Annals of Clinical Microbiology and Antimicrobials最新文献

{"title":"Evaluation of diagnostic performance of comprehensive respiratory virus panel: comparison of next-generation-sequencing to real-time polymerase chain reaction for detection of respiratory viruses.","authors":"Sojin Lee, Yoonjung Kim, Kyung-A Lee","doi":"10.1186/s12941-026-00851-w","DOIUrl":"10.1186/s12941-026-00851-w","url":null,"abstract":"<p><strong>Background: </strong>Respiratory viral infections remain a global health concern, particularly among children, the elderly, and immunocompromised individuals. Although real-time polymerase chain reaction (RT-PCR) is the diagnostic gold standard, its limitations in strain-level typing and mutation tracking highlight the need for complementary approaches such as next-generation sequencing (NGS).</p><p><strong>Methods: </strong>We compared a hybridization-based NGS respiratory virus panel (RVP) in comparison with RT-PCR using 81 nasopharyngeal swab (NPS) specimens. The performance metrics included concordance rates, cycle threshold (Ct)-based stratification, co-infection detection, and strain-level classification.</p><p><strong>Results: </strong>Among the 81 NPS specimens, RT-PCR identified respiratory viruses in 56 cases, including eight co-infections. Excluding co-infections, RVP showed 74.5% positive percent agreement, 92.3% negative percent agreement, and 80.8% overall accuracy. The detection and positive concordance rates declined with higher Ct values, and the sequencing depth also decreased. In co-infections, RVP failed to detect low-titer viruses. Strain-level classification was achieved in 65.5% of the positive samples, by subtyping rhinovirus A and C, respiratory syncytial virus A and B, and influenza A (H1N1 and H3N2).</p><p><strong>Conclusions: </strong>NGS panel tests complement RT-PCR by enabling viral detection and strain typing, thereby offering added value to genomic surveillance and outbreak investigations.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13041287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147281816","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":"Genomic epidemiology and aztreonam-avibactam resistance mechanisms of Proteus mirabilis in china: an eight-year retrospective study.","authors":"Jingyi Guo, Chengjin Wu, Xinyan Tang, Linfang Wang, Yan Qi, Yunsong Yu, Yuexing Tu, Linyue Zhang, Xi Li","doi":"10.1186/s12941-026-00852-9","DOIUrl":"10.1186/s12941-026-00852-9","url":null,"abstract":"<p><strong>Background: </strong>Proteus mirabilis has emerged as an important multidrug-resistant opportunistic pathogen, with the production of metallo-β-lactamases (MBLs) being a major contributor to its broad-spectrum resistance. Although the aztreonam-avibactam (ATM-AVI) combination represents a key therapeutic option against MBL-producing Enterobacteriaceae, the mechanisms underlying ATM-AVI resistance in P. mirabilis has not yet been reported.</p><p><strong>Methods: </strong>A total of 176 multidrug-resistant P. mirabilis isolates were collected from a tertiary hospital in China (2017-2024). Antimicrobial susceptibility testing identified ATM-AVI-resistant isolates (MIC ≥ 8/4 µg/mL). Whole-genome sequencing, gene cloning, RT-qPCR, and copy number analyses were used to determine resistance mechanisms. Growth rate assays evaluated fitness costs, and global phylogenetic analysis elucidated evolutionary and dissemination patterns.</p><p><strong>Results: </strong>Twelve isolates (6.8%, 12/176) were resistant to ATM-AVI, all carrying the bla_PER-4 gene. Cloning experiments confirmed that bla_PER-4 conferred significantly higher ATM-AVI resistance than bla_PER-1. Increased resistance correlated with bla_PER-4 overexpression and gene copy number amplification. Whole-genome analysis showed that bla_PER-4 was embedded in ISCR1-associated class 1 integrons located on both plasmids and chromosomes, with a strain carrying eight tandem chromosomal copies. These structures likely mediated gene amplification via rolling-circle replication and homologous recombination. Phylogenetic analysis revealed that bla_PER-4-positive isolates were mainly associated with the ST135 lineage, suggesting transmission event within hospitals. Global data demonstrated that bla_PER-4-carrying P. mirabilis strains were predominantly found in China (80%, 12/15), while bla_PER-1 strains were more common in the United States.