Microbiology spectrum最新文献

{"title":"Anti-SARS-CoV-2 serology based on ancestral RBD antigens does not correlate with the presence of neutralizing antibodies against Omicron variants.","authors":"Léa Dépéry, Isabelle Bally, Axelle Amen, Benjamin Némoz, Marlyse Buisson, Laurence Grossi, Aurélie Truffot, Raphaële Germi, Delphine Guilligay, Mélanie Veloso, Antoine Vilotitch, Olivier Epaulard, Patrice Morand, Winfried Weissenhorn, Pascal Poignard, Julien Lupo","doi":"10.1128/spectrum.01568-24","DOIUrl":"https://doi.org/10.1128/spectrum.01568-24","url":null,"abstract":"<p><p>Neutralizing antibody titers and binding antibody levels are considered correlates of protection against severe SARS-CoV-2 infection. The clinical utility of serology should be reevaluated in light of the emergence of escape variants, as commercial antibody-binding assays have not been adapted to the virus' antigenic evolution. We compared anti-SARS-CoV-2 antibody titers in four quantitative serological tests based on variable ancestral spike antigens (three in-house ELISAs and the prototype VIDAS SARS-CoV-2 IgG QUANT assay) and neutralization assays against the pseudotyped Wuhan, BA.2, BA.4/5, BQ.1.1, and XBB.1.1 viruses in a cohort of 100 patients infected in 2020 or during the Omicron waves. Binding antibody levels correlated well with neutralizing antibody titers for Wuhan, BA.2, and BA.4/5, but the association decreased for BQ.1.1 and XBB.1 (for the VIDAS assay, Spearman's correlation was 0.82 [95% CI 0.74-0.88] and 0.61 [0.46-0.72] for BA.2 and XBB.1, respectively). In 15% of patients with no neutralizing antibodies against XBB.1, the VIDAS assay still yielded binding antibody levels ranging from 74 to 7,652 binding antibody units/mL. Using an adjusted threshold based on receiver operating characteristic (ROC) curve analysis, the specificity of neutralizing antibody detection increased from 0.15 (95% CI 0.02-0.45) and 0.17 (0.04-0.41) to 0.92 (0.64-1.00) and 0.83 (0.59-0.96) against BQ.1.1 and XBB.1, respectively. Serological tests based on receptor-binding domain antigens from the ancestral virus fail to predict neutralizing activity against the latest circulating Omicron variants. Adapting serological tests may improve their clinical utility in immunocompromised patients.</p><p><strong>Importance: </strong>Anti-SARS-CoV-2 serology was developed in 2020 in response to the COVID-19 pandemic to diagnose SARS-CoV-2 infection and monitor an individual's immunity following natural infection or vaccination. Given the relationship between neutralizing antibody titers and protection against severe infection, many studies have evaluated the correlation between serology tests and neutralization assays in the pre-Omicron era. An important potential clinical use of serology, which explores binding antibodies, is estimating an individual's level of protection against new infection, particularly in immunosuppressed individuals and those at risk of severe COVID. However, in the Omicron era, as new viruses evade the immunity induced by previous infections and vaccination, the correlation between binding antibody levels determined by serological assays developed from ancestral antigens and neutralizing antibody titers against new viruses should be re-examined in order to determine whether these assays should be optimized by adapting antigens to the circulating SARS-CoV-2 strains.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0156824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676056","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 novel <i>Alteromonas</i> phage with tail fiber containing six potential iron-binding domains.","authors":"Chen Yu, Meishun Yu, Ruijie Ma, Shuzhen Wei, Min Jin, Nianzhi Jiao, Qiang Zheng, Rui Zhang, Xuejin Feng","doi":"10.1128/spectrum.00934-24","DOIUrl":"https://doi.org/10.1128/spectrum.00934-24","url":null,"abstract":"<p><p>Viruses play a vital role in regulating microbial communities, contributing to biogeochemical cycles of carbon, nitrogen, and essential metals. <i>Alteromona</i>s is widespread and plays an essential role in marine microbial ecology. However, there is limited knowledge about the interactions of <i>Alteromonas</i> and its viruses (alterophages). This study isolated a novel podovirus, vB_AmeP-R22Y (R22Y), which infects <i>Alteromonas</i> marina SW-47 (T). Phylogenetic analysis suggested that R22Y represented a novel viral