Pub Date : 2026-01-01Epub Date: 2025-12-08DOI: 10.1016/j.jgar.2025.12.004
Muhammad Sharjeel , Memoona Irshad , Azka Rizvi , Altaf Ahmed , Muhammad Jan Leghari
Objective
Rapid identification of lower respiratory tract infection pathogens is critical for initiating early antimicrobial therapy. This study aimed at evaluating the role of multiplex polymerase chain reaction (mPCR) in detecting respiratory pathogens and antimicrobial resistance at a transplant centre.
Methods
The study was a single-centre, retrospective analysis, completed at a tertiary care transplant centre. Data were included from 242 patients admitted with lower respiratory tract infection during a 24-month period. Respiratory specimens were analysed through BioFire PCR. Blood mPCR specimens were excluded (n = 44). Multiplex PCR results were compared with the gold standard of culture and sensitivity testing.
Results
A total of 198 patients were included in the study. The majority had a history of chronic hepatic or renal impairment (n = 95; 48%) or liver/kidney transplantation (n = 57; 28.8%). Chest imaging (n = 162) predominantly revealed pleural effusions (35.2%) and parenchymal infiltrates (28.4%). Most common sample types included sputum (n = 101; 51.0%) and tracheal aspirates (n = 93; 47.0%). Standard culture detected the following pathogens: 290 typical bacteria, 2 atypical organisms, and 95 viral detections. Klebsiella pneumoniae (32.3%) and Escherichia coli (28.8%) were most frequently identified. In n = 102 patients with corresponding culture results, mPCR had sensitivity of 76% and specificity of 59%, with 66.7% concordance between methods. Multiplex PCR and culture identified multiple bacterial species in 38 (37.3%) and 17 (16.7%) cases, respectively. Antimicrobial resistance gene analysis revealed high prevalence of CTX-M (30%), NDM (28%), and OXA-48-like (22%) mutations.
Conclusions
Multiplex PCR pneumonia panel demonstrated high sensitivity in detecting respiratory pathogens but had limitations in its specificity when compared to culture methods.
{"title":"Multiplex PCR pneumonia panel compared to standard culture of respiratory specimens: Retrospective results from a transplant centre","authors":"Muhammad Sharjeel , Memoona Irshad , Azka Rizvi , Altaf Ahmed , Muhammad Jan Leghari","doi":"10.1016/j.jgar.2025.12.004","DOIUrl":"10.1016/j.jgar.2025.12.004","url":null,"abstract":"<div><h3>Objective</h3><div>Rapid identification of lower respiratory tract infection pathogens is critical for initiating early antimicrobial therapy. This study aimed at evaluating the role of multiplex polymerase chain reaction (mPCR) in detecting respiratory pathogens and antimicrobial resistance at a transplant centre.</div></div><div><h3>Methods</h3><div>The study was a single-centre, retrospective analysis, completed at a tertiary care transplant centre. Data were included from 242 patients admitted with lower respiratory tract infection during a 24-month period. Respiratory specimens were analysed through BioFire PCR. Blood mPCR specimens were excluded (<em>n</em> = 44). Multiplex PCR results were compared with the gold standard of culture and sensitivity testing.</div></div><div><h3>Results</h3><div>A total of 198 patients were included in the study. The majority had a history of chronic hepatic or renal impairment (<em>n</em> = 95; 48%) or liver/kidney transplantation (<em>n</em> = 57; 28.8%). Chest imaging (<em>n</em> = 162) predominantly revealed pleural effusions (35.2%) and parenchymal infiltrates (28.4%). Most common sample types included sputum (<em>n</em> = 101; 51.0%) and tracheal aspirates (<em>n</em> = 93; 47.0%). Standard culture detected the following pathogens: 290 typical bacteria, 2 atypical organisms, and 95 viral detections. <em>Klebsiella pneumoniae</em> (32.3%) and <em>Escherichia coli</em> (28.8%) were most frequently identified. In <em>n</em> = 102 patients with corresponding culture results, mPCR had sensitivity of 76% and specificity of 59%, with 66.7% concordance between methods. Multiplex PCR and culture identified multiple bacterial species in 38 (37.3%) and 17 (16.7%) cases, respectively. Antimicrobial resistance gene analysis revealed high prevalence of CTX-M (30%), NDM (28%), and OXA-48-like (22%) mutations.</div></div><div><h3>Conclusions</h3><div>Multiplex PCR pneumonia panel demonstrated high sensitivity in detecting respiratory pathogens but had limitations in its specificity when compared to culture methods.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 179-186"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145723937","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2026-01-08DOI: 10.1016/j.jgar.2026.01.001
Magdalena Gatsch , Charlotte Aldridge , Kasim Allel , Hassanat Mojirola Lawal , Esmita Charani , Emma Pitchforth
Introduction
Antimicrobial resistance (AMR) is a major global health threat addressed through National Action Plans (NAPs) aligned with the WHO Global Action Plan. Despite evidence that women are disproportionately affected – receiving 27% more antibiotic prescriptions than men – gender considerations remain largely absent from AMR policies.
