Microbiology spectrum最新文献

{"title":"<i>Coccidioides</i> genomes from low-incidence states reveal complex migration history across the western United States.","authors":"Emanuel M Fonseca, Shanaya Fox, Adrienne L Carey, Bridget Barker, Marco Marchetti, Megan Hirschi, Kimberly E Hanson, Katharine S Walter","doi":"10.1128/spectrum.01822-25","DOIUrl":"https://doi.org/10.1128/spectrum.01822-25","url":null,"abstract":"<p><p>Coccidioidomycosis (Valley fever), caused by the fungal pathogen <i>Coccidioides</i>, is increasing in incidence across the western United States and parts of the Americas. However, genomic data from low-incidence regions remain scarce, limiting our understanding of the pathogen's dispersal and evolution. To address this gap, we prospectively collected <i>Coccidioides</i>-positive clinical isolates submitted to a national diagnostic laboratory between January 2023 and November 2024. We performed whole-genome sequencing on 27 clinical isolates from Utah, Colorado, and Nevada-states with no previously available <i>Coccidioides</i> genomes-and sequenced an additional 22 isolates from California. For Utah patients, we also reviewed medical records to assess potential travel history. Among the 27 newly sequenced isolates, three were identified as <i>Coccidioides immitis</i> and 24 as <i>Coccidioides posadasii</i>. The <i>C. immitis</i> isolates, all from a single Utah patient, were linked to recent travel to southern California. In contrast, <i>C. posadasii</i> isolates from Utah, Colorado, and Nevada were phylogenetically diverse and dispersed across the species tree. Ancestral state reconstructions suggested multiple independent introductions: at least seven into Utah, two into Nevada, and seven into Colorado. The <i>C. immitis</i> clade likely originated in California (likelihood = 0.96), while <i>C. posadasii</i> traces to Arizona (likelihood = 0.99). These results reveal a complex dispersal history of <i>Coccidioides</i> in the western United States, driven by recurrent introductions rather than a single emergence event. Our study underscores the need for continued genomic surveillance in underrepresented regions to fully capture the evolutionary dynamics of this emerging fungal pathogen.IMPORTANCEValley fever is a fungal disease caused by <i>Coccidioides</i> species, primarily found in arid regions of the western United States and parts of Central and South America. While most genomic studies focus on high-incidence areas, the evolutionary dynamics of the fungus in low-incidence states remain poorly understood. In this study, we analyzed clinical <i>Coccidioides</i> isolates from Utah, Colorado, and Nevada-states with reported cases but limited genomic data. Using whole-genome sequencing and phylogenetic analysis, we found evidence of multiple introductions into each state, likely from neighboring high-incidence regions such as Arizona and California. In Utah, we detected both <i>Coccidioides immitis</i> and <i>Coccidioides posadasii</i>, though the <i>C. immitis</i> case was associated with recent travel. Only <i>C. posadasii</i> was found in Colorado and Nevada. These findings support ongoing dispersal rather than a single introduction and highlight the need for expanded genomic surveillance beyond traditionally endemic regions.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0182225"},"PeriodicalIF":3.8,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global, regional, and national burden of HIV and other sexually transmitted infections among women of childbearing age from 1990 to 2021.","authors":"Xiaoyu Zhang, Chenglong Hu, Yao Liang, Wanguo Dong, Jian Gao, Yu Ji, Chang Cao, Wei Shi, Shuaijie Zhu, Heng Guo, Tianfeng Hua, Hui Li, Min Yang","doi":"10.1128/spectrum.00488-25","DOIUrl":"https://doi.org/10.1128/spectrum.00488-25","url":null,"abstract":"<p><p>Sexually transmitted infections (STIs) represent a significant public health burden, particularly among women of childbearing age. This study aims to analyze the global, regional, and national age-standardized rates of incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for STIs among women aged 15-49 from 1990 to 2021. Data were sourced from the Global Burden of Disease 2021 database, and age-standardized rates were calculated using direct standardization methods. Temporal trends were evaluated through average annual percentage change (AAPC) via jointpoint regression analysis. In 2021, compared with other STIs, HIV/AIDS had the highest age-standardized mortality rate (12.98 per 100,000; 95% CI: 10.04 to 16.84) and DALY rate (829.89; 95% CI: 658.73 to 1,056.91). Trichomoniasis had the highest incidence (6,709.73; 95% CI: 3,676.25 to 10,839.25), and genital herpes had the highest prevalence (17,137.09; 95% CI: 13,485.32-21,121.75). From 1990 to 2021, trichomoniasis showed the sharpest increase in incidence (AAPC: 0.27 [95% CI: 0.25 to 0.30]), while HIV/AIDS had the greatest rise in prevalence (AAPC: 3.50 [3.35 to 3.65]), mortality (AAPC: 1.49 [0.97 to 2.02]), and DALYs (AAPC: 1.52 [1.02 to 2.01]). In contrast, gonococcal infection exhibited the steepest declines in prevalence (AAPC: -0.46 [-0.49 to -0.43]) and mortality (AAPC: -1.16 [-1.34 to -0.97]), while syphilis had the largest decrease in DALYs (AAPC: -1.14 [-1.32 to -0.96]). Regional and national disparities were evident across all metrics. These findings highlight the ongoing and uneven burden of STIs and the need for tailored screening and prevention strategies.