Microbiology spectrum最新文献

{"title":"Effects of different mechanisms on antimicrobial resistance in <i>Pseudomonas aeruginosa</i>: a strategic system for evaluating antibiotics against gram-negative bacteria.","authors":"Yu-Kuo Tsai, Jen-Chang Chang, Jia-Je Li, Esther Yip-Mei Liu, Chang-Phone Fung, Ching-Hsun Wang, Feng-Yee Chang, Jung-Chung Lin, L Kristopher Siu","doi":"10.1128/spectrum.02418-24","DOIUrl":"10.1128/spectrum.02418-24","url":null,"abstract":"<p><p>Our previous studies constructed a strategic system for testing antibiotics against specific resistance mechanisms using <i>Klebsiella pneumoniae</i> and <i>Acinetobacter baumannii</i>. However, it lacked resistance mechanisms specifically expressed only in <i>Pseudomonas</i> species. In this study, we constructed this system using <i>Pseudomonas aeruginosa</i>. In-frame deletion, site-directed mutagenesis, and plasmid transformation were used to generate genetically engineered strains with various resistance mechanisms from two fully susceptible <i>P. aeruginosa</i> strains. Antimicrobial susceptibility testing was used to test the efficacy of antibiotics against these strains in vitro. A total of 31 engineered strains with various antimicrobial resistance mechanisms from <i>P. aeruginosa</i> KPA888 and ATCC 27853 were constructed, and the same antibiotic resistance mechanism showed a similar effect on the MICs of the two strains. Compared to the parental strains, the engineered strains lacking porin OprD or lacking the regulator genes of efflux pumps all showed a ≥4-fold increase on the MICs of some of the 19 antibiotics tested. Mechanisms due to GyrA/ParC mutations and β-lactamases also contributed to their corresponding resistance as previously published. The strains constructed in this study possess well-defined resistance mechanisms and can be used to screen and evaluate the effectiveness of antibiotics against specific resistance mechanisms in <i>P. aeruginosa</i>. Building upon our previous studies on <i>K. pneumoniae</i> and <i>A. baumannii</i>, this strategic system, including a <i>P. aeruginosa</i> panel, has been expanded to cover almost all the important antibiotic resistance mechanisms of gram-negative bacteria that are in urgent need of new antibiotics.IMPORTANCEIn this study, an antibiotic assessment system for <i>P. aeruginosa</i> was developed, and the system can be expanded to include other key pathogens and resistance mechanisms. This system offers several benefits: (i) compound design: aid in the development of compounds that can bypass or counteract resistance mechanisms, leading to more effective treatments against specific resistant strains; (ii) combination therapies: facilitate the exploration of combination therapies, where multiple antibiotics may work synergistically to overcome resistance and enhance treatment efficacy; and (iii) targeted treatments: enable healthcare providers to prescribe more targeted treatments, reducing unnecessary antibiotic use and helping to slow the spread of antibiotic resistance. In summary, this system could streamline the development process, reduce costs, increase the success rate of new antibiotics, and help prevent and control antimicrobial resistance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0241824"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960109/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143556920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of <i>Streptococcus pneumoniae</i> isolates occurring in optochin-susceptible and optochin-resistant variants by analyzing whole-genome sequencing data.","authors":"Sandra Vohrnová, Jana Kozáková, Michal Honskus","doi":"10.1128/spectrum.01939-24","DOIUrl":"10.1128/spectrum.01939-24","url":null,"abstract":"<p><p>The paper presents the study of a set of isolates of <i>Streptococcus pneumoniae</i>, which comprised two heterogeneous subpopulations, one of which was susceptible and the other resistant to optochin. The aim of the study was to compare the results of serotyping, multilocus sequence typing (MLST), ribosomal multilocus sequence typing (rMLST), and variation analysis of these subpopulations and to investigate the genetic probable causes of optochin resistance. The strains studied were cultured from samples taken from patients with invasive pneumococcal disease in the Czech Republic in 2019 and 2020. A total of 10 studied pairs of isolates were subject to serotyping and whole-genome sequencing (WGS). None of the typing methods (serotyping, MLST, or rMLST) applied to pairs of optochin-susceptible