JAC-Antimicrobial Resistance

Background Using a population-based cohort from the Calgary Health Zone (CHZ), Canada, we integrated longitudinal antimicrobial susceptibility and prescribing data with the whole genome sequences of five major pathogens. We aimed to assess how antimicrobial resistance (AMR) responds to prescribing changes and determine which bacterial strains shape these dynamics. Methods We analysed antibiotic prescribing rates, clinical and genomic data from 7,271 Staphylococcus aureus, 1,609 Enterococcus faecalis, 801 Enterococcus faecium, 11,363 Escherichia coli, and 2,319 Klebsiella pneumoniae isolates, associated with bacteraemia episodes in the CHZ between 2006-2022. Genomic clusters (referred to as strains) were identified using StrainGST and assigned to known sequence types (STs) or clonal complexes (CCs). Strain-level incidence, stratified by community-onset (isolates collected [&le;]48h after admission) and hospital-onset (>48h after admission), AMR phenotypes, and prescribing rates were modelled using negative-binomial and binomial regression. Temporal trends were quantified using average annual percentage change (AAPC). Findings Between 2010-2022, fluoroquinolone prescribing declined in both community (AAPC=-6.8% [95% CI -8.1, -5.4]; p<0.0001) and hospital settings (AAPC=-5.1% [-6.5, -3.7]; p<0.0001). This was accompanied by a significant reduction in fluoroquinolone resistance among Gram-positive species. Specifically, S aureus bacteraemia resistant to clinically important antibiotics, cloxacillin, ciprofloxacin, erythromycin, and clindamycin, declined from 2006 to 2022, mostly in hospital-onset cases (AAPC=-16.0%, [-19.3%, -12.7%], p<0.0001). In E coli, ceftriaxone and ciprofloxacin resistance were clustered in ST131 and the emerging ST1193; the latter increased steadily, particularly in community-onset cases (AAPC=17.7%, [0.0%, 30.0%], p<0.0001). CTX-M-27-producing E coli ST131 strains increased (AAPC=23.8%, [17.4%, 30.5%], p<0.0001) between 20082022, while CTX-M-14-producing E coli ST131 declined (AAPC=-15.9%, [-21.3%, -10.2%], p<0.0001) between 2013-2022. These trends were paralleled by an increase in community cephalosporin prescribing (AAPC=7.3%, [4.2%, 10.5%], p<0.0001) between 2010-2022. For K pneumoniae, hypervirulent ST23 was most common (N=88) with an increasing trend in incidence (AAPC=3.0%, [-2.8%, 9.2%]) between 2006-2019. Conclusions The contrasting resistance trends between Gram-positive and Gram-negative species underscore the complexity of AMR control efforts. Effective strategies will require stewardship efforts targeting multiple drug classes, genomic surveillance for emerging resistant strains, and interventions extending beyond hospital settings.

Background. Antibiotic heteroresistance (HR), a resistant subpopulation within a clonal isolate reported susceptible by routine testing, can drive unexplained treatment failure and on-treatment emergence of resistance, yet prospective prevalence data for first-line beta-lactams in Gram-negative bloodstream infection are lacking. We assessed the prevalence and genomic basis of HR to piperacillin, piperacillin/tazobactam, or meropenem among bloodstream isolates reported susceptible by standard-of-care testing. Methods. In this prospective two-centre prevalence study we screened consecutive monomicrobial Gram-negative positive blood cultures at the University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany, and the Fondazione Policlinico Universitario A. Gemelli IRCCS (FPG), Rome, Italy. Enterobacterales and Pseudomonadales reported susceptible by standard-of-care AST were allocated to one investigated beta-lactam (piperacillin, piperacillin/tazobactam or meropenem) according to their routine susceptibility phenotype (Vitek2), and entered a two-tier phenotypic workflow: an agar filter at 0.5x the EUCAST breakpoint in triplicate, followed - if positive - by population analysis profiling (PAP) up to 4x the breakpoint. Heteroresistance was defined as a clonal resistant subpopulation at a frequency of at least 0.5x10-6 surviving in the 4x breakpoint zone. Prevalence was estimated with Wilson-score 95% CIs and compared between centres with Fisher's exact test. Confirmed heteroresistant isolates and their paired susceptible bulk populations underwent short- and long-read whole-genome sequencing, and each resistant/susceptible pair was tested for tandem gene amplification, differential subclonal point variants and structural variation. Findings. 279 isolates were screened (93 at UKE, 186 at Gemelli). The 0.5x breakpoint filter was positive in 22 of 93 isolates (23.7%) at UKE and 66 of 186 (35.5%) at Gemelli. PAP confirmed heteroresistance in 6 of 93 isolates at UKE (6.5%, 95% CI 3.0-13.4) and 27 of 186 at Gemelli (14.5%, 10.2-20.3), a pooled prevalence of 33 of 279 (11.8%, 8.5-16.1); the between-centre difference did not reach significance (Fisher's exact test p=0.051). Heteroresistance was essentially confined to piperacillin/tazobactam: 32 of 150 isolates screened against piperacillin/tazobactam were heteroresistant (21.3%, 15.5-28.6), versus 1 of 71 for piperacillin (1.4%) and 0 of 58 for meropenem. Escherichia coli accounted for 17 of the 33 heteroresistant isolates. In the resistant/susceptible pairs sequenced to date a candidate mechanism was resolved in 18: 13 carried a tandem amplification of a beta-lactamase locus (copy-number ratio 2.4-33.0; amplified units 5-136 kb, most often plasmid-borne and centred on blaTEM-1, blaCTX-M or blaOXA-1), and 5 carried point variants in the AmpC circuit (ampD, ampR, dacB/PBP4) or in efflux components, three of them fixed loss- or gain-of-function changes and three subclonal. Interpretation. Roughly one in eight Gram-negative bloodstream isolates called susceptible to a first-line beta-lactam harboured a resistant subpopulation, and the burden fell almost entirely on piperacillin/tazobactam - the agent most often used empirically in this setting. The dominant genomic substrate was unstable amplification of an existing beta-lactamase gene rather than acquisition of a new resistance determinant, which explains why the phenotype is reversible, invisible to AST and, in principle, quantifiable by copy-number assays at the point of care.

