Microbiology spectrum最新文献

{"title":"ArcA modulates multidrug resistance and compound susceptibility in <i>Klebsiella pneumoniae</i> through ArcB-independent regulation of the SMR efflux pump kpnEF.","authors":"Tongtong Fu, Zheng Fan, Yuchen Chen, Zhoufei Li, Hongbo Liu, Bing Du, Xiaohu Cui, Yanling Feng, Hanqing Zhao, Guanhua Xue, Jinghua Cui, Chao Yan, Lin Gan, Junxia Feng, Ziying Xu, Yang Yang, Zihui Yu, Yuehua Ke, Jing Yuan","doi":"10.1128/spectrum.01499-25","DOIUrl":"https://doi.org/10.1128/spectrum.01499-25","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> has become a major clinical and public health threat due to the increasing prevalence of healthcare-associated infections caused by multidrug-resistant strains. In this study, we demonstrated that the deletion of <i>arcA</i> of ArcAB two-component system diminished the susceptibility of <i>K. pneumoniae</i> to antibiotics, osmotic agents, disinfectants, and structural compounds, which was independent of <i>arcB</i>. RNA-seq analysis revealed a marked upregulation of SMR efflux pump genes <i>kpnEF</i> in the Δ<i>arcA</i> strain compared to the wild-type strain, while the Δ<i>arcB</i> strain exhibited no significant changes. Notably, the deletion of <i>kpnEF</i> in both Δ<i>arcA</i> and wild-type strains abolished their differential susceptibility to antibiotics, osmotic agents, disinfectants, and structural compounds. The EMSA experiments showed that ArcA-P regulated the <i>kpnEF</i> transcriptional expression by directly binding to its promoter region. These findings indicated that ArcA could directly modulate the expression of the KpnEF efflux pump independently of its sensor kinase ArcB. Through phosphorylation level detection and gene knockout experiments, we found that ArcA phosphorylation in the Δ<i>arcB</i> strain was primarily mediated by the AckA-Pta pathway. This study expanded the function of the ArcAB system and provided a critical theoretical foundation for elucidating the mechanisms underlying bacterial antibiotic resistance in <i>K. pneumoniae</i>.IMPORTANCE<i>Klebsiella pneumoniae</i> is an important opportunistic bacterial pathogen, which can acquire a series of antimicrobial resistance (AMR) genes. The emergence of carbapenem-resistant <i>K. pneumoniae</i> (CRKP) posed significant challenges to public health. Polymyxins are often regarded as the last line of defense against CRKP infections. In this study, the deletion of <i>arcA</i>, the regulator of the two-component system ArcAB, increased resistance of <i>K. pneumoniae</i> to antibiotics and decreased susceptibility to osmotic agents, disinfectants, and structural compounds, which was independent of ArcB. Further experiments have shown that ArcA regulated the expression of the small multidrug resistance (SMR) pump KpnEF through direct binding. This process required ArcA phosphorylation, which was independent of ArcB but dependent on the AckA-Pta pathway. This study deepened the regulatory network of ArcAB and provided a new target for the treatment of <i>K. pneumoniae</i>.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0149925"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280658","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":"Correlation of QRDR mutations and MIC levels in fluoroquinolone-resistant <i>Staphylococcus aureus</i> clinical isolates.","authors":"Sohyeong Kim, Xianglan Xuan, Minju Jung, Yujin Park, Soyun Kim, Gaeun Woo, Heechul Park, Sangha Kim, Jiyoung Lee, Min Park, Sunghyun Kim","doi":"10.1128/spectrum.00645-25","DOIUrl":"https://doi.org/10.1128/spectrum.00645-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Antimicrobial resistance is a global health problem. Among various antibiotic-resistant bacteria, &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, particularly methicillin-resistant &lt;i&gt;S. aureus&lt;/i&gt; (MRSA), is a clinically important pathogen responsible for serious infections because of its multidrug resistance (MDR) and association with high mortality rates. The MDR nature of MRSA, including resistance to macrolides, aminoglycosides, fluoroquinolones, and tetracyclines, limits therapeutic choices and poses significant challenges in clinical management. This study aimed to analyze the correlation between mutations in the quinolone resistance-determining region (QRDR) and the minimum inhibitory concentration (MIC) of fluoroquinolone drugs, such as ciprofloxacin and levofloxacin, in MRSA and methicillin-sensitive &lt;i&gt;S. aureus&lt;/i&gt; (MSSA). A total of 63 &lt;i&gt;S&lt;/i&gt;. &lt;i&gt;aureus&lt;/i&gt; clinical strains were isolated from blood