Microbiology spectrum最新文献

{"title":"Further delineation of the etiology of liver abscesses in cattle and indication of hindgut as a potential source of pathogens.","authors":"Harith M Salih, Alyssa Deters, Raghavendra G Amachawadi, Haiyan Wang, Taghreed Mahmood, Xiaorong Shi, Mina Abbasi, Leigh Ann George, Ty E Lawrence, T G Nagaraja","doi":"10.1128/spectrum.02539-25","DOIUrl":"https://doi.org/10.1128/spectrum.02539-25","url":null,"abstract":"<p><p>Liver abscesses (LA) in feedlot cattle are polymicrobial infections, initiated primarily by the translocations of the two subspecies of <i>Fusobacterium necrophorum, necrophorum</i> and <i>funduliforme,</i> and secondarily by <i>Trueperella pyogenes</i> and <i>Salmonella enterica</i> from the rumen into the liver via portal blood. The hindgut has not been investigated as a potential source of LA pathogens. Our objectives were to analyze LA and matched ruminal and colonic epithelial tissues (<i>n</i> = 96), collected at a commercial beef processor immediately after evisceration, to determine culture-based prevalence of pathogens, specifically, <i>Escherichia coli</i>, <i>Klebsiella pneumoniae</i>, <i>Pseudomonas aeruginosa</i>, and <i>Bacteroides fragilis,</i> which have not been targeted before, in addition to <i>F. necrophorum, T. pyogenes,</i> and <i>S. enterica,</i> and quantitative PCR-based prevalence and concentrations of the <i>F. necrophorum</i> subspecies. The subsp. <i>necrophorum</i> was the most dominant species in LA detected by both methods, and concentrations were in the range of 7.0 log<sub>10</sub> colony forming units (CFU). Fusobacterial concentrations were higher in ruminal epithelial than in colonic epithelial tissues, but colonic epithelial tissues yielded more subsp. <i>necrophorum</i> isolates than ruminal epithelial tissues. Of the targeted bacterial species, <i>E. coli</i> was the most dominant, and none of the tissues was positive for <i>B. fragilis</i>. A majority of the isolations of <i>E. coli</i> were after enrichment, suggesting the concentrations were too low to contribute to the abscess development. The data reaffirm that LA are polymicrobial infections, <i>F. necrophorum,</i> specifically <i>necrophorum,</i> is the most dominant species prevalent, and the hindgut is likely to be a source, in addition to the rumen, of pathogens that cause LA.IMPORTANCELiver abscesses (LA) in beef cattle are initiated by entry of bacterial pathogens from the rumen via portal blood. The two most frequently isolated pathogens are the two subspecies of <i>Fusobacterium necrophorum,</i> followed by <i>Trueperella pyogenes</i> and <i>Salmonella enterica</i>. Our objectives were to determine the prevalence of pathogens that have been reported sporadically and have not been targeted before. Liver abscesses and matched ruminal epithelium and colonic epithelial tissues, collected from feedlot cattle at slaughter, were analyzed by culture and PCR methods. The subsp. <i>necrophorum</i> was the most dominant bacterium in liver abscesses. Colonic epithelial tissues yielded more subsp. <i>necrophorum</i> than ruminal epithelial tissues. Although <i>Escherichia coli</i> was the second most prevalent species, a majority of the isolates were obtained after enrichment, indicating low concentrations. Our data reaffirm that <i>F. necrophorum</i> is the dominant species prevalent in LA, and the hindgut is likely to be another source of pathogens","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0253925"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251870","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":"Population-based concordance of <i>Chlamydia trachomatis</i> genotypes between ocular and urogenital samples in Nauru.","authors":"Kym Lowry, Sue-Chen Apadinuwe, Mitchell Starr, Susan Star, Kathleen D Lynch, Anthony W Solomon, Philip Cunningham, Stephen Lambert, David Whiley, John Kaldor, Susana Vaz Nery","doi":"10.1128/spectrum.03205-24","DOIUrl":"https://doi.org/10.1128/spectrum.03205-24","url":null,"abstract":"<p><p><i>Chlamydia trachomatis</i> causes sexually transmitted urogenital infections, as well as ocular infections, the latter mostly spread between children and responsible for the blinding disease trachoma. The strains causing these two types of infection are generally distinct, but there is some evidence that urogenital strains can infect the eye and cause conjunctivitis, possibly indicating transmission on fingers of adults or adolescents to children. In what we believe is the first study of its kind in a setting of