Background: Both over- and under-antibiotic use pose major global health challenges, yet there is no consensus on how to quantify deviations from optimal prescribing or set evidence-based targets. We developed a benchmarking tool for inpatient antibiotic use and evaluated its application in 10 countries. Methods: We developed decision-tree models to estimate expected empiric antibiotic use for 11 indications, based on the WHO AWaRe book for two age groups: 28 days to 12 years and >12 years. We parameterised the models using country-specific antimicrobial resistance estimates in the 10 countries and cross-sectional Global Point Prevalence Survey (Global-PPS) case-mix data from 2021 for 10 countries and from 2015-2022 in a subset of five countries. We then compared estimated expected antibiotic use with observed empiric use (from Global-PPS) in defined daily doses for adults and days of therapy for children, across indications and AWaRe categories. Findings: In 2021, among patients aged >12 years, in all countries but one, observed empiric Access antibiotic use, as a proportion of total antibiotic use, was lower than expected and empiric Watch antibiotic use was higher than expected. Similar patterns were observed in all countries but one in patients aged 28 days to 12 years. The magnitude of discrepancies between expected and observed Access and Watch antibiotic use varied across indications and countries. The median observed-to-expected ratios of usage across countries ranged from 0.3-0.8 for Access antibiotics, and 0.7-5.3 for Watch antibiotics in patients aged >12 years in 2021. Temporal trends from repeated surveys from 2015 to 2022 showed little change in observed-to-expected ratios for Access and Watch antibiotics. Interpretation: This benchmarking tool uses Global-PPS data to quantify differences between observed antibiotic use and WHO AWaRe recommendations. Our tool can be adaptable to local guidelines, provides policy-relevant estimates of expected antibiotic use to support monitoring, procurement planning, and targeted stewardship intervention.

To characterise temporal changes in antimicrobial resistance (AMR) among clinically important bacterial pathogens in Iraq during 2021-2024 and examine their implications for empirical antimicrobial therapy and stewardship. We conducted a retrospective longitudinal analysis of aggregated national AMR surveillance data for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Staphylococcus aureus. Annual resistance proportions were evaluated across clinically relevant antimicrobials. Temporal change was characterised using absolute percentage-point changes and exploratory linear regression. Resistance trajectories were interpreted in relation to empirical treatment options and antimicrobial stewardship. The analysis included 92,338 organism records: 40,496 (43.9%) E. coli, 24,621 (26.7%) S. aureus, 18,223 (19.7%) K. pneumoniae and 8,998 (9.7%) P. aeruginosa. In 2024, ceftriaxone resistance reached 82.9% in E. coli and 65.2% in K. pneumoniae, while ciprofloxacin resistance was 55.4% and 57.9%, respectively. Meropenem resistance reached 37.4% in K. pneumoniae and 62.3% in P. aeruginosa. Conversely, resistance declined for amoxicillin-clavulanate in E. coli (83.5% in 2021 to 57.2% in 2024) and piperacillin-tazobactam in P. aeruginosa (46.4% to 32.9%). Several pathogen-antimicrobial combinations showed marked year-to-year variation, and no temporal trend remained statistically significant after false discovery rate correction. Resistance to several agents central to empirical therapy remains high in Iraq, while substantial carbapenem resistance constrains reliance on carbapenem escalation when resistance to other {beta}-lactams is suspected. Heterogeneous trajectories indicate that empirical recommendations should not rely on single-year national antibiograms alone and support regular integration of national and local resistance surveillance into empirical treatment and antimicrobial stewardship strategies.

