Microbiology spectrum最新文献

{"title":"Performance of a hybrid capture-based target enrichment next-generation sequencing for the identification of respiratory pathogens and resistance-associated genes in patients with severe pneumonia.","authors":"Wei-Yu Hsu, Ting-Wei Kao, Hsin-Ching Cho, Sheng-Yuan Ruan, Tai-Fen Lee, Yu-Tsung Huang, Jung-Yien Chien","doi":"10.1128/spectrum.02130-24","DOIUrl":"10.1128/spectrum.02130-24","url":null,"abstract":"<p><p>Severe pneumonia remains the leading infectious cause of death worldwide. The time-consuming nature and suboptimal sensitivity of sputum cultures hamper prompt pathogen detection for tailored treatments. Advanced techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer rapid genetic pathogen detection and identification of antimicrobial resistance (AMR) genes. However, the performance of hybrid capture-based target enrichment NGS, e<i>.</i>g., Respiratory Pathogen ID/AMR Enrichment Panel (RPIP), for pathogen detection in patients with severe pneumonia remains uncertain. A prospective study involving adults with severe pneumonia was conducted. Respiratory samples from the lower respiratory tract were collected via bronchoalveolar lavage, bronchial washing, or endotracheal tube suction. The performance of RPIP in pathogen and AMR-associated gene detection was compared to that of conventional culture methods and the multiplex PCR-based FilmArray Pneumonia Panel (FilmArray-PN). A total of 83 subjects were enrolled. The most prevalent pathogens detected by RPIP were <i>Rothia mucilaginosa</i>, <i>Stenotrophomonas maltophilia</i>, <i>Pseudomonas aeruginosa;</i> herpes simplex virus-1, cytomegalovirus, and Epstein-Barr virus, and <i>Pneumocystis jirovecii</i>. Overall, the positive and negative agreement rates for bacterial detection were 63.6% and 97.5% between RPIP and culture methods, respectively, and 55.8% and 99.4% between FilmArray-PN and culture methods, respectively. Compared to FilmArray-PN, RPIP exhibited significantly better detection rates for bacteria (<i>P</i> = 0.029), viruses (<i>P</i> < 0.001), and fungi (<i>P</i> < 0.001) and identified additional <i>bla</i><sub>OXA</sub>, <i>bla</i><sub>CMY</sub> as extended-spectrum β-lactamase genes and <i>bla</i><sub>OXA</sub>, <i>bla</i><sub>SHV</sub> as carbapenemase genes. In conclusion, RPIP can sensitively profile respiratory pathogens and is a promising tool for detecting multiple microorganisms and AMR-associated genes in patients with severe pneumonia.IMPORTANCESensitive pathogen detection is pivotal for timely treatment by tailoring adequate antimicrobial agents. Unlike conventional phenotypic approach, novel measures using molecular interrogation appear promising. This study aimed to elucidate the efficacy of a hybrid capture-based target enrichment next-generation sequencing technique (Respiratory Pathogen ID/AMR Enrichment Panel, RPIP) as exemplified in a cohort with severe pneumonia. Pathogen landscape in the population was illustrated by these three methodologies. As compared with multiplex polymerase chain reaction-based FilmArray Pneumonia Panel and conventional culture, RPIP demonstrated significantly improved sensitivity in identifying bacteria, viruses, and fungi. The RPIP also exhibited better performance in identifying different pathogens in patients co-infected with multiple microorganisms. Additionally, the genotypes contributing to","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0213024"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668401","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":"Clinical laboratory evaluation of the Hologic Panther Aptima BV and CV/TV assays for the diagnosis of vaginitis in Dunedin, Aotearoa New Zealand.","authors":"Juliet Elvy, Katelyn Carter, Jenna Paterson, Megan Smith, Gayleen Parslow, James E Ussher","doi":"10.1128/spectrum.01274-24","DOIUrl":"10.1128/spectrum.01274-24","url":null,"abstract":"<p><p>Vaginitis presentations are common, but traditional diagnostic methods are imperfect. Molecular methods for bacterial vaginosis (BV) and vulvovaginal candidiasis (CV) are increasingly available but not commonly utilized in Aotearoa New Zealand. We evaluated the Hologic Aptima BV and CV/<i>Trichomonas vaginalis</i> (TV) assays against our current methods (Gram stain, yeast culture, and Hologic Aptima TV assay) and performed a retrospective BV clinical audit. The BV Aptima assay performed well with high sensitivity (97.5%) and specificity (96.3%) when the indeterminate BV category was excluded. BV indeterminate samples were almost evenly split between positive and negative results when tested on the Aptima BV assay. BV Gram stain interpretation was error prone, with 20% of samples discordant on duplicate examination. Although the Aptima CV assay was highly sensitive, it