samples of sepsis patients. DNA sequence analysis was performed using gDNA extracted from all &lt;i&gt;S. aureus&lt;/i&gt; clinical isolates to identify mutations in the QRDR of &lt;i&gt;gyr&lt;/i&gt;A, &lt;i&gt;gyr&lt;/i&gt;B, &lt;i&gt;par&lt;/i&gt;C, and &lt;i&gt;par&lt;/i&gt;E. The MICs of antimicrobials were determined by the broth microdilution method. Among these genes, only mutations in &lt;i&gt;par&lt;/i&gt;C showed a statistically significant positive correlation with elevated MIC levels, underscoring the primary role of &lt;i&gt;par&lt;/i&gt;C in mediating resistance in our clinical isolates. Notably, all isolates exhibited a substitution at serine 80 (S80) in &lt;i&gt;par&lt;/i&gt;C, and those harboring simultaneous substitutions at both S80 and glutamic acid 84 (E84) demonstrated markedly increased MIC values for both drugs. These findings reinforce previously reported associations between dual mutations and high-level fluoroquinolone resistance, while highlighting the distinct contribution of &lt;i&gt;par&lt;/i&gt;C among the QRDR genes analyzed in this study. Furthermore, we found that the most frequent mutation in the QRDR was the cytosine-to-thymine mutation.IMPORTANCEAntimicrobial resistance is a growing global health crisis, making bacterial infections harder to treat. &lt;i&gt;Staphylococcus aureus&lt;/i&gt;, especially MRSA, is a major concern due to its resistance to multiple antibiotics, including fluoroquinolones like ciprofloxacin and levofloxacin. Our study highlights how specific genetic mutations in the quinolone resistance-determining region (QRDR) influence fluoroquinolone resistance. We found that mutations in the &lt;i&gt;par&lt;/i&gt;C gene, particularly substitutions at serine 80 (S80) and glutamic acid 84 (E84), significantly increase resistance. Understanding these mutations helps predict antibiotic resistance and may guide more effective treatment strategies. By identifying key genetic changes that drive fluoroquinolone resistance, our research contributes to developing improved diagnostic tools and targeted therapies to combat drug-resistant &lt;i&gt;S. aureus&lt;/i&gt; infections. This knowledge is crucial for clinicians and researchers working to contr","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0064525"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280672","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":"Activity of cefiderocol against <i>Pseudomonas aeruginosa</i> from the USA and Europe (2020-2023) with difficult-to-treat resistance phenotype, including those nonsusceptible to recently developed β-lactam/β-lactamase inhibitor combinations: results from the SENTRY antimicrobial surveillance program.","authors":"John H Kimbrough, Maura H Karr, Sean T Nguyen, Boudewijn L M DeJonge, Chris Longshaw, Miki Takemura, Yoshinori Yamano, Mariana Castanheira, Rodrigo E Mendes","doi":"10.1128/spectrum.02079-25","DOIUrl":"https://doi.org/10.1128/spectrum.02079-25","url":null,"abstract":"<p><p>Cefiderocol and the β-lactam/β-lactamase inhibitor (BL-BLI) combinations ceftazidime-avibactam (CAZ-AVI), imipenem-relebactam (IMI-REL), and ceftolozane-tazobactam (TOL-TAZ) are recommended for the treatment of difficult-to-treat resistance (DTR) <i>Pseudomonas aeruginosa</i> by IDSA guidelines. The activity of cefiderocol and the three BL-BLI combinations described above was examined against DTR <i>P. aeruginosa</i> and molecularly characterized subsets collected from the USA and Europe (2020-2023). Approximately 4% of isolates showed a DTR phenotype, and cefiderocol remained active against 98.1% (CLSI breakpoint) of these isolates, whereas the three BL-BLI combinations had susceptibilities of 52.3%-56.0%. A total of 63% of DTR isolates were nonsusceptible to ≥1 of these BL-BLI combinations, and cefiderocol was active against ≥95.5% (CLSI) of these isolates, regardless of the nonsusceptible phenotype(s) to these combinations. In contrast, susceptibilities of the BL-BLI combinations varied from 0.0% to 30.3%. Almost 20% of DTR isolates carried carbapenemases, mostly metallo-β-lactamases, represented by 14 different STs from 15 countries. Cefiderocol had MIC_50/90 of 0.25/2 mg/L against these carbapenemase-carrying DTR isolates and 97.3% (CLSI) of the isolates were susceptible to cefiderocol, whereas <6% of these isolates were susceptible to any of the BL-BLI combinations. MIC_50/90 of cefiderocol against the non-carbapenemase DTR subset was 0.12/1 mg/L, and 98.3% (CLSI) of the isolates were susceptible to cefiderocol, vs 63.7%-69.6% for the BL-BLI combinations. Cefiderocol demonstrated high activity against a