Access microbiology最新文献

{"title":"Effect of antibiotic administration on Blastocystis persistence and gut microbiome-metabolome dynamics in an irritable bowel syndrome longitudinal case study.","authors":"Jamie M Newton, William J S Edwards, Gary S Thompson, Eleni Gentekaki, Anastasios D Tsaousis","doi":"10.1099/acmi.0.000926.v4","DOIUrl":"https://doi.org/10.1099/acmi.0.000926.v4","url":null,"abstract":"<p><p><b>Background.</b> <i>Blastocystis</i>, the most prevalent microbial eukaryote in humans, has a global distribution. Studies have linked its presence with distinct gut microbiome and metabolome profiles compared to those where the organism is absent. However, the interplay of antibiotic administration, <i>Blastocystis</i> and the surrounding gut microbiome remains understudied. This case study aimed to explore antibiotic consumption and the presence of <i>Blastocystis</i> with subsequent changes in the gut microbiome and metabolome of an individual diagnosed with irritable bowel syndrome (IBS). <b>Methods.</b> Stool samples from an IBS patient, collected at 12 time points, were tested for the presence of <i>Blastocystis</i> using real-time PCR targeting the <i>SSU</i>rRNA gene, followed by sequencing of positive samples. Illumina sequencing determined the gut microbiome composition, while one-dimensional proton NMR spectroscopy was used to analyse the metabolome composition. Statistical analyses were conducted to identify relationships between antibiotic consumption, bacterial diversity, metabolome composition and <i>Blastocystis</i> presence. <b>Results.</b> Antibiotics significantly impacted the gut microbiome, with diversity declining early in the antibiotic course, then recovering later and post-course. <i>Blastocystis</i> was detected early, late and post-course but was not detectable mid-course, coinciding with the decline in bacterial diversity. Significant differences were observed between <i>Blastocystis</i>-positive and <i>Blastocystis</i>-negative samples, with bacterial composition significantly changing between samples collected before, early and after the antibiotic course compared to those collected mid-course. Metabolite groups, including short-chain fatty acids, amino acids and succinate, exhibited changes throughout the antibiotic course, indicating that gut metabolite composition is affected by antibiotic consumption. <b>Discussion/Conclusion.</b> While antibiotics did not significantly impact <i>Blastocystis</i> colonization, they did cause a mid-course decline in microbial diversity and <i>Blastocystis</i> presence. The study also revealed significant alterations in important metabolites such as short-chain fatty acids and amino acids throughout the antibiotic course, with an altered metabolome observed post-course. This case study underscores the complex interactions between antibiotics, gut microbiota and metabolites, highlighting the resilience of <i>Blastocystis</i> in the gut ecosystem.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12202796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144532484","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":"Optimizing synthetic cystic fibrosis sputum media for growth of non-typeable Haemophilus influenzae.","authors":"Phoebe Do Carmo Silva, Darryl Hill, Freya Harrison","doi":"10.1099/acmi.0.000979.v3","DOIUrl":"10.1099/acmi.0.000979.v3","url":null,"abstract":"<p><p>Non-typeable <i>Haemophilus influenzae</i> (NTHi) is an early pathogen isolated from the lungs of children with cystic fibrosis (CF). However, its role in the progression of CF lung infection is poorly understood. Additionally, whether it forms biofilms in the lungs of people with CF is an open question. The development of synthetic CF sputum media (SCFM) has given key insights into the microbiology of later CF pathogens, <i>Pseudomonas aeruginosa</i> and <i>Staphylococcus aureus</i>, through replicating the chemical composition of CF sputum. However, the growth of NTHi in these media has not previously been reported. We show that NTHi grows poorly in three variants of SCFM commonly used to induce <i>in vivo</i>-like growth of <i>P. aeruginosa</i> and <i>S. aureus</i> (SCFM1, SCFM2 and SCFM3). The addition of NAD and haemin to SCFM1 and SCFM2 promoted the planktonic growth and biofilm formation of both laboratory and clinical NTHi isolates, and we were able to develop a modified variant of SCFM2 that allows culture of NTHis. We show that NTHi cannot be identified in an established <i>ex vivo</i> model of CF infection, which uses SCFM and porcine bronchiolar tissue. This may in part be due to the presence of endogenous bacteria on the pig lung tissue, which outcompete NTHi, but the lack of selective agar to isolate NTHi from endogenous bacteria, and the fact that NTHi is an exclusively human pathogen, makes it hard to conclude that this is the case. Through spiking modified SCFM2 with filter-sterilized lung homogenate, biofilm growth of clinical NTHi isolates was enhanced. Our results highlight that there are crucial components present in the lung tissue, which NTHi require for growth, which are not present in any published variant of SCFM from the Palmer <i>et al.