Annals of Clinical Microbiology and Antimicrobials最新文献

{"title":"Clinical features of nontuberculous mycobacteria and diagnosis with nanopore targeted sequencing: a retrospective cohort study.","authors":"Xingyu Liu, Tianzhen Wang, Yicheng Guo, Yi Zeng, Weiwei Gao","doi":"10.1186/s12941-026-00876-1","DOIUrl":"https://doi.org/10.1186/s12941-026-00876-1","url":null,"abstract":"<p><strong>Background: </strong>Diagnosing pulmonary non-tuberculous mycobacterial (NTM) disease remains challenging, not only because its clinical manifestations often overlap with those of tuberculosis (TB), but also because its symptoms and signs-such as chronic cough, sputum production, fatigue, and weight loss-can closely resemble those of other common respiratory conditions, including chronic obstructive pulmonary disease (COPD), recurrent pulmonary infections, and chronic bronchitis. This symptomatic overlap often leads to delayed or misdiagnosis, a problem exacerbated by the time-consuming nature of confirmatory culture, which further impedes timely diagnosis.Against the backdrop of a rising incidence of NTM pulmonary disease, Nanopore Targeted Sequencing (NTS) emerges as a promising solution, enabling rapid and comprehensive pathogen detection. This study aims to evaluate the clinical utility of NTS, with a focus on its diagnostic performance, ability to delineate the pathogen spectrum, and reveal polymicrobial co-infections.</p><p><strong>Methods: </strong>In this retrospective study, we analyzed 350 patients suspected with pulmonary NTM infection at Nanjing Second Hospital between 2023 and 2025. We evaluated clinical characteristics, pathogen profiles and co-infections. Bronchoalveolar lavage fluid (BALF), sputum, and tissue specimens were subjected to NTS. The diagnostic performance of NTS was assessed by comparing it with traditional methods, including acid-fast bacillus (AFB) smear, mycobacterial species identification, and conventional culture.</p><p><strong>Results: </strong>Among 350 enrolled patients, 293 were diagnosed with NTM pulmonary disease. The NTM group was significantly older (median age: 61.0 vs. 43.5 years) compared to the non-NTM group (n = 57). NTM patients demonstrated significant cellular immune dysfunction, including lower CD3⁺, CD4⁺ T-cell levels, and CD4⁺/CD8⁺ ratio, alongside a more protracted disease course compared to controls. No significant difference in BMI was observed between the two groups.The most common clinical symptom was productive cough, and imaging predominantly showed patchy parenchymal and nodular shadows. Evaluation of diagnostic performance demonstrated that NTS showed the highest sensitivity (95.9%) and the highest AUC (0.892) among the methods evaluated, although its specificity (82.5%) was slightly lower than that of Mycobacterial culture (84.2%). In contrast, traditional methods such as Mycobacterial culture showed critically low sensitivity (50.5%), despite high specificity. Venn diagram analysis confirmed that NTS detected the highest number of positive cases, supporting its role as a comprehensive diagnostic tool. Furthermore, analysis of co-infections revealed a high frequency (56.0%) of polymicrobial infections among NTM patients, with Mycobacterium tuberculosis and Human Herpesvirus being the most common co-pathogens. Other frequent co-infections included Aspergillus, Candida, and ","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148468510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Specimen-specific distribution of multidrug-resistant organisms and its association with glycemic control in adults with diabetes: a retrospective clinical microbiology study in southern Taiwan.","authors":"Jung-Sheng Chen, Mei-Yin Chou, Siang-Ru Huang, Chien-Sen Liao","doi":"10.1186/s12941-026-00877-0","DOIUrl":"https://doi.org/10.1186/s12941-026-00877-0","url":null,"abstract":"<p><strong>Background: </strong>Patients with diabetes mellitus are susceptible to bacterial infections and may be exposed to repeated or prolonged antimicrobial therapy, which can increase the risk of multidrug-resistant organism (MDRO)-positive cultures. However, the distribution of MDROs across different specimen types and the relationship between glycemic control and MDRO isolation remain insufficiently characterized in regional clinical microbiology settings. This study investigated specimen-specific MDRO profiles and evaluated the association between glycated hemoglobin (HbA1c) levels and MDRO-positive cultures in adults with diabetes.