and optochin-resistant isolates revealed differences in serotype, sequence type, or ribosomal sequence type. The WGS data analysis identified point mutations in ATP (adenosine triphosphate) synthase genes in 8 of the 10 optochin-resistant isolates. In seven optochin-resistant isolates, the mutation was found in the <i>atp</i>C gene and in one isolate in the <i>atp</i>A gene. One of the mutations in the <i>atp</i>C gene has not yet been published in the literature; it is a mutation at position 143T > C with an amino acid change of Val48Ala. In 8 out of the 10 optochin-resistant isolates, the possible genetic basis for resistance was identified, involving point mutations in the <i>atp</i>A and <i>atp</i>C genes. In the remaining two isolates, no clear genetic explanation for the optochin resistance in <i>S. pneumoniae</i> was found, based on current knowledge.</p><p><strong>Importance: </strong>Globally, among the most fundamental tests used for the identification of <i>Streptococcus pneumoniae</i> isolates is determining susceptibility to optochin. In the last 2 decades, optochin-resistant strains have been frequently reported in the literature, which can lead to the misidentification of <i>S. pneumoniae</i>. This study compares whole-genome sequencing data of optochin-susceptible and optochin-resistant subpopulations of <i>S. pneumoniae</i> isolates and investigates the genetic probable causes of resistance in the genomes of optochin-resistant subpopulations.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0193924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960131/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A streamlined procedure for advancing the detection and isolation of <i>Listeria monocytogenes</i> from artificially contaminated ground beef in a single working day.","authors":"Min Lin, Hanhong Dan, Jiewen Guan","doi":"10.1128/spectrum.01577-24","DOIUrl":"10.1128/spectrum.01577-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Listeria monocytogenes&lt;/i&gt;, a rod-shaped Gram-positive bacterium widely distributed in nature, can contaminate foods and represents a foodborne pathogen of public health significance causing a high mortality rate of 20%-30%. Rapid and reliable identification of foods and food-processing environments contaminated with &lt;i&gt;L. monocytogenes&lt;/i&gt; is a crucial step in implementing effective intervention strategies to ensure food safety and limit the transmission of bacteria to humans. This study designed and refined a practical workflow to streamline and accelerate the detection of a low level of &lt;i&gt;L. monocytogenes&lt;/i&gt; present in ground beef. The workflow coupled an abbreviated 5 h culture enrichment in PALCAM liquid medium with physical separation (filtration and centrifugation) to preprocess enrichment samples. Specific capture was achieved using magnetic separation with a bacteriophage endolysin-derived cell wall-binding domain in a Hyglos &lt;i&gt;Listeria&lt;/i&gt; capture kit. Molecular detection was performed using a MicroSEQ &lt;i&gt;L. monocytogenes&lt;/i&gt; RTi-PCR detection kit combined with a nested PCR strategy. Preprocessing of enrichment culture samples using a multi-stage filtration system constructed for the study or commercially available BagFilter Pull-up filter bags, in conjunction with centrifugation, enabled the recovery of ~30 colony-forming units (CFUs) from the enrichment culture of a 25 g ground beef sample artificially contaminated with 1 CFU of &lt;i&gt;L. monocytogenes&lt;/i&gt;. Integration of magnetic separation into the workflow for capturing &lt;i&gt;L. monocytogenes&lt;/i&gt; cells specifically from preprocessed samples and further cleaning up the samples yielded bacterial counts similar to those obtained by direct plating of preprocessed samples. The RTi-PCR-based molecular detection method integrated into the workflow was capable of detecting pure cultures of &lt;i&gt;L. monocytogenes&lt;/i&gt; as low as 12.5 CFUs. Evaluation of the workflow using artificially ground beef demonstrated the consistent detection of &lt;i&gt;L. monocytogenes&lt;/i&gt; within an 8 h workday in a 25 g sample unit containing the cell count as low as 2 CFU following a 5 h culture enrichment.