</p><p><strong>Conclusions: </strong>The bla_PER-4-carrying P. mirabilis, particularly the ST135 clone, represents a high-risk lineage associated with high-level ATM-AVI resistance mediated by gene overexpression and copy number amplification. This finding highlights a novel mechanism of ATM-AVI resistance and underscores the need for continuous genomic surveillance and rational antimicrobial stewardship to prevent its further dissemination.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":""},"PeriodicalIF":3.6,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12955263/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146103697","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":"Coexistence with Staphylococcus aureus modulates the virulence and antibiotic resistance of Pseudomonas aeruginosa.","authors":"Zeinab M Helal, Soha Lotfy Elshaer, Mohammed El-Mowafy, Elsayed E Habib","doi":"10.1186/s12941-025-00843-2","DOIUrl":"10.1186/s12941-025-00843-2","url":null,"abstract":"<p><strong>Background: </strong>In this study, we were aimed to investigate the impact of co-cultures of different bacterial species on bacterial antibiotic resistance and virulence.</p><p><strong>Methods: </strong>The effect of co-cultures of Pseudomonas aeruginosa (Gram-negative bacteria) and Staphylococcus aureus (Gram-positive bacteria) on antibiotic resistance, virulence and biofilm formation in P. aeruginosa was examined in vitro in 14 mixtures. These mixtures were categorized into three groups: Standard category (including standard strains), naturally co-isolated category (co-isolated from the same patient) and random co-culture category (bacterial species from different patients). Additionally, the impact of the standard category on pathogenicity was assessed in vivo using mouse model. Intergroup comparisons were conducted using multiple t-test and comparisons between treated and untreated control isolates grown under the same conditions were made. Survival experiments were analyzed using Mantel-Cox log-rank test.</p><p><strong>Results: </strong>P. aeruginosa survival significantly increased in most of the co-culture mixtures when treated with meropenem (92.9%), ceftazidime (85.7%), cefepime (78.6%), gentamicin (78.6%) and ciprofloxacin (71.4%). Similarly, virulence factor production significantly increased in P. aeruginosa in most of the investigated co-cultures as follows: pyocyanin (71.4%), elastase (71.4%), protease (78.6%), hemolysin (71.4%), lecithinase (78.6%), gelatinase (63.6%) and biofilm (71.4%). At the molecular level, the relative expression of the tested virulence-encoding genes; pelA, lasB and lasA were significantly increased in at least 92.9% of the co-culture mixtures, especially in random ones, compared to their mono-culture, but with varying up-regulation degree (ranging from 1.5 to 96-fold increase).</p><p><strong>Conclusion: </strong>Finally, in vitro investigations for antibiotic resistance and virulence production clearly demonstrated a synergistic interaction between P. aeruginosa and S. aureus in the co-existence mixture. Compared to P. aeruginosa mono-cultures, the co-cultured strains exhibited enhanced resistance profiles and increased expression of key virulence factors, indicating that the simultaneous presence of both species promotes mutual adaptation and potentiation of pathogenic traits. Additionally, in vivo experiments confirmed that the co-infection with S. aureus significantly enhanced the pathogenicity of P. aeruginosa, as indicated by increased mortality rates and higher bacterial counts in lung tissues. Altogether, our results shed light on the impact of the co-existence of microbial species on bacterial virulence and antibiotic resistance.