genus within the <i>Schitoviridae</i> family. R22Y exhibited a broad host range and a relatively large burst size, exerting an important impact on the adaptability and dynamics of host populations. Two auxiliary metabolic genes, encoding Acyl carrier protein and AAA domain-containing protein, were predicted in R22Y, which may potentially assist in host fatty acid metabolism and VB12 biosynthesis, respectively. Remarkably, the prediction of the R22Y tail fiber structure revealed six conserved histidine residues (HxH motifs) that could potentially bind iron ions, suggesting that alterophages may function as organic iron-binding ligands in the marine environment. Our isolation and characterization of R22Y complements the Trojan Horse hypothesis, proposes the possible role of alterophages for marine iron biogeochemical cycling, and provides new insights into phage-host interactions in the iron-limited ocean.IMPORTANCEIron (Fe), as an essential micronutrient, is often a limiting factor for microbial growth in marine ecosystems. The Trojan Horse hypothesis suggests that iron in the phage tail fibers is recognized by the host's siderophore-bound iron receptor, enabling the phage to attach and initiate infection. The potential role of phages as iron-binding ligands has significant implications for oceanic trace metal biogeochemistry. In this study, we isolated a new phage R22Y with the potential to bind iron ions, using <i>Alteromonas</i>, a major siderophore producer, as the host. The tail fiber structure of R22Y exhibits six conserved HxH motifs, suggesting that each phage could potentially bind up to 36 iron ions. R22Y may contribute to colloidal organically complexed dissolved iron in the marine environment. This finding provides further insights into the Trojan Horse hypothesis, suggesting that alterophages may act as natural iron-binding ligands in the marine environment.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0093424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676047","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":"Development of <i>ptxD</i>/Phi as a new dominant selection system for genetic manipulation in <i>Cryptococcus neoformans</i>.","authors":"Muthita Khongthongdam, Tanaporn Phetruen, Sittinan Chanarat","doi":"10.1128/spectrum.01618-24","DOIUrl":"https://doi.org/10.1128/spectrum.01618-24","url":null,"abstract":"<p><p><i>Cryptococcus neoformans</i> is a globally distributed pathogenic fungus posing a significant threat to immunocompromised individuals, particularly those with HIV/AIDS. Effective genetic manipulation tools are essential for understanding its biology and developing new therapies. However, current genetic tools, including the variation of versatile selectable markers, are limited. This study develops and validates the phosphite dehydrogenase gene (<i>ptxD</i>)/phosphite (Phi) selection system as a non-antibiotic selectable marker for genetic manipulation in <i>C. neoformans</i>. A codon-optimized <i>ptxD</i> gene from <i>Pseudomonas stutzeri</i> was cloned under the <i>TEF</i> promoter. Using the transient CRISPR-Cas9 coupled with electroporation system, we integrated the <i>ptxD</i> gene into the <i>C. neoformans</i> genome and assessed the impact of <i>ptxD</i> integration on cell growth and virulence factors. The <i>ptxD</i>/Phi system effectively selected transformed cells on Phi-containing media. Growth assays showed that <i>ptxD</i> integration did not adversely affect cell growth or key virulence factors, including pleomorphism, capsule size, and melanin production. Additionally, we successfully disrupted the <i>ADE2</i> gene using this system, confirming its applicability for gene deletion. Taken together, the <i>ptxD</i>/Phi system provides a robust and versatile tool for genetic manipulation in <i>C. neoformans</i>, facilitating further research into its biology and pathogenicity.IMPORTANCE<i>Cryptococcus neoformans</i> is a type of fungus that can cause serious illnesses in people who have weakened immune systems, like those with HIV/AIDS. To better study this fungus and find new treatments, scientists need tools to change its genes in precise ways. However, the current tools available for this are somewhat limited. This research introduces a new tool called the phosphite dehydrogenase gene/phosphite system, which does not rely on antibiotics to work. It uses a gene from a different bacterium that helps select and grow only the fungus cells that have successfully incorporated new genetic information. This is particularly useful because it does not interfere with the normal growth of the fungus or the features that make it harmful (like its ability to change shape or produce protective coatings). By making it easier and more effective to manipulate the genetics of <i>C. neoformans</i>, this tool opens up new possibilities for understanding how this fungus operates and for developing therapies to combat its infections. This is crucial for improving the treatment of infections in vulnerable populations.