Microbiology spectrum最新文献

{"title":"Survival and safety evaluation of <i>Bifidobacterium longum</i> subsp<i>. longum</i> ZS-8 in healthy adults, determined using PMAxx-qPCR and amplicon sequencing.","authors":"Feng Liu, Biao Dong, Zhongsun Wang, Dan Lin, Huan Xu, Baisheng Ke, Wanying Kang, Yang Jin, Xiuting Huang, Hui Lu, Liqing Zhao, Yun Qian, Liangling Cai, Long Xu, Zhenjiang Zech Xu","doi":"10.1128/spectrum.02861-24","DOIUrl":"https://doi.org/10.1128/spectrum.02861-24","url":null,"abstract":"<p><p>Species-level quantitative PCR (qPCR) provides in-depth knowledge of oral probiotics in the human gastrointestinal tract (GIT). However, it lacks the capability to differentiate exogenous strains from native microbiota, nor can it distinguish between live and dead bacteria. In this study, we employed improved propidium monoazide (PMAxx)-qPCR to evaluate the survival and colonization of <i>Bifidobacterium longum</i> subsp<i>. longum</i> ZS-8 (designated ZS-8) on the strain level in the GIT and its impact on human gut microbiota. By spiking in live and dead ZS-8, we demonstrated that strain-level PMAxx-qPCR could identify and quantify the viable ZS-8 in fecal samples accurately. Using this method, we found that, in healthy humans, oral administration of ZS-8 can transiently survive in the GIT, and multi-layer seamless capsules (MLSC) significantly improve the gastrointestinal tolerance and survivability of ZS-8 compared to its powder form. Furthermore, through selective cultivation and PMAxx-microbiome sequencing, we investigated the response of gut viable microbiome to ZS-8. Results showed that, while the microbiota diversity and total viable counts of <i>Bifidobacterium</i> and <i>Lactobacillus</i> remained stable, certain indigenous species of <i>Bifidobacterium</i> and <i>Lactobacillus</i> increased in abundance, confirming ZS-8's probiotic potential in healthy individuals. Overall, our study demonstrates the effectiveness of combining strain-specific comparative genomics with PMAxx-qPCR for evaluating probiotic survival and colonization in the human gut and highlights the safety of ZS-8 oral administration in healthy individuals.</p><p><strong>Importance: </strong>The survival and colonization of probiotics in the gut are critical for their functional efficacy, yet conventional species-level quantitative PCR (qPCR) fails to distinguish exogenous strains from native microbiota or differentiate live from dead bacteria. By integrating strain-specific comparative genomics with propidium monoazide (PMAxx)-qPCR, we precisely quantified the viability of <i>Bifidobacterium longum</i> ZS-8 at the strain level in the human gut after its oral administration. Our study demonstrated that 1.53-6.90% of cells surviving transit and multi-layer seamless capsules (MLSC) significantly enhanced the gastrointestinal tolerance of ZS-8. While ZS-8 administration did not alter gut microbiota diversity or total viable counts of <i>Bifidobacterium</i> and <i>Lactobacillus</i>, it selectively increased the abundance of specific indigenous beneficial species. This method overcomes the dual limitations of traditional techniques (strain-level specificity and viability discrimination), providing a robust tool for probiotic research. Furthermore, our findings confirm the safety of ZS-8 in healthy individuals and its potential to modulate gut ecology, offering a scientific foundation for personalized probiotic development and clinical translation.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0286124"},"PeriodicalIF":3.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113830","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":"Whole genome study and construction of SHERLOCK detection method for endemic strains of <i>Burkholderia pseudomallei</i> in Hainan based on third-generation sequencing.","authors":"Junjie Hu, Shanshan Xu, Zeng Zeng, Wei Gong, Weihua Xu, Zhichao Ma, Shengmiao Fu, Linhai Li, Bin Xiao, Xinping Chen","doi":"10.1128/spectrum.00592-25","DOIUrl":"https://doi.org/10.1128/spectrum.00592-25","url":null,"abstract":"<p><p><i>Burkholderia pseudomallei (Bp</i>) is a gram-negative bacterium found in soil and surface water. It is also the pathogen that causes melioidosis disease in humans and animals. This study aimed to obtain the whole genome sequence of the endemic strain of <i>Bp</i> in Hainan, using third-generation sequencing (TGS) technology, and elucidate the genome structure, function, and genetic evolution. Additionally, the study aimed to achieve rapid and specific identification of these endemic strains using specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) detection technology, providing a new strategy for the early diagnosis of melioidosis. Utilizing the PacBio platform for TGS technology, we completed whole genome sequencing of 16 <i>Bp</i> strains from Hainan. High-precision and complete genome sequences were obtained through quality control and genome assembly of the sequencing data. Additionally, we established a nucleic acid detection technology platform based on SHERLOCK, which could be completed from nucleic acid extraction to result reading within 1-2 hours, demonstrating good sensitivity and specificity (both are 100%). The lateral chromatography strip method does not require special equipment and holds promise as an immediate screening method for the early diagnosis of melioidosis.