Background: The main cause of urinary tract infections (UTIs) are Gram negative bacteria with Escherichia coli as the leading cause and other important pathogens such as Klebsiella pneumoniae, Pseudomonas aeuriginosa and Enterococcus faecalis. Over the years uropathogens have become resistant to commonly used antibiotics, including penicillin's, cephalosporins and fluoroquinolones. Antimicrobial resistance (AMR) in UTIs is mainly caused by the misuse and overuse of antibiotics, recurrent infections, and healthcare-associated factors such as catheterization. Objectives: The aim of this study was to describe the bacteriological profile and antimicrobial susceptibility patterns of uropathogens isolated from positive urine cultures at Chhatrapati Shivaji Subharti Hospital, Meerut, a tertiary care centre in North India and develop an institutional antibiogram to support empirical prescribing and antibiotic stewardship at this institution. Materials & Methods: The study analysed 50 positive urine culture samples and their antimicrobial susceptibility records from July 2025 to December 2025. The isolates were identified, and antimicrobial susceptibility testing was performed using the disc diffusion method and automated Biomerieux Vitek 2 Compact machine. The collected data was analysed using descriptive statistics and Fisher's exact test. Results: Gram-negative bacteria accounted for 80.0% (40/50) of the culture-positive urine isolates. Escherichia coli was the most frequently isolated uropathogen (n=23, 46.0%), followed by Klebsiella pneumoniae (n=12, 24.0%), Candida spp. (n=6, 12.0%), Enterococcus spp. (n=4,8.0%), Pseudomonas aeruginosa (n=3, 6.0%), and Enterobacter cloacae (n=2, 4.0%). Of the total, 74% (37/50) of isolates came from Inpatient samples. E. coli had a 100% resistance to ampicillin and ceftriaxone, 95.7% to ciprofloxacin and cefepime, and 73.9% to meropenem, with fosfomycin (86.4% sensitive) and colistin (69.6% sensitive) as the only effective antimicrobials. K. pneumoniae had 100% resistance to ceftriaxone, amoxicillin-clavulanate, and piperacillintazobactam; carbapenem resistance ranged from 83.3% to 91.7%, and colistin was the only consistently effective treatment (83.3% sensitive). Of all the 35 tested Enterobacteriaceae isolates, Extended-Spectrum Beta-Lactamases (ESBLs) positivity was 100% with Carbapenem-Resistant Enterobacterales (CRE) positivity at 85.0%. All the bacterial isolates met Multi-drug Resistant (MDR) criteria. 31 of 35 (88.6%) tested Enterobacteriaceae isolates showed ESBL and CRE copositivity. The six strains of Candida demonstrated total sensitivity to all the antifungal drugs used. Conclusion: There is a critical burden of AMR at this hospital with 100% ESBL positivity, 85% CRE, and 100% MDR among all bacterial isolates. This study provides the first baseline institutional antibiogram to guide empirical prescribing and antibiotic stewardship at Chhatrapati Subharti Hospital.

Objective: To determine the prevalence of S. aureus among clinical specimens processed at MeTRH and assess the antimicrobial susceptibility patterns and proportion of MRSA among confirmed isolates. Methods: A retrospective descriptive cross-sectional study was conducted using microbiology laboratory records for clinical specimens submitted for bacteriological culture at MeTRH during the study period. A census approach was used, whereby all eligible laboratory records were included. Clinical specimens were processed using routine microbiological procedures, and suspected S. aureus isolates were identified using conventional methods and the VITEK(R) 2 Compact automated identification system. Antimicrobial susceptibility testing was performed using VITEK(R) 2 Compact, with interpretation based on Clinical and Laboratory Standards Institute criteria. Methicillin resistance was determined phenotypically using cefoxitin susceptibility as the surrogate marker. Data were analysed using frequencies and percentages. Results: A total of 1,082 clinical specimens were analysed, of which 37 yielded S. aureus, giving an overall prevalence of 3.42%. Among the confirmed isolates, 21 (56.8%) were recovered from male patients and 16 (43.2%) from female patients. Pus was the predominant specimen type, accounting for 25 (67.6%) isolates, followed by other specimens at 8 (21.6%) and urine at 4 (10.8%). Antimicrobial susceptibility varied considerably. Resistance was highest to benzylpenicillin and amoxicillin, with 100% resistance among tested isolates. Resistance to amoxicillin-clavulanic acid was 75.0%, while 63.3% of isolates tested were resistant to oxacillin. Susceptibility was relatively high to gentamicin (82.8%), ciprofloxacin (77.3%) and clindamycin (75.0%). All isolates tested against linezolid and vancomycin were susceptible. Among 30 isolates with methicillin susceptibility results, 19 (63.3%) were classified as MRSA and 11 (36.7%) as methicillin-susceptible S. aureus (MSSA). Conclusion: The prevalence of S. aureus among clinical specimens processed at MeTRH was relatively low; however, a substantial proportion of isolates demonstrated antimicrobial resistance, particularly to commonly used {beta}-lactam antibiotics. The high proportion of MRSA is of clinical and public health importance. Routine antimicrobial susceptibility testing, hospital-specific antibiograms, antimicrobial stewardship and strengthened infection prevention and control measures are recommended to support appropriate treatment and limit the spread of resistant S. aureus.