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0161824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142676059","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":"Metagenome-based diversity and functional analysis of culturable microbes in sugarcane.","authors":"Haidong Lin, Liang Wu, Lijun Zhang, Quang Kiet Ta, Peng Liu, Jinkang Song, Xiping Yang","doi":"10.1128/spectrum.01982-24","DOIUrl":"10.1128/spectrum.01982-24","url":null,"abstract":"<p><p>Sugarcane is a key crop for sugar and energy production, and understanding the diversity of its associated microbes is crucial for optimizing its growth and health. However, there is a lack of thorough investigation and use of microbial resources in sugarcane. This study conducted a comprehensive analysis of culturable microbes and their functional features in different tissues and rhizosphere soil of four diverse sugarcane species using metagenomics techniques. The results revealed significant microbial diversity in sugarcane's tissues and rhizosphere soil, including several important biomarker bacterial taxa identified, which are reported to engage in several processes that support plant growth, such as nitrogen fixation, phosphate solubilization, and the production of plant hormones. The Linear discriminant analysis Effect Size (LEfSe) studies identified unique microbial communities in different parts of the same sugarcane species, particularly <i>Burkholderia</i>, which exhibited significant variations across the sugarcane species. Microbial analysis of carbohydrate-active enzymes (CAZymes) indicated that genes related to sucrose metabolism were mostly present in specific bacterial taxa, including <i>Burkholderia</i>, <i>Pseudomonas</i>, <i>Paraburkholderia</i>, and <i>Chryseobacterium</i>. This study improves understanding of the diversities and functions of endophytes and rhizosphere soil microbes in sugarcane. Moreover, the approaches and findings of this study provide valuable insights for microbiome research and the use of comparable technologies in other agricultural fields.</p><p><strong>Importance: </strong>This work utilized metagenomics techniques for conducting a comprehensive examination of culturable microbes and their functional characteristics in various tissues and rhizosphere soil of four distinct sugarcane species. This study enhances comprehension of the diversity and functions of endophytes and rhizosphere soil microbes in sugarcane. Furthermore, the methodologies and discoveries of this work offer new perspectives for microbiome investigation and the use of similar technologies in other agricultural fields.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0198224"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668391","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":"The <i>Neosartorya (Aspergillus) fischeri</i> antifungal protein NFAP2 has low potential to trigger resistance development in <i>Candida albicans in vitro</i>.","authors":"Gábor Bende, Nóra Zsindely, Krisztián Laczi, Zsolt Kristóffy, Csaba Papp, Attila Farkas, Liliána Tóth, Szabolcs Sáringer, László Bodai, Gábor Rákhely, Florentine Marx, László Galgóczy","doi":"10.1128/spectrum.01273-24","DOIUrl":"10.1128/spectrum.01273-24","url":null,"abstract":"<p><p>Due to the increase in the number of drug-resistant <i>Candida albicans</i> strains, new antifungal compounds with limited potential for the development of resistance are urgently needed. NFAP2, an antifungal protein (AFP) secreted by <i>Neosartorya</i> (<i>Aspergillus</i>) <i>fischeri</i>, is a promising candidate. We investigated the ability of <i>C. albicans</i> to develop resistance to NFAP2 in a microevolution experiment compared with generic fluconazole (FLC). <i>C. albicans</i> adapted to only 1× minimum