</p><p><strong>Importance: </strong>Sexually transmitted infections (STIs) pose a significant public health challenge, particularly among women of childbearing age, with substantial impacts on individual health and societal wellbeing. This study provides a comprehensive analysis of the global, regional, and national age-standardized rates of incidence, prevalence, mortality, and disability-adjusted life years (DALYs) for STIs among women aged 15-49 over the past three decades. The findings reveal alarming trends, with HIV/AIDS topping the list in terms of mortality and DALYs and trichomoniasis and genital herpes showing high incidence and prevalence rates. These data highlight the urgent need for targeted screening and preventive interventions to address the disparities in STI burden across regions and countries. By understanding the trends and patterns of STIs, policymakers and healthcare providers can develop effective strategies to reduce the transmission and impact of these infections among women of reproductive age, thereby improving global public health outcomes.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0048825"},"PeriodicalIF":3.8,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Heterologous expression and characterization of synthetic polyester-degrading cutinases from <i>Fusarium</i> spp. in <i>Aspergillus niger</i>.","authors":"Jo-Anne Verschoor, Mark Arentshorst, Antonia J G Regensburg-Tuink, Sjoerd J Seekles, Cees van den Hondel, Johannes H de Winde, Arthur F J Ram","doi":"10.1128/spectrum.02177-25","DOIUrl":"https://doi.org/10.1128/spectrum.02177-25","url":null,"abstract":"<p><p>Cutinases are versatile enzymes with substrate promiscuity, making them promising candidates for the degradation of both natural and synthetic polyesters. While bacterial cutinases have been extensively studied, fungal cutinases remain underexplored, particularly in their enzymatic activity beyond their role in plant virulence. In this study, we investigated four cutinases from two <i>Fusarium</i> strains. Both strains displayed activity on Impranil-DLN, revealing their polyester-degrading potential. The strains were identified as <i>Fusarium oxysporum</i> (strain 38) and <i>Fusarium redolens</i> (strain 62). We characterized two cutinases per strain, tentatively called Cut1 and Cut5. Phylogenetic analysis revealed that both Cut1 clustered together in one branch where the Cut5 variants are closely related to the previously characterized bis(2-hydroxyethyl) terephthalate (BHET)-hydrolyzing enzyme <i>Fo</i>Cut5, providing structural insights and insights into their catalytic potential. We successfully expressed the Cut5 cutinases in <i>Aspergillus niger</i> using a CRISPR-Cas9-based multicopy integration system, resulting in enhanced degradation of Impranil-DLN and tributyrin. Using the same multicopy integration approach, transformants containing multicopy Cut1 variants were obtained but found to produce considerably lower amounts of Cut1, resulting in less activity and disabling further purification. The optimal substrate length, temperature, and pH for both Cut5 enzymes were determined. Additionally, we show activity of the purified Cut5 enzymes on synthetic substrates Impranil-DLN and BHET, suggesting that these fungal cutinases may be valuable for bioremediation. Accelerating the discovery of fungal cutinases and optimizing their expression systems holds promise for future strategies for polymer degradation to reduce agricultural and plastic waste.</p><p><strong>Importance: </strong>Cutinases are promising enzymes for a spectrum of applications due to their substrate promiscuity toward both natural and synthetic polymers. This makes them strong candidates for the development of sustainable solutions to battle environmental pollution. Therefore, the successful production and characterization of novel cutinases is fundamental for understanding their mechanisms and potential applications. In this study, we have identified, produced, and characterized two cutinases from different <i>Fusarium</i> species using a multicopy integration system in <i>Aspergillus niger</i>. Structural characteristics and <i>in vivo</i> and <i>in vitro</i> enzyme activity provide a unique insight into the polyester-degrading activity of these enzymes and how they can contribute to more sustainable solutions to our current waste management and pollution challenges.