high prevalence of both urogenital and ocular infection, we characterized <i>C. trachomatis</i> strains from 107 ocular and 95 urine samples collected through cross-sectional population surveys in Nauru, employing household-based sampling. Ocular samples were collected during a national baseline prevalence survey in 2019 in children aged 1-9 years. Urine samples were collected from adults participating in a national survey before (March 2020) and after (December 2020) a national mass drug administration (MDA) of azithromycin for trachoma in April 2020. We used a cluster survey design to recruit participants, with clusters based on Nauru's districts and a predetermined number of households randomly selected in each cluster. There was no attempt to recruit from the same households across the three survey rounds. Only genotype C, recognized as an ocular strain, was identified in eye specimens from children, whereas six urogenital genotypes (D, E, G, J, Ja, and L1) were detected in adult urine samples, with genotype D most frequent. We, therefore, concluded that, in this highly endemic setting for both urogenital and ocular infection with <i>C. trachomatis,</i> there were two distinct networks of transmission with no evidence of crossover, at least at the population level.IMPORTANCEChlamydia infections are a public health issue with two broad manifestations: ocular infections, mostly found in children, and sexually transmitted infections of the genital tract and anus that can lead to adverse reproductive health outcomes. While generally caused by different <i>C. trachomatis</i> strains, there is some evidence that strains considered to be predominantly sexually transmitted can infect the conjunctiva and cause signs resembling trachoma. Possible strain crossover has raised concern about whether eye infection with genital <i>C. trachomatis</i> strains confers a drive toward visual impairment and blindness, and the potential for such infections to lead to overestimates of trachoma prevalence. In what we believe to be the first study of its kind, we identified distinct ocular strains in pediatric ocular swabs and urogenital strains in adult urine specimens in Nauru and concluded that urogenital <i>C. trachomatis</i> strains are not contributing to ocular disease despite the high prevalence of urogenital chlamydia.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0320524"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251943","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":"Evaluation of a direct method for detecting extended-spectrum β-lactamase using the Cica-beta test on positive blood culture bottles.","authors":"Tomohide Okinaka, Yuji Teshima, Yoshimi Furuno, Miho Takeishi, Ayami Tashiro, Yoko Matsuda, Ayumi Irie, Tomomi Marutani, Hidenobu Koga, Takashi Matono","doi":"10.1128/spectrum.01112-25","DOIUrl":"https://doi.org/10.1128/spectrum.01112-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The global prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is a growing concern, underscoring the need for rapid detection to enable timely, targeted therapy. Conventional methods for ESBL detection, typically involving subculture followed by phenotypic screening and confirmatory tests based on the Clinical and Laboratory Standards Institute guidelines, require extended turnaround times. While rapid molecular diagnostic tests exist, their availability can be limited in some settings due to cost or infrastructure requirements, whereas matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for bacterial identification is more widely adopted. The chromogenic cephalosporin HMRZ-86-based Cica-beta test is a simpler alternative but traditionally requires colonies from subcultures. This study evaluated a direct Cica-beta test using positive blood cultures for rapid extended-spectrum β-lactamase detection. Using bacterial pellets prepared from 109 positive blood cultures of &lt;i&gt;Escherichia coli&lt;/i&gt;, &lt;i&gt;Klebsiella pneumoniae&lt;/i&gt;, &lt;i&gt;Klebsiella oxytoca&lt;/i&gt;, or &lt;i&gt;Proteus mirabilis&lt;/i&gt;, the direct Cica-beta test demonstrated high sensitivity (96.3%, 95% confidence interval [CI]: 81.0-99.9) and specificity (100%, 95% CI: 93.5-100), with a positive predictive value of 100% (95% CI: 81.0-100) and a negative predictive value of 98.8% (95% CI: 93.5-100), when compared to conventional methods. This direct method provides a faster alternative to traditional subculture-based testing, enabling prompt antibiotic adjustments. Although challenges remain, such