</i> Endres and Konstan in JAMA (2022;137:191-1) lineage. Our results may inform future modifications to SCFM recipes to truly mimic the environment of CF lung sputum and thus, to facilitate the study of a wide range of CF pathogens.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181625/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478392","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":"Purulent pleurisy caused by Salmonella enterica subspecies arizonae: a case report.","authors":"Amine Amri, Youssra Boughalem, Elmostafa Benaissa, Yassine Benlahlou, Mariama Chadli","doi":"10.1099/acmi.0.000985.v5","DOIUrl":"10.1099/acmi.0.000985.v5","url":null,"abstract":"<p><p><b>Background.</b> Salmonellosis most commonly presents clinically as typhoid fever or gastroenteritis. Pleuropulmonary infections due to <i>Salmonella</i> are still rare, even though they have often been described in immunocompromised patients. <b>Case presentation.</b> We report a rare case of purulent pleurisy caused by <i>Salmonella enterica</i> subsp. <i>arizonae</i>, occurring in a 50-year-old female with breast cancer who is currently treated with chemotherapy and radiotherapy along with chronic renal failure requiring haemodialysis, who presented with acute chest pain, dyspnoea and haemodynamic instability. After bacteriological identification of <i>Salmonella enterica</i> subsp. <i>arizonae</i> in pleural fluid, antibiotic susceptibility testing was performed. The patient was then started on a broad-spectrum antibiotic, which successfully improved her condition. <b>Conclusion.</b> Our case highlights the implication of <i>Salmonella enterica</i> subsp. <i>arizonae</i> in purulent pleurisy in an immunocompromised patient. An early diagnosis and a proper antibiotic therapy enabled us to reduce the morbidity and mortality risk in our patient.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478393","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":"Draft genome sequence of Flavobacterium aquidurense strain, isolated from untreated wastewater.","authors":"Alexander D H Kingdon, Kara D'Arcy, Anya Breen, Claudia McKeown, Ellie Allman, Priyanka Sharma, Amy McLeman, Adam P Roberts","doi":"10.1099/acmi.0.000976.v3","DOIUrl":"10.1099/acmi.0.000976.v3","url":null,"abstract":"<p><p>Here, we report the draft 5.8 Mb genome sequence of a <i>Flavobacterium aquidurense</i> isolate from untreated wastewater in Liverpool, United Kingdom. The reported isolate has the potential to produce both flexirubin and β-carotene pigments, and contains an additional biosynthetic gene cluster for a putative novel β-lactone. The genome also contains a gene for a putative β-lactamase <i>bla_JOHN-1</i> analogue, and there are multiple copies of a putative novel insertion sequence of the IS<i>3</i> family. This genome adds to a growing resource of <i>Flavobacterium</i> spp<i>.</i> sequencing data which can be utilized to investigate microbial pigment production, antimicrobial resistance genes and mobile genetic elements within this genus.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12181623/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144478391","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 laboratory manual layout: does experiential learning benefit from authentic context?","authors":"Victoria Alice Kate Easton","doi":"10.1099/acmi.0.000955.v4","DOIUrl":"10.1099/acmi.0.000955.v4","url":null,"abstract":"<p><p>Experiential learning is the pedagogic foundation of practical laboratory education. This process of learning through experience enables students to develop a deeper understanding of the theoretical material as well as valuable real-world skills. However, there is often a disconnect between the authentic, real-world context of performing laboratory skills and the method of instruction within higher education. This study developed two student laboratory manuals; one which followed a