Annals of Clinical Microbiology and Antimicrobials最新文献

{"title":"An analysis of the value-added of antibiogram subgroup stratification.","authors":"Connie T Y Xie, Samantha Martinez, Ceylon V Simon, Susan M Poutanen","doi":"10.1186/s12941-025-00787-7","DOIUrl":"10.1186/s12941-025-00787-7","url":null,"abstract":"<p><strong>Background: </strong>Stratified antibiograms are recommended to guide empiric clinical treatment. However, which strata to focus on, the limited number of isolates in identified strata, and the heavy associated workload all pose challenges. This study compares differences in antibiotic susceptibility between a hospital-wide, all-specimens antibiogram and stratified antibiograms in order to identify the value-added of antibiogram stratification.</p><p><strong>Method: </strong>Antibiotic susceptibility of bacterial isolates from 2021 at a quaternary-care academic hospital was obtained from published hospital-wide and unit- and specimen-specific stratified antibiograms. Differences in percent susceptibility by organism and drug between the hospital-wide and stratified antibiograms were calculated. Weighted averages of the difference in percent susceptibility were calculated for each stratified antibiogram compared to the hospital-wide antibiogram and unit-wide antibiograms. Differences were shown through heat maps.</p><p><strong>Results: </strong>When compared to a hospital-wide, all-specimens antibiogram, the emergency department (ED) antibiogram showed higher susceptibility, whereas the intensive care unit (ICU) and, particularly, the transplant unit antibiograms exhibited reduced susceptibility. Compared to unit level antibiograms, further stratification within each unit to specimen-specific (syndromic) antibiograms revealed additional differences. In the ED, urine and respiratory-stratified antibiograms had lower susceptibility and blood had higher susceptibility. Compared to unit-specific antibiograms, in the ICU, all specimen-stratified antibiograms had lower susceptibility and in the transplant unit, antibiograms for all specimens but urine had lower susceptibility.</p><p><strong>Conclusion: </strong>Using a hospital-wide all-specimens antibiogram may both overcall and under call susceptibility leading to poor empiric antimicrobial choices. Specimen-specific antibiograms stratified by unit best inform empiric therapy for specific populations.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"21"},"PeriodicalIF":4.6,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11972497/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787563","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 characteristics, virulence potential, antimicrobial resistance profiles, and phylogenetic insights into Nocardia cyriacigeorgica.","authors":"Chen Yang, Yue-Xin Zheng, Hong-Yi Gu, Hong Chen, Wei Li, Fang Li, Yu-Wang Bi, Jing Chen, Fu-Kun Wang, Qing-Qing Sun, Han-Bing Meng, Zuo-Hao Wu, Shu Yu, Jiang Gu, Yan Cheng","doi":"10.1186/s12941-025-00791-x","DOIUrl":"10.1186/s12941-025-00791-x","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Nocardia cyriacigeorgica, an opportunistic pathogen, is increasingly implicated in human infections. This pathogen predominantly causes pulmonary infections, leading to acute, subacute, or chronic necrotizing suppurative lesions, in severe cases, may progress to disseminated infections. Effective clinical diagnosis, prevention, and treatment strategies require a thorough understanding of its biological characteristics and pathogenic mechanisms. However, despite the rising incidence of nocardial diseases, research on the pathogenicity of N. cyriacigeorgica remains limited, primarily focusing on case reports and epidemiological studies. This study aimed to provide a comprehensive analysis of the genomic features, phylogenetic relationships, antimicrobial resistance profiles, and candidate virulence factors of N. cyriacigeorgica strains to inform future investigations into its pathogenesis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;Whole-genome sequencing was conducted on five N. cyriacigeorgica strains isolated from patients with pulmonary infection at our hospital. This analysis utilized a combination of second-generation Illumina HiSeq and third-generation PacBio sequencing technologies. Additionally, publicly available genomic data from 58 strains in the National Center Biotechnology Information database were integrated, resulting in a dataset of 63 genomes. These genomes were subjected to comparative genomic analyses, including phylogenetic reconstruction, pan-genome evaluation, and gene distribution assessments.