Methods
We conducted a mixed-methods analysis of 132 NAPs published before December 2023. A two-stage approach was used: quantitative keyword frequency analysis of 10 gender-related terms (e.g., sex, gender, women), followed by a qualitative thematic analysis of top-tier NAPs, defined as those scoring ≥3 gender-related terms on a 10-point frequency scale derived from the former quantitative analysis. We also examined the gender composition of NAP curators and assessed correlations between gender representation and keyword inclusion.
Results
Only 14 NAPs (11%) mentioned the term ‘gender’. The most frequent gender-related term was ‘urinary tract infection’ (UTI), appearing in 33% of NAPs. High-scoring NAPs were predominantly from low-income countries (mean score 2.4, SD = 2.2), especially in Africa (mean 2.5, SD = 2.3), compared to upper-middle-income countries (mean 1.1, SD = 1.07) and the Pan-American region (mean 1.0, SD = 0.9). Women were underrepresented among NAP curators: 47 NAPs were led entirely by men, while only 14 were led by women. No significant correlation was found between women’s participation and gender keyword inclusion (β ≈ 0.11, P = 0.449).
Conclusion
Gender remains insufficiently integrated into AMR NAPs. The findings highlight the need for gender awareness policy development and the adoption of an intersectional framework to address overlapping social determinants that shape AMR vulnerability and response.
{"title":"Deconstructing antimicrobial resistance national action plans: A gender-perspective driven mixed-methods analysis","authors":"Magdalena Gatsch , Charlotte Aldridge , Kasim Allel , Hassanat Mojirola Lawal , Esmita Charani , Emma Pitchforth","doi":"10.1016/j.jgar.2026.01.001","DOIUrl":"10.1016/j.jgar.2026.01.001","url":null,"abstract":"<div><h3>Introduction</h3><div>Antimicrobial resistance (AMR) is a major global health threat addressed through National Action Plans (NAPs) aligned with the WHO Global Action Plan. Despite evidence that women are disproportionately affected – receiving 27% more antibiotic prescriptions than men – gender considerations remain largely absent from AMR policies.</div></div><div><h3>Methods</h3><div>We conducted a mixed-methods analysis of 132 NAPs published before December 2023. A two-stage approach was used: quantitative keyword frequency analysis of 10 gender-related terms (e.g., sex, gender, women), followed by a qualitative thematic analysis of top-tier NAPs, defined as those scoring ≥3 gender-related terms on a 10-point frequency scale derived from the former quantitative analysis. We also examined the gender composition of NAP curators and assessed correlations between gender representation and keyword inclusion.</div></div><div><h3>Results</h3><div>Only 14 NAPs (11%) mentioned the term ‘gender’. The most frequent gender-related term was ‘urinary tract infection’ (UTI), appearing in 33% of NAPs. High-scoring NAPs were predominantly from low-income countries (mean score 2.4, SD = 2.2), especially in Africa (mean 2.5, SD = 2.3), compared to upper-middle-income countries (mean 1.1, SD = 1.07) and the Pan-American region (mean 1.0, SD = 0.9). Women were underrepresented among NAP curators: 47 NAPs were led entirely by men, while only 14 were led by women. No significant correlation was found between women’s participation and gender keyword inclusion (β ≈ 0.11, <em>P</em> = 0.449).</div></div><div><h3>Conclusion</h3><div>Gender remains insufficiently integrated into AMR NAPs. The findings highlight the need for gender awareness policy development and the adoption of an intersectional framework to address overlapping social determinants that shape AMR vulnerability and response.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 273-282"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145948968","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-12-15DOI: 10.1016/j.jgar.2025.12.008
Samara Sant’Anna de Oliveira , Camille Alves Brito de Moura , Kaylanne Montenegro , Thereza Cristina da Costa Vianna , Ana Paula Alves do Nascimento , Gerson Gatto de Azeredo Coutinho , Hosana Dau Ferreira de Souza , Claudia Gladys Flores Sejas , Alexander Machado Cardoso , Kayo Bianco , Maysa Mandetta Clementino
Objective
Uropathogenic Escherichia coli (UPEC) poses a significant public health challenge due to increasing antimicrobial resistance (AMR) and severe infections. This study aimed to investigate the genetic heterogeneity and AMR mechanisms of a clinical UPEC strain associated with a fatal healthcare-associated infection.
Methods
Whole-genome sequencing (WGS) was performed on a multidrug-resistant (MDR) UPEC strain isolated from a pediatric patient by using an Illumina Miseq platform. The genome was assembled using Unicycler v0.4.8 and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Genomic analysis included characterisation of the resistome, virulome, and phylogenetic profile using various bioinformatics tools such as ResFinder v4.7.2, VFDB, and PubMLST.