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Consuming foods contaminated with the bacterial pathogen &lt;i&gt;Listeria monocytogenes&lt;/i&gt; can lead to the development of human listeriosis, a severe and life-threatening foodborne illness. Timely detection of &lt;i&gt;L. monocytogenes&lt;/i&gt; present at a low level in foods and food processing environments is a necessary measure to prevent the spread of the &lt;i&gt;Listeria&lt;/i&gt;-associated illness. This study designed and evaluated a multi-step workflow for testing &lt;i&gt;L. monocytogenes&lt;/i&gt; in artificially contaminated food samples. The workflow was composed of a short 5 h culture enrichment, filtration-based sample preprocessing, magnetic separation, a single-tube nested RTi-PCR, and culture plating. It allowed &lt;i&gt;L. monocytogenes&lt;/i&gt; to be detected within 8 h from a 25 g ground beef sample containin","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0157724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Optimizing antibiotic use in MSSA bacteremia: a stewardship-focused approach.","authors":"Victoria L Campodónico","doi":"10.1128/spectrum.03163-24","DOIUrl":"10.1128/spectrum.03163-24","url":null,"abstract":"<p><p>Antimicrobial stewardship is essential for optimizing therapy in bloodstream infections. Methicillin-susceptible <i>Staphylococcus aureus</i> (MSSA) bacteremia requires prompt beta-lactam treatment, and delays in transitioning from empirical anti-MRSA therapy can result in adverse outcomes. Rapid diagnostics like the BioFire Blood Culture Identification (BCID) PCR panel, combined with stewardship interventions, significantly improve care by reducing unnecessary broad-spectrum antimicrobial use. A study by Yetukuri et al. demonstrated that integrating BCID with stewardship efforts reduced time to optimal therapy by 20 h (49 vs 29.1 h, <i>P</i> < 0.001) and shortened both bacteremia duration and anti-MRSA therapy without affecting mortality or hospital stay. These findings emphasize that stewardship programs, including real-time reviews and prescriptive guidance, are critical for translating rapid diagnostic results into timely, targeted treatment. Leveraging stewardship with advanced diagnostics offers a strategic approach to enhancing outcomes and combating antimicrobial resistance.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0316324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960132/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prospective evaluation of real-world performance and clinical impact of the Biofire FilmArray joint infection panel.","authors":"Benjamin Berinson, Konstantin Tanida, Laura Spenke, Lukas Krivec, Johannes Keller, Tim Rolvien, Martin Christner, Marc Lütgehetmann, Martin Aepfelbacher, Till Orla Klatte, Holger Rohde","doi":"10.1128/spectrum.02239-24","DOIUrl":"10.1128/spectrum.02239-24","url":null,"abstract":"<p><p>Limitations of culture-based diagnostic approaches in pathogen detection in joint infections (JI) can be overcome by amplification-based, molecular assays. Recently, a syndromic panel PCR (spPCR) assay (Biofire JI panel; BJA) was approved for pathogen identification from synovial fluid (SF). Here, the performance and the clinical impact of the BJA were assessed in comparison to standard of care diagnostics in a prospective cohort of patients presenting with symptoms consistent with JI. One hundred sixty-five synovial fluids underwent analysis using the BJA. The results were compared with culture-based diagnostics. Discrepant results were re-analyzed using species-specific PCRs or 16S-rDNA sequencing. Clinical data from patients were collected to evaluate the impact on patient management. Twenty-seven of 165 (16.3%) synovial fluid cultures grew bacterial pathogens. In 24/27 cases, the BJA results were concordant. In one case, the cultured pathogen was missed, but three additional pathogens were identified. In 11 culture-negative cases, BJA identified a pathogen. Mean turnaround time in culture-positive samples was 14:11 h and 35:17 h in BJA and culture, respectively. In 11 cases, antibiotic therapy was optimized, based on BJA results. This study demonstrates high sensitivity and specificity (96.3% and 97.8%, respectively) of BJA, as well as a shorter turnaround time than culture-based techniques (21 h faster). Based on analysis of clinical data, antibiotic therapy was optimized due to BJA results in 11 cases. Care must be taken, as important pathogens in prosthetic JI are not included in the panel, restricting its value here.IMPORTANCEPathogen detection is critical for targeted management of joint infections; however, cultural detection of pathogens can be challenging. The Biofire Joint Infection Assay (BJA) is a syndromic panel PCR test that allows culture-independent detection of 31 pathogens. The diagnostic performance and clinical impact were evaluated in a cohort of 160 patients with native and prosthetic joint infections. BJA detected concordant pathogens in 24 of 27 culture-positive cases and enabled the detection of additional pathogens in 11 patients. The time to result was significantly shorter than with standard culture-based diagnostics (14 vs 35 h), and BJA allowed optimization of therapy in 11 patients. The data show that BJA is a relevant addition to the diagnostic options for joint infections. Limitations result from incomplete detection of relevant pathogens, especially in prosthetic joint infections. The use of BJA in daily practice must therefore be accompanied by diagnostic stewardship measures.