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"25 1","pages":"14"},"PeriodicalIF":3.6,"publicationDate":"2026-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12922201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146225305","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 patterns, species-specific correlations, and therapeutic outcomes of nocardiosis in immunocompetent individuals: a systematic analysis based on literature.","authors":"Le Lu, Dongyi Wang, Muzi Li, Xiang Yang, Kailun Zhou, Zhiming Zhao, Chunli Liu, Wei Shang","doi":"10.1186/s12941-026-00849-4","DOIUrl":"10.1186/s12941-026-00849-4","url":null,"abstract":"<p><strong>Background: </strong>Nocardiosis, traditionally an opportunistic infection, lacks comprehensive characterization in immunocompetent individuals. This study aimed to describe and analyze the demographics, clinical features, and outcomes of Nocardia infections in this population based on the literature.</p><p><strong>Methods: </strong>A systematic analysis of 530 immunocompetent Nocardia cases (2020-2024) was conducted using reports from PubMed, CNKI, and MedNexus. Demographics, exposures, clinical characteristics, laboratory, treatment, and outcome were recorded and analyzed.</p><p><strong>Results: </strong>Patients (median age: 59 years; 69.8% male) exhibited pulmonary (46.5%), cutaneous (20.0%), or cerebral (15.7%) involvements. Risk factors included soil/dust exposure (97/530, 18.3%), trauma (44/530, 8.3%), and comorbidities (255/530, 48.1%, e.g., diabetes, bronchiectasis). Cure/improvement (82.6%) group exhibited younger age (P = 0.01) and higher prevalence of local infections (P < 0.001), while more cases of disseminated infection (P < 0.001), N. farcinica (P = 0.01), and unclassified Nocardia spp. (P = 0.02) were in the deterioration/mortality group. Trimethoprim-sulfamethoxazole (71.9%) was the primary therapy. Species-specific patterns demonstrated: N. brasiliensis preferentially linked to cutaneous infections (P < 0.001), N. farcinica to cerebral disease (P < 0.001), and N. cyriacigeorgica to pulmonary involvement (P < 0.001).</p><p><strong>Conclusion: </strong>Nocardiosis in immunocompetent hosts demonstrates distinct risk profiles, site-specific species associations, and prognostic factors. Early diagnosis, species identification, and antimicrobial therapy are critical for optimizing outcomes. This study underscores the need for heightened clinical suspicion and improved diagnostic protocols in non-immunocompromised populations.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"13"},"PeriodicalIF":3.6,"publicationDate":"2026-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12914931/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146046000","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":"Characterization using ultra-deep sequencing of the intra-host distribution of the mutations associated with H. pylori antibiotic resistance.","authors":"Laura Chaufour, Alexandra Herve, Birama Ndiaye, Lucie Karayan-Tapon, Médéric Briand, Frédérique Lartigue, Christophe Burucoa, Maxime Pichon","doi":"10.1186/s12941-025-00840-5","DOIUrl":"10.1186/s12941-025-00840-5","url":null,"abstract":"<p><strong>Introduction: </strong>Helicobacter pylori is a slow-growing, gram-negative strictly pathogenic bacterium, which colonizes the stomachs of half the global population and is responsible for gastritis, peptic ulcer and even adenocarcinoma, Treatment of choice for eradication is a combination of PPIs and multiple antibiotic therapy. Recently, therapeutic failures began to be attributable to increased antibiotic resistance due to mutations in identified genes (rpoB, 16S rRNA coding gene, gyrA, 23S rRNA coding gene, pbp1A, frxA, rdxA).</p><p><strong>Objectives: </strong>This study aimed to determine, using ultra-deep sequencing, the distribution of mutations in patient s hospitalized or undergoing screening for H. pylori.</p><p><strong>Methods: </strong>Gastric biopsies were obtained from two different anatomical regions (antrum/fundus) in 18 patients' samples from 1998 to 2021, in four French hospitals. Following automated extraction, DNA of H. pylori was amplified using multiplexed PCR, before sequencing on the Illumina iSeq100 platform.</p><p><strong>Results: </strong>Antral diversification of H. pylori populations is significantly greater than that at the fundic level for rpoB and rdxA. Fundic diversification of H. pylori populations is significantly greater than that at the antral level for the 23S rRNA coding, rdxA and rpoB genes (p < 0.05), with inter-individual variation.Conversely, the 16S rRNA, frxA, gyrA and pbp1A genes exhibited no significant variation (p > 0.05).