large and contemporary collection of DTR <i>P. aeruginosa</i>, regardless of carbapenemase status. The three currently recommended BL-BLI combinations for treating certain <i>P. aeruginosa</i> infections demonstrated limited activity and high degree of cross-resistance.IMPORTANCECefiderocol and the β-lactam/β-lactamase inhibitor (BL-BLI) combinations ceftazidime-avibactam (CAZ-AVI), imipenem-relebactam (IMI-REL), and ceftolozane-tazobactam (TOL-TAZ) are recommended for the treatment of difficult-to-treat resistance (DTR) <i>Pseudomonas aeruginosa</i> by IDSA guidelines. However, this study shows that cefiderocol demonstrated high activity against a large collection of <i>P. aeruginosa</i>, including DTR isolates. In contrast, the three currently recommended BL-BLI combinations had limited activity, especially against isolates carrying carbapenemase genes, and high degree of cross-resistance. Cefiderocol also sustained activity against a diverse array of isolates with various BL-BLI nonsusceptible phenotypes, and regardless of carbapenemase status. These findings support the use of cefiderocol as a first treatment option for infections caused by DTR <i>P. aeruginosa</i>.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0207925"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280626","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":"Establishment of an RAA-CRISPR/Cas12a assay based on <i>CpSge1</i> for rapid detection of <i>Cryphonectria parasitica</i>.","authors":"Haoyu Wu, Xiaorong Lin, Chengming Tian, Dianguang Xiong","doi":"10.1128/spectrum.01079-25","DOIUrl":"https://doi.org/10.1128/spectrum.01079-25","url":null,"abstract":"<p><p>Chestnut blight disease caused by <i>Cryphonectria parasitica</i> is a serious branch disease that occurs worldwide, especially in Europe and North America. In recent years, chestnut blight disease has also been severe and even posed a great threat to the healthy development of chestnut orchards in some areas of China. Accurate and rapid detection of <i>C. parasitica</i> during the initial stages of the disease is helpful to take corresponding prevention and control measures in advance. In this study, we selected the <i>CpSge1</i> (Gti1/Pac2 transcription factor family) of <i>C. parasitica</i> as the detection target and established a rapid and visual detection system of <i>C. parasitica</i> that combined the recombinase-aided amplification (RAA) and CRISPR/Cas12a, called <i>CpSge1</i>-RAA-CRISPR/Cas12a. The system allows for the specific detection of <i>C. parasitica</i> in approximately 60 mins, with visualization of results. The detection sensitivity of this system was found to be 1 pg/µL. We combined the RAA-CRISPR/Cas12a with a lateral flow dipstick, which also showed specific, high sensitivity, and fast characters. In conclusion, the RAA-CRISPR/Cas12a assay has great potential to be a method for early diagnosis and on-site detection of <i>C. parasitica</i>, especially for areas where specialized equipment is lacking.IMPORTANCEA rapid, highly sensitive, and visualized detection system of <i>Cryphonectria parasitica</i> was established by using the RAA-CRISPR/Cas12a method based on the C-terminal variable regions of a fungal-specific transcription factor <i>CpSge1</i>. The detection system was performed at a constant temperature condition of 37°C, which provides important support for the diagnosis of chestnut blight diseases in the field.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0107925"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280710","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":"Sugar-induced cell death is temperature dependent and conserved in <i>Saccharomyces cerevisiae</i> and <i>Candida</i> species.","authors":"Raveena Parbhudayal, Hai-Ping Cheng","doi":"10.1128/spectrum.01568-25","DOIUrl":"https://doi.org/10.1128/spectrum.01568-25","url":null,"abstract":"<p><p>Yeast sugar-induced cell death (SICD) is a phenomenon whereby cells lose viability in the presence of glucose and the absence of other nutrients to support their growth. Both stationary- and exponential-phase cells of <i>Saccharomyces cerevisiae</i> undergo SICD. The majority of studies on SICD are focused on <i>S. cerevisiae</i>; however, since glucose is a universal carbon source for yeast, we hypothesized that a similar response may be seen in other species of yeast. In this study, we sought to conduct a comparative analysis of SICD in <i>S. cerevisiae</i> and <i>Candida</i> spp. We first established that SICD is prevalent in <i>S. cerevisiae</i> and <i>Candida</i> spp.; however, this phenomenon is highly