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0223924"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reevaluation of the gastrointestinal methanogenic archaeome in multiple sclerosis and its association with treatment.","authors":"Pei Yee Woh, Yehao Chen, Christina Kumpitsch, Rokhsareh Mohammadzadeh, Laura Schmidt, Christine Moissl-Eichinger","doi":"10.1128/spectrum.02183-24","DOIUrl":"10.1128/spectrum.02183-24","url":null,"abstract":"<p><p>The role of the gut archaeal microbiome (archaeome) in health and disease remains poorly understood. Methanogenic archaea have been linked to multiple sclerosis (MS), but prior studies were limited by small cohorts and inconsistent methodologies. To address this, we re-evaluated the association between methanogenic archaea and MS using metagenomic data from the International Multiple Sclerosis Microbiome Study. We analyzed gut microbiome profiles from 115 MS patients and 115 healthy household controls across Buenos Aires (27.8%), Edinburgh (33.9%), New York (10.4%), and San Francisco (27.8%). Metagenomic sequences were taxonomically classified using kraken2/bracken and a curated profiling database to detect archaea, specifically <i>Methanobrevibacter</i> species. Most MS patients were female (80/115), aged 25-72 years (median: 44.5), and 70% were undergoing treatment, including dimethyl fumarate (<i>n</i> = 21), fingolimod (<i>n</i> = 20), glatiramer acetate (<i>n</i> = 14), interferon (<i>n</i> = 18), natalizumab (<i>n</i> = 6), or ocrelizumab/rituximab (<i>n</i> = 1). We found no significant differences in overall archaeome profiles between MS patients and controls. However, treated MS patients exhibited higher abundances of <i>Methanobrevibacter smithii</i> and <i>M.</i> sp900766745 compared to untreated patients. Notably, <i>M.</i> sp900766745 abundance correlated with lower disease severity scores in treated patients. Our results suggest that gut methanogens are not directly associated with MS onset or progression but may reflect microbiome health during treatment. These findings highlight potential roles for <i>M. smithii</i> and <i>M.</i> sp900766745 in modulating treatment outcomes, warranting further investigation into their relevance to gut microbiome function and MS management.IMPORTANCEMultiple sclerosis (MS) is a chronic neuroinflammatory disease affecting the central nervous system, with approximately 2.8 million people diagnosed worldwide, mainly young adults aged 20-30 years. While recent studies have focused on bacterial changes in the MS microbiome, the role of gut archaea has been less explored. Previous research suggested a potential link between methanogenic archaea and MS disease status, but these findings remained inconclusive. Our study addresses this gap by investigating the gut archaeal composition in MS patients and examining how it changes in response to treatment. By focusing on methanogens, we aim to uncover novel insights into their role in MS, potentially revealing new biomarkers or therapeutic targets. This research is crucial for enhancing our understanding of the gut microbiome's impact on MS and improving patient management.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0218324"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974365/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Clostridioides</i> (<i>Clostridium</i>) <i>difficile</i> infection in hospitalized adult patients in Cambodia.","authors":"Lengsea Eng, Deirdre A Collins, Kefyalew Addis Alene, Sotharith Bory, Youdaline Theng, Pisey Vann, Sreyhuoch Meng, Setha Limsreng, Archie C A Clements, Thomas V Riley","doi":"10.1128/spectrum.02747-24","DOIUrl":"10.1128/spectrum.02747-24","url":null,"abstract":"<p><p>Despite high levels of global concern, little is known about the epidemiology of <i>Clostridioides</i> (<i>Clostridium</i>) <i>difficile</i> infection (CDI) in