</p><p><strong>Discussion: </strong>This first study using in-house high-throughput sequencing of H. pylori on clinical biopsies from the same patients reinforces the hypothesis that the bacterial population within the same host is heterogeneous. The presence of minority variants justifies the need for at least two biopsies to ensure robust testing of the H. pylori antibiotic susceptibility profile.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"4"},"PeriodicalIF":3.6,"publicationDate":"2026-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12853736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146028219","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":"The impact of the timing of mNGS-guided antibiotic adjustment on clinical outcomes in ICU patients with severe community-acquired pneumonia: a retrospective study.","authors":"Yong Sun, Kai Guo, Jing Tang, Junjie Zhao, Xiaojing Zhang, Youqin Yan, Lingmin Yuan, Yi Zhang, Canhu Qiu, Jian Luo, Juan Chen, Honglong Fang","doi":"10.1186/s12941-026-00848-5","DOIUrl":"10.1186/s12941-026-00848-5","url":null,"abstract":"<p><strong>Background: </strong>Severe community-acquired pneumonia (SCAP) remains a major cause of intensive care unit (ICU) admission and mortality. Prompt pathogen identification and timely administration of appropriate antimicrobial therapy are essential for improving patient outcomes. Although metagenomic next-generation sequencing (mNGS) enables rapid pathogen detection, the prognostic impact of the timing of mNGS-guided antibiotic adjustment remains unclear.</p><p><strong>Methods: </strong>We conducted a multicenter retrospective study of ICU patients diagnosed with SCAP who underwent both bronchoalveolar lavage fluid (BALF) mNGS and conventional microbiological tests (CMTs). Patients were categorized into early (≤ 72 h) and late (> 72 h) antibiotic adjustment groups based on the interval from ICU admission to the time of antibiotic adjustment guided by mNGS results. Subgroup analyses were performed according to immune status.</p><p><strong>Results: </strong>In our study, mNGS significantly outperformed conventional microbiological tests (CMTs) in pathogen detection (92.70% vs. 57.18%, P < 0.001), with a particularly higher yield for mixed infections (51.63% vs. 19.14%, P < 0.001). Early mNGS-guided antibiotic adjustment was associated with a significantly reduced 28-day mortality compared to late adjustment (41.98% vs. 53.76%, P = 0.037). Furthermore, multivariate logistic regression analysis confirmed early adjustment as an independent protective factor for 28-day mortality (adjusted OR = 0.44, 95% CI: 0.23-0.83, P = 0.011). In the immunocompromised subgroup, early mNGS-guided adjustment was associated with significantly lower 28-day mortality than late adjustment (39.29% vs. 60.00%, P = 0.029), with a significant interaction observed between timing and immune status (P = 0.042).</p><p><strong>Conclusion: </strong>Early mNGS-guided antibiotic adjustment is associated with improved survival among ICU patients with SCAP. This benefit is more pronounced in immunocompromised patients, underscoring the importance of early mNGS application to guide antimicrobial decision-making in this vulnerable population.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"12"},"PeriodicalIF":3.6,"publicationDate":"2026-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12895937/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145997240","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 impact of altered gut microbiota and metabolite profiles on mortality in patients with candidemia: a prospective observational pilot cohort study.","authors":"Soo Hyun Park, Seung Min Park, Jin Woong Suh, Jeong Yeon Kim, Jang Wook Sohn, Young Kyung Yoon","doi":"10.1186/s12941-026-00850-x","DOIUrl":"10.1186/s12941-026-00850-x","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota plays an important role in defending against infectious diseases. However, data on the clinical implications of the microbiome profiles in patients with candidemia remain limited. In this study, we investigated the association between the intestinal microbiome and mortality in patients with candidemia.