Public genomic repositories can support antimicrobial resistance (AMR) surveillance, but unequal sampling can bias interpretation. We characterised AMR determinants, multicountry genomic cluster overlap and surveillance gaps across Africa using an NCBI Pathogen Detection snapshot retrieved on 24 August 2026 for 55 African Union member states. Records were validated and deduplicated by BioSample, and complete AMRFinderPlus calls were summarised across five United Nations M49 subregions and eight overlapping regional economic communities (RECs). Country-pair cluster overlap was assessed using the Jaccard index, while project-based and composition-standardised sensitivity analyses evaluated repository bias. The dataset contained 86,829 unique BioSamples from 51 states; South Africa, Malawi and Kenya contributed 55.8%. Complete extended-spectrum {beta}-lactamase calls were detected in 21,513 isolates and carbapenemase calls in 4,642. blaCTX-M-15 dominated the ESBL profile, while NDM and OXA types predominated. Seventy clusters contained carbapenemase-positive isolates from at least two countries. A shared REC covered all participating countries in 38 clusters, while 32 crossed REC boundaries. Normalised country-pair overlap was low, with a maximum Jaccard index of 9.5%. Project balancing reduced the Northern African carbapenemase estimate from 32.3% to 17.9% and the Eastern African ESBL estimate from 36.9% to 12.5%. Public repositories identify determinants and clusters for investigation but do not estimate prevalence or transmission. AMR surveillance should combine national confirmation, regional institution-led investigation where countries share an REC, and continent-wide coordination through Africa CDC for cross-REC signals, supported by representative One Health sampling, standardised metadata and sustained African sequencing capacity.

Background: Antimicrobial resistance (AMR) is a growing global health threat, and India's high antibiotic consumption makes public knowledge, attitudes, and practices (KAP) a critical determinant of stewardship outcomes. Existing Indian KAP evidence is drawn from small, localised cohorts, leaving a gap in nationwide, digitally-sourced data. This study aimed to describe antibiotic-related knowledge, attitudes and self-reported practices among users of a digital healthcare platform in India, examine demographic and regional variation, and identify potential areas for future stewardship interventions. Methods: A cross-sectional survey was conducted among adult users of the Tata 1mg platform (December 2025-February 2026), with participants invited via an in-app banner. Knowledge and attitude were each scored on a 0-4 scale (4 items); practice was scored as a percentage of applicable items answered favourably, with scoring adjusted for branching logic based on antibiotic-access route. Of 10,726 respondents who started the survey, 4,883 completed it (45.5%). City of residence was mapped to one of six regions (India's five statutory Zonal Council zones plus a North-Eastern region) for 4,187 respondents. Associations with demographic characteristics were assessed using multivariable linear regression, and regional differences were assessed using one-way ANOVA. A parallel survey of 256 physicians was conducted to enable patient-provider comparison. Results: Mean scores were: knowledge 2.28 (SD 1.19), attitude 0.91 (SD 1.14), practice 44.9% (SD 33.4); attitude, not knowledge, was the weakest domain. Older age was associated with higher scores across all domains (practice: B=12.52, p<0.001 for age [&ge;]65 vs. 18-34); city tier was independently associated with lower knowledge and attitude (Tier 3 vs. Tier 1: p=0.010 and p<0.001, respectively). Regional differences were non-significant for knowledge and practice but significant for attitude (F=2.56, p=0.026, ^2=0.003), driven by lower scores in the North-Eastern region. In the parallel physician survey, 55.5% of respondents estimated that more than half of their patients self-medicated before consultation. Conclusion: In this platform-based sample, attitudes were the weakest domain, not knowledge, and 42.0% said their last antibiotic did not come on a doctor's recommendation. The findings may inform digital stewardship touchpoints, such as point-of-purchase guidance and prescription verification, in line with India's National Action Plan on Antimicrobial Resistance 2.0. As a cross-sectional survey of platform users, it cannot establish the relative contributions of knowledge, beliefs and access pathways to antibiotic use.

Objective. To identify antimicrobial stewardship targets by triangulating provider knowledge and practice, government-facility prescribing indicators and patient-reported treatment experience in three districts of Chhattisgarh, India. Methods. We analysed three independently sampled cross-sectional components: a provider survey (171 providers), a World Health Organization and International Network for Rational Use of Drugs assessment (600 encounters at 20 government facilities) and patient exit interviews (371 consultations). We used descriptive indicators and multivariable ordinal or binary logistic regression. Findings. Among providers, 149 of 163 (91.4%) recognized antimicrobial resistance, but 131 of 163 (80.4%) reported providing antibiotics for colds or sore throats to at least some patients. Guideline familiarity was not associated with less frequent provision (adjusted common odds ratio [aOR], 1.13; 95% confidence interval [CI], 0.57-2.24; P=0.725). Government facilities prescribed antibiotics in 329 of 600 encounters (54.8%), with a facility range of 16.7-80.0%. In exit interviews, 131 of 142 informal-provider consultations (92.3%) involved a reported injection; informal providers accounted for 131 of 181 reported injections (72.4%). Clear or very clear instructions were associated with satisfaction (aOR: 13.66; 95% CI: 6.37-29.28; P<0.001). Conclusion. High awareness coexisted with frequent self-reported antibiotic provision, wide facility variation and sector-specific injection exposure. Stewardship programmes should diagnose local drivers before selecting interventions and prospectively evaluate adapted decision support, audit and feedback, independent drug information, informal-provider engagement and communication training.