Cambodia. This study aimed to identify the prevalence and risk factors for CDI, and molecular types of <i>C. difficile</i> in hospitalized adults at Calmette Hospital, Phnom Penh, Cambodia. Stool samples were collected from 263 hospitalized adults between June and September 2022 and tested for <i>C. difficile</i> using direct and enrichment cultures. PCR toxin genes <i>tcdA, tcdB, cdtA</i>, and <i>cdtB,</i> and amplification of the 16s-23s rRNA intergenic spacer region for ribotyping, were performed on all <i>C. difficile</i> isolates. <i>C. difficile</i> was isolated from 24% (63/263) of samples, and most isolates were non-toxigenic (67%, 42/63). The five most predominant toxigenic <i>C. difficile</i> ribotypes (RTs) were RTs 046 (8%, 5/63), 017 (6%, 4/63), 056 (5%, 3/63), 014/020 (5%, 3/63), and 012 (3%, 2/63), and prominent non-toxigenic RTs were QX011 (14%, 9/63), 010 (8%, 5/63), 009 (3%, 2/63), QX021 (3%, 2/63), and QX002 (3%, 2/63). Risk factors significantly associated with CDI included diabetes (odds ratio [OR] = 2.48, 95% confidence interval [CI]: 1.16-5.30) and hospitalization >24 h within the last 3 months before testing (OR = 3.89, 95% CI: 1.79-8.43). It was concluded that most participants from whom <i>C. difficile</i> was isolated were colonized only; however, a high prevalence of asymptomatic carriage could contribute to silent transmission in healthcare settings and communities. Genotypic identification of local <i>C. difficile</i> strains is necessary for a better understanding of the epidemiology of CDI and the importance of <i>C. difficile</i>.</p><p><strong>Importance: </strong><i>Clostridioides difficile</i> is a significant cause of diarrhea worldwide, initially as a hospital-acquired infection and, more recently, as a community-associated infection. Risk factors for hospital-acquired <i>C. difficile</i> infection include antimicrobial consumption, extended hospitalization, age ≥ 65 years, and proton pump inhibitor treatment. While much is known about <i>C. difficile</i> in high-income countries, little is known and there has been less interest in this infection in Asia due to the lack of data. Thus, investigating the prevalence and risk factors for <i>C. difficile</i> and characterizing <i>C. difficile</i> strains from hospitalized adults is necessary in Asian countries such as Cambodia. Diabetes and hospitalization >24 h within the last 3 months were identified as risk factors for <i>C. difficile</i> colonization/infection. The high prevalence of non-toxigenic strains and asymptomatic carriage of <i>C. difficile</i> in this country were notable. Further studies are warranted to gain better insights into this infection in Cambodia.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0274724"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Performance of ddPCR-GNB for microbial diagnosis of suspected bloodstream infection due to the four most common gram-negative bacteria: a prospective, multicenter study.","authors":"Shan-Shan Weng, Ling Lin, Jian-Feng Xie, Bang-Chuan Hu, Xue-Qing Ma, Jiang Xia, Yan Jiang, Hua Zhou, Xiao-Yan Wu, Yu-Hong Jin, Guo-Qiu Wu, Yi Yang, Ren-Hua Sun, Yun-Song Yu, Dong-Dong Zhao","doi":"10.1128/spectrum.01015-24","DOIUrl":"10.1128/spectrum.01015-24","url":null,"abstract":"<p><p>We aimed to validate the performance of ddPCR-GNB, a plasma droplet digital PCR panel targeting the four most common gram-negative bacteria, for patients with suspected bloodstream infection (BSI). Patients suspected of having BSIs were prospectively enrolled. The results of blood culture and ddPCR-GNB were compared, and cases with discordant results were arbitrated on the basis of additional microbiological results and clinical evidence. A total of 1,041 patients were enrolled. Blood culture and ddPCR-GNB results were positive for targeted bacteria in 6.3% and 31.7% of patients, respectively. The overall per-patient sensitivity and specificity of ddPCR-GNB for proven BSIs were 98.5% (95% CI, 91.9% to 99.9%) and 72.8% (95% CI, 69.9% to 75.5%), respectively; the negative predictive value was 99.9% (95% CI, 99.2% to 100%). The discordant results included 265 cases (25.5%) with negative companion blood culture results but positive ddPCR-GNB results and one case vice versa. A total of 23.7% of the cases were attributed to probable (<i>n</i> = 126) or possible (<i>n</i> = 121) BSIs. If both probable and possible BSIs were assumed to be true positives, the per-patient specificity of ddPCR-GNB would be 97.5%. The ddPCR-GNB panel demonstrated excellent microbial diagnostic performance in identifying targeted bacteria for patients with suspected BSI.