Access microbiology最新文献

{"title":"Draft genome sequences of four potential new species of the genus Bradyrhizobium isolated from root nodules of native legumes in Costa Rican forests.","authors":"Rachelle Fernández-Vargas, Sara Jiménez-Alpízar, Valeria Leandro-Arce, Bradd Mendoza-Guido, Keilor Rojas-Jimenez","doi":"10.1099/acmi.0.000990.v3","DOIUrl":"10.1099/acmi.0.000990.v3","url":null,"abstract":"<p><p>Here, we report the draft genome sequences of four <i>Bradyrhizobium</i> spp. isolates obtained from root nodules of the native legumes <i>Pentaclethra macroloba</i>, <i>Chamaecrista nictitans</i>, <i>Erythrina fusca</i> and <i>Zygia engelsingii</i> in tropical forests of Costa Rica. Genomes ranged from 8.6 to 9.8 Mb with GC contents between 62.8% and 63.8%. Phylogenomic analysis, along with average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) comparisons, confirmed that these isolates represent potential new species. ANI values ranged from 88.3% to 90.3%, and dDDH values from 28.8% to 41.8%, compared with their closest <i>Bradyrhizobium</i> species. Functional annotation revealed some genes related to nitrogen fixation (<i>nifA</i>, <i>nifB</i>, <i>nifH</i>) and nodulation capacity (<i>nodB</i>, <i>nodC</i>, <i>nodJ</i>). These results provide insights into the diversity and symbiotic capabilities of <i>Bradyrhizobium</i> in tropical ecosystems.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12084545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144096137","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":"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":"Classification of unsequenced Mycobacterium tuberculosis strains in a high-burden setting using a pairwise logistic regression approach.","authors":"Isabel Rancu, Benjamin Sobkowiak, Joshua L Warren, Nelly Ciobanu, Alexandru Codreanu, Valeriu Crudu, Caroline Colijn, Ted Cohen, Melanie H Chitwood","doi":"10.1099/acmi.0.000964.v3","DOIUrl":"10.1099/acmi.0.000964.v3","url":null,"abstract":"<p><p>Over the past three decades, molecular epidemiological studies have provided new opportunities to investigate the transmission dynamics of <i>Mycobacterium tuberculosis</i>. In most studies, a sizable fraction of individuals with notified tuberculosis cannot be included, either because they do not have culture-positive disease (and thus do not have specimens available for molecular typing) or because resources for conducting sequencing are limited. A recent study introduced a regression-based approach for inferring the membership of unsequenced tuberculosis cases in transmission clusters based on host demographic and epidemiological data. This method was able to identify the most likely cluster to which an unsequenced strain belonged with an accuracy of 35%, although this was in a low-burden setting where a large fraction of cases occurred among foreign-born migrants. Here, we apply a similar model to <i>M. tuberculosis</i> whole-genome sequencing data from the Republic of Moldova, a setting of relatively high local transmission. Using a maximum cluster span of ~40 single nucleotide polymorphisms (SNPs) and a cluster size cutoff of <i>n</i>≥10, we could best predict the specific cluster to which each clustered case was most likely to be a member with an accuracy of 17.2 %. In sensitivity analyses, we found that a more restrictive (~20 SNPs threshold) or permissive (~80 SNPs) threshold did not improve performance. We found that increasing the minimum cluster size improved prediction accuracy. These findings highlight the challenges of transmission inference in high-burden settings like Moldova.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12163731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144304265","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":"Erratum: 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.0.001048","DOIUrl":"https://doi.org/10.1099/acmi.0.001048","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1099/acmi.0.000995.v3.].</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":"001048"},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281734/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692972","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":"Gummatous mitral valve endocarditis from tertiary syphilis.","authors":"Nisha George, Daniel Pan, Shirley Sze, Caroline Williams, Zein El-Dean, Victor Zlocha, Elizabeth Webb, Manish Pareek","doi":"10.1099/acmi.0.000817.v3","DOIUrl":"10.1099/acmi.0.000817.v3","url":null,"abstract":"<p><p>A 50-year-old Romanian gentleman presented with fever, myalgia and 30 kg weight loss. He was treated for syphilis after acquiring it 16 years ago. On examination, there was a pansystolic murmur in the axilla, and the patient had an ataxic gait. Blood tests showed raised inflammatory markers. However, standard investigations for infective endocarditis, including multiple blood cultures, serological titres for fastidious organisms and antibody tests were negative. A computed tomography (CT) of the chest, abdomen and pelvis demonstrated hepatosplenomegaly with multiple splenic infarcts. A magnetic resonance imaging (MRI) of the head with contrast showed multiple punctate enhancement in the bilateral hemispheres with leptomeningeal enhancement. Transthoracic echocardiogram demonstrated a large vegetation leading to severe mitral regurgitation. Serum treponemal antibodies were positive; <i>Treponema pallidum</i> particle agglutination (TPPA) was positive at 1 : 1280, and rapid plasma reagin (RPR) 1 : 4 treponemal IgM was negative; lumbar puncture syphilis serology was negative. The patient was treated with an extensive period of intravenous antibiotics, in addition to a prosthetic metallic valve replacement, where unusual ragged calcified valvular tissue was observed. Tertiary syphilis is a difficult diagnosis to confirm, since it can often be indolent and occur in areas of the body where it may go unnoticed. In our case, a diagnosis of probable syphilitic endocarditis was made from a combination of the history, an initial increase in the size of the lesion following antibiotic therapy and observation of likely gumma on the mitral valve during surgery. In such cases, surgery in addition to optimal antimicrobial therapy is necessary for effective treatment. This case adds to the current literature that treatment with penicillin is likely inadequate to prevent late complications.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281932/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692973","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":"Primary iliac bone tuberculosis: a case report.","authors":"Hajar Dahou, Fataou Saley Younoussa, Imane Aragon, Salma El Aouadi, Yahya El Harras, Elmostafa Benaissa, Yassine Ben Lahlou, Abdelaali Bahadi, Jamal El Fenni, Adil Maleb, Mariama Chadli, Mostafa Elouennass","doi":"10.1099/acmi.0.000844.v3","DOIUrl":"10.1099/acmi.0.000844.v3","url":null,"abstract":"<p><p>Tuberculosis (TB) remains one of the world's leading causes of morbidity and mortality. It occurs in both pulmonary and extra-pulmonary forms. Primary iliac bone TB remains a rare clinical entity, even in endemic areas. The diagnosis of the disease can be challenging due to its similarity to other bone diseases. We report a rare case of primary iliac bone TB in a 63-year-old patient who was on peritoneal dialysis and had a medical history of hypertension and type II diabetes, which was complicated by diabetic retinopathy and diabetic kidney disease. Magnetic resonance imaging revealed osteomyelitis in the iliac bone, while real-time polymerase chain reaction using the GeneXpert^® system on a gluteal collection sample confirmed the diagnosis of TB. The integration of advanced molecular tools, such as GeneXpert^®, represents significant progress, enabling rapid and accurate diagnosis of TB and facilitating early initiation of treatment.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281756/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692974","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":"Corrigendum: Tossing the coin of extended-spectrum β-lactamase: prevalence of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from patients with sepsis.","authors":"Beatrice Achan, Tonny Luggya, Robert Innocent Ebwongu, Simon Sekyanzi, Henry Kajumbula","doi":"10.1099/acmi.0.001047","DOIUrl":"https://doi.org/10.1099/acmi.0.001047","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1099/acmi.0.000962.v3.].</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":"001047"},"PeriodicalIF":0.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692971","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}