</p><p><strong>Importance: </strong>Melioidosis is a highly pathogenic infectious disease caused by a gram-negative bacterium of <i>Burkholderia pseudomallei</i> (<i>Bp</i>). The traditional gold standard for diagnosing melioidosis is still isolation and culture from clinical samples. Although this method has high specificity, it has low sensitivity and is time-consuming, which often leads to misdiagnosis or missed diagnosis of melioidosis, affecting subsequent treatment. In this study, recombinase polymerase amplification technology and clustered regularly interspaced short palindromic repeats/Cas13a technology were combined to establish the Specific High-sensitivity Enzymatic Reporter Unlocking detection technology, which can achieve rapid and accurate identification of <i>Bp</i>, providing a new method for the early diagnosis of melioidosis.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0059225"},"PeriodicalIF":3.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113832","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":"STING-mediated antiviral response: insights into MVA replication control in avian cells.","authors":"Teresa Brusco, Valentina Menci, Carmen Caiazza, Anna Maria Petrone, Renata Palladino, Matteo Faticanti, Veronica Bignone, Concetta Ambrosino, Elisa Scarselli, Massimo Mallardo, Loredana Siani, Valentino Ruzza","doi":"10.1128/spectrum.00075-25","DOIUrl":"https://doi.org/10.1128/spectrum.00075-25","url":null,"abstract":"<p><p>The safety-tested Modified Vaccinia virus Ankara (MVA) is a well-characterized mutant virus widely used in fundamental research to elucidate the functions of Poxvirus host-interaction factors. Beyond its safety profile, MVA is an attractive viral vector for vaccine development due to its genetic stability and ability to efficiently infect antigen-presenting cells, such as dendritic cells and tumor cells. In this report, we investigated the interplay between MVA and the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) antiviral pathway in chicken fibroblast cell lines (wild-type DF-1 and knock-out STING) to verify whether manipulation of the STING axis could impact MVA replication and cell responses. Our findings demonstrate that STING-mediated signaling plays a role in contrasting the replication of MVA. Upon MVA infection, the loss of STING hampered the expression of type I interferons (IFNs) and, in turn, interferon-stimulated gene 15 (ISG15) and interferon-induced transmembrane protein 3 (IFITM3). In line with these results, the expression of early and late MVA genes was enhanced, and DNA replication occurred earlier and was more abundant. Interferon regulatory factor 1 (IRF1) and myeloid differentiation primary response 88 (MyD88) were significantly induced by MVA infection in STING-KO cells, indicating that their responses to MVA infection are independent of the cGAS/STING axis. Collectively, these results refine our knowledge of MVA-host interaction in chicken fibroblasts and offer insights to guide strategies for enhancing Poxvirus vaccine vector production.IMPORTANCEGiven the context-dependent nature of STING antiviral activity, it is critical to broaden the investigation in order to clarify the virus-host response mechanisms across different species, particularly in chicken fibroblasts, to provide insights into MVA-based vaccine production improvements.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0007525"},"PeriodicalIF":3.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113775","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":"Molecular characterization of carbapenem-resistant Enterobacterales (CRE) and <i>in vitro</i> activity of novel beta lactams against CRE isolates from Malaysia.","authors":"Fairuz Abdul Rashid, Nurzam Suhaila Che Hussin, Nurul Fathiyah Zaipul Anuar, Noraziah Sahlan, Navindra Kumari Palanisamy, Fadzilah Mohd Nor","doi":"10.1128/spectrum.00553-25","DOIUrl":"https://doi.org/10.1128/spectrum.00553-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Knowledge gap on the susceptibility of novel β-lactam agents (cefiderocol, ceftazidime-avibactam, imipenem-cilastatin-relebectam, and aztreonam) against carbapenem-resistant Enterobacterales (CRE) has been recognized. This study aimed to genotypically characterize CRE isolates and investigate the novel β-lactam activity against CRE. CRE is defined as Enterobacterales that is phenotypically non-susceptible to any carbapenems, including imipenem, meropenem, and ertapenem. A total of 154 CRE isolates were collected from two tertiary centers in Malaysia from October 2023 to May 2024. Carbapenemase-producing