</p><p><strong>Importance: </strong>This is the first multicentral study to validate the clinical performance of ddPCR in etiological diagnosis of bloodstream infection. The results showed that ddPCR has high sensitivity and increased detection rate compared with blood culture. The study proved the potential of the ddPCR method in microbial diagnoses.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0101524"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960046/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Activation of gut FXR improves the metabolism of bile acids, intestinal barrier, and microbiota under cholestatic condition caused by GCDCA in mice.","authors":"Xing-Ming Xie, Bang-Yan Zhang, Shu Feng, Zi-Jun Fan, Guo-Ying Wang","doi":"10.1128/spectrum.03150-24","DOIUrl":"10.1128/spectrum.03150-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Abnormal bile acid (BA) metabolism is involved in liver fibrosis. In a previous study, we discovered that the hydrophobic BA glycochenodeoxycholate (GCDCA) induced liver fibrosis and that GW4064, an agonist of farnesoid X receptor (FXR), alleviated liver fibrosis caused by GCDCA. However, the impacts of GCDCA on liver BAs, gut BAs, the intestinal barrier, and the gut microbiota are unclear, and obtaining this information would provide additional information into the role of GCDCA in the development of liver fibrosis. In the present study, ultra-performance liquid chromatography‒tandem mass spectrometry revealed that mice administered GCDCA by gavage had higher levels of total and primary liver BAs than those in the control group, and a significant reduction in primary liver BAs was observed in the GCDCA + GW4064 group compared with those in the GCDCA group. Compared with those in the control group, the mice administered GCDCA by gavage had greater levels of total and primary BAs in the gut, especially T-alpha-MCA and T-beta-MCA, and no significant differences in the terminal ileum were observed between the GCDCA and GCDCA + GW4064 groups. Immunohistochemistry indicated that GCDCA administration inhibited gut FXR and FGF15 expression, whereas GW4064 activated gut FXR and promoted FGF15 expression. Moreover, immunohistochemistry revealed that GCDCA administration decreased mucin2, claudin-1, occludin, and ZO-1 expression, whereas GW4064 restored their expression. 16S rDNA sequencing revealed that the alpha diversity of the microbiota did not significantly differ among the three groups, but differences in the beta diversity of the microbiota were observed among the three groups. At the phylum level, GCDCA significantly disturbed the gut microbiota, as indicated by reductions in Desulfobacterota, Bacteroidota, and Actinobacteria in the GCDCA group compared with those in the control group. However, significantly increased abundances of Proteobacteria, Cyanobacteria, and Patescibacteria were noted in the GCDCA group compared with the control group. GW4064 administration significantly improved the microbiota structure at the phylum level. The efficacy of GW4064 was also observed at the genus level. Correlation analyses revealed fewer relationships between the gut microbiota and gut BAs, whereas the gut microbiota was more closely related to liver BAs in the GCDCA and GW4064 intervention groups. Together, GCDCA induced cholestasis and disturbed BA metabolism in the gut and liver, as well as the intestinal barrier and structure of the gut microbiota. Activation of gut FXR improved intestinal barrier injury and alleviated BA metabolism dysfunction and dysbacteriosis caused by GCDCA under cholestatic conditions.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Glycochenodeoxycholate (GCDCA) is a hydrophobic bile acid (BA) in humans and is highly increased in the serum and stool of liver fibrosis patients. However, the effects of GCDCA were not comprehensively inves","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0315024"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Correction for Snoeyenbos-West et al., \"Cultivating efficiency: high-throughput growth analysis of anaerobic bacteria in compact microplate readers\".","authors":"Oona L O Snoeyenbos-West, Christina R Guerrero, Makaela Valencia, Paul Carini","doi":"10.1128/spectrum.03322-24","DOIUrl":"10.1128/spectrum.03322-24","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0332224"},"PeriodicalIF":3.7,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11960441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}