Results
The isolate has a genome with a size of 4,681,240 bp, a GC content of 50.60% and harbour seven plasmids. Genomic analysis revealed multiple genetic determinants contributing to a multidrug-resistant profile, including efflux systems, enzymatic target alterations, and antibiotic transporter modifications. Adhesin genes (fimH, afaA-D, lpfA, fdeC, csgA), hemolysins (hlyE, hlyF), iron acquisition systems (iucC, iutA, sitA), and genes related to antimicrobial peptide degradation (ompT, traJ) and colicin production (cma, cvaC) were identified. Resistance to heavy metals (tellurium, copper/silver, arsenic) was also detected. These findings characterise the isolate as a highly virulent, multidrug-resistant, and environmentally resilient emerging UPEC clone.
Conclusions
This study highlights the convergence of virulence, AMR, and environmental adaptability in an ST131-H30 UPEC strain. The findings underscore the critical need for comprehensive genomic surveillance, infection control strategies to mitigate the public health impact of MDR E. coli.
{"title":"Genomic insights into a multidrug-resistant uropathogenic Escherichia coli ST131-H30 strain associated with a fatal healthcare-associated infection","authors":"Samara Sant’Anna de Oliveira , Camille Alves Brito de Moura , Kaylanne Montenegro , Thereza Cristina da Costa Vianna , Ana Paula Alves do Nascimento , Gerson Gatto de Azeredo Coutinho , Hosana Dau Ferreira de Souza , Claudia Gladys Flores Sejas , Alexander Machado Cardoso , Kayo Bianco , Maysa Mandetta Clementino","doi":"10.1016/j.jgar.2025.12.008","DOIUrl":"10.1016/j.jgar.2025.12.008","url":null,"abstract":"<div><h3>Objective</h3><div>Uropathogenic Escherichia coli (UPEC) poses a significant public health challenge due to increasing antimicrobial resistance (AMR) and severe infections. This study aimed to investigate the genetic heterogeneity and AMR mechanisms of a clinical UPEC strain associated with a fatal healthcare-associated infection.</div></div><div><h3>Methods</h3><div>Whole-genome sequencing (WGS) was performed on a multidrug-resistant (MDR) UPEC strain isolated from a pediatric patient by using an Illumina Miseq platform. The genome was assembled using Unicycler v0.4.8 and was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Genomic analysis included characterisation of the resistome, virulome, and phylogenetic profile using various bioinformatics tools such as ResFinder v4.7.2, VFDB, and PubMLST.</div></div><div><h3>Results</h3><div>The isolate has a genome with a size of 4,681,240 bp, a GC content of 50.60% and harbour seven plasmids. Genomic analysis revealed multiple genetic determinants contributing to a multidrug-resistant profile, including efflux systems, enzymatic target alterations, and antibiotic transporter modifications. Adhesin genes (fimH, afaA-D, lpfA, fdeC, csgA), hemolysins (hlyE, hlyF), iron acquisition systems (iucC, iutA, sitA), and genes related to antimicrobial peptide degradation (ompT, traJ) and colicin production (cma, cvaC) were identified. Resistance to heavy metals (tellurium, copper/silver, arsenic) was also detected. These findings characterise the isolate as a highly virulent, multidrug-resistant, and environmentally resilient emerging UPEC clone.</div></div><div><h3>Conclusions</h3><div>This study highlights the convergence of virulence, AMR, and environmental adaptability in an ST131-H30 UPEC strain. The findings underscore the critical need for comprehensive genomic surveillance, infection control strategies to mitigate the public health impact of MDR <em>E. coli.</em></div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 175-178"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145774901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Antimicrobial resistance (AMR) is a pressing global health challenge, particularly affecting low- and middle-income countries. This study aims to evaluate the spread of AMR both across time and across different regions of the world.
Methods
We analysed clinical isolates from 65 countries. A country-specific time-series forecasting (i.e. seasonal autoregressive integrated moving average (SARIMA), long short-term memory (LSTM), and seasonal autoregressive integrated moving average-LSTM hybrid models) were performed for Acinetobacter baumannii in Argentina (2004–2030) as a case study to demonstrate model applicability for national-level prediction. Moreover, interrupted time series regression was applied to predict antibiotic-resistance trends and assess the global impact of national action plans.
Results
Southeast Asia and Africa exhibited the highest AMR burdens, with Indonesia (0.65), Egypt (0.52), and Malawi (0.49) having the highest resistance scores. An income-based gradient was observed across key pathogens, third-generation cephalosporin and carbapenem-resistant Escherichia coli, Klebsiella pneumoniae, and A. baumannii were significantly more prevalent in low- and middle-income countries. Gender-wise analysis revealed significantly higher resistance rates in males across most antibiotics, especially levofloxacin. Age-stratified analyses revealed higher resistance in elderly populations, particularly to fluoroquinolones and β-lactams. Forecasting for A. baumannii in Argentina (2004–2030) indicated a continued upward resistance across β-lactam and fluoroquinolones, with LSTM achieving the lowest root mean square error across five antibiotics. The interrupted time series revealed a prenational action plan decline but no significant postimplementation change.
Conclusion
This study provides a comprehensive data-driven framework to monitor and forecast AMR, evaluate policy interventions, and, hence, suggest targeted interventions and strategies for each income group and region, moving beyond the one-size-fits-all approach.
