JAC-Antimicrobial Resistance

BackgroundElectronic prescribing registries are widely used for antimicrobial stewardship surveillance. Existing indicators predominantly measure structure or process, while validated outcome indicators remain rare. The present study evaluates how well rule-based measures capture clinically meaningful postdiagnostic antibiotic decision making in pediatric febrile urinary tract infection. MethodsWe conducted a retrospective, multicenter validation study including all empirically treated febrile UTI episodes across three Swedish pediatric emergency departments. Prescribing outcomes were classified using registry rules and compared with outcomes determined by clinician review and laboratory findings. Guidance Ratio (GR) and Discontinuation Ratio (DR) were calculated monthly and in aggregate for both clinically validated- and registry rule classifications. ResultsIn total, 909 febrile UTI episodes were included across all sites. The rule-based GR was 49%. GR increased consistently with stronger diagnostic evidence. Among the 431 episodes with clinician-adjudicated follow-up, 63% resulted in guided treatment; 28% discontinued treatment, and 9% lacked follow-up documentation. The rule-based algorithm showed a sensitivity of 0.78 and a specificity of 1.00 for identifying guided outcomes. Monthly rule-based GR tracked validated temporal patterns but underestimated absolute values. A calibration function substantially improved agreement. ConclusionsRule-based indicators captured overall prescribing patterns but underestimated the level of prescribing concordant with guidelines. Validation against clinician reviewed reference data enabled calibration and improved the interpretability of indicators based on registry data for antimicrobial stewardship.

BackgroundAntimicrobial resistance (AMR) surveillance is essential for quantifying and monitoring the burden of AMR among World Health Organization (WHO) priority pathogens. We analysed Tunisian AMR surveillance system (TARSS) data across five sentinel hospitals from 2014 to 2022. MethodsWe conducted a retrospective isolate-level analysis for Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter spp. Temporal, ward, and specimen associations were quantified using multivariable logistic regression models. Sex and age categories were explored in secondary models due to missingness. Temporal trends were assessed using Cochran-Armitage test, and co-resistance was summarised for third-generation cephalosporin and carbapenem phenotypes. We also evaluated temporal dynamics of 3GCR and CR profiles. ResultsA total of 35,525 E. coli, 14,325 K. pneumoniae, 9,679 P. aeruginosa, and 5,597 Acinetobacter spp. were reported to TARSS between 2014 and 2022. Mean annual MDR prevalence was high for Acinetobacter spp. (85.1%), moderate for K. pneumoniae (45.5%) and for P. aeruginosa (27.1%), and lower for E. coli (17.5%). Adjusted models indicated increased odds of resistance to several antibiotics, whereas E. coli showed decreased odds. Intensive care unit (ICU) and blood isolates were associated with higher odds of resistance in all pathogens. ConclusionThis nine-year multi-hospital analysis reveals a high prevalence of AMR across the four WHO priority pathogens, settings, and specimen types, with increasing resistance for some pathogen-antibiotic combinations. The higher odds of clinically important resistance amongst ICU and blood isolates support the use of ward-level antibiograms and stratified stewardship and infection prevention measures.

Objectives: Optimising parenteral antimicrobial use is central to antimicrobial resistance (AMR) control, yet its appropriateness is difficult to assess. We aimed to develop a quantitative indicator to evaluate the appropriateness of parenteral antimicrobial therapy in hospitalised patients with bloodstream infections. Methods: We developed the Susceptibility-Spectrum Discrepancy Index (S2DI), reflecting the discrepancy between antimicrobial susceptibility of blood culture isolates and the spectrum width of prescribed agents. Using a database from 67 National Hospital Organization hospitals in Japan, we identified patients with Staphylococcus aureus or Escherichia coli bacteraemia from 2017 to 2023. An expert panel of 10 infectious disease physicians independently ranked antimicrobial susceptibility (A) and spectrum width of commonly used agents (B). S2DI was defined as B minus A on day 7 after treatment initiation, with values closer to zero indicating more appropriate therapy. S2DI was calculated for individual cases, aggregated at the hospital level, and analysed using linear mixed-effects models with hospital-level random effects. Results: A total of 4,505 S. aureus and 9,563 E. coli bacteraemia cases were included. Median S2DI was 1 (IQR 0-1) for S. aureus and 2 (IQR 0-3) for E. coli. For both pathogens, later calendar years were significantly associated with more favourable S2DI, suggesting gradual improvement in antimicrobial use. In E. coli bacteraemia, female sex and younger age were also associated with more appropriate therapy. Conclusions: Although variation across hospitals persists, appropriateness of parenteral antimicrobial use has improved over time. S2DI is a simple metric that may support optimisation of antimicrobial use.