dependent on temperature, which may explain why this phenotype was perhaps missed previously in <i>C. albicans</i>. We found that glucose is a universal inducer of cell death in all tested strains, but other carbon sources may also lead to cell death to a lesser extent. Additionally, cells transferred to a glucose-only solution induce a dramatic decline in extracellular pH, which may not be directly associated with cell death. Together, our data suggest that SICD is a fundamental and conserved mechanism in yeast.IMPORTANCESince the discovery of the yeast metacaspase, <i>YCA1</i>, research on cell death and aging in <i>Saccharomyces cerevisiae</i> has expanded significantly. Increasing evidence demonstrates similarities between yeast and mammalian cell death. A less discussed type of cell death is sugar-induced cell death (SICD). SICD is a phenomenon observed in <i>S. cerevisiae</i>, whereby cells transferred to water-only remain viable for many days; however, when transferred to glucose-only solutions, there is a rapid loss of viability. Studies on SICD in yeast have been focusing mostly on <i>S. cerevisiae</i>. In this study, we expand the systematic characterization of SICD in <i>Saccharomyces</i> to pathogenic <i>Candida</i> spp. The extension of SICD in pathogenic yeast raises the possibility of this mechanism being of potential interest in therapeutic development.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0156825"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280627","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":"Novel model to predict risk of invasive fungal infection and fungal prophylaxis timing.","authors":"Xinyu Zuo, Xinyuan Ma, Miao Zhang, Richeng Mao, Jiexian Ma","doi":"10.1128/spectrum.02958-24","DOIUrl":"https://doi.org/10.1128/spectrum.02958-24","url":null,"abstract":"<p><p>Patients on immunosuppressive drugs or those who are critically ill are at high risk for invasive fungal infections (IFIs). The assessment of IFI risk and the initiation of prophylaxis in these patients remain unclear. A nomogram model was developed to evaluate clinical and immune indicators in relation to IFI risk and validated by immunocompromised patients. High-risk patients, as identified by the model, were selected for a prospective randomized study to assess the efficacy of the model and timing of fungal prophylaxis initiation. Patients deemed high risk received either fluconazole or a placebo until IFI occurrence or risk downgrade for 90 days. We compared the incidence of IFI and mortality between the two groups. The nomogram, created from a training cohort (<i>n</i> = 384), included age, IgG level, and CD4⁺ cell count as predictive indicators of IFI and was validated in a separate cohort (<i>n</i> = 281) with an area under the curve of 0.723. A total of 265 patients were recruited into the prospective study, with 163 high-risk patients randomly assigned to receive either fluconazole (<i>n</i> = 83) or a placebo (<i>n</i> = 80). The model had a positive predictive value of 48.8% and a negative predictive value of 90.2%. High-risk IFI defined by this model could be reduced to the low-risk cohort level with fluconazole prophylaxis (<i>P</i> < 0.01). This nomogram model reliably predicts the risk of IFI and timing of mycoprophylaxis in immunocompromised patients. Targeted mycoprophylaxis significantly reduces the incidence of IFI, particularly yeast infections, and may help to prevent fungal colonization.</p><p><strong>Importance: </strong>We still lack enough evidence to decide when and how to begin fungal prophylaxis in immunocompromised patients. A model based on immune function indicator is an effective tool for predicting risk of invasive fungal infection (IFI) in immunocompromised patients. Patients were collected to evaluate the performance of the model retrospectively and prospectively.</p><p><strong>Clinical trials: </strong>This study is registered with the Chinese Clinical Trial Registry as ChiCTR2400079810.