{"title":"Global prediction of antimicrobial resistance trends using statistical and machine learning models: Evaluating national action plan policy impacts through interrupted time series analysis","authors":"Linta Khalid , Kashif Saleem , Saima Mushtaq , Iltaf Hussain , Zamir Hussain , Zainab Hussain , Rehan Zafar Paracha , Amjad Khan , Jie Chang , Yu Fang , Imran Sajid","doi":"10.1016/j.jgar.2025.11.022","DOIUrl":"10.1016/j.jgar.2025.11.022","url":null,"abstract":"<div><h3>Objective</h3><div>Antimicrobial resistance (AMR) is a pressing global health challenge, particularly affecting low- and middle-income countries. This study aims to evaluate the spread of AMR both across time and across different regions of the world.</div></div><div><h3>Methods</h3><div>We analysed clinical isolates from 65 countries. A country-specific time-series forecasting (i.e. seasonal autoregressive integrated moving average (SARIMA), long short-term memory (LSTM), and seasonal autoregressive integrated moving average-LSTM hybrid models) were performed for <em>Acinetobacter baumannii</em> in Argentina (2004–2030) as a case study to demonstrate model applicability for national-level prediction. Moreover, interrupted time series regression was applied to predict antibiotic-resistance trends and assess the global impact of national action plans.</div></div><div><h3>Results</h3><div>Southeast Asia and Africa exhibited the highest AMR burdens, with Indonesia (0.65), Egypt (0.52), and Malawi (0.49) having the highest resistance scores. An income-based gradient was observed across key pathogens, third-generation cephalosporin and carbapenem-resistant <em>Escherichia coli, Klebsiella pneumoniae</em>, and <em>A. baumannii</em> were significantly more prevalent in low- and middle-income countries. Gender-wise analysis revealed significantly higher resistance rates in males across most antibiotics, especially levofloxacin. Age-stratified analyses revealed higher resistance in elderly populations, particularly to fluoroquinolones and β-lactams. Forecasting for <em>A. baumannii</em> in Argentina (2004–2030) indicated a continued upward resistance across β-lactam and fluoroquinolones, with LSTM achieving the lowest root mean square error across five antibiotics. The interrupted time series revealed a prenational action plan decline but no significant postimplementation change.</div></div><div><h3>Conclusion</h3><div>This study provides a comprehensive data-driven framework to monitor and forecast AMR, evaluate policy interventions, and, hence, suggest targeted interventions and strategies for each income group and region, moving beyond the one-size-fits-all approach.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 214-226"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145800582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2026-01-04DOI: 10.1016/j.jgar.2025.12.018
Yu Liu , Xu Zheng , Binwei Wu
Objectives
Enterococci are significant hospital pathogens, posing a serious global public health threat. This study aimed to analyze the in vitro susceptibility of enterococcal isolates to eight commonly used antibiotics and to explore cross-resistance patterns in vancomycin-resistant enterococci (VRE), including their heterogeneity across geographic regions, clinical wards, and infection sites.
Methods
Utilizing data from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program (2019–2023), this study analyzed 18,043 enterococcal isolates (12,007 Enterococcus faecalis and 6,036 Enterococcus faecium) from 59 countries across six continents. We assessed in vitro susceptibility to eight common antibiotics and evaluated VRE cross-resistance patterns.
Results
: E. faecalis showed susceptibility rates greater than 95% to ampicillin, daptomycin, linezolid, teicoplanin, tigecycline, and vancomycin. In contrast, E. faecium exhibited susceptibility greater than 90% only for linezolid and tigecycline. The vancomycin resistance rate in E. faecium was 25.4%, significantly higher than in E. faecalis (1.22%), with notable multidrug cross-resistance. Geographically, North America displayed the highest vancomycin resistance rate in E. faecium (53.25%), while Asia showed the highest linezolid resistance rate in this species (2.9%). ICU and non-pediatric patients generally exhibited higher resistance rates, and genitourinary specimens showed slightly higher resistance than those from other sites.
Conclusions
Enterococcal resistance varies significantly across species, regions, and clinical environments. The extensive cross-resistance in VRE poses a major challenge to clinical treatment. Tigecycline and linezolid remain highly effective in vitro globally. To slow the spread of resistant strains, it is crucial to enhance resistance monitoring in high-risk regions and populations, while optimizing antibiotic usage strategies.
