Access microbiology最新文献_第3页

Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity. 大山雀和蓝山雀的粪便宏基因组提供了对宿主、饮食、病原体和微生物多样性的深入了解。

Access microbiology Pub Date : 2025-04-28 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000910.v3

Mark J Pallen, Alise Jany Ponsero, Andrea Telatin, Cara-Jane Moss, David Baker, Darren Heavens, Gabrielle L Davidson

{"title":"Faecal metagenomes of great tits and blue tits provide insights into host, diet, pathogens and microbial biodiversity.","authors":"Mark J Pallen, Alise Jany Ponsero, Andrea Telatin, Cara-Jane Moss, David Baker, Darren Heavens, Gabrielle L Davidson","doi":"10.1099/acmi.0.000910.v3","DOIUrl":"https://doi.org/10.1099/acmi.0.000910.v3","url":null,"abstract":"Background. The vertebrate gut microbiome plays crucial roles in host health and disease. However, there is limited information on the microbiomes of wild birds, most of which is restricted to barcode sequences. We therefore explored the use of shotgun metagenomics on the faecal microbiomes of two wild bird species widely used as model organisms in ecological studies: the great tit (Parus major) and the Eurasian blue tit (Cyanistes caeruleus). Results. Short-read sequencing of five faecal samples generated a metagenomic dataset, revealing substantial variation in composition between samples. Reference-based profiling with Kraken2 identified key differences in the ratios of reads assigned to host, diet and microbes. Some samples showed high abundance of potential pathogens, including siadenoviruses, coccidian parasites and the antimicrobial-resistant bacterial species Serratia fonticola. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from Isospora spp., while metagenome-assembled genomes documented new prokaryotic species. Conclusions. Here, we have shown the utility of shotgun metagenomics in uncovering microbial diversity beyond what is possible with 16S rRNA gene sequencing. These findings provide a foundation for future hypothesis testing and microbiome manipulation to improve fitness in wild bird populations. The study also highlights the potential role of wild birds in the dissemination of antimicrobial resistance.","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038002/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053766","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}

引用次数: 0

Genome sequence of antibiotic-resistant Klebsiella quasipneumoniae FSFC0558: a novel sequence type (ST8212). 耐药准肺炎克雷伯菌FSFC0558基因组序列：一个新的序列类型（ST8212）。

Access microbiology Pub Date : 2025-04-25 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000944.v3

Daniel Robins, Richard N Goodman, Ralfh Pulmones, Upendo O Kibwana, Joel Manyahi, Bjørn Blomberg, Nina Langeland, Sabrina Moyo, Adam P Roberts

引用次数: 0

Opportunities for microbiology citizen science: lessons learnt from three pilot projects. 微生物学公民科学的机会：三个试点项目的经验教训。

Access microbiology Pub Date : 2025-04-16 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000899.v3

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

{"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":"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.","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}

引用次数: 0

Comparative genomics analysis of six Cutibacterium acnes strains isolated from contaminated platelet concentrates. 从污染血小板浓缩物中分离的6株痤疮表皮杆菌的比较基因组学分析。

Access microbiology Pub Date : 2025-04-08 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000938.v3

Annika Flint, Dilini Kumaran, Kelly Weedmark, Franco Pagotto, Sandra Ramirez-Arcos

{"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":"Cutibacterium acnes 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, C. acnes 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 C. acnes 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.","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}

引用次数: 0

Detection of vanA genes in vancomycin-susceptible Enterococcus faecium isolates: implications for additional testing. 万古霉素敏感粪肠球菌中vanA基因的检测：附加检测的意义。

Access microbiology Pub Date : 2025-04-01 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000959.v4

Victoria Jordan, Hemalatha Varadhan

引用次数: 0

A novel case of Staphylococcus pseudintermedius aortitis. 假性葡萄球菌性主动脉炎1例。

Access microbiology Pub Date : 2025-03-28 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000912.v3

Dione Jones, Matthew Lim, Maxwell Olenski

引用次数: 0

A rare case of Aerococcus urinae native valve endocarditis. 尿气球菌原生瓣膜心内膜炎1例。

Access microbiology Pub Date : 2025-03-27 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000863.v4

Sofie Goes, Kim Callebaut, Denis Pierard, Ingrid Wybo, Deborah De Geyter, Astrid Muyldermans, Jolien Geers, Laura Kerselaers, Thomas Demuyser

{"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":"Background. Aerococcus urinae was initially considered a commensal of the urinary tract, but there is now increasing evidence for its involvement in urinary tract and systemic infections. A. urinae endocarditis has a non-negligible mortality rate and occurs mainly in patients with underlying conditions or the presence of extraneous material. Case presentation. 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 A. urinae. 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 A. urinae endocarditis. Conclusion. A. urinae 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.","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}

引用次数: 0

RSYD-BASIC: a bioinformatic pipeline for routine sequence analysis and data processing of bacterial isolates for clinical microbiology. RSYD-BASIC：用于临床微生物学常规细菌分离序列分析和数据处理的生物信息学管道。

Access microbiology Pub Date : 2025-03-21 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000646.v6

Kat Steinke, Karina Gravgaard Thomsen, Silje Vermedal Hoegh, Sanne Løkkegaard Larsen, Karina Kubel Vilhelmsen, Thøger Gorm Jensen, Marianne Nielsine Skov, Thomas Vognbjerg Sydenham

{"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":"Background. 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. Results. 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 in vitro 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. Conclusion. 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.","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}

引用次数: 0

Antimicrobial effect of blue light on antibiotic-sensitive and drug-resistant Escherichia coli: a novel isotropic optical fibre. 蓝光对抗生素敏感和耐药大肠杆菌的抗菌作用：一种新型各向同性光纤。

Access microbiology Pub Date : 2025-03-19 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000967.v3

Megan H Goh, Joseph J Connolly, Antonia F Chen, Robert A Rabiner, Santiago A Lozano-Calderon

{"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":"Background. 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 Escherichi coli (AS-Ec) and ESBL-producing E. coli (ESBL-Ec). Methods. 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. Results. 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 (P=0.043) and 3.74±0.21 (P=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 (P=0.034) and 2.53±0.22 (P=0.037) at 60 min for LP-ABL and HP-ABL, respectively. Conclusions. 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.","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}

引用次数: 0

Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia. 埃塞俄比亚Wolaita屠宰牛疑似结核病变分枝杆菌的分离和遗传分析。

Access microbiology Pub Date : 2025-03-18 eCollection Date: 2025-01-01 DOI: 10.1099/acmi.0.000915.v3

Melese Yilma Zaba, Sebsib Neway, Damien Farrell, Eva Denion, Viktor Perets, Melaku Tilahun, Kidist Bobosha, Joseph P Cassidy, Asefa Asmare, Stephen V Gordon

{"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":"Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis 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 M. bovis in lesions from four animals and M. tuberculosis in lesions from one animal. The M. bovis and M. tuberculosis isolates showed genetic similarity to previously identified MTBC lineages in Ethiopia. The presence of M. tuberculosis 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 M. bovis and M. tuberculosis.","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}

引用次数: 0