genes (&lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VIM&lt;/sub&gt;, and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP&lt;/sub&gt;,) were detected using PCR. Susceptibility to β-lactams was determined using disc diffusion. Of 154 CRE isolates, 102 (66.2%) were carbapenemase-producing carbapenem-resistant Enterobacterales (CP-CRE). &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; (76/102; 74.5%), &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48-like&lt;/sub&gt; (17/102; 16.7%), &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; & &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48-like&lt;/sub&gt; (8/102; 7.8%), and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; & &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VIM&lt;/sub&gt; (1/102; 1.0%) were identified among the CP-CRE isolates. The proportion of CRE isolates that exhibited susceptibility towards cefiderocol, ceftazidime-avibactam, and imipenem-cilastatin-relebactam was 86.4% (133/154), 41.6% (64/154), and 26.0% (40/154), respectively. Among &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt;-harboring isolates, cefiderocol (57/76; 75.0%) demonstrated superior activity compared with ceftazidime-avibactam (3/76; 3.9%) and imipenem-cilastatin-relebectam (1/76; 1.3%). Among isolates harboring &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48-like&lt;/sub&gt;, cefiderocol, ceftazidime-avibactam, and imipenem-cilastatin-relebectam demonstrated 100% (17/17), 70.6% (12/17), and 17.6% (3/17) susceptibility, respectively. Nine isolates that harbored two genes (eight &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; + &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48-like&lt;/sub&gt;, one &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; + &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VIM&lt;/sub&gt;) demonstrated 100% susceptibility to cefiderocol but 100% resistance to ceftazidime-avibactam and imipenem-cilastatin-relebectam. The ceftazidime-avibactam plus aztreonam combination achieved 100% susceptibility in isolates harboring metallo-β-lactamases-producing genes; &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; (76/76; 100%), &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; + &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48-like&lt;/sub&gt; (8/8; 100%), and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; + &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VIM&lt;/sub&gt; (1/1; 100%). &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;NDM&lt;/sub&gt; was the most prevalent gene causing CRE. Cefiderocol has the greatest activity compared with other investigated β-lactams.IMPORTANCECarbapenem-resistant Enterobacterales (CRE) has been recognized as a priority and public health concern requiring urgent attention for the development of effective antimicrobial resistance (AMR) prevention and control strategies. Differentiating between carbapenemase-producing CRE (CP-CRE) and non-CP-CRE, along with identifying carbapenemase-prod","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0055325"},"PeriodicalIF":3.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113745","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":"Rapid direct disk diffusion testing for antibiotic resistance in urinary tract infections: a bacterial concentration-adjusted approach.","authors":"Henning Sabersky-Müssigbrodt, Seoras Russell, Nina Wantia, Oliver Hayden","doi":"10.1128/spectrum.00888-25","DOIUrl":"https://doi.org/10.1128/spectrum.00888-25","url":null,"abstract":"<p><p>Urinary tract infections are among the most prevalent bacterial infections worldwide, typically diagnosed using clinical symptoms, dipstick tests, and laboratory methods requiring standardized bacterial suspensions for antibiotic susceptibility testing (AST). This study evaluated two rapid disk diffusion methods for urine samples that incorporate bacterial concentration into the analysis, eliminating the need for standardized suspensions. The threshold-adapted approach compares inhibition zones to concentration-specific breakpoints derived from reference strains, while the regression-based method transforms inhibition zones at various concentrations into predicted standard (0.5 McFarland) values using a linear model. In both methods, urine and antibiotic disks are applied to one agar plate for disk diffusion, while a separate plate determines bacterial concentration, enables isolation, and supports matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) analysis. This simultaneous processing reduces diagnostic time by 18-24 hours. The approaches were compared with traditional disk diffusion testing using defined bacterial suspensions, reference strains, and clinical urine samples. In trials using defined suspensions from 0.5 McFarland to 10<b>³</b> CFU/mL, the threshold-adapted method achieved 94.7% and 94.1% categorical agreement for susceptible and resistant bacteria, respectively; the regression-based