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Phylogenetic analysis identified five major clades within N. cyriacigeorgica. ANI analysis further subdivided clade B into five distinct subgroups. Pan-genome analysis revealed clade-specific orthogroups in the distribution of genes assigned to Clusters of Orthologous Groups, with clade A containing the highest number of clade-specific gene families. Comparative genomic analysis uncovered several potential pathogenic genes implicated in host cell invasion, phagosomal maturation arrest, and intracellular survival within macrophages, which were conserved across all analyzed strains. Notable differences in the distribution of enterobactin-encoding genes were observed among the clades. The mce3C gene also displayed variable distributions across clades; however, no correlation was established between its presence and strain source. Among the 63 strains, 27 were found to harbor both mce3C and mce4F genes, which were categorized into five distinct patterns. Furthermore, antibiotic resistance genes, including VanSO, VanRO, erm(O)-Irm, srmB, ermH, bcl, bla1, and cmIR, demonstrated clade-specific distribution patterns. Notably, the genes erm(O)-Irm, srmB, and ermH were associated with the isolation origin of the strains.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;This study provides a comprehensive evaluation of the genomic characteristics, potential virulence factors, antimicrobial resistance genes","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"22"},"PeriodicalIF":4.6,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11972502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143787571","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":"TROJAN-MDR: in vitro activity of cefiderocol and comparators against multidrug-resistant Enterobacterales and Pseudomonas aeruginosa strains in Southern France, evaluation of available testing methods performances.","authors":"Massinissa Benyahia, Chloé Magnan, Vincent Jean-Pierre, Romaric Larcher, Adeline Boutet-Dubois, Marie Gaillard, Hélène Marchandin, Stéphanie Genieyz, Madjid Morsli, Jean-Philippe Lavigne, Alix Pantel","doi":"10.1186/s12941-025-00785-9","DOIUrl":"10.1186/s12941-025-00785-9","url":null,"abstract":"<p><strong>Background: </strong> Cefiderocol, a newly introduced siderophore cephalosporin, exhibits activity against various multidrug-resistant (MDR) Gram-negative bacilli (GNB), including producers of Ambler class A, B and D carbapenemases. The TROJAN-MDR study aimed to (i) compare the in vitro activity of cefiderocol with other last-resort antibiotics against a well-characterized collection of Enterobacterales and Pseudomonas aeruginosa strains from Southern France, and (ii) assess the performance of available cefiderocol antimicrobial susceptibility testing (AST) methods.</p><p><strong>Methods: </strong>The collection comprised 127 Enterobacterales from various clones, including 119 carbapenemase producers (93.7%), and 53 MDR P. aeruginosa. The minimum inhibitory concentrations (MICs) of cefiderocol were determined using the UMIC^® broth microdilution method (BMD) as the reference. Comparators MICs were measured using Sensititre™ EUMDRXXF plates and Liofilchem strips for aztreonam-avibactam. Results were interpreted according to EUCAST breakpoints, with CLSI breakpoints also used for cefiderocol. The performance of the ComASP^® BMD and disk diffusion on two different Mueller-Hinton media (Bio-Rad and BD) were evaluated according to ISO 20776-2:2007 and 2021.</p><p><strong>Results: </strong>Cefiderocol demonstrated potent activity on Enterobacterales (81.9% susceptible) and P. aeruginosa (84.9%) using EUCAST breakpoints. Among Enterobacterales, the most effective comparators were colistin, aztreonam-avibactam, meropenem-vaborbactam, and amikacin, with susceptibility rates of 99.2%, 98.4%, 85%, and 76.4%, respectively. For P. aeruginosa, only colistin exhibited better activity (100%). The disk diffusion method showed superior performance on BD medium compared to Bio-Rad. The ComASP^® method did not provide sufficient performance to be considered reliable.