</p><p><strong>Methods: </strong>This retrospective clinical microbiology study was conducted at a regional teaching hospital in southern Taiwan. Culture-positive isolates obtained from adult patients between January and December 2023 were reviewed. After predefined exclusions, 1989 isolates from abscess, urine, sputum, and blood specimens were included. The analysis focused on six predefined clinically monitored MDRO phenotypes routinely reported by the hospital clinical microbiology laboratory and infection-control program. Diabetes status was determined from documented physician diagnosis in the electronic medical record and/or laboratory evidence consistent with national diagnostic criteria. Poor glycemic control was defined as HbA1c > 8.0%. Bacterial identification and antimicrobial susceptibility testing were performed using the VITEK-2 Compact automated system, with confirmatory disk diffusion testing when indicated. Associations among diabetes status, specimen type, demographic factors, biochemical parameters, and MDRO-positive cultures were analyzed using chi-square tests, t tests, and logistic regression models.</p><p><strong>Results: </strong>Among 1989 culture-positive isolates, 902 were obtained from patients with diabetes and 1087 from patients without diabetes. The overall MDRO-positive proportions were 19.5% in the diabetes group and 17.5% in the non-diabetes group. Urine was the most frequent specimen source in patients with diabetes. MDRO distribution differed significantly by specimen type. Methicillin-resistant Staphylococcus aureus predominated in abscess and blood specimens, vancomycin-resistant Enterococcus predominated in urine specimens, and carbapenem-resistant Acinetobacter baumannii and carbapenem-resistant Pseudomonas aeruginosa were frequent in sputum specimens. In patients with diabetes, HbA1c > 8.0% was associated with increased odds of MDRO-positive cultures after adjustment for age, sex, and specimen type (adjusted odds ratio, 2.82; 95% confidence interval 1.84-4.32; p < 0.001). Routine lipid markers and uric acid were not significantly associated with MDRO status.</p><p><strong>Conclusions: </strong>Poor glycemic control was associated with MDRO-positive cultures in adults with diabetes. These findings support specimen-specific MDRO surveillance and suggest that glycemic-cont","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148429688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Incidence, mortality and risk factors of invasive pulmonary aspergillosis in critically ill patients during the COVID-19 era: a global systematic review and meta-analysis.","authors":"Zijing Zhou, Bin Luo, Xiwen Zhang, Qing Li, Yingzi Huang, Yi Yang, Haibo Qiu, Ming Xue, Jianfeng Xie","doi":"10.1186/s12941-026-00878-z","DOIUrl":"https://doi.org/10.1186/s12941-026-00878-z","url":null,"abstract":"<p><strong>Background: </strong>Invasive pulmonary aspergillosis (IPA) represents a growing threat to critically ill patients, with mortality rates exceeding 50%. The burden of IPA has been exacerbated during the COVID-19 era due to prolonged ICU stays and widespread use of immunosuppressive therapies. This systematic review and meta-analysis aimed to synthesize global evidence on the incidence, mortality, and risk factors of IPA in ICU patients.</p><p><strong>Methods: </strong>Observational studies reporting IPA incidence, mortality, or risk factors in ICU settings from their inception between November 1, 2019 to October 11, 2024 for eligible studies were retrieved from PubMed, Embase, Web of Science, and Cochrane Library. Study quality was assessed using the Newcastle-Ottawa Scale (NOS). Meta-analyses were performed using R software to calculate pooled estimates with 95% confidence intervals (CI). Multiple subgroup analysis was conducted.