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0217725"},"PeriodicalIF":3.8,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Validation and subcellular localization of previously predicted type III secreted effector proteins in <i>Chlamydia trachomatis</i>.","authors":"Paige N McCaslin, Shelby E Andersen, Parker Smith, Mary M Weber, Robert Faris","doi":"10.1128/spectrum.01616-25","DOIUrl":"https://doi.org/10.1128/spectrum.01616-25","url":null,"abstract":"<p><p>The obligate intracellular bacterium <i>Chlamydia trachomatis</i> (<i>C.t</i>.) is the leading cause of bacterial sexually transmitted infections and infectious blindness worldwide. <i>C.t</i>. replicates within a specialized membrane-bound compartment known as the inclusion and employs a type III secretion system (T3SS) to deliver effector proteins into the host cell. These effectors reprogram host cellular processes to create an environment conducive to bacterial replication. Until recently, <i>C.t</i>. was genetically intractable, limiting efforts to identify effector proteins secreted during infection. As a result, early studies relied on heterologous expression in surrogate T3SS-component bacteria such as <i>Yersinia pseudotuberculosis</i>, <i>Shigella flexneri</i>, or <i>Salmonella enterica</i> serovar Typhimurium to assess secretion potential. With the advent of genetic tools for use in <i>C.t.</i>, we are now able to directly assess whether previously identified effectors are translocated during <i>C.t</i>. infection. Using three complementary approaches-the adenylate cyclase assay, β-lactamase assay, and glycogen synthase kinase assay-we identified 11 secreted effectors and 10 potentially secreted effectors. Of these 21 secreted factors, 10 displayed unique localization patterns when ectopically expressed in mammalian cells. Together, these findings define a core set of secreted effectors <i>C.t</i>. effectors that warrant further functional characterization.</p><p><strong>Importance: </strong>This study systematically identifies and validates <i>Chlamydia trachomatis</i> type III secreted effectors, confirming secretion for 11 proteins and identifying 12 additional candidates. Using multiple complementary translocation assays, we directly assess secretion in the native bacterial context, revealing key effectors that target specific host compartments. Notably, several effectors localize to the nucleus or cytoplasm, suggesting distinct roles in host cell manipulation. Our findings refine the known effector repertoire and provide critical insights into how <i>C. trachomatis</i> remodels host organelles to sustain infection. By emphasizing experimentally verified secretion rather than surrogate systems, this work strengthens the foundation for future mechanistic studies and therapeutic targeting.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0161625"},"PeriodicalIF":3.8,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145355358","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening microbial inhibitors of <i>Pseudogymnoascus destructans</i> in Northern China.","authors":"Shaopeng Sun, Mingqi Shan, Zihao Huang, Yihan Lv, Zizhen Wei, Mingqi Shen, Keping Sun, Zhongle Li, Jiang Feng","doi":"10.1128/spectrum.01241-25","DOIUrl":"https://doi.org/10.1128/spectrum.01241-25","url":null,"abstract":"<p><p>White-nose syndrome is caused by <i>Pseudogymnoascus destructans,</i> leading to the near extinction of multiple bat populations in North America. This fungal pathogen has also been detected in China, but the prevalence and loads are relatively low in the hosts and environment. Previous studies have screened bat skin microbiomes in China to identify microbes that inhibit the growth of <i>P. destructans</i>. However, there is limited information on bacterial genera that possess properties that inhibit <i>P. destructans</i> in bat cave environments in China, particularly regarding antifungal metabolic pathways. We isolated 29 bacterial strains that have the ability to inhibit growth of <i>P. destructans</i> from the skin of bats and soil samples in China. These strains primarily belonged to several genera, including <i>Acinetobacter</i>, <i>Pseudomonas</i>, and <i>Serratia</i>. Gas chromatography-mass spectrometry analysis identified volatile organic compounds from strains that inhibit <i>P. destructans</i>, showing that 100 µL of α-Pinene, 2-Undecanone, 2-Nonanone, 2,5-Dimethylpyrazine, as well as 10 µL Benzaldehyde and Thujone, completely inhibited the growth of <i>P. destructans</i> and caused morphological damage to the mycelium. The soluble secondary metabolites from the antagonistic strains indicated that the