traditionally linear 'week by week' format, and another which took inspiration from a publication format and listed the protocols in a distinct 'methods' section. The effect the change of layout had on student learning was assessed through analysis of student summative assessment and interaction with the online learning environment. Additionally, the effect on student confidence and perceived technical skills development was assessed through a student survey. The differences in layout resulted in no significant differences in student assessment performance but did result in higher levels of engagement with the online learning environment. The student survey reported an increase in technical confidence (21%) and skill (31%) with the authentic 'methods' section layout changes compared to the traditional format. The increase in student engagement, confidence and perceived skill shows that experiential learning benefits from placing the information in an authentic context.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144328308","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":"Culture harder: use more specimens to increase methicillin-resistant Staphylococcus aureus culture yield relative to PCR.","authors":"Arvette E Mitchell, Arpit P Patel, Jennifer DiCandilo, Zachary W Rebollido, Matthew A Pettengill","doi":"10.1099/acmi.0.000918.v4","DOIUrl":"10.1099/acmi.0.000918.v4","url":null,"abstract":"<p><p>Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) causes considerable morbidity and mortality in both community-acquired and healthcare-associated infections, but detecting colonization with MRSA has been shown to improve patient outcomes in certain clinical settings. MRSA colonization detection has been carried out in a variety of ways, with molecular assays having superior sensitivity in most studies relative to culture, but culture is disadvantaged in some comparisons by utilization of low specimen volumes. We compared a commercial molecular assay to both low-volume (10 µl) and high-volume (650 µl) cultures and found that increasing the volume utilized for culture led to the detection of 25% more cases than low-volume culture.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12134384/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144236368","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 cautionary tale of false-positive histoplasma urine antigen in an HIV patient: a case report.","authors":"Mohammad Z Khrais, Jake Smith, Tanmay Gandhi, Shahrukh Arif, Juan Carlos Rico","doi":"10.1099/acmi.0.000929.v3","DOIUrl":"10.1099/acmi.0.000929.v3","url":null,"abstract":"<p><p><b>Introduction.</b> Coccidioidomycosis, or Valley fever, is a fungal disease caused by <i>Coccidioides</i> species, prevalent in parts of the southwestern United States. It usually results from inhaling spores from soil and is a common cause of pneumonia in these regions. <b>Case Presentation.</b> We present a unique case of coccidioidomycosis in an immunodeficient male patient secondary to human immunodeficiency virus infection with poor adherence to anti-retroviral treatment. After presenting with non-specific symptoms and pre-syncope, he was initially diagnosed with pneumonia based on chest X-ray findings, but his symptoms failed to improve with antibiotics. He was treated for presumed pulmonary histoplasmosis following a positive histoplasma urine antigen test. However, the patient worsened clinically. Following a computed tomography scan demonstrating a large necrotic lung consolidation, fungal stain and culture of tissue biopsied through endobronchial ultrasound confirmed coccidioidomycosis. The patient received 2 weeks of liposomal amphotericin with clinical improvement before discharge with itraconazole. <b>Conclusion.</b> The histoplasma antigen test can be falsely positive due to cross-reaction with other fungal infections like blastomycosis, paracoccidioidomycosis or talaromycosis, and less frequently, coccidioidomycosis or aspergillosis. Diagnosis of coccidioidomycosis requires a high index of suspicion outside the expected geographic distribution in the appropriate clinical setting. Our case highlights the risk of false-positive antigen test results and the importance of invasive diagnostics, including bronchoscopy to obtain fungal cultures, if the diagnosis remains uncertain.