</p><p><strong>Results: </strong>Fifty-six studies involving 15,385 ICU patients (2,381 IPA cases) were included. The pooled incidence of IPA was 11.9% (95% CI: 9.7-14.6%). Subgroup analyses revealed higher incidence in mechanically ventilated patients (15.0%, 95% CI: 11.7-19.0%). Factors associated with an increased risk of IPA included male sex (OR = 1.29), smoking history (OR = 1.52), chronic lung diseases (OR = 1.30), chronic kidney disease (OR = 1.70), chronic liver disease (OR = 1.79), heart disease (OR = 1.20), malignant tumor (OR = 1.75), hematological malignancy (OR = 2.65), glucocorticoids use before ICU (OR = 2.13), immunosuppression (OR = 2.26), EORTC host factors (OR = 2.13), vasopressor use (OR = 3.28), mechanical ventilation (OR = 3.69), and renal replacement therapy (OR = 2.31). The overall mortality rate was 59.6% (95% CI: 55.0-64.0%), escalating to 61.9% in mechanically ventilated patients. Mortality-associated factors included age ≥ 65 years (OR = 2.85), ICU-administered glucocorticoids (OR = 1.95) and mechanical ventilation (OR = 1.93).</p><p><strong>Conclusions: </strong>During the COVID-19 era, IPA remains a life-threatening complication in critically ill patients, particularly those with COVID-19, and is associated with immunosuppression, organ dysfunction, and invasive therapies. Our findings, predominantly reflecting CAPA epidemiology, generate the hypothesis that early screening in high-risk populations and tailored antifungal strategies warrant prospective evaluation to determine whether they improve outcomes.</p><p><strong>Trial registration: </strong>Ethical approval and patient consent were not required for this meta-analysis, as it was based on previously published studies. The protocol for this meta-analysis was registered on PROSPERO: International prospective register of systematic reviews (CRD42025631579).</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148418120","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effectiveness of cefazolin versus anti-staphylococcal β-lactam for treating methicillin-susceptible Staphylococcus aureus pneumonia in critically ill patients admitted to intensive care units: a multicenter cohort study.","authors":"Sufyan M Alomair, Khalid Al Sulaiman, Aisha Alharbi, Rahaf Alqahtani, Hatun M Labban, Nader Damfu, Sultan Alotaibi, Huda J Aljedaani, Shahad A Alshamrani, Rahaf R Altalhi, Rana F Albadrani, Khalid M Alkharfy, Deem A Alkaoud, Nada F Alshehri, Enas Munshi, Nadine Alanazi, Shahad S Almutairi, Maha A Alanizi, Sarah A Almugbil, Lujain M Almatrafi, Asmaa A Almehmadi, Maram A Alzahrani, Marah Almutairi, Munirah F Alhmoud, Hadeel M Alharbi, Ohoud Aljuhani","doi":"10.1186/s12941-026-00873-4","DOIUrl":"https://doi.org/10.1186/s12941-026-00873-4","url":null,"abstract":"<p><strong>Introduction: </strong>Critically ill patients carry a high risk of infections and related complications, which significantly increase mortality. For patients with confirmed methicillin-susceptible Staphylococcus aureus (MSSA) pneumonia, the optimal definitive β-lactam therapy remains controversial. To date, clinical evidence comparing the effectiveness of cefazolin against other antistaphylococcal β-lactam antibiotics in the intensive care unit (ICU) setting is limited. Therefore, this study aimed to evaluate the clinical effectiveness of cefazolin versus non-cefazolin β-lactam antibiotics for treating MSSA pneumonia in critically ill adults.</p><p><strong>Methods: </strong>We conducted a multicenter, retrospective cohort study from January 2016 to July 2021 at three tertiary hospitals in Saudi Arabia. The study included adult intensive care unit (ICU) patients with confirmed MSSA respiratory infections who received definitive, targeted anti-MSSA β-lactam therapy. Eligible patients were categorized into two groups based on the specific antibiotic received (cefazolin vs. non-cefazolin β-lactam antibiotics). The primary outcome was treatment failure, while all other endpoints were considered secondary. Logistic, linear, and negative binomial regression analyses were utilized to analyze the study's endpoints, as appropriate.