</p><p><strong>Conclusions: </strong>Cefiderocol was highly active against a large collection of MDR GNB, including high-risk clones. It is crucial to assess susceptibility to this last-resort antibiotic using a validated method when considering clinical use.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"20"},"PeriodicalIF":4.6,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662246","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":"Molecular and genetic features of a bla_NDM-1 and bla_SHV-12 coharboring hypermucoviscous Klebsiella pneumoniae of serotype K2 and ST65.","authors":"Yuting Kang, Qiujie Li, Wanting Ma, Chao Xu, Zhuoran Qiu, Wei Jia, Pengtao Wang","doi":"10.1186/s12941-025-00789-5","DOIUrl":"10.1186/s12941-025-00789-5","url":null,"abstract":"<p><strong>Purpose: </strong>This study aimed to assess the resistance phenotype, virulence phenotype, and genetic characteristics of a bla_NDM-1 and bla_SHV-12 co-harboring ST65 K2 Klebsiella pneumoniae (KP114), which was isolated from General hospital of Ningxia Medical University.</p><p><strong>Methods: </strong>Antibiotic susceptibility test was determined by Vitek 2 Compact system. Multilocus Sequence typing (MLST), antimicrobial resistance and virulence genes were examined by PCR and Sanger sequencing. The virulence of KP114 was evaluated through string test, macrophage phagocytosis assay, serum resistance assay, and mouse infection model. Whole-genome sequencing was performed for further analysis of genetic information.</p><p><strong>Results: </strong>The presence of the bla_NDM-1 and bla_SHV-12 genes in KP114 confered resistance to multi-antibiotics. The hypervirulence of KP114 was demonstrated through various in vitro experiments and in vivo mouse infection model. KP114 was found to harbor two distinct plasmids: a drug-resistant plasmid (pKP114-NDM), classified as the IncX3 type, which contained various transfer elements including type IV coupling protein (T4CP) and type IV secretion system (T4SS), and a virulence plasmid (pKP114-vir) that exhibited a high sequence similarity with pLVPK. The results of the conjugation experiment showed that resistance and virulence traits were successfully transferred from KP114 to Escherichia coli EC600 and J53.</p><p><strong>Conclusions: </strong>We reported a Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) strain of ST65 K2 serotype carrying the bla_NDM-1 and bla_SHV-12, which exhibited hypervirulence and drug resistance with potential for transmission. This finding allows improved clinical surveillance and control of this clone, thereby holding considerable value for clinical treatment.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"19"},"PeriodicalIF":4.6,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11921603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655976","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":"Beyond the gut: a comprehensive meta-analysis on Helicobacter pylori infection and cardiovascular complications.","authors":"Somayeh Yaslianifard, Fatemeh Sameni, Kimia Kazemi, Yousef Atefpour, Bahareh Hajikhani, Ali Baradaran Bagheri, Shahrooz Yazdani, Masoud Dadashi","doi":"10.1186/s12941-025-00788-6","DOIUrl":"10.1186/s12941-025-00788-6","url":null,"abstract":"<p><strong>Background: </strong>Helicobacter pylori (H. pylori) is known to induce chronic inflammatory conditions, and interactions between the host immune system and pathogen have diverted attention toward investigating its correlation with extra-gastrointestinal disorders.</p><p><strong>Objective: </strong>The present study aimed to assess the rate of H. pylori infection in cardiovascular disease (CVD) through a systematic review and meta-analysis.</p><p><strong>Methods: </strong>We conducted a large-scale meta-analysis to determine the prevalence rates of H. pylori infection in vascular diseases. Articles from PubMed/Medline, Web of Science, and Embase databases published between 2000 and 2023 were included for analysis. We used multiple independent observers to extract data, calculated the pooled frequency of H. pylori in vascular diseases using a random effect model, and reported the results as a weighted average based on the study population. The main outcome measures were presented with 95% confidence intervals (CI).