as the potential misclassification of certain β-lactamases, such as AmpC, this approach offers a promising, cost-effective strategy for rapid diagnosis. It has the potential to improve patient outcomes by facilitating timely and appropriate antimicrobial therapy. Further multicenter studies are necessary to validate these findings.IMPORTANCEExtended-spectrum β-lactamase-producing Enterobacterales pose significant challenges in clinical practice due to their resistance to β-lactam antibiotics and association with increased mortality in bloodstream infections. Rapid and accurate identification of these organisms remains crucial for guiding initial antimicrobial therapy and improving patient outcomes. Conventional testing methods are time-consuming, and advanced molecular techniques, such as FilmArray, are costly and not universally available. This study evaluated a novel application of the chromogenic cephalosporin HMRZ-86-based Cica-beta test, a direct method using bacterial pellet from positive blood cultures for extended-spectrum β-lactamase detection. It demonstrated high diagnostic accuracy, with sensitivity and specificity comparable to conventional and FilmArray methods, while significantly reducing result turnaround time. This cost-effective, rapid diagnostic tool offers practical advantages in diverse clinical settings and resource-limited environment","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0111225"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of plasmid-mediated tigecycline resistance <i>tet</i>(x4) and New Delhi metallo-β-lactamase (NDM) in an <i>Escherichia coli</i> isolate from Canada.","authors":"Laura F Mataseje, Nicole Lerminiaux, Allison McGeer, Jennie Johnstone, Susan Poutanen, Erin McGill, Yves Longtin","doi":"10.1128/spectrum.00976-25","DOIUrl":"https://doi.org/10.1128/spectrum.00976-25","url":null,"abstract":"<p><p>Rapid spread of carbapenemase-producing Enterobacterales is a global health threat for which tigecycline is one of the few remaining therapeutic options. Resistance by <i>tet</i>(x4) is particularly worrisome, given its presence on mobile genetic elements. Here we report on a tigecycline-resistant <i>Escherichia coli</i> strain isolated from a patient returning from Pakistan. A <i>tet</i>(x4) gene was found on an IncFII plasmid isolated from an ST410 <i>E. coli</i> co-harboring NDM-5. The combination of carbapenemase and <i>tet</i>(x4) is concerning.IMPORTANCETigecycline is one of the few last-resort therapeutic options available for treating multidrug-resistant gram-negative bacterial infections, particularly of interest in carbapenemase-producing isolates. Mobile tigecycline resistance is still relatively rare, especially in North America and among clinical isolates. Here we describe the identification of a high-risk clone (<i>E. coli</i> ST410) in Canada that contains the tigecycline resistance gene <i>tet</i>(x4) on an IncFII plasmid and <i>bla</i>_NDM-5 on a separate IncFIB plasmid. Here, we highlight a rare resistance gene in combination with a carbapenemase, both of which are plasmid mediated, complicating antimicrobial treatment options.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0097625"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>In vitro</i> activity of cefiderocol against nosocomial <i>Acinetobacter baumannii</i>.","authors":"Barbara Ymaña, Rocío Egoávil-Espejo, Rosario Huerto-Huánuco, Rosario Oporto-Llerena, Carla A Alonso, Angie K Castillo, Luciano A Palomino-Kobayashi, Carmen Valera-Krumdieck, Gabriela Soza, Tamin Ortiz-Gomez, Patricia Gonzales, María López, Gina Salvador-Luján, Beatriz Rojo-Bezares, Martin Casapia, Paula Toledano, Joseph Pinto, Maria Ramos Chirinos, Yolanda Sáenz, Maria J Pons, Joaquim Ruiz","doi":"10.1128/spectrum.00844-25","DOIUrl":"https://doi.org/10.1128/spectrum.00844-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The emergence and spread of third-/fourth-generation cephalosporin and/or carbapenem-resistant &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; have become a significant global public health concern, making new treatment alternatives necessary. Thus, the present study aimed to assess &lt;i&gt;in vitro&lt;/i&gt; cefiderocol activity against clinical isolates of &lt;i&gt;A. baumannii&lt;/i&gt; and analyze their relationship with extended-spectrum β-lactamases (ESBLs) and carbapenemases. Ninety-five &lt;i&gt;A. baumannii&lt;/i&gt; clinical isolates were included in the study. Susceptibility to 12 antimicrobial agents was established by automated methods