lacked specificity compared with Gram stain (83.5%) but was similar to culture (91.2%). Our BV clinical audit showed that patients with a BV indeterminate result were less likely to be treated for BV than those with a positive result, meaning more women may be treated for BV if this assay were implemented. Overall, implementation may improve laboratory workflow and consistency of reporting, but cost may be a barrier. The clinical impact of changing methods needs to be considered.IMPORTANCEIn this paper, we evaluate the performance of the Aptima molecular assays against current Gram stain and culture methods, as well as a clinical audit to determine the potential clinical impact of implementation. Although molecular methods are increasingly used in other countries, New Zealand has not yet adopted this approach. Importantly, we found Gram stain for bacterial vaginosis (BV) to be error prone, with 20% of Gram stain results discordant on repeat examination. We show the potential for molecular methods to increase BV diagnoses and improve reproducibility and consistency of reporting which, according to our clinical audit results, would lead to more women being treated for this dysbiosis condition overall.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0127424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668384","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":"Etoposide targets 2A protease to inhibit enterovirus 71 replication.","authors":"Qinqin Liang, Sai Shi, Qingjie Zhang, Yaxin Wang, Sheng Ye, Binghong Xu","doi":"10.1128/spectrum.02200-24","DOIUrl":"https://doi.org/10.1128/spectrum.02200-24","url":null,"abstract":"<p><p>Enterovirus 71 (EV71) is a major pathogen that causes hand, foot, and mouth disease (HFMD) in infants and children. Notably, no clinically approved drugs specifically target EV71. The EV71 2A protease (2A^pro), a cysteine protease produced by the virus, is essential for the virus' replication and has a significant impact on the functioning of host cells. Thus, it presents a valuable target for the discovery of antiviral medications. In this study, based on the monomers and their derivatives in the Library of Traditional Chinese Medicine (TCM), we performed virtual screening and biological experiments. We identified a derivative of a traditional herbal monomer, Etoposide, commonly isolated from the roots and rhizomes of <i>Podophyllum</i> spp. Etoposide inhibited replication of EV71 A, B, C, and CVA16 viruses in a concentration-dependent manner in a variety of cell lines with minimal cytotoxicity. Furthermore, both molecular dynamics simulations and site-directed mutagenesis assays revealed that Etoposide inhibited the activity of the EV71 2A protease by mainly binding to two residues, Y89 and P107. The findings indicate that Etoposide serves as a promising inhibitor of the EV71 2A^pro, demonstrating strong antiviral properties and positioning itself as a formidable candidate for clinical trials against EV71.IMPORTANCEWe first used a drug screening approach focused on monomeric compounds and their derivatives from traditional Chinese medicine to identify an EV71 2A^pro inhibitor-Etoposide. We then performed biological experiments to validate that Etoposide suppresses the replication of the EV71 virus in a concentration-dependent manner with minimal cytotoxicity to various cell lines. Remarkably, it shows inhibitory activity against EV71 A, B, C, and CVA16, suggesting that Etoposide may be a potential broad-spectrum inhibitor. We revealed a novel mechanism that Etoposide inhibits EV71 proliferation by targeting 2A^pro, and the interactions with Y89 and P107 are of great importance. The findings suggest that Etoposide serves as a promising inhibitor of EV71 2A^pro, demonstrating significant antiviral properties. It stands out as a strong candidate for broad-spectrum applications in clinical research.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0220024"},"PeriodicalIF":3.7,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647898","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":"Characteristic alterations of gut microbiota and serum metabolites in patients with chronic tinnitus: a multi-omics analysis.","authors":"Jiang Wang, Jia-Hui Xiang, Xu-Yuan Peng, Min Liu, Le-Jia Sun, Min Zhang, Li-Yuan Zhang, Zhi-Bin Chen, Zheng-Quan Tang, Lei Cheng","doi":"10.1128/spectrum.01878-24","DOIUrl":"10.1128/spectrum.01878-24","url":null,"abstract":"<p><p>Chronic tinnitus is a central nervous system disorder. Currently, the effects of gut microbiota on tinnitus remain unexplored. To explore the connection between gut microbiota and tinnitus, we conducted 16S rRNA sequencing of fecal microbiota and serum metabolomic analysis in a cohort of 70 patients with tinnitus and 30 healthy volunteers. We used the weighted