</p><p><strong>Methods: </strong>This prospective, observational, pilot cohort study enrolled adult patients with culture-confirmed candidemia. Fecal samples were collected within 5 days of diagnosis and analyzed using 16 S ribosomal RNA gene sequencing for microbiota profiling and gas chromatography-mass spectrometry for metabolomic analysis. Multivariate logistic regression was used to identify predictors of in-hospital mortality, defined as death during hospitalization.</p><p><strong>Results: </strong>Fifty-nine patients with candidemia were analyzed, and the in-hospital mortality rate was 40.7%. The median Shannon diversity index of the gut microbiota was significantly lower in non-survivors than that in survivors (P = 0.009). Linear discriminant analysis revealed 11 bacterial species that differed significantly between the two groups. Among the 111 fecal metabolites, only 3-isopropoxy-hexamethyl-tetrasiloxane differed significantly between the survivors and non-survivors (P = 0.007). Septic shock (adjusted odds ratio: 10.59; 95% confidence interval, 1.70-65.97), underlying malignancy (7.79 [1.41-43.10]), and Shannon diversity index (0.40 [0.19-0.84]) were significant predictors of in-hospital mortality.</p><p><strong>Conclusions: </strong>Low gut bacterial diversity is independently associated with mortality in patients with candidemia. These preliminary findings warrant confirmation through larger, well-powered studies.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"11"},"PeriodicalIF":3.6,"publicationDate":"2026-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12896107/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145994261","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":"Pathogen-specific IgE-reactive cytosolic allergenic epitopes of Aspergillus fumigatus for immunodiagnostic/immunotherapeutic applications against allergic aspergillosis.","authors":"Priya Koundal, Sunita Manhas, Shahbaz Aman, Shafiul Haque, Bharat Singh, Shakeel Ahmed Mohammed, Michael Oellerich, Hardeep S Tuli, Seema Ramniwas, Mehak Dangi, Abdul R Asif","doi":"10.1186/s12941-025-00846-z","DOIUrl":"10.1186/s12941-025-00846-z","url":null,"abstract":"<p><p>Aspergillus fumigatus is a significant fungal pathogen responsible for allergic bronchopulmonary aspergillosis (ABPA), a global respiratory disease characterized by high morbidity and mortality. Accurate diagnosis of ABPA remains challenging due to the overlap of clinical and radiological features with other respiratory infections. This study aimed to identify A. fumigatus specific antigens and epitopes to advance immunodiagnostic and immunotherapeutic strategies for ABPA. Clinically confirmed ABPA patients were recruited, and their sera were tested for immunoreactivity against A. fumigatus crude and recombinant allergens. Proteomic analysis was done by employing two-dimensional electrophoresis (2DE) immunoblotting of A. fumigatus cytosolic fractions using sera from 10 individual patients. IgE-reactive spots identified via Q-TOF mass spectrometry revealed 18 allergenic proteins. Among these, two known allergens (Asp-f12 and Asp-f22) and three predicted allergens (sorbitol/xylulose-reductase, Hsp70-chaperone Hsp88, and Hsp70) exhibited cross-reactivity with allergens from other fungi. Notably, 13 allergenic proteins demonstrated significant immunoreactivity specific to ABPA patient sera. In silico epitope analysis identified 9 A. fumigatus specific B-cell and 4 T-cell epitopes with antigenic potential. Molecular docking studies confirmed the binding of representative B-cell and T-cell epitopes to their respective receptors (B-cell receptor and MHC-II complex), demonstrating receptor-specific interactions. These findings highlight pathogen-specific allergens and epitopes that could serve as valuable resources for developing targeted immunodiagnostic and immunotherapeutic tools. This approach may improve the clinical management of ABPA and help reduce its global disease burden.