{"title":"In vitro activity of vancomycin and other commonly used Antibiotics against clinical isolates of Enterococcus faecalis and Enterococcus faecium: Data from the antimicrobial testing leadership and surveillance (ATLAS) program from 2019 to 2023","authors":"Yu Liu , Xu Zheng , Binwei Wu","doi":"10.1016/j.jgar.2025.12.018","DOIUrl":"10.1016/j.jgar.2025.12.018","url":null,"abstract":"<div><h3>Objectives</h3><div>Enterococci are significant hospital pathogens, posing a serious global public health threat. This study aimed to analyze the in vitro susceptibility of enterococcal isolates to eight commonly used antibiotics and to explore cross-resistance patterns in vancomycin-resistant enterococci (VRE), including their heterogeneity across geographic regions, clinical wards, and infection sites.</div></div><div><h3>Methods</h3><div>Utilizing data from the Antimicrobial Testing Leadership and Surveillance (ATLAS) program (2019–2023), this study analyzed 18,043 enterococcal isolates (12,007 <em>Enterococcus faecalis</em> and 6,036 <em>Enterococcus faecium</em>) from 59 countries across six continents. We assessed in vitro susceptibility to eight common antibiotics and evaluated VRE cross-resistance patterns.</div></div><div><h3>Results</h3><div><em>: E. faecalis</em> showed susceptibility rates greater than 95% to ampicillin, daptomycin, linezolid, teicoplanin, tigecycline, and vancomycin. In contrast, <em>E. faecium</em> exhibited susceptibility greater than 90% only for linezolid and tigecycline. The vancomycin resistance rate in <em>E. faecium</em> was 25.4%, significantly higher than in <em>E. faecalis</em> (1.22%), with notable multidrug cross-resistance. Geographically, North America displayed the highest vancomycin resistance rate in <em>E. faecium</em> (53.25%), while Asia showed the highest linezolid resistance rate in this species (2.9%). ICU and non-pediatric patients generally exhibited higher resistance rates, and genitourinary specimens showed slightly higher resistance than those from other sites.</div></div><div><h3>Conclusions</h3><div>Enterococcal resistance varies significantly across species, regions, and clinical environments. The extensive cross-resistance in VRE poses a major challenge to clinical treatment. Tigecycline and linezolid remain highly effective in vitro globally. To slow the spread of resistant strains, it is crucial to enhance resistance monitoring in high-risk regions and populations, while optimizing antibiotic usage strategies.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 254-263"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145905990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2025-11-20DOI: 10.1016/j.jgar.2025.11.013
Chahrazed Belhout , Claudia Aldeia , Vincent Perreten , Andrea Endimiani
Objectives
Paenimyroides ceti is a newly defined species belonging to the Flavobacteriaceae family. It was originally isolated from the lung and liver of two beaked whales. Here, we report the first complete circular genome of a P. ceti and provide insights into its antimicrobial resistance determinants.
Methods
P. ceti strain MC-ZM-24 was isolated from homogenized tissues of Zophobas morio larvae. Antimicrobial susceptibility tests were determined by broth microdilution and carbapenemase production was assessed by Blue-Carba test. Whole-genome sequencing (WGS) was obtained using both the Illumina short and Oxford Nanopore long-read technologies. A hybrid genome assembly was generated with Unicycler and subsequently annotated using the NCBI Prokaryotic Genome Annotation Pipeline. Antimicrobial resistance genes were identified using AMRFinder and ResFinder. Known metallo-β-lactamase (MBL) protein sequences deposited in NCBI GenBank and UniProt databases were compared with that of strain MC-ZM-24.
Results
The genome comprised a single circular chromosome of 3,274,043-bp, with 3,053 genes, and exhibited a GC content of 35.56%. Phenotypically, the strain was multidrug-resistant, non-susceptible to carbapenems and produced a carbapenemase. WGS analysis identified a unique chromosomal bla gene encoding a MBL that harbors the conserved subclass B1 motifs, but shares low sequence identity with previously described MBL enzymes.
Conclusions
The complete genome of P. ceti MC-ZM-24 expands our understanding of Paenimyroides ecology and evolution. It also highlights an intrinsic subclass B1 β-lactamase, extending the repertoire of chromosomal MBLs in Flavobacteriaceae. This new MBL will require further detailed characterization.
目的：拟黄杆菌属黄杆菌科新定义种。它最初是从两只喙鲸的肺和肝脏中分离出来的。在这里，我们报告了第一个完整的圆形基因组P. ceti和提供洞察其抗菌素耐药性决定因素。方法：从莫蠓幼虫匀浆组织中分离出ceti P. MC-ZM-24菌株。用微量肉汤稀释法测定其药敏试验，用蓝碳水化合物试验测定其碳青霉烯酶产量。全基因组测序（WGS）采用Illumina短读和Oxford Nanopore长读技术。使用Unicycler生成杂交基因组组装，随后使用NCBI原核基因组注释管道进行注释。采用AMRFinder和ResFinder对耐药基因进行鉴定。将NCBI GenBank和UniProt数据库中已知的金属β-内酰胺酶（MBL）蛋白序列与菌株MC-ZM-24进行比较。结果：该基因组全长3274043 -bp，包含3053个基因，GC含量为35.56%。表型上，该菌株多重耐药，对碳青霉烯类不敏感，并产生碳青霉烯酶。WGS分析发现了一个独特的染色体bla基因编码MBL，该基因包含保守的B1亚类基序，但与先前描述的MBL酶具有低序列同一性。结论：P. ceti MC-ZM-24的全基因组扩展了我们对拟金线虫生态学和进化的认识。它还强调了一个内在的B1 β-内酰胺酶亚类，扩展了黄杆菌科染色体MBLs的库。这种新的MBL需要进一步的详细描述。