</p><p><strong>Results: </strong>In 87 included studies, the prevalence of H. pylori infection in vascular diseases was 56.7% worldwide. 14.25% of H. pylori isolates harbored the cagA gene. The predominant vascular complication was coronary artery disease (CAD) (31.07%), primarily documented in Europe. This meta-analysis revealed a declining emphasis on studying the association of H. pylori infection with vascular disease in recent times.</p><p><strong>Conclusion: </strong>According to this meta-analysis, H. pylori infection has a high frequency in CVD and may increase the risk of vascular diseases. However, further research is required, particularly in nations with limited data.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"18"},"PeriodicalIF":4.6,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11916874/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143655938","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":"In vitro activity of rifampicin, rifapentine and rifabutin in combination with their 25-deacetyl-metabolites against various Mycobacterium tuberculosis lineages.","authors":"Charlotte Genestet, Chloé Bourg, Elisabeth Hodille, Olivier Bahuaud, Florence Ader, Sylvain Goutelle, Oana Dumitrescu","doi":"10.1186/s12941-025-00784-w","DOIUrl":"10.1186/s12941-025-00784-w","url":null,"abstract":"<p><strong>Objectives: </strong>Rifamycin agents (rifampicin (RIF), rifapentine (RFP), rifabutin (RFB)) are the cornerstone of tuberculosis (TB) therapy. Rifamycins are metabolized into 25-deacetyl-metabolites, which have been described has active and may contribute to in vivo drug effect. However, little is known about the combined effect of rifamycins and their metabolites across different Mycobacterium tuberculosis complex (MTBC) lineages.</p><p><strong>Methods: </strong>This study included 14 MTBC strains representing the main lineages. Minimum inhibitory concentrations (MICs) were determined using microdilution assays for the three rifamycins and their metabolites. A checkerboard assay was used to assess drug interactions, with the fractional inhibitory concentration (FIC) index calculated for synergy or antagonism.</p><p><strong>Results: </strong>MICs varied across rifamycins, RIF and its metabolite showed the highest MICs, followed by RFP and RFB and their respective metabolites. FIC indices for rifamycin-metabolite combinations indicated additive effects (FIC between 0.5 and 1.25), with no antagonism observed, even at clinically relevant metabolite-to-parent drug ratios, and without impact of MTBC lineage.</p><p><strong>Conclusions: </strong>Rifamycin metabolites exhibit additive effects with parent drugs, potentially enhancing bactericidal activity. This highlights that rifamycin susceptibility testing should account for both parent drugs and their metabolites, as these metabolites also exhibit antimicrobial activity. Additionally, these findings support further pharmacokinetic/pharmacodynamic studies to optimize TB treatment regimens, particularly in relation to metabolite-to-parent drug ratios in patients.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"16"},"PeriodicalIF":4.6,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530821","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, genomic analysis and preclinical evaluation of the lytic Staphylococcus bacteriophage PSK against methicillin-resistant Staphylococcus aureus wound isolate.","authors":"Abanoub A Zanaty, Tarek Dishisha, Mohamed Abd El-Gawad El-Sayed-Ahmed, Maha M Abdel-Fattah, Kawkab A Ahmed, Karim Abdelkader","doi":"10.1186/s12941-025-00783-x","DOIUrl":"10.1186/s12941-025-00783-x","url":null,"abstract":"<p><strong>Background: </strong>The dissemination of multi-drug-resistant bacteria, particularly Methicillin-resistant Staphylococcus aureus (MRSA), necessitates exploring new alternatives for their control. Bacteriophages are promising antibiotic alternatives with unique features. Here, we have performed a comprehensive characterization of a newly isolated bacteriophage (PSK) and compared its therapeutic potential with vancomycin in vivo.