Objective As antimicrobial resistance (AMR) continues to threaten global public health, bacteriophage therapy products (BTPs) offer a promising alternative to conventional antimicrobials. However, translation into routine clinical practice requires best practice standards for manufacturing and quality control to ensure the consistent safety, quality, and reliability of personalised BTPs produced for individual patients or small cohorts. Design A modified Delphi methodology was used to develop consensus statements, engaging experts from Australia's National Bacteriophage Therapy Regulatory Working Group across the fields of clinical microbiology, phage biology, good manufacturing practice (GMP), regulatory science, and government. The process comprised three iterative phases: (1) structured statement development, (2) an anonymous REDCap survey, and (3) a hybrid consensus meeting. The strength of evidence and recommendations was assessed using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) framework. Results Consensus was reached on 35 statements to provide best practice manufacture and quality control guidance for BTPs. These statements address requirements for phage identification and characterisation; define the point at which GMP-aligned processes commence for ubiquitous phages; outline quality control expectations for phage active pharmaceutical ingredient (pAPI) production and maintenance of BTP and host cell repositories. Additional guidance covers quality management systems, including documentation, traceability, and governance. Conclusion These consensus statements provide comprehensive best practice recommendations for the manufacture and quality control of BTPs in Australia. By promoting consistent, safe, and quality-assured approaches to personalised BTPs, they aim to facilitate clinical implementation while remaining aligned with existing international pharmacopoeial standards and regulatory frameworks.

Background: Optimising sampling frames for genomic surveillance of E. coli and Klebsiella may support interventions to mitigate bloodstream infections (BSIs), but approaches to estimating sample size and how these relate to bacterial population diversity at multiple genetic levels (strain/plasmid/antimicrobial resistance genes [ARGs]) are lacking. Methods: Using systematically collected, regionally-stratified, whole genome sequencing data from a 6-month genomic survey of English E. coli/Klebsiella BSI isolates (n=1,939; NEKSUS), we used Bayesian approaches to estimate the sample sizes required to capture genetic diversity at strain- (MLST, fastBAPS clusters), plasmid- and ARG-levels, using two diversity measures: 'coverage' (i.e. proportion of the bacterial population/plasmids/ARGs represented by features observed in the sample), and the number/proportion of unique features observed at varying surveillance sample sizes. Our method is available as a user-friendly R Shiny application, EpiSENTRY (https://01a0c3dd-90d2-e597-58a5-51391a468387.share.connect.posit.cloud/). Findings: Randomly sampling 1,400 E. coli/Klebsiella BSI isolates each achieved [&ge;]80% coverage of bacterial lineages and ARGs (i.e. capture features constituting [&ge;]80% of the population) at 95% certainty, but captured lower proportions of unique features (28% MLSTs, 59% fastBAPS clusters, 19% plasmid subcommunities, and 57% ARGs for E. coli; 49%, 87%, 50% and 83% for Klebsiella, respectively). Sample sizes required for 80% coverage of E. coli plasmid populations were higher than MLSTs (1,928 [95% CrI: 1,837-2,025] vs 1,351 [1,230-1,472]), while for Klebsiella, estimates were lower for plasmids (1,115 [1,052-1,181] vs 1,422 [1,331-1,515] for MLSTs). Lower sample sizes adequately captured 80% coverage of fastBAPS clusters and ARGs (649 [575-727] and 27 [23-30], respectively, for E. coli; 113 [84-145] and 83 [72-96] for Klebsiella), due to feature-specific frequency distributions. Klebsiella BSIs were more diverse than E. coli, with sampling 10.9% vs 3.2% of total annual BSIs in England needed to reach 80% MLST coverage. Plasmid populations and Klebsiella MLSTs were region-specific, emphasising the need for regionally-representative sampling. Interpretation: Bayesian analysis facilitates estimates of context-specific genomic surveillance sample sizes. Cost-effective targets for coverage require further optimisation.