{"title":"Full genome of Paenimyroides ceti strain MC-ZM-24 producing a new subclass B1 metallo-β-lactamase","authors":"Chahrazed Belhout , Claudia Aldeia , Vincent Perreten , Andrea Endimiani","doi":"10.1016/j.jgar.2025.11.013","DOIUrl":"10.1016/j.jgar.2025.11.013","url":null,"abstract":"<div><h3>Objectives</h3><div><em>Paenimyroides ceti</em> is a newly defined species belonging to the <em>Flavobacteriaceae</em> family. It was originally isolated from the lung and liver of two beaked whales. Here, we report the first complete circular genome of a <em>P. ceti</em> and provide insights into its antimicrobial resistance determinants.</div></div><div><h3>Methods</h3><div><em>P. ceti</em> strain MC-ZM-24 was isolated from homogenized tissues of <em>Zophobas morio</em> larvae. Antimicrobial susceptibility tests were determined by broth microdilution and carbapenemase production was assessed by Blue-Carba test. Whole-genome sequencing (WGS) was obtained using both the Illumina short and Oxford Nanopore long-read technologies. A hybrid genome assembly was generated with Unicycler and subsequently annotated using the NCBI Prokaryotic Genome Annotation Pipeline. Antimicrobial resistance genes were identified using AMRFinder and ResFinder. Known metallo-β-lactamase (MBL) protein sequences deposited in NCBI GenBank and UniProt databases were compared with that of strain MC-ZM-24.</div></div><div><h3>Results</h3><div>The genome comprised a single circular chromosome of 3,274,043-bp, with 3,053 genes, and exhibited a GC content of 35.56%. Phenotypically, the strain was multidrug-resistant, non-susceptible to carbapenems and produced a carbapenemase. WGS analysis identified a unique chromosomal <em>bla</em> gene encoding a MBL that harbors the conserved subclass B1 motifs, but shares low sequence identity with previously described MBL enzymes.</div></div><div><h3>Conclusions</h3><div>The complete genome of <em>P. ceti</em> MC-ZM-24 expands our understanding of <em>Paenimyroides</em> ecology and evolution. It also highlights an intrinsic subclass B1 β-lactamase, extending the repertoire of chromosomal MBLs in <em>Flavobacteriaceae</em>. This new MBL will require further detailed characterization.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 109-111"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145581683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-01-01Epub Date: 2026-02-09DOI: 10.1016/j.jgar.2026.01.009
{"title":"ISAC News and Updates","authors":"","doi":"10.1016/j.jgar.2026.01.009","DOIUrl":"10.1016/j.jgar.2026.01.009","url":null,"abstract":"","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages ii-iii"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147394328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Community-acquired pneumonia (CAP) remains a major global health concern, particularly in regions with rising antimicrobial resistance (AMR). In Lebanon, increasing resistance among respiratory pathogens complicates management, limiting treatment options and worsening clinical and economic outcomes. This expert panel review assessed recent national AMR data to adapt CAP treatment recommendations to the Lebanese context. The 2019 ATS/IDSA guidelines and their 2025 update were reviewed; while most recommendations were retained, empiric antibiotic choices were adjusted for key pathogens based on local resistance patterns. The proposed management algorithm stratifies patients by disease severity, care setting, and AMR risk, integrating pathogen-specific risk factors into clinical decisions. By contextualizing international guidance to local epidemiology and healthcare infrastructure, these recommendations aim to optimize targeted therapy, support antimicrobial stewardship, and preserve antibiotic efficacy in Lebanon’s evolving resistance landscape.
{"title":"Adapting international evidence-based guidelines to local challenges: A Lebanese perspective on the latest American Thoracic Society and Infectious Diseases Society of America (ATS/IDSA) community-acquired pneumonia antibacterial therapy recommendations","authors":"Rana Attieh , Joe Nahal , Rola Husni , Jacques E. Mokhbat , Jamil Barhoun , Joumana Kmeid , Mona Youssef , Zahi Helou , Wael Zorkot , Nassab Fakhreddine , Fatima Baalbaki , Nazih Bizri , Hanine Mansour , Dania Abdallah , Rima Moghnieh","doi":"10.1016/j.jgar.2025.11.005","DOIUrl":"10.1016/j.jgar.2025.11.005","url":null,"abstract":"<div><div>Community-acquired pneumonia (CAP) remains a major global health concern, particularly in regions with rising antimicrobial resistance (AMR). In Lebanon, increasing resistance among respiratory pathogens complicates management, limiting treatment options and worsening clinical and economic outcomes. This expert panel review assessed recent national AMR data to adapt CAP treatment recommendations to the Lebanese context. The 2019 ATS/IDSA guidelines and their 2025 update were reviewed; while most recommendations were retained, empiric antibiotic choices were adjusted for key pathogens based on local resistance patterns. The proposed management algorithm stratifies patients by disease severity, care setting, and AMR risk, integrating pathogen-specific risk factors into clinical decisions. By contextualizing international guidance to local epidemiology and healthcare infrastructure, these recommendations aim to optimize targeted therapy, support antimicrobial stewardship, and preserve antibiotic efficacy in Lebanon’s evolving resistance landscape.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 98-108"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145557031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Studies of carbapenem-resistant Pseudomonas aeruginosa (CRPA)-harbouring OXA-48-like carbapenemases are rare. The study aimed to report the emergence and characterization of a novel high-risk clone of CRPA-harbouring OXA-48-like from India.
