Access microbiology最新文献

{"title":"Is the Zika virus re-emerging as a distinct genetic lineage in India?","authors":"Pradeep Kumar N, Ajithlal P M, Prasanta Saini, Aiswarya R S, Abidha Suresh, Philip Samuel, Balasubramaniam R, Jessu Mathew, Sonia T, Amju K P, Raju K H K, Veerapathiran A, Selvam A, Balaji T, Ashwani Kumar","doi":"10.1099/acmi.0.000857.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000857.v4","url":null,"abstract":"<p><p>An outbreak of Zika fever occurred in Thiruvananthapuram City, Kerala, India, during 2021. At the request of the Kerala state health administration, we investigated the same, towards proposing requisite containment strategies for the disease outbreak. Epidemiological investigations indicated a clustering pattern of Zika fever cases with the presumed index case from a multi-speciality hospital in the city. Preliminary reports on the same had been already reported elsewhere during 2021. Further, entomological surveys carried out evinced the predominant mosquito species in the city, viz. <i>Aedes albopictus</i> (65.55%), <i>Aedes aegypti</i> (22.0%) and <i>Aedes vittatus</i> (12.0%) were naturally infected with Zika virus (ZIKV), the minimum infection rates being 17.9, 7.8 and 3.6, respectively. Also, trans-ovarian transmission was recorded in both <i>Ae. aegypti</i> and <i>Ae. albopictus</i>. This is the first report on the detection of ZIKV from <i>Ae. albopictus</i> in India. Analysis of phylogenetically informative genes of the ZIKV genome indicated the emergence of a distinct lineage of the Asian strain of virus, with five unique non-synonymous mutations, viz. 'A22T' and 'I160M' (pre-membrane) and 'D348N', 'T470A' and 'V473L' (envelope), that were involved in the outbreak. The altered gene expression pattern and evolutionary implications of these unique mutations remain to be investigated. Genetic analysis of the virus isolates from this and other investigations carried out on sporadic outbreaks of ZIKV in the country subsequently indicated that ZIKV is re-emerging as a distinct genetic lineage in India. These findings and other recent reports on ZIKV outbreaks warrant an urgent need for a systematic countrywide surveillance strategy, towards the prevention/preparedness/containment of a massive outbreak of this emerging neurovirulent arboviral disease.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12078788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144083133","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":"Cardiac tamponade revealing tuberculous pericarditis: a case report.","authors":"Oumaima Skalante, Mariam Hachimi Idrissi, Soukaina Cherkaoui, Elmostafa Benaissa, Yassine Ben Lahlou, Mariama Chadli","doi":"10.1099/acmi.0.000983.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000983.v4","url":null,"abstract":"<p><p>Tuberculosis remains a major public health issue in Morocco. Pulmonary tuberculosis is the most common form, but various extrapulmonary forms exist. Tuberculous pericarditis is a rare form of extrapulmonary tuberculosis that can be complicated by cardiac tamponade, pericardial constriction or their combination, which can threaten the patient's life. Its clinical and radiological signs are nonspecific, and the clinical presentation can be misleading and incomplete, sometimes even with an initial tamponade. We report the case of a 68-year-old female patient admitted for intense retrosternal chest pain associated with acute dyspnoea, evolving in the context of unquantified weight loss and general deterioration. Additionally, she reported a history of fever and night sweats. Clinical examination revealed a conscious, febrile, hypotensive, tachycardic, polypneic patient with good oxygen saturation, signs of right heart failure and muffled heart sounds on auscultation. Chest X-ray revealed cardiomegaly, and the ECG showed diffuse low voltage. Given the presence of Beck's triad suggestive of cardiac tamponade, a transthoracic echocardiogram was performed, revealing a large pericardial effusion with a 'swinging heart'. A chest CT scan also confirmed the large pericardial effusion. The diagnosis of cardiac tamponade was made based on the clinical and radiological findings, and pericardial drainage was performed, after which the patient showed clinical improvement. PCR GenXpert MTB/RIF Ultra detected the presence of <i>Mycobacterium tuberculosis</i> in the pericardial fluid, with no resistance to rifampicin. Culture was positive for <i>M. tuberculosis</i>. The diagnosis of tuberculous pericarditis was, thus, confirmed, and the patient was started on quadruple antituberculosis therapy with good clinical progress.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12048714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065545","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":"Novel hot spring Thermoproteota support vertical inheritance of ammonia oxidation and carbon fixation in Nitrososphaeria.","authors":"T Slosser, M Wenick, E Markert, E Trembath-Reichert, L M Ward","doi":"10.1099/acmi.0.000931.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000931.v4","url":null,"abstract":"<p><p>Aerobic ammonia oxidation is crucial to the nitrogen cycle and is only known to be performed by a small number of bacterial lineages [ammonia-oxidizing bacteria (AOB)] and a single lineage of archaea belonging to the <i>Nitrososphaeria</i> class of <i>Thermoproteota</i> [ammonia-oxidizing Archaea (AOA)]. Most cultivated AOA originate from marine or soil environments, but this may capture only a limited subset of the full diversity of this clade. Here, we describe several genomes of AOA from metagenomic sequencing of a hot spring microbial mat, representing several poorly characterized basal lineages that may be important for understanding the early evolution of archaeal ammonia oxidation. These genomes include a novel genus most closely related to <i>Nitrososphaera</i> as well as novel species belonging to the genera <i>Nitrosotenuis</i>, <i>Nitrososphaera</i> and <i>Nitrosotalea</i>. Furthermore, the distributions and phylogenetic relationships of key metabolic genes support a history of vertical inheritance of ammonia oxidation and carbon fixation from the last common ancestor of crown group AOA.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12041475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144045296","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":"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":"<p><p><b>Background.</b> 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 (<i>Parus major</i>) and the Eurasian blue tit (<i>Cyanistes caeruleus</i>). <b>Results.</b> 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 <i>Serratia fonticola</i>. From metagenome assemblies, we obtained complete mitochondrial genomes from the host species and from <i>Isospora</i> spp., while metagenome-assembled genomes documented new prokaryotic species. <b>Conclusions.</b> 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.</p>","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}

{"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":"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}