Enteric fever is endemic to many low- and middle-income countries (LMICs), particularly those in sub-Saharan Africa, South and South-East Asia. The causative agents are typhoidal serovars of Salmonella enterica, including Typhi (S. Typhi) and Paratyphi A (SPA). There are no vaccines currently licensed for SPA, leaving antimicrobials as the only therapeutic option. Multi-drug resistance (MDR) S. Typhi is increasingly prevalent, but to date has not been detected in SPA. In Australia, cases of SPA are notifiable. Here we report on the genomic epidemiology of 208 cases of SPA in returned travellers to Australia, and their close contacts, from 2018 to 2025. A total of 15 unique genotypes were detected, and these were correlated with geographical regions of reported travel. There was a low incidence of antimicrobial resistance with only a single isolate carrying acquired resistance genes. Mutations in quinolone resistance determining regions were common across the genotypes, detected in 95.7% of isolates. A single isolate in a traveller returning from India was resistant to several first line antibiotics including: ampicillin, amoxicillin plus clavulanic acid, ceftriaxone, azithromycin and ciprofloxacin. The isolate carried a plasmid encoding an extended spectrum beta-lactamase (blaCTX-M-231), two macrolide resistance genes (mphA and ermB) and a quinolone resistance gene (qnrS1). Elements of the pangenome were explored, with stable maintenance of small plasmids encoding hypothetical proteins detected in four genotypes. Copy number variation in genes encoding surface antigen biosynthesis genes were detected in six genotypes. These biosynthesis genes are targets for one of the two SPA vaccines in development, and the potential variation in surface antigens could have implications for vaccine efficacy. Linking epidemiological data with genomic studies of SPA provides an opportunity to improve understanding of the emergence, spread and risk of drug-resistant SPA infections, and to better inform empirical treatment guidelines in returned travellers.

Objectives- Among clinical methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infection (BSI) strains, we sought to determine the prevalence of {beta}-lactam-{beta}-lactamase inhibitor (BLBLI) susceptibility, and its association with oxacillin susceptibility, genotypic factors, and patient characteristics. Methods- Clinical MRSA BSI strains were tested for susceptibility to penicillin-clavulanate by Etest (n=117, 36% of the dataset) and to oxacillin by disk diffusion assay (n=328, 100%). Penicillin-clavulanate susceptibility was defined as MIC [&le;]2mg/L and oxacillin disk susceptibility as an inhibition zone > 6mm. All strains were whole-genome sequenced, and alleles of mecA annotated. The sensitivity and specificity of the oxacillin disk to predict penicillin-clavulanate 'susceptibility' were assessed. Clinical and genomic associations with BLBLI 'susceptibility' were assessed by calculating odds-ratios (OR). Results -We found 73/117 (62%) and 205/328 (62%) strains to be 'susceptible' to penicillin-clavulanate and oxacillin disk, respectively. Oxacillin disk susceptibility and penicillin-clavulanate susceptibility were highly correlated (sensitivity 97.3% and specificity 95.5%). We therefore used oxacillin disk susceptibility as a proxy for penicillin-clavulanate susceptibility. Comparative genomics of the mecA gene uncovered 8 alleles. The oxacillin disk 'susceptible' phenotype was associated with specific mecA alleles, community-associated MRSA sequence-types (OR 72.8, 95%CI 35.4-162), community acquisition of infection (OR 2.09, 95% CI 1.03-4.27), lower Charlson Comorbidity Index (OR 0.90, 95% CI 0.82-0.98) and SOFA (sequential organ failure assessment) scores at presentation (OR 0.88, 95% CI 0.79-0.98). Conclusion - BLBLI 'susceptibility' is common among MRSA strains and is strongly associated with the strain genotype. Infections caused by BLBLI 'susceptible' strains are associated with specific patients' characteristics, namely younger age, fewer comorbidities, acquisition in the community and milder presentations.

Background Antimicrobial-resistant Gram-negative bacteria pose a major threat to global health. In the WHO Bacterial Priority Pathogen List (BPPL) 2024, several species were classified as critical or high priority for research and development of new antimicrobial therapeutics and diagnostics. However, access to well-characterised and clinically relevant bacterial isolate panels remains an unmet need for development and validation. Methods We constructed five panels of Gram-negative bacterial isolates, cultured from samples originally referred to the UK Health Security Agency Antimicrobial Resistance and Healthcare-Associated Infections Reference Unit for analysis between 2014 and 2025. For each isolate, antimicrobial susceptibilities were determined against a range of clinically relevant antibiotics, including third-generation cephalosporins, carbapenems, colistin and other last-line antibiotics. WGS was performed on all isolates, and previously described resistance determinants were characterised. Results The five panels consist of 145 isolates and represent 81 sequence types across Escherichia coli (30 isolates), Klebsiella pneumoniae (30 isolates), carbapenem-resistant Acinetobacter baumannii (30 isolates), carbapenem-resistant Pseudomonas aeruginosa (30 isolates), and a mixed panel of other healthcare-associated Enterobacterales species (25 isolates). Panels are highly representative of globally relevant strains, including those currently in circulation and on the WHO BPPL 2024, and of resistance mechanisms of public health importance. Conclusion The panels provide a diverse, comprehensive set of multidrug-resistant Gram-negative bacterial isolates, representative of strains currently in circulation globally. Selected isolates carry a breadth of important resistance mechanisms and are highly relevant to the current epidemiological landscape. The isolates and associated metadata are available to industry, academia, and other laboratories for use in developing novel antimicrobial compounds and diagnostic assays.