Methods
Identification, AST, phenotypic detection of carbapenemases and WGS using Ion-Torrent-S5 platform were carried out. Analyses included ResFinder, VFDB, MLST, PAst, Phastest and CRISPR/Cas. SNP-based phylogenetic analysis with global OXA-48-like-harbouring CRPA genomes was carried out by CSI Phylogeny and iTOL for visualization.
Results
The clinical MDR strain of CRPA AMRIR00655 belonged to a novel sequence type ST5217 and serotype O11. Phenotypic tests followed by WGS revealed the presence of dual carbapenemases, OXA-181 (serine-carbapenemase) and VIM-2 (zinc-carbapenemase), both located on chromosome. blaOXA-181 resides between chromosomal genes encoding RodZ and PAP2 in P. aeruginosa, confirming chromosomal integration.4,261 bp of blaOXA-181-bearing contig-DNA showed 100% homology to K. pneumoniae plasmid pKP3-A. ISEcp1 was present on upstream and on downstream, △lysR, △ereA and repA genes were detected. blaVIM-2 was located within class 1 integron along with aacC6-II, dfrB5, aac(3)-Id, tniC in surrounding regions and 13,242 bp showing 100% identity to P. aeruginosa chromosome. Presence of other ARGs (blaPAO, blaOXA-488,aph(3′')-Ib, aph(6)-Id, crpP, catB7, fosA, sul2) and efflux-pump genes might explain its MDR phenotype. Virulence factors including T3SS (PscF, PopB, PopD, PcrV) and its effectors (ExoT, ExoU, ExoY) indicated the pathogenic potential of ST5217. Core genome analysis showed that ST5217 was closest with other high-risk clones ST1339 and ST773-harbouring blaOXA-48-like.
Conclusions
To the best of our knowledge, this is the first report of blaOXA-181-harbouring novel high-risk clone of CRPA ST5217/ExoU+/O11 in India which emphasises the spread of OXA-181 among bacteria other than Enterobacteriaceae-family and warrant close monitoring.
{"title":"Genomic analysis of a novel high-risk ST5217/ExoU+/O11 clone of carbapenem-resistant OXA-181- and VIM-2-producing Pseudomonas aeruginosa in India","authors":"Subhasree Roy , Souvik Nandy , Daichi Morita , Ranjan Kumar Nandy , Balaji Veeraraghavan , Kamini Walia , Santasabuj Das , Sulagna Basu","doi":"10.1016/j.jgar.2025.12.002","DOIUrl":"10.1016/j.jgar.2025.12.002","url":null,"abstract":"<div><h3>Objectives</h3><div>Studies of carbapenem-resistant <em>Pseudomonas aeruginosa</em> (CRPA)-harbouring OXA-48-like carbapenemases are rare. The study aimed to report the emergence and characterization of a novel high-risk clone of CRPA-harbouring OXA-48-like from India.</div></div><div><h3>Methods</h3><div>Identification, AST, phenotypic detection of carbapenemases and WGS using Ion-Torrent-S5 platform were carried out. Analyses included ResFinder, VFDB, MLST, PAst, Phastest and CRISPR/Cas. SNP-based phylogenetic analysis with global OXA-48-like-harbouring CRPA genomes was carried out by CSI Phylogeny and iTOL for visualization.</div></div><div><h3>Results</h3><div>The clinical MDR strain of CRPA AMRIR00655 belonged to a novel sequence type ST5217 and serotype O11. Phenotypic tests followed by WGS revealed the presence of dual carbapenemases, OXA-181 (serine-carbapenemase) and VIM-2 (zinc-carbapenemase), both located on chromosome. <em>bla</em><sub>OXA-181</sub> resides between chromosomal genes encoding RodZ and PAP2 in <em>P. aeruginosa</em>, confirming chromosomal integration<em>.</em>4,261 bp of <em>bla</em><sub>OXA-181</sub>-bearing contig-DNA showed 100% homology to <em>K. pneumoniae</em> plasmid pKP3-A. IS<em>Ecp1</em> was present on upstream and on downstream, △<em>lysR,</em> △<em>ereA</em> and <em>repA</em> genes were detected. <em>bla</em><sub>VIM-2</sub> was located within class 1 integron along with <em>aacC6-II, dfrB5, aac(3)-Id, tniC</em> in surrounding regions and 13,242 bp showing 100% identity to <em>P. aeruginosa</em> chromosome. Presence of other ARGs (<em>bla</em><sub>PAO</sub>, <em>bla</em><sub>OXA-488,</sub> <em>aph(3′')-Ib, aph(6)-Id, crpP, catB7, fosA, sul2</em>) and efflux-pump genes might explain its MDR phenotype. Virulence factors including T3SS (PscF, PopB, PopD, PcrV) and its effectors (ExoT, ExoU, ExoY) indicated the pathogenic potential of ST5217. Core genome analysis showed that ST5217 was closest with other high-risk clones ST1339 and ST773-harbouring <em>bla</em><sub>OXA-48-like</sub>.</div></div><div><h3>Conclusions</h3><div>To the best of our knowledge, this is the first report of <em>bla</em><sub>OXA-181</sub>-harbouring novel high-risk clone of CRPA ST5217/ExoU+/O11 in India which emphasises the spread of OXA-181 among bacteria other than Enterobacteriaceae-family and warrant close monitoring.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 158-161"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145742985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Tuberculosis (TB) remains a leading infectious cause of death, with drug-resistant TB threatening control gains worldwide Rapid, accurate prediction of resistance to first-line agents is essential to guide therapy.