</p><p><strong>Results: </strong>A total of 54 patients were included in the study, evenly distributed with 27 patients in the cefazolin group and 27 in the alternative anti-MSSA β-lactam group. The treatment failure rate was significantly higher in the cefazolin group compared to the non-cefazolin β-lactam antibiotics group (OR 5.73; 95% CI (1.303-25.191), p = 0.02). Moreover, the rate of re-escalation to other antibiotics was higher in the cefazolin group (OR 17.98; 95% CI (2.731-118.425), p = 0.002). No significant difference was found in time to defervescence, or MSSA recurrence infection rate within three months. In addition, in-hospital and 30-day mortality rates, ICU re-admission, length of stay, and ventilator-free days were not statistically significant different between the two groups.</p><p><strong>Conclusion: </strong>In critically ill patients with MSSA pneumonia, cefazolin was associated with higher rates of treatment failure and re-escalation compared to non-cefazolin β-lactams antibiotics. Further studies with a larger sample size are needed to validate these findings.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148409991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rare emergence of delamanid resistance in multidrug-/rifampicin-resistant tuberculosis patients receiving delamanid-containing regimens: a prospective multicentric study in China.","authors":"Wei Shu, Qingshan Cai, Yuping Huang, Yuanhong Xu, Yuanyuan Shang, Ruixia Liang, Liang Yan, Lin Wang, Long Jin, Yi Pei, Zhongfeng Huang, Shanshan Li, Yufeng Wang, Mengqiu Gao, Liang Li, Yu Pang","doi":"10.1186/s12941-025-00820-9","DOIUrl":"10.1186/s12941-025-00820-9","url":null,"abstract":"<p><strong>Background: </strong>Delamanid (DLM) is a promising drug recommended for treatment of multidrug-/rifampicin-resistant tuberculosis (MDR/RR-TB). However, there are very little data about the emergence of drug resistance in patients with the use of DLM-containing regimens. The study aimed to monitor the dynamics of susceptibility of MTB to DLM and investigate the potential mechanism conferring decreased susceptibility.</p><p><strong>Methods: </strong>A prospective cohort study was conducted, enrolling MDR/RR-TB patients with culture-confirmed diagnoses across 10 study sites. Serial sputum samples were collected from participants receiving DLM-containing regimens at baseline (treatment initiation), week 2, week 4, and every 4 weeks thereafter until treatment completion. The in vitro susceptibility of Mycobacterium tuberculosis isolates to DLM was assessed using the BACTEC MGIT 960 system.</p><p><strong>Results: </strong>A total of 263 MDR/RR-TB patients were included from 2020 to 2024 in the present study, favorable outcomes were recorded in 187 patients (71.1%). The distribution of minimal inhibit concentration (MIC) for a bacterial population to DLM was unimodal, and most isolates tested had a MIC value of < 0.015 µg/mL. The MIC₅₀ and MIC₉₀ of MTB isolates were 0.03 and 0.06 µg/mL, respectively. Using the 0.12 µg/mL as a proposed epidemiological cutoff value, the resistance to DLM was found in 0.76% (2/263) of MTB isolates and no mutations were identified within loci conferring DLM resistance. Additionally, the remaining 81 (30.8%) with serial isolates were included in our analysis. 70 out of 81 patients exhibited no change in DLM MICs. In contrast, the reduced susceptibility to DLM was noted in 11 patients, defined as no less than 2-fold increase in MIC value compared with that of baseline.</p><p><strong>Conclusions: </strong>Primary DLM resistance was rare (0.76%), and resistance emergence during treatment was infrequent, though some cases of reduced susceptibility were observed.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"25 1","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13326454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148374279","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical characteristics and temporal trends of meropenem and piperacillin/tazobactam heteroresistance in Pseudomonas aeruginosa isolates.","authors":"Yali Fan, Huilan Li, Xiaoyue Liang, Jia Xie, Biyu Lin, Zheng Liang, Weifeng Liu, QinJin Wang, Tian Zhong, Ying Chen, Shuping Nie, Chao Wu","doi":"10.1186/s12941-026-00875-2","DOIUrl":"https://doi.org/10.1186/s12941-026-00875-2","url":null,"abstract":"<p><strong>Background: </strong>Heteroresistance (HR) to commonly used anti-pseudomonal agents in Pseudomonas aeruginosa has been reported in cross-sectional epidemiological surveys; however, longitudinal studies investigating the long-term epidemiological dynamics and clinical correlates of this adaptive phenotype are still lacking. This retrospective time-series study aims to systematically explore the HR phenotypic profiles and temporal dynamic of clinical P. aeruginosa isolates against piperacillin/tazobactam (TZP) and meropenem (MEM), and further clarify their potential clinical correlates.