</p><p><strong>Methods: </strong>Sewage samples were processed and enriched with the MRSA S. aureus SK1 strain in a search for isolation of a lytic bacteriophage. The isolated bacteriophage was assessed in vitro in terms of thermal and pH stability and kinetic parameters using absorption and one step growth curve assays. Moreover, its potential antibacterial activity was evaluated against S. aureus SK1 lone and in combination of standard of care antibiotics used for treatment of wound infections. We further analyzed its genome to exclude the presence of any potential toxin or antibiotic resistance genes. Finally, its antibacterial potential and capability to alleviate wound infection were assessed using a murine wound-infection model.</p><p><strong>Results: </strong>The lytic bacteriophage (PSK) was isolated as a new species of the genus Rosenblumvirus with a genome size of 17,571 bp that is free from potential resistance or virulence genes. PSK displays infectivity against 4/10 S. aureus strains including two vancomycin-resistant strains. Moreover, it demonstrates favorable infection kinetics of fast adsorption with latent period and burst size of 20 min and 123 PFU/infected cell, respectively. Stability analysis revealed thermal stability up to 60 °C with wide pH range stability (4-11). In vitro, PSK kills S. aureus SK1 with multiplicity of infection (MOI) as low as 10^- 4 with an overall mutation frequency of 2.47 × 10^- 6 CFU/mL that is further improved when combined with 0.25× MIC of oxacillin, fusidic acid or vancomycin. In vivo, a single dose of PSK in murine wound infection model exhibited a comparable performance to four doses of vancomycin, when treatment started 2 h post-infection. However, when applied 2 days post-infection, PSK demonstrates superior antibacterial activity (up to 4.58 log unit count reduction) and enhances wound closure and tissue healing.</p><p><strong>Conclusion: </strong>These findings represent PSK as a potential vancomycin alternative effective in treating S. aureus- induced wound infections.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"17"},"PeriodicalIF":4.6,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11871620/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531191","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":"Major blood stream infection-causing bacterial pathogens, antimicrobial resistance patterns and trends: a multisite retrospective study in Asmara, Eritrea (2014-2022).","authors":"Yosan Gebremeskel Andemichael, Eyorusalem Tsehaye Habtetsion, Hagos Hayelom Gulbet, Maedn Hailemariam Eman, Oliver Okoth Achila, Samuel Tekle Mengistu, Azania Werede Andemichael, Abrehet Marikos Buthuamlak, Eyob Yohannes Garoy, Berhe Tesfai, Mohammed Elfatih Hamida","doi":"10.1186/s12941-025-00780-0","DOIUrl":"10.1186/s12941-025-00780-0","url":null,"abstract":"<p><strong>Background: </strong>An important knowledge gap exists on the epidemiology of blood stream infections (BSIs) in low-middle-income countries (LMICs). In this retrospective analysis, we evaluated the etiology, antimicrobial resistance (AMR) and trends of BSIs in Eritrea.</p><p><strong>Methods: </strong>The study reviewed 9-year records (January 2014- December 2022) of 3153 patients with blood culture results available in the National Health Laboratory (NHL) archives. Relevant data included age, sex, hospital/care center, and year.</p><p><strong>Result: </strong>During the surveillance period, we examined data from 3153 patients (1797 (57.0%) men vs. 1356 (43.0%) females, and 1.2 years (Q1: 0.01 months - Q3: 15 years). Of the samples submitted, 1026 (35.5%) samples were positive for the presence of pathogens (663(64.6%) pathogens vs. 363 (35.4%)) potential contaminants. In decreasing frequency, the most common isolates were: Coagulase-negative Staphylococcus (CoNs), 189 (28.6%); Klebsiella spp., 120 (18.2%); Escherichia coli, 66 (10.0%); Citrobacter spp., 48 (7.3%); Staphylococcus aureus, 47(7.1%); Pseudomonas aeruginosa, 34 (5.1%); and Salmonella spp., 33(5.1). The relative prevalence of BSIs changed somewhat over time (p-value < 0.001) with the isolation of multiple isolates trending upward from 2018 and onwards. Additional findings included the likely presence of extended spectrum beta lactamase (ESBL), high frequency of methicillin resistant Staphylococcus aureus (MRSA) (37(80.4%) and high rate of resistance to gentamicin (363(62.5%) and fluoroquinolones. Furthermore, the multiple antimicrobial resistances (MAR) index was relatively high (mean = 0.55, SD: ±0.23) with wide species-level variation. In a related density cluster analysis, we demonstrated a time-dependent increase in the diversity of resistotypes.