inhibitory concentration (MIC) of NFAP2, which can be considered tolerance rather than resistance, compared with 32× MIC of FLC. Genome analysis revealed non-silent mutations in only two genes in NFAP2-tolerant strains and in several genes in FLC-resistant strains. Tolerance development to NFAP2 did not influence cell morphology. The susceptibility of NFAP2-tolerant strains did not change to FLC, amphotericin B, micafungin, and terbinafine. These strains did not show altered susceptibility to AFPs from <i>Penicillium chrysogenum</i>, except one which had less susceptibility to <i>Penicillium chrysogenum</i> antifungal protein B. FLC-resistant strains had decreased susceptibility to terbinafine and NFAP2, but not to other drugs and AFPs from <i>P. chrysogenum</i>. NFAP2-tolerant and FLC-resistant strains showed decreased and increased NFAP2 binding and uptake, respectively. The development of tolerance to NFAP2 decreased tolerance to cell wall, heat, and UV stresses. The development of FLC resistance increased tolerance to cell wall stress and decreased tolerance to heat and UV stresses. Tolerance to NFAP2 did not have significant metabolic fitness cost and could not increase virulence, compared with resistance to FLC.IMPORTANCEDue to the increasing number of (multi)drug-resistant strains, only a few effective antifungal drugs are available to treat infections caused by opportunistic <i>Candida</i> species. Therefore, the incidence of hard-to-treat candidiasis has increased dramatically in the past decade, and the demand to identify antifungal compounds with minimal potential to trigger resistance is substantial. The features of NFAP2 make it a promising candidate for the topical treatment of <i>Candida</i> infection. Data on the development of resistance to antifungal proteins in <i>Candida albicans</i> are lacking. In this study, we provide evidence that NFAP2 has a low potential to trigger resistance in <i>C. albicans in vitro</i>, and the developed tolerance to NFAP2 is not associated with severe phenotypic changes compared with development of resistance to generic fluconazole. These results suggest the slow emergence of NFAP2-resistant <i>Candida</i> strains, and NFAP2 can reliably be used long-term in the clinic.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0127324"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668459","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":"Lack of activity of HIV-1 integrase strand-transfer inhibitors on recombinase activating gene (RAG) activity at clinically relevant concentrations.","authors":"Sally Demirdjian, Vincent N Duong, Jennifer N Byrum, Arabinda Nayak, Cooper B McKinney, Jason K Perry, Christian Callebaut, Karla K Rodgers, Brie Falkard, Joy Y Feng","doi":"10.1128/spectrum.02468-24","DOIUrl":"10.1128/spectrum.02468-24","url":null,"abstract":"<p><p>Human immunodeficiency virus 1 (HIV-1) infection remains a global health concern, with nearly 30 million people on antiretroviral (ARV) treatment. Integrase strand-transfer inhibitors (INSTIs) that block HIV-1 integrase are crucial components of first-line combination ARV therapies recommended in most international guidelines and have significantly improved HIV-1 treatment due to their efficacy and safety. This study evaluates potential off-target effects of INSTIs on recombinase activating genes (RAG1 and RAG2), which are essential for adaptive immune system function. We performed a comprehensive assessment of the off-target effects of clinically approved INSTIs on RAG activity, utilizing both biochemical and cellular assays. We purified the first catalytically active recombinant human core RAG1-RAG2 complex and tested it in the presence of the co-factor human HMGB1 protein for the gel-based biochemical RAG DNA cleavage assay. Additionally, we optimized an extrachromosomal V(D)J recombination cellular assay using murine mCherry-core RAG1, full-length murine mCherry-RAG2, and a plasmid substrate green fluorescent protein (GFP) reporter system, transfecting them into cells in the absence or presence of inhibitors. This setup enabled high-throughput analysis of V(D)J recombination for multiple compounds in a dose-response manner via flow cytometry. Physiologically relevant concentrations of INSTIs were examined for their potential impact on RAG activity and V(D)J recombination, with approved INSTIs showing minimal to no effects on recombinase