</p><p><strong>Methods: </strong>We comprehensively analyzed 380 non-duplicate clinical strains collected from a tertiary hospital between 2011 and 2024. The disk diffusion and Etest gradient diffusion methods were used for the preliminary determination of HR incidence rates in clinical isolates against six anti-pseudomonal antibiotics. Population analysis profiling (PAP) assays was further performed to assess the temporal dynamics and phenotypic characteristics of HR to TZP MEM. HR was defined as the presence of resistant subpopulations with an MIC at least eightfold higher than that of the dominant population at a frequency of ≥ 1 × 10⁻⁷. Subsequently, univariate and multivariate regression analyses were performed to identify clinical factors associated with HR and non-HR strains.</p><p><strong>Results: </strong>Preliminary screening indicated that 55% of the tested strains exhibited the HR phenotype, whereas confirmatory assays further verified that 49.5% of the isolates displayed HR to either TZP or MEM. The HR detection rate for MEM peaked at 35.3% during 2017-2019, followed by a gradual decline, reaching a minimum of 24.04% during the 2020-2022 pandemic. Meanwhile, the HR rate to TZP initially increased, then decreased, peaking at 43.1% during 2017-2019 and subsequently declining to 27.8%. In addition, multivariate regression analysis identified that male gender and prior antiviral exposure were independently associated with decreased risk of HR, whereas prior fluoroquinolone antibiotics exposure was independently associated with an increased risk.</p><p><strong>Conclusion: </strong>Our findings highlight the widespread prevalence, distinct temporal dynamics, and diverse phenotypic features of HR, and underscore the potential clinical value of integrating HR screening into antimicrobial susceptibility testing, particularly for high-risk patient populations, to better guide therapy and mitigate the risk of treatment failure.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148337510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Convergent evolution of ST2 and ST164 mediates dissemination of the bla_NDM-1/bla_OXA-23 profile in Acinetobacter baumannii.","authors":"Ren Liu, Guilin Jin, Feng Yu, Hui Tan, Fang Yuan, Peiwen Zhang, Yinyi Chen, Liang Xiao, Xiaojun Yang","doi":"10.1186/s12941-026-00872-5","DOIUrl":"https://doi.org/10.1186/s12941-026-00872-5","url":null,"abstract":"<p><strong>Background: </strong>The convergence of the potent carbapenemase genes bla_NDM-1 and bla_OXA-23 in carbapenem-resistant Acinetobacter baumannii (CRAB) poses a critical threat. However, the dissemination patterns and evolutionary drivers of this dual-carbapenemase profile remain unclear.</p><p><strong>Methods: </strong>We performed a comprehensive genomic analysis of a global collection of 1820 high-quality public WGS-derived CRAB isolates (2001-2024) harbouring acquired non-OXA carbapenemase genes. Topological congruence between bla_NDM-1- and bla_OXA-23-positive phylogenies was assessed via normalized Robinson-Foulds (nRF) distance. Ecological diversity metrics (e.g., Shannon entropy) combined with Bayesian and hypergeometric models quantified host-lineage restriction. The evolutionary dynamics of a colistin-resistant ST2 sublineage (PmrB T232I) were inferred using Skygrowth coalescent analysis. Geographic divergence was assessed via PERMANOVA and genome-wide association study (GWAS).