Access microbiologyPub Date : 2025-06-26eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000972.v4
Susan V Grooters, Dixie F Mollenkopf, Gregory A Ballash, Thomas E Wittum
{"title":"The impact of zinc supplementation on carbapenem MICs among bacteria expressing IMP metallo-beta-lactamase.","authors":"Susan V Grooters, Dixie F Mollenkopf, Gregory A Ballash, Thomas E Wittum","doi":"10.1099/acmi.0.000972.v4","DOIUrl":"10.1099/acmi.0.000972.v4","url":null,"abstract":"<p><p>Antibiotic-resistant infections cause an estimated 2.8 million illnesses and 35,900 deaths annually in the USA. Carbapenems are a class of antibiotics that are generally reserved to treat life-threatening invasive infections including sepsis. Accurate diagnosis of carbapenem-resistant infections is critical for early and appropriate treatment. <i>bla</i> <sub>IMP</sub> encodes bacterial production of the IMP metallo-beta-lactamase (MBL), which can confer resistance to all the beta-lactams including carbapenems. Zinc is an essential co-factor in the IMP MBL enzymatic hydrolysis of carbapenems. Tests for the presence of IMP carbapenemase, such as the Carba NP, include zinc sulphate (ZnSO<sub>4</sub>) although broth dilution methods for determining MIC for carbapenems may vary. We hypothesized that ZnSO<sub>4</sub> availability would improve the accuracy of carbapenem MIC determination for bacteria expressing <i>bla</i> <sub>IMP</sub>. Thus, the objective of this study was to determine if supplemental ZnSO<sub>4</sub> affects the carbapenem MICs of <i>Enterobacterales</i>, <i>Alteromonadales</i> and <i>Moraxellales</i> expressing <i>bla</i> <sub>IMP</sub>. Isolates utilized for this study were originally recovered from environmental samples collected at farms, wastewater treatment plants and surface water. They were selected based on phenotypic non-susceptibility to carbapenems and genetic confirmation of bacterial carriage of <i>bla</i> <sub>IMP</sub>. Cation-adjusted Mueller-Hinton broth suspensions of each isolate standardized to a 0.5 MacFarland standard were tested with and without ZnSO<sub>4</sub> added at 0.1 mmol l<sup>-1</sup> concentration to determine MICs using standard extended-spectrum beta-lactamase microbroth dilution MIC panels. Although we observed that <i>Morganellaceae</i> imipenem MICs were higher (<i>P</i><0.001) than those from other bacteria harbouring <i>bla</i> <sub>IMP</sub>, the inclusion of supplemental ZnSO<sub>4</sub> did not influence carbapenem MIC. This suggests that supplemental ZnSO<sub>4</sub> will not improve the accuracy of carbapenem MICs in environmental bacteria expressing IMP carbapenemase. Additional research will be required to identify important factors that may influence the expression of carbapenemase including IMP and the accurate determination of clinical MICs, which is critical to appropriate therapeutic decision-making.</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/PMC12281849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692980","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}
Access microbiologyPub Date : 2025-06-26eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000926.v4
Jamie M Newton, William J S Edwards, Gary S Thompson, Eleni Gentekaki, Anastasios D Tsaousis
{"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":"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}
Access microbiologyPub Date : 2025-06-20eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000979.v3
Phoebe Do Carmo Silva, Darryl Hill, Freya Harrison
{"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}
Access microbiologyPub Date : 2025-06-20eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000976.v3
Alexander D H Kingdon, Kara D'Arcy, Anya Breen, Claudia McKeown, Ellie Allman, Priyanka Sharma, Amy McLeman, Adam P Roberts
{"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<sub>JOHN-1</sub></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}
Access microbiologyPub Date : 2025-06-18eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000902.v3
Prashantha Hebbar, Oh Bi Han, Ng Xin Yan, Dominic Kay, Kwa Yee Chu, James Sy-Keen Woon, Pang Kok Lun, Shama Prasada Kabekkodu, Alevoor S Bharath Prasad, Bharathi Prakash, Nadine Nograles, Mahibub Mahamadsa Kanakal, Michaela Goodson, Shubhada Nagaraja, Roshan Mascarenhas
{"title":"Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia.","authors":"Prashantha Hebbar, Oh Bi Han, Ng Xin Yan, Dominic Kay, Kwa Yee Chu, James Sy-Keen Woon, Pang Kok Lun, Shama Prasada Kabekkodu, Alevoor S Bharath Prasad, Bharathi Prakash, Nadine Nograles, Mahibub Mahamadsa Kanakal, Michaela Goodson, Shubhada Nagaraja, Roshan Mascarenhas","doi":"10.1099/acmi.0.000902.v3","DOIUrl":"10.1099/acmi.0.000902.v3","url":null,"abstract":"<p><p>The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed <i>Pseudomonadota</i> (67-69%), <i>Bacteroidota</i> (6-8%), <i>Bacillota</i> (5-8%), <i>Campylobacterota</i> (4-5%), <i>Acidobacteriota</i> (3-4%), <i>Planctomycetota</i> (2-4%) and <i>Actinomycetota</i> (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of <i>Burkholderiaceae</i>, <i>Bacillaceae</i> and <i>Enterobacteriaceae</i> suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.</p>","PeriodicalId":94366,"journal":{"name":"Access microbiology","volume":"7 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12281800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144692975","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}
Access microbiologyPub Date : 2025-06-17eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000955.v4
Victoria Alice Kate Easton
{"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}
Access microbiologyPub Date : 2025-06-03eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000918.v4
Arvette E Mitchell, Arpit P Patel, Jennifer DiCandilo, Zachary W Rebollido, Matthew A Pettengill
{"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}
Access microbiologyPub Date : 2025-05-28eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.000929.v3
Mohammad Z Khrais, Jake Smith, Tanmay Gandhi, Shahrukh Arif, Juan Carlos Rico
{"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}
Access microbiologyPub Date : 2025-05-28eCollection Date: 2025-01-01DOI: 10.1099/acmi.0.001025.v3
Ryan R Wick, Louise M Judd, Timothy P Stinear, Ian R Monk
{"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}