. Linezolid is a last-resort antimicrobial used in human clinical settings, and florfenicol is commonly used in veterinary clinical settings. The present study sought to evaluate the potential of florfenicol in veterinary use to select for linezolid-resistant bacteria. The growth and fitness of linezolid-resistant bacteria harbouring mobile linezolid-resistance genes were assessed in the presence and absence of florfenicol using <i>Enterococcus faecalis</i> and <i>Enterococcus faecium</i>, respectively. The bacterial strains harboured wild and cloning plasmids carrying mobile linezolid-resistance genes, which reduced their susceptibility to linezolid and florfenicol. The acquisition of plasmids carrying mobile linezolid-resistance genes improved bacterial growth in the presence of florfenicol and conferred fitness costs in its absence. Florfenicol imposes a selection pressure on bacteria harbouring plasmids carrying mobile linezolid-resistance genes. Hence, the appropriate use of florfenicol in veterinary clinical settings is important to control the dissemination of mobile linezolid-resistance genes and to ensure the sustained effectiveness of linezolid against multidrug-resistant bacteria, including vancomycin-resistant enterococci in human clinical settings.</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/PMC12282029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692970","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":"Effect of the incubation time on blood culture results and bacterial pathogens causing bloodstream infections among children attending Sekou Toure Regional Referral Hospital in Mwanza, Tanzania.","authors":"James Thomas, Albert Wasira, Darus Maarafu, Faustin Igogo, Eunice Emmanuel, Roza Ernest, Martha F Mushi, Stephen E Mshana","doi":"10.1099/acmi.0.000942.v3","DOIUrl":"10.1099/acmi.0.000942.v3","url":null,"abstract":"<p><p><b>Background.</b> A one hour delay in initiating appropriate antimicrobial treatment increases the mortality rate of patients with bloodstream infections by 2%. This highlights the risk associated with manual blood culture methods, as they tend to have long turnaround time, with an initial incubation period of 18-24 h, leading to delays in obtaining diagnostic results. This study examined the impact of incubation time on blood culture results and analysed the patterns of the pathogens causing bloodstream infections (BSIs) among children attending Sekou Toure Regional Referral Hospital (SRRH), Mwanza, Tanzania <b>Methodology.</b> A hospital-based, descriptive cross-sectional study was conducted at SRRH from May to July 2024. The conventional blood culture method, using in-house prepared brain heart infusion broth with slight modifications on the initial time of the blind subculture (at 8, 24 and 120 h) was done to isolate the pathogens causing BSIs. Descriptive data analysis was performed using STATA software version 15. <b>Results.</b> The study enrolled 302 children with clinical diagnosis of BSIs. Of these, 160 (53%) were male, with a median age of 6 years interquartile range [IQR] 1-7 years. Fever was the predominant clinical sign reported in 259 (85.8%) children. Microbiologically confirmed BSIs were detected in 90 (29.8%) children. Among them, 51.1% (46/90) were detected through blind subculture after 8 h of initial incubation. An additional 31 (34.4%) and 13 (14.4%) were detected after 24 h and 120 h of incubation, respectively. The most frequently isolated pathogens were <i>Klebsiella pneumoniae</i> (25.6%, 23/90) and <i>Staphylococcus aureus</i> (24.4%, 22/90). Gram-negative bacteria (GNB) formed the majority (71.1%, 64/90) of the isolated pathogens, with 62.5% (40/64) showing resistance to third-generation cephalosporin (3GC). Additionally, 45.5% (10/22) of the <i>S. aureus</i> strains were methicillin-resistant <i>S. aureus</i>. <b>Conclusion.</b> Blind subculture after 8 h of initial incubation correctly detected more than half of the children with microbiologically confirmed BSIs. Incorporating blind subculture on MacConkey agar supplemented with 2 µg ml^-1 cefotaxime (MCA-C) after 8 h of incubation resulted in the correct treatment of half of the children with BSIs caused by GNB within 24 h. In areas with high prevalence of 3GC resistance, blind subculture within 8 h should include MCA-C for appropriate treatment within 24 h.</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/PMC12281735/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692969","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}