</p><p><strong>Conclusion: </strong>This study highlights the considerable health burden of AMR/or MDR in BSIs in Eritrea. Additionally, it underscores the urgent need for enhanced laboratory capacity, surveillance, institutionalisation of antibiotic stewardship programs, and robust infection control programs in hospitals across the country. The need for multidisciplinary research was also highlighted.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"15"},"PeriodicalIF":4.6,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846260/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472075","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":"Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.","authors":"Jinfeng Yuan, Liping Ma, Juan Du, Hailin Sun, Shanshan Li, Gang Zhou, Guanhua Rao, Fengshuo Sun, Wangyang Chen, Hui Miao, Dan Tian, Changhao Cheng, Yan Wang, Liang Li, Lifeng Li, Yu Pang","doi":"10.1186/s12941-025-00782-y","DOIUrl":"10.1186/s12941-025-00782-y","url":null,"abstract":"<p><p>Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"13"},"PeriodicalIF":4.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439766","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":"Diagnostics, resistance and clinical relevance of non-tuberculous mycobacteria unidentified at the species level by line probe assays: a bi-national study.","authors":"Matúš Dohál, Nils Wetzstein, Michaela Hromádková, Simona Mäsiarová, Erik M Rasmussen, Peter Kunč, Mária Škereňová, Igor Porvazník, Ivan Solovič, Stefan Niemann, Jarmila Hnilicová, Juraj Mokrý, Věra Dvořáková, Margo Diricks","doi":"10.1186/s12941-025-00781-z","DOIUrl":"10.1186/s12941-025-00781-z","url":null,"abstract":"<p><strong>Objectives: </strong>While the reported incidence of non-tuberculous mycobacterial (NTM) infections is increasing, the true prevalence remains uncertain due to limitations in diagnostics and surveillance. The emergence of rare and novel species underscores the need for characterization to improve surveillance, detection, and management.</p><p><strong>Methods: </strong>We performed whole-genome sequencing (WGS) and/or targeted deep-sequencing using the Deeplex Myc-TB assay on all NTM isolates collected in Slovakia and the Czech Republic between the years 2019 to 2023 that were unidentifiable at the species level by the routine diagnostic line probe assays (LPA) GenoType CM/AS and NTM-DR. Minimal inhibitory concentrations against amikacin, ciprofloxacin, moxifloxacin, clarithromycin, and linezolid were determined, and clinical data were collected.</p><p><strong>Results: </strong>Twenty-eight cultures from different patients were included, of which 9 (32.1%) met the clinically relevant NTM disease criteria. The majority of those had pulmonary involvement, while two children presented with lymphadenitis. Antimycobacterial resistance rates were low. In total, 15 different NTM species were identified, predominantly rare NTM like M. neoaurum, M. kumamotonense and M. arupense. Notably, clinically relevant M. chimaera variants were also identified with WGS and Deeplex-Myc TB, which, unlike other M. chimaera strains, appeared to be undetectable by LPA assays. Deeplex detected four mixed infections that were missed by WGS analysis. In contrast, WGS identified two novel species, M. celatum and M. branderi, which were not detected by Deeplex-Myc TB. Importantly, one of these novel species strains was associated with clinically relevant pulmonary disease.</p><p><strong>Discussion: </strong>Our study demonstrates the clinical relevance of uncommon NTM and the effectiveness of targeted deep-sequencing combined with WGS in identifying rare and novel NTM species.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"24 1","pages":"14"},"PeriodicalIF":4.6,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11834575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143439863","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}