bioactive compounds were predominantly small-molecule organic substances. Whole-genome sequencing of these antagonistic strains revealed that the most enriched potential antifungal gene clusters were associated with bacteriocins, siderophores, and β-lactones. β-Lactones were the primary gene cluster against <i>P. destructans</i>, and chitinases may play a crucial role in the antifungal process.IMPORTANCEBat skin and environmental microbiota may influence the colonization and persistence of <i>Pseudogymnoascus destructans</i>, thereby potentially affecting the occurrence of white-nose syndrome. Examining differences in these gene clusters contributes to understanding variation in the capacity of bacterial groups to have characteristics that inhibit <i>P. destructans</i>. This study lays the foundation for further exploration and elucidation of the mechanisms by which bacteria from bat skin and roosting environments suppress <i>P. destructans</i> growth <i>in vitro</i>.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0124125"},"PeriodicalIF":3.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hemolytic activity and antibiotic resistance profiles of <i>Staphylococcus aureus</i> isolates from clinical patients.","authors":"Yen-Hsi Lai, Chih-Chen Kao, Min Yi Wong, Tsung-Yu Huang, Yu-Hui Lin, Chien-Wei Chen, Yao-Kuang Huang","doi":"10.1128/spectrum.02074-25","DOIUrl":"https://doi.org/10.1128/spectrum.02074-25","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> is a common human pathogen that can cause vascular and skin infections, and patients undergoing hemodialysis are particularly susceptible to vascular access infections caused by <i>S. aureus</i>. Hemolysins are important virulence factors, and antibiotic resistance poses challenges for treatment. In this study, <i>S. aureus</i> isolates were collected from hemodialysis patients with vascular access, such as arteriovenous grafts, tunneled-cuffed catheters, and arteriovenous fistulas, as well as from non-vascular access infection (VAI) patients. The hemolytic phenotype and eight antibiotic susceptibility of these isolates were tested, and PCR was used to detect hemolysin (<i>hla</i>, <i>hlb</i>, <i>hld</i>, and <i>hlgC</i>/<i>B</i>) and antibiotic resistance genes (<i>accA-aphD</i>, <i>tetM</i>, and <i>tetK</i>). The results showed that methicillin-resistant <i>S. aureus</i> (MRSA) and methicillin-susceptible <i>S. aureus</i> (MSSA) isolates exhibited only β- and γ-hemolytic phenotypes. The <i>hla</i> and <i>hld</i> genes were the most frequently detected hemolysin genes, whereas <i>hlb</i> was the least common. Over 80% of both MRSA and MSSA isolates exhibited resistance to ampicillin, with multidrug resistance observed more frequently in MRSA. Distinct antibiotic resistance gene patterns were observed in MRSA and MSSA isolates. Despite these differences in gene patterns, no obvious differences were found between VAI and non-VAI patients, or between MRSA and MSSA isolates. These findings provide a better understanding of the hemolytic characteristics and antibiotic susceptibility of <i>S. aureus</i> isolates collected from hemodialysis and non-hemodialysis patients, contributing to more targeted and effective treatment strategies.IMPORTANCE<i>Staphylococcus aureus</i> is a common human pathogen, and dialysis patients are at higher risk of infection compared to the general population because this bacterium can colonize medical devices and vascular access catheters. Among its various virulence factors, hemolysins play a crucial role by damaging host cells and helping the bacteria evade immune defenses. The widespread use of antibiotics has led to the emergence of antibiotic-resistant <i>S. aureus</i>, especially methicillin-resistant <i>S. aureus</i>, further complicating treatment. This study aims to investigate the types of hemolysins, the distribution of hemolysin and antibiotic resistance genes, and antibiotic resistance patterns in <i>S. aureus</i> isolates from patients with vascular access-related and non-vascular access infections, providing a reference for infection control and treatment strategies.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0207425"},"PeriodicalIF":3.