and/or disk diffusion, while that of colistin was determined following microdilution and that of cefiderocol by microdilution using iron-depleted broth. The presence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;CTX-M&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;PER&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VEB&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;GES&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;VIM&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMI&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;NDM&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-23G&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-24G&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48G&lt;/sub&gt;, and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-58G&lt;/sub&gt; was established by PCR. The results showed extremely high levels of resistance (&gt;80%) to all the tested antibacterial agents except colistin (11.6%) and cefiderocol (Clinical and Laboratory Standards Institute [CLSI]: 0%; US Food and Drug Administration [FDA]: 1.1%). Following FDA criteria, 22.1% of isolates were intermediate to cefiderocol, with 68.4% of isolates surpassing the European Committee on Antimicrobial Susceptibility Testing epidemiological cut off. Seven colistin-resistant isolates were only susceptible to cefiderocol following CLSI breakpoints, four of them qualifying as cefiderocol-intermediate following FDA breakpoints. No association between the presence of ESBLs or carbapenemases and cefiderocol minimum inhibitory concentration levels was observed. The present results show the potential utility of cefiderocol in the treatment of &lt;i&gt;A. baumannii&lt;/i&gt; infections, highlighting the need for judicious use and continuous surveillance to prevent the emergence of cefiderocol-resistant &lt;i&gt;A. baumannii&lt;/i&gt; clones.IMPORTANCEAntibiotic resistance is a silent pandemic challenging the treatment of infectious diseases worldwide, but also other medical practices, as, for instance, organ transplantation procedures. In Peru, current levels of antimicrobial resistance are worrisome. In this scenario, we have determined the &lt;i&gt;in vitro&lt;/i&gt; activity of cefiderocol against a series of &lt;i&gt;Acinetobacter baumannii&lt;/i&gt; exhibiting high levels of resistance to commonly used antibiotics. This activity is independent of the presence of the most common extended-spectrum beta-lactamases or carbapenemases. Obtained results showed the potential of cefiderocol to become an alternative for the treatment of this type of microorganism, but the high number of isolates bordering the considered breakpoint, despite the lack of use of cefiderocol in the c","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0084425"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251877","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>Caenorhabditis elegans</i> AWC neuron-mediated chemosensation negatively modulates dormancy during <i>Salmonella fepB</i> mutant infection.","authors":"Swarupa Mallick, Jasmin Pradhan, Chamjailiu Daimai, Vidya Devi Negi","doi":"10.1128/spectrum.00420-25","DOIUrl":"https://doi.org/10.1128/spectrum.00420-25","url":null,"abstract":"<p><p>In our earlier work, we demonstrated that continuous 8-day exposure of <i>Caenorhabditis elegans</i> to a <i>Salmonella enterica</i> serovar Typhimurium <i>fepB</i> mutant strain negatively regulates dauer larva development in the second generation of the population. Our current study aims to understand how specific chemosensory neurons in <i>C. elegans</i> recognize the <i>∆fepB Salmonella</i> Typhimurium strain and undergo plasticity in response to infection. We observed the olfactory preference of <i>C. elegans</i> toward the pathogenic wild type <i>Salmonella</i> (WT-STM). However, prolonged exposure showed enhanced lawn occupancy of nematodes in the ∆<i>fepB</i> strain with better associative learning response than the WT-STM counterpart. We also observed upregulation of chemosensory genes <i>odr-7</i>, <i>ceh-36</i>, <i>daf-11</i>, <i>tax-2</i>, and <i>tax-4</i> at 24 hours post ∆<i>fepB</i> infection. However, continuous exposure to defective olfactory neuron mutants of the <i>C. elegans</i> emphasizes AWC neurons' participation in sensing the Δ<i>fepB</i> strain, ultimately mediating plasticity in <i>C. elegans</i>' second generation. Our research shows how the olfactory neurons of <i>C. elegans</i> detect <i>Salmonella</i> Typhimurium upon encounter and adjust their behavior accordingly. Furthermore, it highlights the strong connection between the chemosensory neurons of nematodes and the bacterial signals that regulate host physiology for survival.