Carbapenem-resistant Escherichia coli (CR-E. coli) is an emerging One Health threat, but recent shifts in predominant lineages and genomic links between clinical and food reservoirs in Hong Kong remain poorly defined. We analyzed 271 CR-E. coli isolates from four hospitals (2022-2026) and 585 isolates recovered from 4,917 retail food samples (2022-2025). Isolates underwent antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing, resistance-gene and plasmid profiling, core-genome SNP phylogenetics, and comparative genomics. Food isolates were mainly from raw pork (268/585, 45.8%) and raw chicken (231/585, 39.5%). blaNDM-5 was detected in 527/585 (90.1%) food and 241/271 (88.9%) clinical isolates. ST69 was the most frequent defined sequence type in both collections, representing 44/585 (7.5%) food and 36/271 (13.3%) clinical isolates, in contrast to the heterogeneous lineages and carbapenemases previously reported in Hong Kong. Applying a predefined [&le;]50-pairwise-SNP threshold for close genomic relatedness, core-genome phylogeny of 80 ST69 isolates identified two major mixed-source clusters collectively comprising 28 clinical and 27 food isolates. Clustered isolates showed similar antimicrobial resistance profiles, carried blaNDM-5 and blaTEM-1, and were associated with IncI1 MLST | ST136 plasmids. Comparative analyses showed >99.85% average nucleotide identity and broad conservation of the blaNDM-5-associated plasmid backbone across sources. These findings indicate the emergence of blaNDM-5-carrying ST69 as a prominent CR-E. coli lineage in Hong Kong and demonstrate close genomic relatedness between selected clinical and retail food isolates. Although transmission direction have not been inferred yet, the findings support integrated One Health surveillance and source-tracing across clinical, food, animal, and environmental sectors.

Objectives: To determine whether methicillin-resistant Staphylococcus aureus (MRSA) recov-ered from wastewater, as a proxy for community carriage, and clinical settings represent distinct populations and whether their comparison provides insight into distinctions between healthcare-associated (HA-) and community-associated (CA-) MRSA. Methods: We analyzed whole-genome sequences from 115 MRSA isolates collected in Switzer-land between 2021 and 2024, including 89 from three hospitals and 26 from six wastewater treatment plants serving the hospital catchment areas. We compared the phylogenetic relatedness, sequence types (STs), SCCmec types, spa types, antimicrobial resistance genes (ARGs), and viru-lence factors between the two sources. Results: Amongst all isolates, few were closely genetically related, with only 5% (273/6,105) of the pairwise comparisons differing by [&le;]15 core-genome single nucleotide polymorphisms. Amongst the 89 clinical isolates, there were 23 STs and 46 spa types as compared to 6 STs and 9 spa types amongst the 26 wastewater isolates. All wastewater isolates (100%, or 26/26) and most clinical isolates (64%, or 57/89) were SCCmec IV, historically associated with CA-MRSA. Pan-ton-Valentine Leukocidin genes, which historically indicated virulence associated with CA-MRSA, were detected in 37% (43/115) of isolates, including 40% (36/89) of clinical isolates and 27% (7/26) of wastewater isolates. One wastewater ST (ST97, 6/26 isolates) was phylogenetically distinct from all clinical isolates and corresponds to a known livestock-associated MRSA lineage, while other STs identified in wastewater are known to circulate in livestock or communities (ST22, ST88, ST1482). Conclusions: Our findings highlight the effectiveness of clinical surveillance in monitoring MRSA epidemiology in Switzerland, with most major lineages, antimicrobial resistance determi-nants, and virulence factors identified in wastewater also present among clinical isolates. Notably, wastewater isolates shared sequence types with known livestock and CA-MRSA lineages. This suggests wastewater supplements traditional methods in understanding community circulation but provides limited unique insight into clinical circulation.

Predicted probabilities of antibiotic susceptibility to known or suspected pathogens can be used to support antibiotic selection. Patient demographic, clinical, and prior microbiologic history can be used to generate location-specific prediction models. For three Canadian tertiary care institutions we fit and evaluated models for predicting Gram-negative antibiotic susceptibilities to common antimicrobial agents based on previously established model structures. A web-based application was developed to permit visualization of antibiotic susceptibility predictions and support antibiotic decision-making.