method achieved 100% for susceptible and 88.2% for resistant bacteria. When urine was applied directly, both methods showed 93.7% true susceptible and 94.1% true resistant agreement with standard testing. By integrating inhibition zone size, antibiotic, species, and bacterial concentration, these rapid AST methods streamline urine diagnostics and show high agreement with standard testing-highlighting their potential as practical alternatives to conventional AST, particularly in resource-limited settings where reduced diagnostic time and simplified laboratory procedures can significantly improve patient care.IMPORTANCEAntibiotic susceptibility testing (AST) for urinary tract infections typically requires time-consuming standardization of bacterial suspensions, delaying targeted treatment. Prior direct susceptibility testing (DST) approaches have largely overlooked the inoculum effect, testing at a single, arbitrary concentration and risking misclassification of both resistant and susceptible isolates. This study presents two rapid disk diffusion methods that systemically incorporate bacterial concentration into the analysis, enabling direct testing from urine samples without prior inoculum adjustment. Both approaches demonstrated high agreement with standard AST and reduced diagnostic time by up to 24 hours. These concentration-aware methods may streamline susceptibility testing workflows, particularly in resource-limited settings, and represent a practical advancement toward faster, clinically reliable DST.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0088825"},"PeriodicalIF":3.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145113782","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":"Increased intestinal permeability and bile acid accumulation via inhibition of the FXR-SHP pathway contribute to coumarin-induced systemic inflammation.","authors":"Na Shou, Dandan Wu, Qi Wang, Ping Huang, Qiwen Lin, Senao Hou, Keyi Fu, Wenqian Xu, Jiyu Zhang, Zunji Shi","doi":"10.1128/spectrum.01415-25","DOIUrl":"https://doi.org/10.1128/spectrum.01415-25","url":null,"abstract":"<p><p>Coumarin causes severe poisoning in animals, affecting the development of agriculture and animal husbandry. Coumarin induces hepatotoxicity, but the inflammatory mechanism of coumarin is unclear. Here, we explored the effects of coumarin on systemic and hepatic inflammation. Our study found that coumarin reduced the abundance of <i>Akkermansia muciniphila</i>. The number of colonic goblet cells and the expression of <i>Claudin 1</i> and <i>ZO-1</i> were decreased in coumarin-treated groups, increasing intestinal permeability. Coumarin elevated the expression of lipopolysaccharide (LPS) biosynthesis genes and serum LPS. These changes increased oxidative stress indicators and total BA (TBA) in the liver. Coumarin inhibited <i>Fxr</i> and <i>Shp</i> expressions in the liver, thereby promoting cholesterol 7-alpha hydroxylase (<i>Cyp7a1</i>) transcription and upregulating TBA level. Collectively, coumarin induced systemic and hepatic inflammation by decreasing tight junction protein and colonic goblet cells, increasing LPS biosynthesis genes of gut microbiota and serum LPS, and elevating TBA level via the <i>Fxr-Shp</i> pathway.IMPORTANCECoumarin, a compound found in <i>Melilotus officinalis</i>, a high-quality forage plant crucial to animal husbandry, has raised safety concerns due to its potential for severe animal poisoning and liver toxicity. It is not clear about the mechanism of coumarin-induced systemic inflammation and liver inflammation. This research aims to elucidate the mechanisms of coumarin-induced systemic and hepatic inflammation, which is of significant importance for the development of agriculture and animal husbandry. In agriculture, understanding how coumarin affects the gut microbiota and intestinal barrier function could lead to the development of new varieties of <i>Melilotus officinalis</i> with lower coumarin concentrations, thus improving its safety as a forage crop.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0141525"},"PeriodicalIF":3.8,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086456","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 new gold rush in clinical diagnostics: from standard laboratory assays to fast and accurate point-of-care (POC) methods.","authors":"Hui-Chen Foreman","doi":"10.1128/spectrum.01887-25","DOIUrl":"https://doi.org/10.1128/spectrum.01887-25","url":null,"abstract":"<p><p>Integrating two point-of-care (POC)-amenable technologies, namely, multiple cross displacement amplification (MCDA) and gold nanoparticle-based lateral flow biosensors (AuNPs-LFB), has demonstrated excellent detection of hepatitis B virus (HBV) and hepatitis C virus (HCV). In a recent study, Zhang et al. (H. Zang, Y. Shi, Z. Wu, Q. Zhao, et al., Microbiol Spectr 13:e01738-24, 2025, https://doi.org/10.1128/spectrum.01738-24) developed a novel, single-tube, multiplex MCDA-AuNPs-LFB assay that targets the HBV S gene and the HCV 5'-UTR region. The assay operates under isothermal conditions at 64°C for 35 min, and the AuNPs-LFB assay permits a visual interpretation of results. This platform achieves an analytical sensitivity comparable to lab-based quantitative PCR but with shorter turnaround time, reduced cost, operational simplicity, and undetectable cross-reactivity to anatomically relevant, non-target pathogens, making it highly suitable for decentralized POC diagnostic applications. The success of hybrid systems in simplifying nucleic acid testing while increasing portability indicates a potential transition in clinical diagnosis from centralized tech-centered labs to local clinics, field testing, and even home care.