</p><p><strong>Results: </strong>Co-occurring acquired carbapenemase genes dominated the cohort, with the combination of bla_NDM-type and bla_OXA-23-like genes accounting for 64.7% (1178/1820) of isolates. This prevalence was primarily driven by the specific bla_NDM-1/bla_OXA-23 profile (n = 1080), overwhelmingly restricted to two clones: the internationally disseminated ST2 (n = 644) and the regionally prevalent ST164 (n = 209). An integrated triad of evidence-topological congruence (nRF = 0.346, p < 0.001), a mathematically stark collapse in lineage diversity upon dual-gene acquisition, and extreme statistical enrichment (Bayes factors 7.8 × 10¹⁹-1.5 × 10²²)-demonstrates that this dual-resistance phenotype does not diffuse randomly via horizontal transfer. Instead, it is profoundly constrained within these specific accommodating clonal frameworks. Within the dominant ST2 clone, a colistin-resistant high-risk sublineage exhibited a 'gene load-selection continuum', where a subgroup with an expanded resistome paradoxically maintained a higher effective population size, highlighting the role of genomic plasticity. Geographic origin explained 46.5% of accessory genome variance (PERMANOVA p < 0.001), highlighting strong geographic stratification of accessory genomes.</p><p><strong>Conclusions: </strong>The widespread dissemination of the bla_NDM-1/bla_OXA-23 profile is mediated by the convergent expansion of ST2 and ST164, acting as dominant clonal drivers. This study provides a framework for clone-specific epidemiological hitchhiking and highlights the need to refine surveillance to prioritize the genomic tracking of these key lineages. The retrospective nature of public data may influence prevalence estimates, but the core clonal dissemination pattern remains robust.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300672","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigation of atypical microbial agents in patients with sterile pyuria.","authors":"Elif Seren Tanrıverdi, Yusuf Yakupoğulları, Ayten Gündüz, Barış Otlu","doi":"10.1186/s12941-026-00874-3","DOIUrl":"https://doi.org/10.1186/s12941-026-00874-3","url":null,"abstract":"<p><strong>Background: </strong>To determine the frequency of microbial DNA detection in patients with sterile pyuria and evaluate the association of leukocyte count and leukocyte esterase (LE) test results with physicians' treatment decisions.</p><p><strong>Methods: </strong>This prospective cross-sectional study was conducted over two months in the microbiology laboratories of two university hospitals. Urine samples from 201 patients with sterile pyuria (≥ 10 leukocytes/ml and/or LE positivity with negative urine culture) and 180 controls (no growth in culture and no pyuria) were analyzed. Multiplex PCR targeting 14 potential pathogens was performed. Demographic data, PCR results, and physicians' treatment decisions were recorded. Chi-square tests and logistic regression assessed associations between laboratory findings and treatment decisions.</p><p><strong>Results: </strong>PCR detected at least one potential pathogen in 50.2% of sterile pyuria patients compared to 10% of controls (p < 0.05). Treatment initiation was more frequent in the patient group than in controls (43.3% vs. 30%, p < 0.05). Logistic regression demonstrated that leukocyte counts ≥ 10/ml were significantly associated with PCR positivity (OR = 6.84, p < 0.05) and the physician's treatment decisions (OR = 2.59, p < 0.05). The most common pathogens in patients were Ureaplasma urealyticum (21.9%), Mycoplasma hominis (12.9%), and Gardnerella vaginalis (10.9%), predominantly in adult women with both elevated leukocyte counts and positive LE tests. Although PCR positivity was significantly associated with treatment initiation, the correlation was weak (r = 0.33), indicating that treatment decisions were influenced by additional clinical factors.</p><p><strong>Conclusions: </strong>Molecular testing detected DNA from Ureaplasma, Mycoplasma, and G. vaginalis frequently in sterile pyuria, particularly in adult women; these findings indicate candidate microorganisms requiring clinical correlation.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":5.2,"publicationDate":"2026-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148300690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficacy and safety of intravenous combined with aerosolized colistimethate sodium for carbapenem-resistant organism-induced pneumonia: a retrospective study.","authors":"Ji Liu, Wei Wang, Xun Deng, Xiaoyu Lin, Xun Yu, Ran Fu, Yong Wang, Shumei Sun","doi":"10.1186/s12941-026-00863-6","DOIUrl":"https://doi.org/10.1186/s12941-026-00863-6","url":null,"abstract":"<p><strong>Background: </strong>Polymyxins are regarded as the last-resort antibiotics for treating resistant Gram-negative bacteria. Colistimethate sodium (CMS) is commonly used for carbapenem-resistant organism (CRO)-induced pulmonary infection. However, the polycationic/hydrophilic structure of intravenous injection (IV-CMS) limits its penetration into lung parenchyma, whereas aerosol inhalation (AER-CMS) has high alveolar penetration and minimal systemic dispersion. Currently, post-marketing monitoring of the clinical efficacy and safety of IV + AER CMS is limited. We aimed to evaluate the efficacy and safety of IV + AER CMS (Tianyun^®; Chiatai Tianqing Pharma Jiangsu, China) in the treatment of CRO-induced pulmonary infections.