Background Rising antimicrobial resistance (AMR) in the African region contributes to high morbidity and mortality. Continuous national AMR surveillance is critical in understanding the spread of AMR and informing policies on containment. We present results of national AMR surveillance in Kenya Methods Passive surveillance was prospectively conducted in 20 sites in Kenya between 2021 and 2025. Sites included national and sub-national level tertiary public and private hospital laboratories. Non-duplicate isolates of WHO priority Gram-negative and Gram-positive pathogens were included in this analysis. Bacterial isolates were identified using either conventional identification methods, Analytical Profile Index or automated systems while antimicrobial susceptibility testing was performed using the Kirby-Bauer disk diffusion method or automated systems and interpreted using the Clinical and Laboratory Standards Institute guidelines. The primary outcomes were the proportions of various priority bacteria isolated and the proportions resistant to commonly used antibiotics. Results Between 2021 and 2025, there were 15,124 priority pathogens isolated with 7,592 (50.2%) from urine, 5,430 (35.9%) from blood (35.9%), and 1,784 (11.8%) from respiratory specimens. Escherichia coli and Klebsiella pneumoniae accounted for 76.3% of the priority pathogens. Resistance to 3rd generation cephalosporins was 63.2% for Escherichia coli and 79.1% for Klebsiella pneumoniae for the period 2021 to 2025 while carbapenem-resistance was 30.4% for Klebsiella pneumoniae and 7.2% for Escherichia coli. Resistance to carbapenems by Klebsiella pneumoniae increased from 17.9% in 2021 to 35.9% in 2025 while Methicillin resistance in Staphylococcus aureus increased from 36.5% in 2021 to 56.4% in 2025. Conclusion Resistance to critical antibiotics is a significant problem in Kenya, with alarming rates of Methicillin Resistant Staphylococcus aureus and carbapenem resistant Klebsiella pneumoniae. Ugent and sustained infection prevention and control measures and appropriate antimicrobial stewardship activities should be instituted across all health facilities in the country. There is need for improved access to antibiotics with activity against these resistant pathogens.

Background: Overuse of antibiotics accelerates antimicrobial resistance (AMR), threatening public health. Poland faces challenges with high antibiotic use; therefore, understanding people's antibiotic-related behaviours and beliefs would help identify targets for interventions. This study aims to identify sociodemographic and psychosocial correlates of antibiotic use among a representative sample of adults in Poland. Methods: The study employed an exploratory survey design. Adults in Poland (N=1,000) were randomly sampled, ensuring the representativeness of the Polish general population. Data were collected using a pretested questionnaire, administered through computer-assisted telephone interviews. Quantitative data were analysed descriptively and using a logistic regression. Free-text data were analysed using content analysis. Results: 31.6% of respondents used oral antibiotics in the preceding year, most commonly for respiratory tract infections (RTIs). Higher age, higher household income level, and education level were identified as predictors of increased antibiotic use, with increasing age being the most prominent factor. The belief that antibiotics accelerate recovery from RTIs and expectations for antibiotic prescriptions were found to be associated with greater antibiotic use. Encouragingly, 92.9% of respondents reported trusting their doctors, 51.5% that doctors explained why antibiotics were unnecessary for particular infections, and 57.1% were willing to engage in such discussions. While 76.5% of respondents reported awareness of antibiotic resistance, descriptions of the concept were often flawed. Conclusions: Key areas of focus for future interventions include addressing attitudes and behaviours of middle-aged (35-65) and older (66+ years old) adults, managing patient expectations regarding recovery and prescriptions, and correcting fundamental misconceptions about AMR.

Irrational prescribing can compromise patient safety, medicine availability, and antimicrobial stewardship. At a public district hospital in southwestern Uganda, a 2019 internal audit prompted by recurrent stock-outs found approximately three medicines per outpatient prescription, four per inpatient prescription, and antibiotics in about 60% of outpatient prescriptions. We implemented a six-month quality improvement initiative to increase prescribing concordant with the Uganda Clinical Guidelines (UCG) and improve key indicators of rational medicine use among outpatients. From January to November 2021, we conducted an uncontrolled before-and-after quality improvement evaluation. Prescription records were selected by systematic random sampling at baseline and six-month endline. We reviewed 350 baseline and 101 endline outpatient prescriptions. The primary outcome was prescription concordance with UCG. Secondary outcomes included antibiotic prescribing, number of medicines per encounter, generic prescribing, and injection use. Adjusted analyses accounted for age, sex, and diagnostic group. Following root-cause analysis, the hospital quality improvement (QI) team implemented prescriber education, provided clinicians with soft-copy PDF versions of the UCG and essential medicines lists, restricted prescribing to recognized clinicians with signature verification, and instituted periodic prescription audit and feedback. Guideline-concordant prescribing increased from 43.7% to 76.2% (adjusted change, +32.8 percentage points; 95% CI, 21.9-43.8; aPR=1.82; 95% CI, 1.51-2.20). Antibiotic prescribing decreased from 83.4% to 65.3% (adjusted change, -17.9 points; 95% CI, -27.8 to -8.0; aPR=0.80; 95% CI, 0.70-0.91). Mean medicines per encounter decreased from 3.35 to 2.66 (adjusted mean difference, -0.61; 95% CI, -0.79 to -0.43), while prescriptions containing only generic medicines increased from 78.6% to 94.1% (adjusted change, +13.6 points; 95% CI, 5.8-21.4). Guideline-concordant prescribing increased, while antibiotic use and medicine burden declined and generic prescribing improved. Antibiotic use nevertheless remained high, underscoring the need for continued stewardship, audit, and iterative QI.