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0295824"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280634","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":"NsrM (All0345) and NsrX (Alr1976), two FurC (PerR)-targeted transcriptional regulators, modulate nitrogen metabolism and heterocyst differentiation genes in the cyanobacterium <i>Anabaena</i> sp. strain PCC 7120.","authors":"Jorge Guío, Marta Acero, Anindita Bandyopadhyay, Deng Liu, Himadri B Pakrasi, Isabelle Michaud-Soret, M Teresa Bes, Emma Sevilla, María F Fillat","doi":"10.1128/spectrum.02311-25","DOIUrl":"https://doi.org/10.1128/spectrum.02311-25","url":null,"abstract":"<p><p>The control of nitrogen metabolism in the model cyanobacterium <i>Anabaena</i> sp. strain PCC7120 is a complex process orchestrated by master regulators such as NtcA, HetR, and FurC (PerR). These proteins establish complex networks with secondary regulators, finely tuning cellular metabolism in response to diverse, often undefined environmental signals. The XRE-like Alr1976 and the MerR-like All0345 proteins are two predicted transcriptional regulators regulated by FurC. While All0345 is widespread, both proteins have homologs conserved across several bacterial phyla, with <i>alr1976</i> often followed by a gene encoding a Zn-metalloprotease. Previous transcriptomic analyses showed that <i>furC</i> overexpression affected <i>alr1976</i> expression slightly more under nitrogen-deficient conditions, while changes in <i>all0345</i> expression were exclusively observed under N deficiency, pointing them as critical candidates for understanding the finer details of nitrogen control in <i>Anabaena</i>. This work shows that both Alr1976 (NsrX) and All0345 (NsrM) are potentially modulated by NtcA and work as nitrogen secondary regulators. Electrophoretic mobility shift assays and transcriptomic analyses of ∆<i>nsrX</i> and ∆<i>nsrM</i> deletion strains indicate that both regulators act as repressors of key genes involved in nitrogen metabolism and heterocyst development. Notably, the ∆<i>nsrM</i> strain showed earlier heterocyst formation at 24 h of nitrogen step-down. NsrX and NsrM display distinct requirements for optimal DNA-binding activity to nitrogen metabolism genes (presence of Mn and reducing environment, respectively), suggesting they respond to different environmental stimuli. This differential signal integration likely enables master regulators FurC and NtcA to exert more precise control over shared targets, thereby refining the intricate network of nitrogen metabolic regulation in <i>Anabaena</i>.</p><p><strong>Importance: </strong>Filamentous, nitrogen-fixing cyanobacteria are valuable organisms for biotechnology applications and as models for the study of multicellularity in prokaryotes. Understanding the regulation of nitrogen fixation and heterocyst development is essential for optimizing their use in synthetic biology and as biofertilizers. This study identifies two novel nitrogen secondary regulators, Alr1976 (NsrX) and All0345 (NsrM), as part of the intricate regulatory circuit governing nitrogen metabolism in the model cyanobacterium <i>Anabaena</i> sp. strain PCC7120. Genes encoding NsrX and NsrM are regulated by both FurC (PerR) and NtcA, therefore taking part in the NtcA-PerR network that modulates nitrogen metabolism and heterocyst differentiation genes.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0231125"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280682","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":"Frequent high-level rifaximin resistance in <i>Escherichia coli</i> associated with long-term treatment of patients with liver cirrhosis: a prospective, controlled study.","authors":"L Boll, W V Kern, S Schuster, M Schultheiß, C Schneider, M Vavra, R Thimme, S Rieg, J Camp","doi":"10.1128/spectrum.03347-24","DOIUrl":"https://doi.org/10.1128/spectrum.03347-24","url":null,"abstract":"<p><p>We conducted a prospective, controlled study to assess the prevalence of high-level rifaximin resistance in intestinal <i>Escherichia coli (E. coli</i>) among patients with liver cirrhosis (LC). Rectal swabs were collected from consenting adult LC patients at Freiburg University Medical Center. Swabs were cultured on MacConkey agar plates supplemented with rifaximin at two concentrations (32 µg/mL and 256 µg/mL), and pink/red colonies were identified as <i>E. coli</i> using standard methods. Minimum inhibitory concentrations (MICs) of rifaximin and a panel of additional agents were determined using microdilution assays. Of the 100 patients enrolled, 49 received rifaximin (median duration 22 weeks), and 51 served as controls. Patients receiving rifaximin had more advanced LC (Child B/C, 75% vs. 50%) and more frequent concurrent antibiotic use (22% vs. 12%). High-level rifaximin-resistant <i>E. coli</i> strains were recovered from 67% (33/49) of rifaximin-treated patients, compared to 12% (6/51) of controls (<i>P</i> < 0.001). Cross-resistance to rifampicin was complete, with no clear associations with other resistance phenotypes. A subset of five high-level resistance swabs was assessed for homogeneity of colonization by randomly picking <i>E. coli</i> strains from a non-supplemented