</p><p><strong>Importance: </strong>Bacteria act as food signals for the <i>Caenorhabditis elegans</i>. Our work gives insight into how worms' olfactory neurons recognize pathogen <i>Salmonella</i> Typhimurium exposure and modulate behavioral plasticity, giving a better survival strategy against the pathogens. How specific chemosensory neurons in worms recognize the ∆<i>fepB</i> strain and undergo behavioral plasticity in response to infection. Furthermore, it highlights the strong connection between the chemosensory neurons of worms and the bacterial signals that regulate host physiology for survival when exposed to mutant strain infection, which might be under check in wild-type bacteria for their own benefit in an evolutionary adaptation. This mechanism might help the worm to select the pathogenic or non-pathogenic microbes as food and avoid infection-mediated lethality.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0042025"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251890","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 machine learning-based predictive model for multilobar pulmonary consolidation induced by macrolide-resistant <i>Mycoplasma pneumoniae</i> pneumonia caused by the 23S rRNA A2063G mutation.","authors":"Yan Guo, Yonghan Luo","doi":"10.1128/spectrum.02458-25","DOIUrl":"https://doi.org/10.1128/spectrum.02458-25","url":null,"abstract":"<p><p>This study aims to develop a machine learning (ML)-based predictive model for assessing the risk of multilobar pulmonary consolidation in children with macrolide-resistant <i>Mycoplasma pneumoniae</i> pneumonia (MRMP) caused by the 23S rRNA A2063G mutation, a subgroup underrepresented in prior studies. A total of 404 MRMP cases diagnosed between October 2024 and February 2025 were included in this study. Key clinical characteristics, including laboratory test results, symptoms, and treatment outcomes, were extracted from electronic medical records. Six ML models, including Logistic Regression, Naive Bayes, K-Nearest Neighbors, Multilayer Perceptron, Random Forest, and XG-Boost, were developed to predict multilobar pulmonary consolidation. Least absolute shrinkage and selection operator (LASSO) regression was used to select relevant variables. Model performance was then evaluated using receiver operating characteristic (ROC) curves and decision curve analysis (DCA). Finally, Sharpley Additive Explanations was used for model interpretability. XG-Boost demonstrated the highest predictive performance with an area under the ROC curve of 0.976 and 0.904 in the training and validation sets, respectively, showing a high sensitivity of 0.97, specificity of 0.81, accuracy of 0.94, and an F1 score of 0.95. Key predictors identified for multilobar pulmonary consolidation included the top 10 variables: C-reactive protein, lactate dehydrogenase, fibrinogen, platelet count, albumin, hemoglobin, creatinine, aspartate aminotransferase, interleukin-6, and oxygen therapy. DCA showed that the model also exhibited strong clinical utility. The XG-Boost predictive model offers a robust tool for identifying high-risk children with MRMP caused by the 23S rRNA A2063G mutation. By integrating clinical features, the model enhances early risk stratification and can support clinical decision-making, improving the accuracy and efficiency of treatment plans.IMPORTANCEMacrolide-resistant <i>Mycoplasma pneumoniae</i> pneumonia caused by the 23S rRNA A2063G mutation poses a significant threat to pediatric health, often leading to severe multilobar pulmonary consolidation. This study develops a high-performance machine learning model (XG-Boost) that accurately predicts this complication using key clinical indicators such as C-reactive protein, lactate dehydrogenase, and IL-6. With an area under the ROC curve of 0.976, the model enables early risk stratification, guiding clinicians in optimizing treatment for high-risk children. By improving diagnostic precision and intervention timing, this tool can reduce disease severity, minimize hospital stays, and enhance patient outcomes. The interpretability of the model via Sharpley Additive Explanations analysis further ensures its clinical applicability, making it a valuable advancement in managing antibiotic-resistant pediatric pneumonia.