activity. Consequently, the findings support the continued use of INSTIs in HIV-1 treatment without substantial concern for adverse effects on V(D)J recombination and immune system function.IMPORTANCEINSTIs are a crucial component of antiretroviral treatments for HIV-1 infection. This study provides a careful and thorough analysis of the impact of approved INSTIs on recombinase activating gene (RAG1 and RAG2) activity, which plays a pivotal role in the adaptive immune system. The concentrations tested were derived from several clinical studies and accounted for the maximum free fraction of the drug available in patients. This approach ensures that our findings are directly applicable to clinical scenarios by providing meaningful insights into the potential drug side effects in patients. We developed biochemical and cellular assays to measure the impact of INSTIs on RAG activity. All tested INSTIs did not inhibit RAG at supratherapeutic concentrations in the RAG1/RAG2 biochemical cleavage and cellular V(D)J recombination assays. Our assessment supports the continued use of INSTIs in HIV-1 treatments without concern for adverse effects.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0246824"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668390","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":"Prior immunity to <i>Ureaplasma urealyticum</i> protects against respiratory infection in immunosuppressed mice.","authors":"Maha Y Al-Jabri, Robin Patel, Derek Fleming","doi":"10.1128/spectrum.01763-24","DOIUrl":"10.1128/spectrum.01763-24","url":null,"abstract":"<p><p><i>Ureaplasma</i> species can cause systemic infections in immunocompromised hosts, including lung transplant recipients. Here, we investigated the impact of prior exposure to <i>Ureaplasma urealyticum</i> on the risk of <i>U. urealyticum</i> and <i>Ureaplasma parvum</i> infection in mice subjected to an immunosuppression regimen similar to that administered to solid organ transplant recipients. Mice were immunized with three intramuscular injections of <i>U. urealyticum</i>, with control mice injected with adjuvant only. Following immunization, mice received tacrolimus, mycophenolate mofetil, and methylprednisolone, and then were challenged with <i>U. urealyticum</i> or <i>U. parvum</i> intraperitoneally and intratracheally over 6 days. Relative <i>U. urealyticum</i> antibody levels in plasma were assessed over time, and lungs were harvested at sacrifice for bacterial load quantification, assessed using a color-changing unit assay. <i>U. urealyticum</i> antibody levels were higher in immunized compared with control animals (<i>P</i> < 0.0001), even when animals were immunosuppressed. <i>U. urealyticum</i> and <i>U. parvum</i> lung burden was reduced in immunized compared with control mice (~6 log₁₀ reduction for <i>U. urealyticum</i> and <1 log₁₀ reduction for <i>U. parvum</i>; <i>P</i> = 0.008 and 0.046, respectively). In summary, this study shows that prior exposure to live <i>U. urealyticum</i> provides some protection against infection with <i>U. urealyticum</i>.IMPORTANCE<i>Ureaplasma</i>-induced hyperammonemia syndrome is a rare but potentially deadly complication of solid organ transplantation, especially lung transplantation. The pathophysiology of this relatively recently recognized condition is poorly understood, and it is unclear what factors may influence patient susceptibility. This study investigates the possible protective effects of prior exposure to <i>Ureaplasma urealyticum</i> in a mouse model subjected to an immunosuppression regimen similar to that given to lung transplant recipients. The findings show that prior exposure could provide protection against <i>Ureaplasma</i> lung infection.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0176324"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668407","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":"Tackling the unyielding: testing two novel approaches against NDM-producing Enterobacterales and <i>Pseudomonas aeruginosa</i> isolates collected in India.","authors":"Yamuna Devi Bakthavatchalam, Bijayini Behera, Anand Shah, Purva Mathur, Raja Ray, Bashir Ahmed Fomda, Kamini Walia, Balaji Veeraraghavan","doi":"10.1128/spectrum.00497-24","DOIUrl":"10.1128/spectrum.00497-24","url":null,"abstract":"<p><p>The <i>in vitro</i> activity of two novel antibiotics with different modes of action, (i) siderophore