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of intratumoral bacteria correlated with hepatitis B virus (HBV) levels: a prognostic indicator for patient outcomes in hepatocellular carcinoma patients.","authors":"Yuan Dang, Jingyun Huang, Xing Peng, Yingchao Wang, Jianmin Wang","doi":"10.1128/spectrum.01188-25","DOIUrl":"https://doi.org/10.1128/spectrum.01188-25","url":null,"abstract":"<p><p>Hepatocellular carcinoma (HCC) is a prevalent liver cancer associated with global health. The tumor microenvironment's (TME) microbial composition significantly influences HCC's development and prognosis. This study analyzed bacterial 16S rRNA genes from liver cancer patients' tumor, adjacent tumor, and normal tissues, revealing distinct microbiome profiles between tumor and normal tissues. HCC microbiota was more abundant, with <i>Bacteroides</i>, <i>Ochrobactrum</i>, <i>Akkermansia</i>, and <i>Lactobacillus</i> as the most prevalent genera. Hepatitis B virus (HBV)-positive (HBV+) and HBV-negative (HBV-) HCC tissues showed different microbial network patterns, with <i>Bacteroides</i> enrichment in HBV+ tissues being associated with HCC prognosis. HBV is associated with clinicopathological features and serves as an independent prognostic factor in HCC. The study underscores the microbiota's complexity in HCC and the potential of HBV as a prognostic biomarker post-surgery. This study provides critical insights into the relationship between the microbiota within the TME and HCC, a leading cause of cancer-related mortality. By identifying distinct microbiome profiles in HCC patients, particularly the enrichment of <i>Bacteroides</i> in HBV-positive tissues, our research not only uncovers the complexity of microbial interactions in liver cancer but also highlights the potential of using HBV status as a prognostic biomarker. This could significantly inform personalized treatment strategies and improve clinical outcomes for HCC patients, emphasizing the relevance of microbiome-based diagnostics and therapies in oncology.IMPORTANCEIn our study of the tumor microenvironment (TME) in hepatocellular carcinoma (HCC), we used DNA sequencing of bacterial 16S rRNA genes to analyze microbial compositions in tumor, adjacent tumor, and normal tissues from 213 liver cancer patients. Fluorescence <i>in situ</i> hybridization confirmed the presence of microbiota within tumors. Our results showed significant differences in microbiome profiles between tumor and normal tissues, with increased abundance of <i>Bacteroides</i>, <i>Ochrobactrum</i>, <i>Akkermansia</i>, and <i>Lactobacillus</i> in the HCC TME. Hepatitis B virus (HBV) status further stratified these differences, with <i>Bacteroides</i> significantly enriched in HBV-positive tissues and correlating with patient prognosis. Additionally, <i>Bacteroides</i> and <i>Akkermansia</i> showed interdependent population changes. Clinicopathological features, such as tumor size, were associated with HBV status, identifying HBV infection as an independent prognostic factor. These findings highlight the HCC microbiota's complexity and suggest HBV status as a potential prognostic biomarker, opening avenues for personalized therapeutic strategies.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0118825"},"PeriodicalIF":3.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>In vitro</i> persistence of clinical methicillin-resistant <i>Staphylococcus aureus</i> isolates from bone and joint infections after exposure to daptomycin, telavancin, and vancomycin.","authors":"Aliaa Fouad, Joseph L Kuti, Christian M Gill","doi":"10.1128/spectrum.01576-25","DOIUrl":"https://doi.org/10.1128/spectrum.01576-25","url":null,"abstract":"<p><p>Bacterial persistence is linked to chronic infections caused by methicillin-resistant <i>Staphylococcus aureus</i> (MRSA). Understanding the persister profiles of daptomycin, telavancin, and vancomycin is crucial because MRSA bone and joint infections (BJIs) are associated with recurrence and treatment failure. Persister formation was assessed using quantitative <i>in vitro</i> assays against six clinical BJI MRSA isolates and a quality control ATCC strain. Assays were performed using a mid-exponential phase of bacteria challenged with steady-state drug concentrations of the three agents. Persisters were quantified as the percent survival quantifiable at 24 h compared with the respective control. Persisters were also quantified after three serial passages of daptomycin pre-exposure. The percent survival identified at 24 h was ≤21.7% with no significant differences between daptomycin, telavancin, and vancomycin in quantitative persister assays without daptomycin pre-exposure. After 3 days of <i>in vitro</i> daptomycin pre-exposure, the 24 h percent survival significantly increased compared with no pre-exposure in two isolates for the daptomycin group (100% vs 1% and 4.8% vs 0.2%, respectively). The 24 h percent persister was significantly higher in daptomycin compared with vancomycin and telavancin in four isolates. There was no significant increase in 24 h percent persister for telavancin and vancomycin after daptomycin pre-exposure. Daptomycin, telavancin, and vancomycin resulted in similar bacterial survival at 24 h at clinically achievable concentrations. Daptomycin pre-exposure did not alter persistence for telavancin and vancomycin. Considering differences in persister generation, further clinical studies are justified to help differentiate these anti-MRSA agents