gene co-expression network method to analyze the relationship between the gut microbiota and the serum metabolites. The random forest technique was utilized to select metabolites and gut taxa to construct predictive models. A pronounced gut dysbiosis in the tinnitus group, characterized by reduced bacterial diversity, an increased Firmicutes/Bacteroidetes ratio, and some opportunistic bacteria including <i>Aeromonas</i> and <i>Acinetobacter</i> were enriched. In contrast, some beneficial gut probiotics decreased, including Lactobacillales and Lactobacillaceae. In serum metabolomic analysis, serum metabolic disturbances in tinnitus patients and these differential metabolites were enriched in pathways of neuroinflammation, neurotransmitter activity, and synaptic function. The predictive models exhibited great diagnostic performance, achieving 0.94 (95% CI: 0.85-0.98) and 0.96 (95% CI: 0.86-0.99) in the test set. Our study suggests that changes in gut microbiota could potentially influence the occurrence and chronicity of tinnitus, and exert regulatory effects through changes in serum metabolites. Overall, this research provides new perceptions into the potential role of gut microbiota and serum metabolite in the pathogenesis of tinnitus, and proposes the \"gut-brain-ear\" concept as a pathomechanism underlying tinnitus, with significant clinical diagnostic implications and therapeutic potential.IMPORTANCETinnitus affects millions of people worldwide. Severe cases may lead to sleep disorders, anxiety, and depression, subsequently impacting patients' lives and increasing societal healthcare expenditures. However, tinnitus mechanisms are poorly understood, and effective therapeutic interventions are currently lacking. We discovered the gut microbiota and serum metabolomics changes in patients with tinnitus, and provided the potential pathological mechanisms of dysregulated gut flora in chronic tinnitus. We proposed the innovative concept of the \"gut-brain-ear axis,\" which underscores the exploration of gut microbiota impact on susceptibility to chronic tinnitus through serum metabolic profile modulation. We also reveal novel biomarkers associated with chronic tinnitus, offering a new conceptual framework for further investigations into the susceptibility of patients, potential treatment targets for tinnitus, and assessing patient prognosis. Subsequently, gut microbiota and serum metabolites can be used as molecular markers to assess the susceptibility and prognosis of tinnitus.Furthermore, fecal transplantation may be used to treat tinnitus.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0187824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647881","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":"Transcriptional profiles of <i>Microcystis</i> reveal gene expression shifts that promote bloom persistence in <i>in situ</i> mesocosms.","authors":"Lauren E Krausfeldt, Paisley S Samuel, Robert P Smith, Hidetoshi Urakawa, Barry H Rosen, Rita R Colwell, Jose V Lopez","doi":"10.1128/spectrum.01369-24","DOIUrl":"https://doi.org/10.1128/spectrum.01369-24","url":null,"abstract":"<p><p>Harmful algal blooms caused by cyanobacteria threaten aquatic ecosystems, the economy, and human health. Previous work has tried to identify the mechanisms that allow blooms to form, focusing on the role of nutrients. However, little is known about how introduced nutrients influence gene expression <i>in situ</i>. To address this knowledge gap, we used <i>in situ</i> mesocosms initiated with water experiencing a <i>Microcystis</i> bloom. We added pulses of nutrients that are commonly associated with anthropogenic sources to the mesocosms for 72 hours and collected samples for metatranscriptomics to examine how the physiological function of <i>Microcystis</i> and bloom status changed. The addition of nitrogen (N) as urea, but not the addition of PO₄, resulted in conspicuous bloom persistence for at least 9 days after the final introduction of nutrients. The addition of urea initially resulted in the upregulation of photosynthesis machinery, as well as phosphate, carbon, and N transport and metabolism. Once <i>Microcystis</i> presumably became N-replete, upregulation of amino acid metabolism, microcystin biosynthesis, and other processes associated with biomass generation occurred. These capacities coincided with the upregulation of toxin-antitoxin systems, CRISPR-<i>cas</i> genes, and transposases suggesting that phage defense and genome rearrangement are critical in bloom persistence. Overall, our results show the stepwise transcriptional response of a <i>Microcystis</i> bloom to the introduction of nutrients, specifically urea, as it is sustained in a natural setting. The transcriptomic shifts observed herein may serve as markers of the longevity of