cefiderocol and (ii) β-lactam-enhancer mechanism-based cefepime/zidebactam, was tested against New Delhi Metallo-β-lactamase (NDM)-producing Enterobacterales and <i>Pseudomonas aeruginosa</i> collected in India. Minimum inhibitory concentrations of antibiotics against multicentric NDM-producing <i>Escherichia coli</i> (<i>n</i> = 117), <i>Klebsiella pneumoniae</i> (<i>n</i> = 103), and <i>P. aeruginosa</i> (<i>n</i> = 72) were determined by the reference broth microdilution method. Among <i>E. coli</i>, 111 isolates were NDM-alone, and six were NDM + OXA-48-like producers. Among <i>K. pneumoniae</i>, 47 and 56 isolates were NDM-alone and NDM + OXA-48-like producers, respectively. All <i>E. coli</i> isolates harbored four amino acid inserts in their penicillin-binding protein 3. Using the highest susceptible breakpoint among CLSI, FDA, and EUCAST interpretive criteria, cefiderocol susceptibility was 39.3%, ≤80%, and 57%, for NDM ± OXA-48-like-producing <i>E. coli</i>, NDM ± OXA-48-like-producing <i>K. pneumoniae,</i> and NDM-producing <i>P. aeruginosa</i>, respectively. At a cefepime break point of ≤8 mg/L, 100% of Enterobacterales and ≥90% of <i>P. aeruginosa</i> isolates were cefepime/zidebactam-susceptible. NDM being a dominant carbapenemase among Enterobacterales and <i>P. aeruginosa</i> in India, the variable activity of cefiderocol against NDM producers is a concern. Post approval, cefepime/zidebactam could offer a promising treatment option against NDM producers.</p><p><strong>Importance: </strong>Metallo-β-lactamases are therapeutically challenging due to the limited treatment options. Against such isolates, currently approved newer β-lactam/β-lactamase inhibitor combinations are ineffective. In this study, we tested siderophore cephalosporin, cefiderocol, which utilizes an unconventional iron uptake pathway for efficient cellular penetration, and cefepime/zidebactam that utilizes novel β-lactam enhancer mechanisms for overcoming diverse carbapenemases. Cefiderocol showed limited activity against <i>Escherichia coli</i> isolates co-harboring New Delhi metallo-β-lactamase (NDM) with PBP3 insert, dual carbapenemase (NDM with OXA-48 like)-producing <i>Klebsiella pneumoniae</i>, and NDM-producing <i>Pseudomonas aeruginosa</i> isolates, while cefepime/zidebactam potently inhibited NDM-producing Enterobacterales and <i>P. aeruginosa</i> isolates. NDM being a dominant carbapenemase among Enterobacterales and <i>P. aeruginosa</i> in India, the variable activity of cefiderocol against NDM producers is a concern. Post approval, cefepime/zidebactam could offer a promising treatment option against NDM producers.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0049724"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668416","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 of deep learning models in predicting the nugent score to diagnose bacterial vaginosis.","authors":"Naoki Watanabe, Tomohisa Watari, Kenji Akamatsu, Isao Miyatsuka, Yoshihito Otsuka","doi":"10.1128/spectrum.02344-24","DOIUrl":"10.1128/spectrum.02344-24","url":null,"abstract":"<p><p>The Nugent score is a commonly used diagnostic tool for bacterial vaginosis. However, its accuracy depends on the skills of laboratory technicians. This study aimed to evaluate the performance of deep learning models in predicting the Nugent score to improve diagnostic consistency and accuracy. In total, 1,510 vaginal smear images collected from a hospital in Japan between 2021 and 2023 were assessed. Each image was annotated by laboratory technicians into one of four categories based on the Nugent score-normal vaginal flora, no vaginal flora, altered vaginal flora, or bacterial vaginosis. Deep learning models were developed to predict these categories, and their performance was compared to that of technician annotations. The deep learning models demonstrated 84% accuracy at 400× magnification and 89% at 1,000× magnification. The 1,000× model was further optimized and tested on an independent set of 106 images. After optimization, the advanced model achieved 94% accuracy, outperforming the average 92% accuracy of the technicians. The agreement between the advanced model predictions and technicians was 92% for normal vaginal flora, 100% for no vaginal flora, 91% for altered vaginal flora, and 100% for bacterial vaginosis. Overall, our findings suggest that deep learning models