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"7"},"PeriodicalIF":3.6,"publicationDate":"2026-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12882445/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145987570","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":"Fatal multi-drug-resistant gram-negative bacterial pneumonia among adults hospitalized àt Mulago National Referral Hospital, Uganda: an autopsy study.","authors":"Wellington Mutumba, Henry Kajumbula, Robert Lukande, Sam Kalungi, Bakeera Semmuli, Grace Banturaki, Damalie Nakanjako","doi":"10.1186/s12941-025-00839-y","DOIUrl":"10.1186/s12941-025-00839-y","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Pneumonia, responsible for three million deaths annually worldwide, remains a leading cause of death from hospital-acquired infections. Unfortunately, treatment in most cases is empirical and not based on microbiological data because of difficulty in obtaining reliable lower respiratory tract specimens as they are frequently contaminated by upper respiratory tract bacterial flora. We examined aseptically collected lung specimens from decedents with fatal pneumonia to (a) isolate the multi-drug-resistant gram-negative bacteria (MDR GNB) and analyze their antimicrobial susceptibility profiles and resistance phenotypes to beta-lactams and (b) determine the factors associated with fatal MDR GNB pneumonia.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;This was a cross-sectional, descriptive autopsy-based study conducted between June-December 2024 at the Mulago National Referral Hospital mortuary and the Clinical Microbiology Laboratory at Makerere University College of Health Sciences, Kampala, Uganda. Deceased adults, within a postmortem interval not exceeding 20 hours, with an ante-mortem diagnosis of pneumonia or other lower respiratory tract infections were included. Lung tissue and or aspirates were collected, processed, and analyzed microbiologically for bacterial identification, susceptibility testing, and detection of resistance phenotypes to beta lactams.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Overall, 120 adults died during hospitalization at Mulago Hospital with a primary diagnosis of pneumonia in the period of June to December 2024; of whom 60/100 (50%) were female. The mean age was 50.2 (16.6) years, and the median duration of hospitalization was 42.5 (Inter-quartile range 19.0-80.0) hours. Nearly half (53/120, 44%) were referrals from private health care facilities while 43 (35.8%) were from public health care facilities. Thirty-two (32/120, 26.7%) were confirmed to be living with HIV and 59/120 (49%) had other co-morbidities. One hundred three (103/120, 85.8%) had received empirical antibiotic treatment without microbiological investigations. Bacteria isolated from lung tissue/aspirates were Klebshiella pneumoniae species in 54(45.0%) patients, Escherichia coli in 33(27.5%), Pseudomonas aeruginosa in 17(14.2%) and Acinetobacter species in 12(10.0%) of the patients. The bacteria isolates were resistant to most of the antibiotics used for empirical therapy with resistance to Ceftriaxone at 86.7%, Piperacillin-tazobactam at 44.2%, Coamoxiclav 46.7% and Meropenem at 21.7%. Amikacin and Tigecycline had the least resistance at 20% and 14.3% respectively. Overall, Cabarpenem resistance (defined by resistance to either Imipenem or Meropenem or Ertapenem) was observed in 60/120 (50%) of patients. Patients who had pneumonia with co-morbidities were 2.5 times more likely to have Cabarpenem resistance; Odds Ratio, OR (95% Confidence interval (CI) 2.51(1.07 to 5.87); p value =0.033 and patients who were referred from private health care f","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"9"},"PeriodicalIF":3.6,"publicationDate":"2026-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12888371/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145958204","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":"Transient AdeABC-mediated eravacycline resistance in carbapenem-resistant Acinetobacter baumannii ST2: a mutation-independent efflux pump adaptation.","authors":"Xu Yang, Nanhao He, Anwarul Haque, Ying Mai, Jiong Wang, Shunian Xiao, Chao Zhuo","doi":"10.1186/s12941-025-00847-y","DOIUrl":"10.1186/s12941-025-00847-y","url":null,"abstract":"","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":" ","pages":"8"},"PeriodicalIF":3.6,"publicationDate":"2026-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12888453/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145958294","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}