MacConkey agar plate. Homogeneous colonization with high-level rifaximin-resistant <i>E. coli</i> was found in 80% of cases. The prevalence of high-level rifaximin-resistant intestinal <i>E. coli</i> in LC patients on long-term rifaximin treatment is extremely high (67% vs. 12%). While rifaximin may remain effective in preventing hepatic encephalopathy (HE), its potential use in preventing spontaneous bacterial peritonitis might be severely limited by the emergence of resistance.IMPORTANCEThis study highlights the emergence of antibiotic-resistant <i>E. coli</i> as an important consequence of long-term rifaximin use in patients with liver cirrhosis: the development of antibiotic resistance in gut bacteria. Rifaximin is commonly used to prevent complications like hepatic encephalopathy (HE) by targeting gut bacteria. However, this research shows that prolonged use can lead to the emergence of highly resistant <i>E. coli</i> strains, potentially compromising the drug's effectiveness and limiting its utility in preventing HE and infections, such as spontaneous bacterial peritonitis. By identifying specific resistance patterns and genetic mutations, this study highlights the need for cautious use of rifaximin and further research into balancing its benefits with the risks of resistance. These findings contribute to a broader understanding of how antibiotics affect gut bacteria over time and offer a basis for exploring strategies to preserve the effectiveness of this important medication for patients with advanced liver disease.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0334724"},"PeriodicalIF":3.8,"publicationDate":"2025-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145280716","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 post-reactive structures of <i>Leishmania major</i> UDP-sugar pyrophosphorylase provide insights into the product release mechanism.","authors":"Ohm Prakash, Jana Führing, Petra Baruch, Roman Fedorov, Françoise H Routier","doi":"10.1128/spectrum.00911-25","DOIUrl":"https://doi.org/10.1128/spectrum.00911-25","url":null,"abstract":"<p><p>Biosynthesis of the nucleotide sugars UDP-glucose (UDP-Glc) and UDP-galactose (UDP-Gal) is intimately connected and essential for the viability of trypanosomatid parasites. In the genus <i>Leishmania</i>, it is controlled by the UDP-glucose pyrophosphorylase (UGP) and UDP-sugar pyrophosphorylase (USP). In contrast to UGP, USP has a broad substrate specificity and may generate several UDP-sugars <i>in vitro,</i> including UDP-Glc and UDP-Gal. This enzyme, present in protozoan parasites (including <i>Leishmania</i> species and <i>Trypanosoma cruzi</i>) and in plants, most likely plays a role in salvaging monosaccharides. In order to gain a detailed mechanistic understanding of USPs, we determined high-resolution X-ray structures of <i>Leishmania major</i> USP (<i>Lm</i>USP) in post-reactive states. Several positions of the byproduct pyrophosphate (PP<i>i</i>) were identified and revealed a product release channel in the forward reaction, as well as the geometries of post-reactive Michaelis product complexes. The conformational changes of functional loops (hinge loop-1, hinge loop-2, and the nucleotide-binding loop) showed dynamic effects accompanying the product release process. Structural information about the post-reactive states of <i>Lm</i>USP also includes the metastable binding position of a magnesium (Mg²⁺) ion in the active site. The proposed product release mechanism was substantiated by molecular dynamics simulations and can serve as a model for other UDP-sugar pyrophosphorylases.IMPORTANCETo survive in the hostile environment of the sandfly gut, the parasite <i>Leishmania</i> relies on a range of phosphoglycans made of mannose-phosphate and galactose. In these glucose-limiting conditions, mannogen potentially serves as a reservoir for the synthesis of these crucial glycoconjugates, whereas galactose likely arises from recycling. The enzyme UDP-sugar pyrophosphorylase (USP) is responsible for the activation of this monosaccharide. This enzyme has a relaxed specificity and converts UTP and a range of sugar-1-phosphate to the corresponding UDP-sugar and pyrophosphate (PP<i>i</i>). Here, we determined high-resolution X-ray structures of <i>Leishmania major</i> USP (<i>Lm</i>USP) in post-reactive states. The data provide insight into the product release mechanism for UDP-sugar pyrophosphorylases. Considering the conservation of the residues involved in the coordination of PP<i>i</i> amongst USP enzymes, this mechanism is relevant for all USPs. This work completes our knowledge of the catalytic mechanism of trypanosomatid uridylyltransferases, which are genetically validated drug targets.