blooms while providing insight into why <i>Microcystis</i> blooms over other cyanobacteria.IMPORTANCEHarmful algal blooms represent a threat to human health and ecosystems. Understanding why blooms persist may help us develop warning indicators of bloom persistence and create novel mitigation strategies. Using mesocosm experiments initiated with water with an active bloom, we measured the stepwise transcription changes of the toxin-producing cyanobacterium <i>Microcystis</i> in response to the addition of nutrients that are important in causing blooms. We found that nitrogen (N), but not phosphorus, promoted bloom longevity. The initial introduction of N resulted in the upregulation of genes involved in photosynthesis and N import. At later times in the bloom, upregulation of genes involved in biomass generation, phage protection, genomic rearrangement, and toxin production was observed. Our results suggest that <i>Microcystis</i> first fulfills nutritional requirements before investing energy in pathways associated with growth and protection against competitors, which allowed bloom persistence more than a week after the final addition of nutrients.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0136924"},"PeriodicalIF":3.7,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142648026","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":"High level non-carbapenemase carbapenem resistance by overlaying mutations of <i>mexR</i>, <i>oprD,</i> and <i>ftsI</i> in <i>Pseudomonas aeruginosa</i>.","authors":"Yan Yang, Xue Li, Lang Sun, Xiu-Kun Wang, You-Wen Zhang, Jing Pang, Guo-Qing Li, Xin-Xin Hu, Tong-Ying Nie, Xin-Yi Yang, Jian-Hua Liu, Gerrit Brandis, Xue-Fu You, Cong-Ran Li","doi":"10.1128/spectrum.01398-24","DOIUrl":"https://doi.org/10.1128/spectrum.01398-24","url":null,"abstract":"<p><p>Carbapenem-resistant <i>Pseudomonas aeruginosa</i> (CRPA) is a global threat, but the mechanism of non-carbapenemase carbapenem resistance is still unclear. In the current study, we investigated the contributions of point mutations in <i>mexR</i>, <i>oprD</i>, and <i>ftsI</i> to carbapenem resistance in <i>P. aeruginosa</i> during <i>in vivo</i> evolution studies with consecutive clinical isolates. Real-time qPCR and Electrophoretic Mobility Shift Assay demonstrated that MexR (Gln55Pro) mutation increased MexAB efflux pump genes expression by altering MexR's binding capacity, leading to a four- to eight-fold increase in meropenem MIC in the Pae d1 Green ∆<i>mexR</i> and PAO1∆<i>mexR</i> mutants. The OprD (Trp415*) truncation affected porin structure, and the constructed mutant Pae d1 Green <i>oprD</i> Trp415* increased meropenem MIC by 16-fold (from 0.25 to 4 µg/mL). The contribution of <i>ftsI</i> mutation to meropenem resistance was confirmed by clinical linkage analysis and was estimated to cause a two-fold increase in meropenem MIC by comparing the resistant clinical isolate with the Pae d1 Green <i>oprD</i> Trp415*∆<i>mexR</i> double mutant. The study found that the oprD Trp415* allele alone accounts for the imipenem MIC in clinical isolates, while the ∆<i>mexR</i> and <i>ftsI</i> Arg504Cys alleles do not contribute to imipenem resistance. In conclusion, we identified and explored the contributions of <i>mexR</i>, <i>oprD,</i> and <i>ftsI</i> mutations to high level non-carbapenemase carbapenem resistance in <i>P. aeruginosa</i>. These findings highlight the interplay of different mutations in causing non-carbapenemase carbapenem-resistance in <i>P. aeruginosa</i>.</p><p><strong>Importance: </strong>The emergence of carbapenem-resistant <i>Pseudomonas aeruginosa</i> (CRPA) poses a significant global health threat, complicating treatment options for infections caused by this pathogen. Understanding the mechanisms behind non-carbapenemase carbapenem resistance is critical for developing effective therapeutic strategies. This study provides crucial insights into how specific point mutations in key genes-<i>mexR</i>, <i>oprD</i>, and <i>ftsI</i>-contribute to carbapenem resistance, particularly the MexR (Gln55Pro) mutation's effect on efflux pump expression and the OprD (Trp415*) truncation's impact on porin structure. The findings elucidate the complex interplay of these mutations, highlighting their roles in conferring high-level resistance, and underscore the imperative for continued research to inform therapeutic strategies against CRPA infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0139824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647920","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":"Expression of Concern for Nazir et al., \"Characterization, taxonomic classification, and genomic analysis of two newly isolated bacteriophages with potential to infect <i>Escherichia