</p><p><strong>Methods: </strong>This is a multi-center retrospective study. Patients with CRO-induced pulmonary infection who received IV + AER CMS/IV-CMS alone between 2021 and 2023 were enrolled. The primary endpoint was clinical response rate, and secondary endpoints included clinical cure rate, length of stay, mortality, and incidence of adverse events (pigmentation, hypersensitivity, renal toxicity, neurotoxicity, and bronchospasm).</p><p><strong>Results: </strong>There were 101 patients in IV + AER CMS group and 108 patients in IV-CMS group. The clinical response rate in IV + AER CMS group was significantly higher than that in IV-CMS group (78.57% vs. 60.00%, p = 0.017). There were no significant differences in clinical cure rate, length of stay and 28-day all-cause mortality between two groups. No significant differences in the incidence of adverse events were observed between two groups.</p><p><strong>Conclusions: </strong>The clinical response rate of IV + AER CMS for CRO-induced pulmonary infection is higher than that of IV-CMS and no increased risk of renal toxicity, demonstrating good tolerability of AER-CMS in clinical practice.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148248884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A longitudinal analysis of Clostridioides difficile virulence profiles across three geographic regions in Israel (2020-2022).","authors":"Orna Schwartz, Avi Peretz, Maya Azrad","doi":"10.1186/s12941-026-00868-1","DOIUrl":"https://doi.org/10.1186/s12941-026-00868-1","url":null,"abstract":"<p><strong>Background: </strong>Clostridioides difficile infection (CDI) is one of the leading infectious diarrhea worldwide. C. difficile pathogenicity is mediated by various virulence factors, including toxins and biofilm formation. This study included 313 C. difficile isolates that were previously collected from four medical centers. We aimed to investigate the prevalence, distribution, and associations of virulence factors in C. difficile strains from both healthcare-associated (HA)- and community-acquired (CA)-CDI patients across Israel from 2020 to 2022.</p><p><strong>Methods: </strong>Multi-locus sequence typing (MLST) and whole-genome sequencing (WGS) were performed for strain classification and virulence gene detection. Toxin and biofilm production were also characterized.</p><p><strong>Results: </strong>Sequence type (ST) 42 (12.5%) and ST2 (11.5%) were the most prevalent strains. Toxin production patterns were significantly associated with setting of infection acquisition (p < 0.0001). Isolates producing both toxin A and B were 2.5-fold more common among HA-CDI strains, while toxin-A-producers were more frequent in CA-CDI. Biofilm was produced by 96.9% of isolates, with strong biofilm-producing strains significantly more prevalent in hospitals (p < 0.001). Furthermore, isolates producing both toxins A and B were predominantly moderate or strong biofilm producers (p < 0.0001). agrD presence was significantly associated with ST, toxin production patterns and biofilm-production capacity (p < 0.0001 for ST and biofilm, p = 0.0016 for toxins).</p><p><strong>Conclusions: </strong>This study revealed a high diversity of C. difficile strains in Israel and demonstrated that virulence factor patterns differ significantly across STs and the acquisition setting. The differences between HA-CDI and CA-CDI isolates in some virulence factors underscores the importance of continuous epidemiological surveillance to guide tailored treatment and prevention strategies.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148194365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}