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0188725"},"PeriodicalIF":3.8,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>Coxiella burnetii</i> and <i>Bartonella</i> species serology of febrile patients with an established infectious or inflammatory diagnosis in Sudan, Nepal, and Cambodia.","authors":"Carl Boodman, Sophie Edouard, Johan van Griensven, Kanika Deshpande Koirala, Basudha Khanal, Suman Rijal, Narayan Raj Bhattarai, Sayda El Safi, Thong Phe, Kruy Lim, Pascal Lutumba, François Chappuis, Cédric P Yansouni, Achilleas Tsoumanis, Barbara Barbé, Marjan van Esbroeck, Kristien Verdonck, Marleen Boelaert, Nitin Gupta, Pierre-Édouard Fournier, Emmanuel Bottieau","doi":"10.1128/spectrum.01675-25","DOIUrl":"https://doi.org/10.1128/spectrum.01675-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;i&gt;Coxiella burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; species cause febrile illness and infective endocarditis in low- and middle-income countries (LMICs). This study investigated whether seropositivity to &lt;i&gt;C. burnetii&lt;/i&gt; or &lt;i&gt;Bartonella&lt;/i&gt; could be detected among patients with persistent fever for which an infectious or inflammatory etiological diagnosis had been previously established in three LMICs. Our study tested sera from Cambodian, Nepalese, and Sudanese participants using indirect immunofluorescent antibody assays (IFA) for &lt;i&gt;C. burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt;. Seropositivity rates for both pathogens were assessed across tropical and inflammatory etiologies of fever and compared to ubiquitous bacterial infections considered as a \"reference group,\" as they were not expected to cause serologic cross-reactivity. A total of 1,313 individuals underwent IFA, including 560/1,313 (42.7%) from Sudan, 432 (32.9%) from Nepal, and 321 (24.5%) from Cambodia. Overall, 57 (4.3%) and 60 (4.6%) participants tested positive for &lt;i&gt;C. burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; species, respectively. Forty-four (3.4%) individuals tested positive for both &lt;i&gt;C. burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; species (75.4% positive agreement). &lt;i&gt;C. burnetii&lt;/i&gt; positivity did not differ significantly between the three countries (&lt;i&gt;P&lt;/i&gt; = 0.44), while &lt;i&gt;Bartonella&lt;/i&gt; seropositivity was predominantly identified in Nepal (&lt;i&gt;P&lt;/i&gt; &lt; 0.001). Compared to the reference group, &lt;i&gt;C. burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; seropositivity were more common among participants with visceral leishmaniasis, &lt;i&gt;P. falciparum&lt;/i&gt; malaria, leptospirosis, brucellosis, scrub typhus, and systemic lupus erythematosus (SLE), though only statistically significant for the latter two diagnoses. Further studies are necessary to investigate &lt;i&gt;C. burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; seropositivity in LMICs and to disentangle cross-reactivity, previous infection, or co-infection.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;&lt;i&gt;Coxiella burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; spp. are important but under-recognized causes of febrile illness and infective endocarditis in low- and middle-income countries (LMICs). This study evaluated the seroprevalence of these pathogens among patients with confirmed causes of persistent fever in Sudan, Nepal, and Cambodia. Despite the diagnostic utility of serologic testing for these infections, its performance in LMICs-where co-infections and background seropositivity are common-remains poorly characterized. The findings suggest notable seropositivity for &lt;i&gt;C. burnetii&lt;/i&gt; and &lt;i&gt;Bartonella&lt;/i&gt; among patients with a set of tropical and inflammatory diagnoses, including visceral leishmaniasis, &lt;i&gt;Plasmodium falciparum&lt;/i&gt; malaria, leptospirosis, brucellosis, scrub typhus, and systemic lupus erythematosus. These results highlight the potential for cross-reactivity and underscore the need for context-specific validation. Enhanced understanding of serologic test characteristics is esse","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0167525"},"PeriodicalIF":3.8,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086246","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":"Activated