The objective of this meta-analysis is to evaluate the diagnostic performance of machine learning (ML) algorithms trained on genomic data for predicting phenotypic resistance to the antitubercular drugs.
Methods
We searched 4 databases for original studies applying ML to whole-genome or targeted sequencing for resistance prediction against rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STM), and other routinely tested drugs. Random-effects meta-analyses (REML) pooled sensitivity and specificity; Area Under Curve (AUC) was meta-analysed after logit transformation. Publication bias was examined via funnel plots plus Egger’s and Begg’s tests with trim-and-fill adjustment.
Results
Seven eligible studies were included. Pooled performance was strongest for RIF and INH (RIF: sensitivity 0.90, specificity 0.95; INH: sensitivity 0.88, specificity 0.93). EMB and STM showed lower sensitivities despite reasonable AUCs. Forest plots for AUC (including logit scale), sensitivity, and specificity demonstrated drug-wise variation. Across studies, specificity (mean ≈ 0.92) exceeded sensitivity (mean ≈ 0.75). Bias diagnostics revealed marked funnel plot asymmetry; trim-and-fill imputation added 22, 29, and 23 studies for AUC, sensitivity, and specificity, respectively, yielding adjusted pooled estimates of ∼0.89 (AUC), 0.70 (sensitivity), and 0.93 (specificity).
Conclusions
ML models trained on genomic data demonstrate high diagnostic accuracy and robust discriminative ability for predicting first-line drug resistance—particularly for RIF and INH—although sensitivity remains variable across drugs and model types. Standardized external validation and calibration are needed before broad clinical deployment.
{"title":"Integrative machine learning approaches with genomic data for predicting antitubercular drug resistance: A systematic review and meta-analysis","authors":"Rohan Shrivastava , Kashmi Sharma , Somesh Mishra , Poonam Parihar , Gobardhan Das , Khushhali Menaria Pandey , Anand Kumar Maurya , Vineet Kumar Sharma , Anamika Mishra , Sandeep Kushwaha , Rekha Khandia , Kuldeep Singh Yadav , Anvita Gupta Malhotra , Amit Agrawal , Jitendra Singh , Megha Katare Pandey","doi":"10.1016/j.jgar.2025.11.021","DOIUrl":"10.1016/j.jgar.2025.11.021","url":null,"abstract":"<div><h3>Objectives</h3><div>Tuberculosis (TB) remains a leading infectious cause of death, with drug-resistant TB threatening control gains worldwide Rapid, accurate prediction of resistance to first-line agents is essential to guide therapy.</div><div>The objective of this meta-analysis is to evaluate the diagnostic performance of machine learning (ML) algorithms trained on genomic data for predicting phenotypic resistance to the antitubercular drugs.</div></div><div><h3>Methods</h3><div>We searched 4 databases for original studies applying ML to whole-genome or targeted sequencing for resistance prediction against rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STM), and other routinely tested drugs. Random-effects meta-analyses (REML) pooled sensitivity and specificity; Area Under Curve (AUC) was meta-analysed after logit transformation. Publication bias was examined via funnel plots plus Egger’s and Begg’s tests with trim-and-fill adjustment.</div></div><div><h3>Results</h3><div>Seven eligible studies were included. Pooled performance was strongest for RIF and INH (RIF: sensitivity 0.90, specificity 0.95; INH: sensitivity 0.88, specificity 0.93). EMB and STM showed lower sensitivities despite reasonable AUCs. Forest plots for AUC (including logit scale), sensitivity, and specificity demonstrated drug-wise variation. Across studies, specificity (mean ≈ 0.92) exceeded sensitivity (mean ≈ 0.75). Bias diagnostics revealed marked funnel plot asymmetry; trim-and-fill imputation added 22, 29, and 23 studies for AUC, sensitivity, and specificity, respectively, yielding adjusted pooled estimates of ∼0.89 (AUC), 0.70 (sensitivity), and 0.93 (specificity).</div></div><div><h3>Conclusions</h3><div>ML models trained on genomic data demonstrate high diagnostic accuracy and robust discriminative ability for predicting first-line drug resistance—particularly for RIF and INH—although sensitivity remains variable across drugs and model types. Standardized external validation and calibration are needed before broad clinical deployment.</div></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":"46 ","pages":"Pages 148-157"},"PeriodicalIF":3.2,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145756841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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