coli</i>\".","authors":"","doi":"10.1128/spectrum.02252-24","DOIUrl":"https://doi.org/10.1128/spectrum.02252-24","url":null,"abstract":"","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0225224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142647918","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":"Discovery and characterization of complete genomes of 38 head-tailed proviruses in four predominant phyla of archaea.","authors":"Tianqi Xu, Yimin Ni, Hailing Li, Shuang Wu, Shuling Yan, Lanming Chen, Yongxin Yu, Yongjie Wang","doi":"10.1128/spectrum.00492-24","DOIUrl":"https://doi.org/10.1128/spectrum.00492-24","url":null,"abstract":"<p><p>Archaea play a significant role in natural ecosystems and the human body. Archaeal viruses exert a considerable influence on the structure and composition of archaeal communities and their associated ecological environments. The present study revealed the complete genomes of 38 archaeal head-tailed proviruses through comprehensive data mining. The hosts of these proviruses were identified as belonging to the following four dominant phyla: <i>Halobacteriota</i>, <i>Thermoplasmatota</i>, <i>Thermoproteota</i>, and <i>Nanoarchaeota</i>. In addition to the 14 proviruses of halophilic archaea related to the <i>Graaviviridae</i> family, the remaining proviruses exhibited limited genetic similarities to known (pro)viruses, suggesting the existence of 14 potential novel families. Of the 38 archaeal proviruses, 30 have the potential to lyse host cells. Eleven proviruses contain genes linked to antiviral defense mechanisms, including those involved in restriction modification (RM), clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) nucleases, defense island system associated with restriction-modification (DISARM), and DNA degradation (Dnd). Moreover, auxiliary metabolic genes were identified in the proviruses of <i>Bathyarchaeia</i> and <i>Halobacteriota</i> archaea, including those involved in carbohydrate and amino acid metabolism. Our findings indicate the diversity of archaeal viruses, their interactions with archaeal hosts, and their roles in the adaptation of the host.IMPORTANCEThe field of archaeal virology has seen a rapid expansion through the use of metagenomics, yet the diversity of these viruses remains largely uncharted. In this study, the complete genomes of 38 novel archaeal proviruses were identified for the following four dominant phyla: <i>Halobacteriota</i>, <i>Thermoplasmatota</i>, <i>Thermoproteota</i>, and <i>Nanoarchaeota</i>. Two families and six genera of Archaea were the first to be identified as hosts for viruses. The proviruses were found to contain diverse genes that were involved in distinct adaptation strategies of viruses to hosts. Our findings contribute to the expansion of the lineages of archaeal viruses and highlight their intricate interactions and essential roles in enabling host survival and adaptation to diverse environmental conditions.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0049224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639225","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":"Performance evaluation of the high-throughput quantitative Alinity m Epstein-Barr virus assay.","authors":"D Yitzchak Goldstein, Mark M Sasaki, Momka Narlieva, Nhi Nhan, Tianxi Liu, April Kegl, Tanjina Akter, Tanisha Dickerson, Eriel Thornton, Patricia Jim, Stephen Young, Danijela Lucic, Julie W Hirschhorn","doi":"10.1128/spectrum.01507-24","DOIUrl":"https://doi.org/10.1128/spectrum.01507-24","url":null,"abstract":"<p><p>Molecular testing for Epstein-Barr virus (EBV) infection is a cornerstone of care to prevent adverse outcomes in immunocompromised patients, including transplant recipients. We evaluated the analytical and clinical performance of the quantitative Alinity m EBV assay for plasma sample testing on the fully automated Alinity m platform. Assay lower limit of detection and precision were determined using commercially available panels in plasma. Alinity m EBV detected 100% of panels at 1.3 Log IU/mL, and precision ranged from 1.9% to 5.2% coefficients of variance (SD ≤ 0.14 Log IU/mL). Remnant-de-identified specimens initially tested with the Eurofins Viracor EBV Laboratory Developed Test (LDT) (<i>n</i> = 357), ELITech EBV LDT (<i>n</i> = 113), University of Washington (UW) LDT (<i>n</i> = 151), or Roche cobas EBV assay (<i>n</i> = 148) were subsequently tested with the Alinity m EBV assay. Comparison of the Alinity m EBV assay and Eurofins Viracor EBV assay demonstrated a correlation coefficient of 0.762 and mean bias of -0.48 Log IU/mL, comparison of the Alinity m EBV assay with UW LDT demonstrated a correlation coefficient of 0.970 and mean bias of -0.24 Log IU/mL, and comparison of the Alinity m EBV assay with cobas EBV demonstrated a correlation coefficient of 0.964 and mean bias of 0.35 Log IU/mL. The Alinity m EBV assay demonstrated high precision across the analytical measurement range and produced comparable results to the EBV test of record assays. These findings support the utility of the fully automated Alinity m EBV assay in transplant patient management.