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0245825"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251895","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":"Transcription factor RonA-driven GlcNAc catabolism is essential for growth, cell wall integrity, and pathogenicity in <i>Aspergillus fumigatus</i>.","authors":"Xiufang Gong, Xinwei Ge, Qijian Qin, Bin Wang, Linqi Wang, Cheng Jin, Wenxia Fang","doi":"10.1128/spectrum.00122-25","DOIUrl":"https://doi.org/10.1128/spectrum.00122-25","url":null,"abstract":"<p><p><i>Aspergillus fumigatus,</i> a saprophytic mold, demonstrates metabolic versatility by utilizing diverse carbon sources to sustain its growth and pathogenic potential. While N-acetylglucosamine (GlcNAc), an ubiquitous amino sugar, serves as a vital nutrient, its catabolic pathway in <i>A. fumigatus</i> remains unexplored. Here, we identified core components of this pathway, including GlcNAc-6-phosphate deacetylase (DacA), glucosamine-6-phosphate deaminase (NagA), and the transcription factor RonA. The expressions of <i>dacA</i>, <i>nagA</i>, and <i>ronA</i> were strongly induced when GlcNAc was the sole carbon source. Both Δ<i>dacA</i> and Δ<i>nagA</i> mutants exhibited abolished growth under GlcNAc condition, whereas the Δ<i>ronA</i> mutant exhibited pleiotropic defects, including severe growth defects, impaired polarity, delayed development, reduced cell wall integrity, and decreased virulence in a <i>Galleria mellonella</i> infection model. The deletion of <i>ronA</i> resulted in enhanced immune clearance and exacerbated inflammatory responses. Conidial cell wall analysis revealed that Δ<i>ronA</i> conidia displayed aberrant cell wall architecture, primarily characterized by increased surface protein exposure and significantly reduced melanin. Collectively, our findings highlight RonA's critical role in GlcNAc catabolism, conidial cell wall integrity, and the pathogenesis of <i>A. fumigatus</i>, providing novel insights into antifungal drug development.IMPORTANCE<i>Aspergillus fumigatus</i> is a major human fungal pathogen known for its ability to cause a wide range of diseases, primarily due to its exceptional adaptability to diverse environments. This study identifies DacA and NagA as key enzymes in GlcNAc catabolism, while the transcription factor RonA is essential for growth, sporulation, and cell wall stress response on GlcNAc. Beyond regulating GlcNAc catabolism, RonA was found to play a pivotal role in modifying the conidial cell wall structure, influencing host-pathogen interactions, including immune modulation and pathogenicity. These findings highlight RonA as a potential therapeutic target for treating <i>A. fumigatus</i> infections.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0012225"},"PeriodicalIF":3.8,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145251952","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":"Urogenital microbiome, intracellular bacterial communities, and their contribution to urinary tract infections.","authors":"Luciana Robino, Nicolás Navarro, Nicole Canales-Huerta, María José González, Erlen Cruz, Rafael Sauto, Cecilia Morales, Florencia Neffa, Javier Zeballos, Gerdhard L Jessen, Pablo Zunino, Paola Scavone","doi":"10.1128/spectrum.01247-25","DOIUrl":"https://doi.org/10.1128/spectrum.01247-25","url":null,"abstract":"<p><p>The urinary tract was long considered a sterile environment, but recent studies have revealed the presence of diverse microbial communities in healthy individuals collectively known as the urinary microbiome or urobiome. Although the urobiome has been studied primarily in populations from North America, Europe, and Asia, little is known about its characteristics in Latin America. In this work, we conducted a descriptive analysis of the urobiome of 77 adults, 40 females, and 37 males with and without symptoms of urinary tract infections (UTI) from Uruguay using a strategy that includes expanded quantitative uroculture, 16S rRNA gene sequencing from urine, and intracellular bacterial community evaluation. The microbial profiles revealed a wide diversity in the bacterial community composition, including both <i>Lactobacillus</i>-dominated and diverse non-<i>Lactobacillus</i> communities. Notably, several genera frequently associated with health or disease, such as <i>Gardnerella</i>, <i>Staphylococcus</i>, <i>Streptococcus</i>, and <i>Escherichia</i>, were detected in many samples. We also observed associations between community types and host factors, such as gender, presence of symptoms, and IBC. These findings contribute to expanding our understanding of the human urobiome and highlight