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182686","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":"Are reads required? High-precision variant calling from bacterial genome assemblies.","authors":"Ryan R Wick, Louise M Judd, Timothy P Stinear, Ian R Monk","doi":"10.1099/acmi.0.001025.v3","DOIUrl":"10.1099/acmi.0.001025.v3","url":null,"abstract":"<p><p>Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related <i>Staphylococcus aureus</i> isolates sequenced on Illumina and Oxford Nanopore Technologies platforms. By benchmarking multiple assembly and variant-calling pipelines against a ground truth dataset, we found that read-based methods consistently achieved high accuracy. Assembly-based approaches performed well in some cases but were highly dependent on assembly quality, as errors in the assembly led to false-positive variant calls. These findings underscore the need for improved assembly techniques before the potential benefits of assembly-based variant calling (such as reduced computational requirements and simpler data management) can be realized.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12120141/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182529","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":"Crystalline lens dislocation as a presenting sign of Streptococcus pyogenes invasive infections.","authors":"Paulina Liberman, Jacob G Light, Shazia Dharssi, Tracy Howard, Jennifer Lu, Patricia J Simner, Karen C Carroll, Cheng-Ying Ho","doi":"10.1099/acmi.0.000903.v4","DOIUrl":"10.1099/acmi.0.000903.v4","url":null,"abstract":"<p><p><b>Introduction.</b> To describe two cases of crystalline lens dislocation as a presenting feature of invasive group A <i>Streptococcus</i> (GAS) infection and its management. <b>Case presentation.</b> We report on a 58-year-old woman and a 36-year-old man who presented in 2024 with acute vision loss and severe ocular and systemic symptoms. Both patients were found to have lens dislocation and were diagnosed with invasive GAS infection. The 58-year-old woman had a complicated clinical course leading to enucleation, while the 36-year-old man responded favourably to early and aggressive treatment with systemic and intravitreal antibiotics. The responsible GAS strains were sequence type (ST) 28 and ST433, respectively. <b>Conclusion.</b> These cases highlight the importance of recognizing crystalline lens dislocation as a potential sign of ocular GAS infection. Two specific strain types of GAS associated with these findings, ST28 and ST433, are reported. In patients with GAS sepsis presenting with corneal oedema and zonular loss, clinicians should immediately initiate treatment, including intravitreal antibiotic injections and systemic therapy. Prompt and aggressive management can be crucial in preserving ocular structures.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176344","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":"Multi-metal-resistant Staphylococcus warneri strain TWSL_1: revealing heavy metal-resistant genomic features by whole-genome sequencing and analysis.","authors":"Dilani Chathurika Dissanayake, Naduviladath Vishvanath Chandrasekharan, Champika Dilrukshi Wijayarathna","doi":"10.1099/acmi.0.000954.v5","DOIUrl":"10.1099/acmi.0.000954.v5","url":null,"abstract":"<p><p>This study explores the genomic basis of heavy metal resistance in <i>Staphylococcus warneri</i> strain TWSL_1, isolated from industrial textile effluent. The strain exhibited strong resistance to Cd²⁺, Pb²⁺ and Cu²⁺, with MICs of 50, 1,200 and 75 mg l^-1, respectively. Whole-genome sequencing revealed a 2.66 Mb genome with 2,567 CDSs and a 99.81% average nucleotide identity to <i>S. warneri</i> WS479. Comparative genomic analysis at the genus level revealed that <i>S. warneri</i> strain TWSL_1 possesses a unique and expanded repertoire of heavy metal resistance genes, including the cadmium efflux system accessory protein and cadmium resistance protein, which are absent in pathogenic <i>Staphylococcus</i> sp. used for the comparison. Phylogenetic analysis confirmed its classification within <i>S. warneri</i>, with strong bootstrap support (100). Functional annotation highlighted metabolic versatility and stress response capabilities, supporting its adaptation to metal-rich environments. <i>S. warneri</i> TWSL_1 demonstrated high Pb²⁺ removal efficiency, reducing concentrations by over 70%. These findings highlight <i>S. warneri</i> TWSL_1 as a promising candidate for heavy metal bioremediation with potential applications in environmental detoxification and monitoring strategies.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12117009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144176478","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}