</p>","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0091125"},"PeriodicalIF":3.8,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145275356","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":"Emergence and dissemination of <i>bla</i>_KPC-31 and <i>bla</i>_PAC-2 among different species of Enterobacterales in Colombia: a new challenge for the microbiological laboratories.","authors":"Betsy E Castro, Elsa De la Cadena, Janneth J Escobar-Arcos, Juan C García-Betancur, Natalia Restrepo-Arbeláez, Christian Pallares, María J López, Angela Pescador, Juan Escobar T, Lorena Matta-Cortes, Adriana C Palacios-Larrota, María Virginia Villegas","doi":"10.1128/spectrum.01805-25","DOIUrl":"https://doi.org/10.1128/spectrum.01805-25","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Ceftazidime/avibactam (CZA) is a promising treatment option for infections caused by carbapenem-resistant Enterobacterales (CRE). However, CZA resistance is increasingly reported worldwide, largely due to the emergence of KPC variants and increase of metallo-β-lactamases (MBL). This study describes the mechanisms associated with CZA resistance in circulating Enterobacterales isolates from Colombia, highlighting the challenge this represents for microbiological identification. Between 2021 and 2024, 68 CZA-resistant Enterobacterales isolates were identified by automated methods in seven Colombian cities. Resistance to CZA was subsequently confirmed by broth microdilution and E-test. Carbapenemase production was evaluated using phenotypic tests, such as the mCIM test, Carba NP, lateral flow assay, and qPCR (&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;VIM&lt;/sub&gt;, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;IMP&lt;/sub&gt;, and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;OXA-48&lt;/sub&gt;). Whole-genome sequencing was performed on 15 isolates that tested negative for MBL genes. Whole-genome sequencing of these 15 isolates revealed a variety of resistance determinants: six isolates harbored &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC-31&lt;/sub&gt;, one &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC-33&lt;/sub&gt;&lt;i&gt;,&lt;/i&gt; one &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC-8&lt;/sub&gt;, five harbored &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;PAC-2&lt;/sub&gt;, and two co-harbored &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;PAC-2&lt;/sub&gt; and &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC-2&lt;/sub&gt;. Notably, &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;PAC-2&lt;/sub&gt; was located on an IncQ plasmid. However, some of these variants were not detected by phenotypic assays, likely due to their low or undetectable carbapenemase activity. CZA resistance in non-MBL producing Enterobacterales in Colombia is primarily mediated by the presence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;KPC-31&lt;/sub&gt; and emergence of &lt;i&gt;bla&lt;/i&gt;&lt;sub&gt;PAC-2&lt;/sub&gt;. These resistance mechanisms pose significant diagnostic, therapeutic, and epidemiological challenges, as they frequently go undetected by conventional microbiological methods. In this context, enhanced molecular surveillance and improved diagnostic strategies are urgently needed to enable early detection, guide antimicrobial therapy, and support infection control and stewardship efforts.IMPORTANCEAntibiotic resistance is a serious global health threat. Ceftazidime/avibactam (CZA) is a key treatment option for multidrug-resistant (MDR) Enterobacterales often used when other antibiotics fail. However, bacteria are now developing resistance to this drug as well, making infections increasingly difficult to treat. In this study, we examined CZA-resistant bacteria from multiple cities in Colombia and found uncommon resistance genes across several bacterial species. These genes are frequently missed, as they often do not test positive due to the limitations of most routinely used laboratory tests. Importantly, some of these genes can be transferred between bacteria, increasing the likelihood of indiscriminate dissemination in the hospital setting. Therefore, our findings highlight the urgent need for improved diagnosti","PeriodicalId":18670,"journal":{"name":"Microbiology spectrum","volume":" ","pages":"e0180525"},"PeriodicalIF":3.8,"publicationDate":"2025-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145275287","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}