have the potential to diagnose bacterial vaginosis with an accuracy comparable to that of laboratory technicians.IMPORTANCEBacterial vaginosis is a global health issue affecting women, causing symptoms such as abnormal vaginal discharge and discomfort. The Nugent score is a standard method for diagnosing bacterial vaginosis and is based on the manual interpretation of Gram-stained vaginal smears. However, this method relies on the skill and experience of trained professionals, leading to variability in results and poses significant challenges for settings with limited access to experienced technicians. The results of this study indicate that deep learning models can predict the Nugent score with high accuracy, offering the potential to standardize the diagnosis of bacterial vaginosis. By reducing observer variability, these models can facilitate reliable diagnoses, even in settings where experienced personnel are scarce. Although validation is needed on a larger scale, our results suggest that deep learning models may represent a new approach for diagnosing bacterial vaginosis.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0234424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668404","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":"Improvement of a MALDI-TOF database for the reliable identification of <i>Candidozyma auris</i> (formally <i>Candida auris</i>) and related species.","authors":"Hui-Hui Zhu, Miao-Miao Liu, Teun Boekhout, Qi-Ming Wang","doi":"10.1128/spectrum.01444-24","DOIUrl":"10.1128/spectrum.01444-24","url":null,"abstract":"<p><p>Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a promising technique for the rapid identification microorganisms. The aim of this study was to create a new database for the accurate identification of <i>Candidozyma auris</i> (formerly known as <i>Candida auris</i>) and 11 species of the <i>Candidozyma haemuli</i> species complex, including <i>C. chanthaburiensis</i>, <i>C. duobushaemuli</i>, <i>C. haemuli</i>, <i>C. heveicola</i>, <i>C. khanbhai</i>, <i>C. konsanensis</i>, <i>C. metrosideri</i>, <i>C. ohialehuae</i>, <i>C. pseudohaemuli</i>, <i>C. ruelliae</i>, and <i>C. vulturna</i>. Seventy-one <i>Candidozyma</i> isolates from different national institutions were studied. Thirty-seven strains were used to create a MALDI-TOF (microTyper MS) database using the formic acid extraction method. The validation of this database was performed with 34 other strains of the genus <i>Candidozyma</i>, and the result was compared with the identification results when using DBRs v1.0.0.4 (Tianrui, China). Our library allowed a 100% identification of the evaluated strains with all strains showing log scores of >2.0. Repeatability and reproducibility tests result showed a coefficient of variation of the log score values of less than 5%. The MALDI-TOF MS system can identify <i>C. auris</i> and related species quickly and accurately. This method will play a crucial role in accurately diagnosing infectious agents of the genus <i>Candidozyma</i> in clinical practice.</p><p><strong>Importance: </strong>Importance <i>Candidozyma auris</i>, also known as <i>Candida auris</i>, has quickly spread across the world, and prompt identification of <i>C. auris</i> from infected individuals is critical. However, a standard identification method is lacking for the identification of <i>C. auris</i> in clinical and public health laboratories. To make matters worse, its biochemical assimilation profile was found to be similar to that of closely related and even no-related species, leading to frequent misidentification. To improve diagnostics of this and closely related species, we created a database of reference mass spectra resulting in the efficient and correct identification of all <i>Candidozyma</i> species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Moreover, potential pathogenic species of <i>Candidozyma</i> can be effectively identified by MALDI-TOF MS, and differentiated from non-clinically relevant phylogenetic relatives. Thus, MALDI-TOF MS may help expedite laboratory diagnosis and treatment of <i>C. auris</i> and related species of clinical importance and help the clinician to decide on early treatment.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0144424"},"PeriodicalIF":3.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142668387","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}