carbon ameliorates type 2 diabetes via metabolic remodeling of the gut microbiota.","authors":"Cai-Xia Zhao, Yu-Tong Wu, Yin Wang, Jian-Qiang Su","doi":"10.1128/spectrum.03109-24","DOIUrl":"https://doi.org/10.1128/spectrum.03109-24","url":null,"abstract":"<p><p>Type 2 diabetes (T2D) is a major public health concern worldwide, and there has been increasing attention on the role of natural dietary drugs in diabetes therapy. However, the effects of these drugs on gut microbial composition, functional potentials, and metabolisms remain unclear. Improved carbohydrate and amino acid metabolism, regulated inflammatory mediators, with simultaneous reduction in detrimental compounds were observed in the significantly promoted group of gut bacteria after conducting integrated 16S rRNA sequencing and metabolomic analyses in T2D Goto-Kakizak (GK) rats and healthy Wistar rats that were exposed to four natural dietary drugs (highly porous activated carbon, wheatgrass, dandelion, and corn stigma), while the endotoxin-producing bacteria were inhibited by dietary drugs, especially for the activated carbon diet, which resulted in metabolic changes and anti-inflammatory effects that decreased both high-fat diet-induced obesity and blood glucose. These findings highlight the effectiveness of natural dietary drugs, with a particular emphasis on activated carbon, and establish a foundation for tailoring the use of these drugs in T2D therapy.IMPORTANCEOur findings highlight the significant hypoglycemic effect of activated carbon, demonstrating its potential to remodel the gut microbiota, improve carbohydrate and amino acid metabolism, regulate inflammatory mediators, and reduce detrimental compounds such as lipopolysaccharide (LPS). These results suggest that dietary intervention with activated carbon could be a noninvasive and accessible method for improving diabetes management, providing novel insights into the role of natural dietary drugs in metabolic health and diabetes therapy.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0310924"},"PeriodicalIF":3.8,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086416","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":"Lower airway microbiota compositions and diversity among ventilator-associated pneumonia patients across COVID-19 epidemic phases: a retrospective study.","authors":"Shengyu Hao, Chujun Zhou, Yilin Wei, Yuxian Wang, Pan Jiang, Jieqiong Song, Ming Zhong","doi":"10.1128/spectrum.00076-25","DOIUrl":"https://doi.org/10.1128/spectrum.00076-25","url":null,"abstract":"<p><p>Ventilator-associated pneumonia (VAP) is a major cause of morbidity in critically ill patients, and the SARS-CoV-2 infection has influenced the lung microbiome. This study aimed to examine the lower respiratory tract microbiome in VAP patients during different phases of the Shanghai COVID-19 epidemic. A total of 175 patients were included and divided into pre-epidemic (Pre), during-epidemic (Dur), and post-epidemic (Post) groups for analysis. Bronchoalveolar lavage fluid and serum were analyzed using next-generation sequencing. The intensive care unit (ICU) mortality rates were 48.3% (Pre group), 60.3% (Dur group), and 28.8% (Post group). Cytokine levels were lower in the Post group compared to the Pre group. <i>Acinetobacter</i>, <i>Candida</i>, and <i>Herpes Simplex Virus 1</i> (<i>HSV-1</i>) were the most frequently detected organisms. The prevalence of <i>Klebsiella pneumoniae</i>, <i>Enterococcus faecium</i>, <i>Aspergillus fumigatus</i>, and <i>HSV-1</i> was higher in the Dur group. α-Diversity of bacteria was significantly lower in the Dur group (<i>P</i> < 0.05), indicating reduced microbiome diversity. Multivariable Cox regression analysis identified APACHE II score (hazard ratio [HR] = 1.04, <i>P</i> = 0.029) and maximum bacterial load (HR = 1.67, <i>P</i> = 0.046) as independent risk factors for ICU mortality. This study highlights changes in microbiome composition across epidemic phases, which may inform treatment strategies.IMPORTANCEWith the development of next-generation sequencing technology, it is increasingly being applied in clinical practice, especially in evaluating the prognosis of severe infections and co-infections. This study characterized the composition of microorganisms in the lower respiratory tract of ventilator-associated pneumonia (VAP) patients across three phases of the COVID-19 epidemic. Our study emphasizes that the relative abundance of bacteria, fungi, and viruses in bronchoalveolar lavage fluid of VAP patients may vary with the progression of the local epidemic and host immune status. These findings provide a mechanistic basis for optimizing targeted therapies in VAP management during infectious disease outbreaks.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0007625"},"PeriodicalIF":3.8,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086414","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}