the need to consider geographic and cultural diversities when characterizing microbial communities and their implications for health.IMPORTANCEThe concept of a sterile urinary tract has been challenged by the discovery of complex microbial communities in urine samples from healthy individuals. Most existing studies on the urinary microbiome focus on populations in the Global North, resulting in limited data from Latin America. Here, we present the first study characterizing the urobiome of an adult Uruguayan population using 16S rRNA gene sequencing. By analyzing associations between bacterial community types and individual metadata, we provide insights into the diversity and structure of urinary microbiota in a previously understudied population. These results broaden the current understanding of the urobiome and emphasize the importance of including diverse populations in microbiome research to achieve a more comprehensive and representative view of microbial contributions to health and disease.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0124725"},"PeriodicalIF":3.8,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239149","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>Streptomyces</i> sp. BI87 from human gut: potent anticancer activities and divergence from known <i>Streptomyces</i> lineages.","authors":"Yu-Hui Wang, Hong-Tao Xu, Miao-Wei Liu, Bao-Juan Yuan, Xin-Yu Gao, Xing-Hua Zhang, Hong-Da Tian, Hao Yu, Jin-Ru Lai, Liang Liu, Randal N Johnston, Gui-Rong Liu, Shu-Lin Liu","doi":"10.1128/spectrum.00858-25","DOIUrl":"10.1128/spectrum.00858-25","url":null,"abstract":"<p><p>Cancer is among the deadliest diseases with few truly curative therapies. Recent studies have shown that the human intestinal microbiota contains bacteria that exhibit potent suppressive effects on cancer or coordinate anticancer functions with the immune system. However, whether the peculiar anticancer trait was acquired stochastically by a strain of a non-anticancer bacterial species or an intrinsic property of a phylogenetic lineage of bacteria remained unclear. In this study, we compared a human gut isolate <i>Streptomyces</i> sp. BI87, which had highly effective anticancer activities, with the type strain of <i>Streptomyces albidoflavus</i>, DSM 40455^T, which was most closely related to BI87 among 30 type strains of the genus <i>Streptomyces</i> but did not show any detectable anticancer activities. We found that, although BI87 and DSM 40455^T had >99% 16S rDNA sequence similarity, they are phylogenetically separated by a genetic boundary into distinct natural species as evaluated by the 3Cs definition of bacterial species based on the ratio of common genes with zero sequence degeneracy. In addition to the anticancer activities, BI87 encodes several biological characteristics different from DSM 40455^T, including those of antibacterial and antiviral spectra, secondary metabolites, structural composition in the cell wall, and major cellular fatty acids. Based on the genomic and phenotypic distinctions of BI87 from closely related <i>Streptomyces</i> strains, we propose that the anticancer bacterial strain BI87 represents a new lineage at the natural species level within the genus <i>Streptomyces</i>.IMPORTANCEThe characterization of the anticancer bacterial strain, <i>Streptomyces sp</i>. BI87, isolated from a healthy human, suggests the prevalent existence of anticancer microbes in the gut microbiome of humans, which may be nurtured and harnessed for cancer prevention or treatment without the need for the introduction of engineered and non-indigenous microbes to a person or the use of radio- or chemo-therapies. Also important is the finding that a close relative of BI87, <i>Streptomyces albidoflavus</i> DSM40455^T, does not express appreciable anticancer properties in the same <i>in vitro</i> and <i>in vivo</i> experiments, demonstrating that <i>Streptomyces</i> sp. BI87 represents a novel bacterial lineage with selective suppressive activities on cancer, at the phylogenetic level of natural species. Genomic comparisons between BI87 and DSM40455^T demonstrate that phylogenetic delineation of closely related bacteria needs to be conducted at the level of natural species rather than OTUs, as an OTU may contain phenotypically or even phylogenetically radically distinct bacteria.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0085825"},"PeriodicalIF":3.8,"publicationDate":"2025-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12502529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}