</p><p><strong>Importance: </strong>Epstein-Barr virus (EBV) infection and reactivation are associated with increased risk for post-transplant lymphoproliferative disorders (PTLD) in transplant recipients with the development of PTLD occurring predominantly within a year of transplant. Quantitative PCR for EBV is used to monitor the viral load of EBV with a negative result as a good negative predictor of PTLD. Nucleic acid amplification tests (NAATs) with high sensitivity and specificity are available on fully automated high-throughput instruments to provide accurate quantitation and improve test result turn-around time. This study evaluates the analytical and clinical performance of one such NAAT, the Alinity m EBV assay.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0150724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639172","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":"Antimicrobial susceptibility testing of <i>Dermabacter hominis</i>.","authors":"Tim Kintzinger, Dennis Knaack, Sören Schubert, Uwe Groß, Robin Köck, Frieder Schaumburg","doi":"10.1128/spectrum.01827-24","DOIUrl":"https://doi.org/10.1128/spectrum.01827-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Dermabacter hominis,&lt;/i&gt; a short gram-positive rod, is a part of the human skin flora, but can also cause infections (e.g., skin and soft tissue infections, bone and joint infections, abscesses, peritoneal dialysis-associated peritonitis, and bacteremia). Only limited data are available for antimicrobial resistance rates. Although CLSI does include coryneform genera in &lt;i&gt;Corynebacterium&lt;/i&gt; spp. clinical breakpoints, they point out that only limited data are available on resistance rates. The aim of this study was to assess the minimal inhibitory concentration (MIC) of clinical isolates of &lt;i&gt;D. hominis&lt;/i&gt; and to deduce breakpoints for disk diffusion. &lt;i&gt;D. hominis&lt;/i&gt; (n = 30) from five laboratories in Germany were tested by broth microdilution and disk diffusion method. MICs were interpreted according to current clinical breakpoints for &lt;i&gt;Corynebacterium&lt;/i&gt; spp. or pharmacokinetic-pharmacodynamic breakpoints (EUCAST). To deduce breakpoints for disk diffusion, MICs were correlated with inhibition zone diameters. All isolates were susceptible to vancomycin, rifampicin, and linezolid (100%, &lt;i&gt;n&lt;/i&gt; = 30/30). Lower susceptibility rates were found for ampicillin (83%, &lt;i&gt;n&lt;/i&gt; = 25/30) followed by ceftriaxone (37%, &lt;i&gt;n&lt;/i&gt; = 11/30) and clindamycin (27%, &lt;i&gt;n&lt;/i&gt; = 8/30). All isolates were resistant to benzylpenicillin and daptomycin. Good correlations between disk diffusion and MIC (suggested breakpoints for susceptibility in brackets) were found for ampicillin (S ≥ 10 mm), ceftriaxone (S ≥ 24 mm), clindamycin (S ≥ 19 mm), levofloxacin (I ≥ 24 mm), linezolid (S ≥ 29 mm), rifampicin (S ≥ 38 mm), and vancomycin (S ≥ 21 mm). Due to limited variances in both MIC values and inhibition zone diameters, no disk diffusion breakpoint could be deduced for gentamicin and benzylpenicillin in our dataset. &lt;i&gt;D. hominis&lt;/i&gt; has favorable susceptibility rates for vancomycin, rifampicin, and linezolid and shows correlations between MIC and disk diffusion diameter for selected antimicrobial agents. Thus, the development of clinical breakpoints for disk diffusion appears feasible.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Dermabacter hominis&lt;/i&gt; can cause infections in humans (e.g., skin and soft tissue infections, bone and joint infections, abscesses, peritoneal dialysis-associated peritonitis, and bacteremia). Currently, only limited data are available regarding the resistance rates of this specific pathogen. Data for the easy accessible disk diffusion method are missing. We were able to provide additional data on resistance rates of clinical &lt;i&gt;D. hominis&lt;/i&gt; isolates to common antimicrobial agents and correlate these with disk diffusion diameters to derive breakpoints to further improve the antimicrobial susceptibility testing for this specific pathogen. In addition to that, we created a current overview of resistance rates from the existing literature. Our data provide deeper insight into resistance rates and antimicrobial susceptibility testing of thi","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0182724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142639220","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}