in the treatment of MRSA BJIs.IMPORTANCEBacterial persistence has been associated with relapsing infections, including infections caused by MRSA. Chronic infections, such as bone and joint infections, are associated with high rates of recurrence, and persistence may play a role. Although daptomycin, telavancin, and vancomycin are widely used for the treatment of bone and joint infections, their persister potential has not been assessed under the same experimental conditions. The present study sought to assess the <i>in vitro</i> persister potential of daptomycin, telavancin, and vancomycin against clinical MRSA from bone and joint infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0157625"},"PeriodicalIF":3.8,"publicationDate":"2025-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A retrospective evaluation of the BIOFIRE FilmArray Blood Culture Identification 2 panel for the detection of pathogenic yeasts.","authors":"Emily Puumala, Noelle H Adler, Sharon M Deml, Nancy L Wengenack","doi":"10.1128/spectrum.02258-25","DOIUrl":"https://doi.org/10.1128/spectrum.02258-25","url":null,"abstract":"<p><p>Bloodstream infections (BSIs) caused by opportunistic yeasts, namely those of the genus <i>Candida</i>, demonstrate strikingly high mortality rates and require early therapeutic intervention to optimize patient outcomes. Advancements in microbiological diagnosis of BSIs have introduced rapid molecular methods, including multiplex PCR panels, to detect common organisms directly from blood culture media. The BIOFIRE FilmArray Blood Culture Identification 2 (BCID2) assay is one such method and detects seven of the most common yeast species responsible for fungemia, enabling timelier therapeutic optimization by clinicians. Here, we evaluated the clinical performance of BCID2 for yeast identification from positive blood cultures between 2021 and 2025 at a tertiary medical center, compared to the reference standard method, which couples subculturing and diagnostic mass spectrometry. A total of 252 individual yeast identification events were confirmed using the reference method during our study period, 33 (13%) of which represent organisms that lack BCID2 PCR-based targets and 219 (87%) represent organisms targeted by this assay. Of the 219 identifications compatible with the BCID2 panel targets, 209 (95%) were correctly identified. Discordance between BCID2 and the reference method commonly stemmed from the inability of BCID2 to target all yeasts encountered clinically in blood culture, as well as its reduced accuracy in cultures where >1 yeast is present. Overall, these data suggest that the BCID2 assay is a rapid and accurate method to identify the most common organisms causing yeast BSI from blood culture; however, subculture-based reference techniques are important complementary tools in the clinical microbiology laboratory.IMPORTANCEInvasive fungal diseases, including bloodstream infections (BSIs) caused by yeasts, are increasing in prevalence alongside the growing global population of immunocompromised individuals. Prompt and targeted treatment is necessary for effective management of yeast BSI, and microbiological diagnostics play an important role in tailoring patient treatment. Rapid molecular assays that simultaneously detect multiple pathogens associated with a specific syndrome are attractive strategies to expedite pathogen identification. This includes the BIOFIRE FilmArray Blood Culture Identification 2 (BCID2) assay, which detects 33 organisms including 7 yeasts commonly associated with fungemia, directly from blood culture media. Its performance has been well established for the detection of bacteria and bacterial resistance markers from blood cultures. Here, we provide a yeast-specific snapshot into the microbiological performance of BCID2, highlighting its accuracy as well as limitations in detecting medically important yeasts compared to standard culture-based identification from a four-year specimen cohort collected in a tertiary care hospital.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0225825"},"PeriodicalIF":3.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346272","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic study of food waste anaerobic digestion.","authors":"Oluwatomisin A Akinsola, Samuel O Dahunsi, Ebenezer L Odekanle","doi":"10.1128/spectrum.02087-25","DOIUrl":"https://doi.org/10.1128/spectrum.02087-25","url":null,"abstract":"<p><p>This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as <i>Lactobacillus</i> and <i>Clostridia,</i> dominating the early stages of digestion, followed by methanogenic archaea like <i>Methanomicrobia</i> in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0208725"},"PeriodicalIF":3.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145346315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}