Antimicrobial resistance (AMR) is classified by the World Health Organization (WHO) as one of humanity's ten global public health threats. This review aimed to estimate the prevalence, temporal trends and regional distribution of AMR in WHO priority bacteria across human, animal and environmental sources in Cameroon. This review was conducted following PRISMA 2020 guidelines, with the protocol registered in PROSPERO. A systematic literature search was conducted in Google Scholar, PubMed, African Journals Online, Hinari, and Africa indexus Medicus. Random effects models were used to estimate pooled prevalence and 95% confidence intervals (CIs), with subgroup analyses by bacterial source, region, and sampling period. Of 1566 articles screened, 115 met the inclusion criteria. The reported data encompassed 16 bacteria-antibiotic combinations in 16,948 isolates. Globally, third-generation cephalosporin (3GC) resistance in E. coli was the most prevalent (49.0%, 95% CI: 39.0-60.0%, I2=97.7%), reaching 77.0% (95% CI: 46.0-98.0%, I2=95.6%) in environmental isolates. The pooled prevalence of ESBL production in all included Enterobacterales was 37.0% (95% CI: 30.0-45.0%). Most of the highest resistance rates were observed in the Littoral region. The resistance rates between 2016 and 2025 were significantly higher than those from 2000 to 2015. These increases were more marked in fluoroquinolone-resistant Salmonella spp (1.0% to 48.0%, I2=97.3%, p<0.001), carbapenem-resistant E. coli (0% to 15%, I2=93.5%, p<0.001), and 3GC-resistant E. coli (34.0% to 64.0%, I2=97.6%, p=0.003). Antimicrobial resistance in WHO priority bacteria in Cameroon is high, unevenly distributed across regions and significantly increasing over time. These results underscore the crucial need for strengthened AMR surveillance to curb the growing threat of AMR in Cameroon.

Background: Metronidazole (MTZ) is a first-line antibiotic for several enteric infections. Its use is common in low-income countries, where most primary-care consultations are conducted by nurses. However, increasing resistance among some enteric pathogens is a growing concern. Using WHO guidelines, we conducted a register-based cross-sectional study to assess MTZ prescribing practices and their determinants in public and private primary healthcare facilities in South Benin. Methods: We performed a register-based cross-sectional study covering the year 2020 in 11 primary healthcare facilities (5 public and 6 private) in Abomey-Calavi, South Benin, following WHO recommendations. In total, 200 visits per facility were selected using systematic random sampling. The primary outcome was the prevalence of MTZ prescription. Determinants of MTZ prescription were identified using multivariable logistic regression analysis. Results: In total, 2,200 medical visits were analyzed. The median age of patients was 19 years, and 57% were female. Antimalarials were prescribed in 52% of visits. Antibacterial agents were prescribed in the majority of visits, with MTZ being the second most frequently prescribed antibiotic (18%), after aminopenicillins (27%). In multivariable analysis, digestive symptoms (adjusted odds ratio [aOR], 8.65; 95% confidence interval [CI], 6.49-11.6), genitourinary symptoms (aOR, 6.84; 95% CI, 3.18-15.0), and skin lesions (aOR, 2.39; 95% CI, 1.58-3.60) were independently associated with increased odds of MTZ prescription. In contrast, fever (aOR, 0.66; 95% CI, 0.49-0.87), respiratory symptoms (aOR, 0.44; 95% CI, 0.26-0.71), and malaria (aOR, 0.21; 95% CI, 0.15-0.28) were associated with decreased odds. Visits in the private sector were also associated with higher odds of MTZ prescription compared with the public sector (aOR, 2.31; 95% CI, 1.78-3.02). Conclusion: MTZ is the second most commonly prescribed antibiotic in primary care in the study area, with its use largely driven by digestive symptoms. Further studies are needed to assess the appropriateness of this prescription. Additionally, research is warranted to understand better the determinants of higher antimicrobial prescribing in the private healthcare sector.

BACKGROUNDAutomated antimicrobial susceptibility testing (AST) systems are crucial for accurate, timely detection of drug-resistant microbial isolates. This meta-analysis assessed the performance of the BD Phoenix ("Phoenix", BD Diagnostic Solutions), Vitek(R) 2 ("Vitek 2", bioMerieux), and DxM MicroScan WalkAway ("MicroScan", Beckman Coulter, Inc.) AST systems relative to common reference methodology. METHODSA systematic literature search in Ovid (MEDLINE and Embase) yielded 275 unique (not duplicated) records, with 44 additional records retrieved from handsearching; 39 studies met inclusion criteria. Categorical agreement (CA), essential agreement (EA), very major errors (VMEs), and major errors (MEs) for the three instruments were compared to a common reference method. Ratios of proportions were analyzed using random-effect meta-regression. RESULTSThe instruments did not differ significantly in CA, EA, or ME. Vitek 2 showed a higher overall VME rate than Phoenix ([~]44% higher; Vitek 2-to-Phoenix ratio = 1.44; p=0.062 [approaching significance]) and MicroScan (74% higher; ratio = 1.74; p=0.045). No appreciable difference was observed for VME between Phoenix and MicroScan. Subgroup analyses should be interpreted cautiously due to limited overall significance indicating varying performance across systems. Vitek 2 generally had higher relative VMEs for gram-negative organisms and lower relative VMEs for gram-positive organisms, whereas Phoenix showed the opposite pattern. MicroScan had relatively low VMEs when stratified by Clinical and Laboratory Standards Institute (CLSI) criteria; no differences in VMEs were observed using European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria. CONCLUSIONAlthough some VME differences were noted, overall performance of the three systems was comparable. Organism- and drug-specific VME patterns--and updates to CLSI criteria over time--highlight the importance of continued monitoring of current breakpoints for all three instruments.

Introduction: Antibiotic misuse is a major driver of antimicrobial resistance (AMR), contributing to an estimated 1.27 million deaths globally. In Kenya, inappropriate antibiotic use is shaped by health-seeking behaviors and sociodemographic factors. However, little is known about how adults with productive coughs seek and use antibiotics, or how sociodemographic factors underpin these practices. This study explored antibiotic-seeking pathways, usage patterns, and the sociodemographic factors influencing these practices among adults with productive coughs attending selected chest and tuberculosis clinics in Nairobi County, Kenya. Methodology: A facility-based cross-sectional study was conducted among 400 adults ([&ge;]18 years) with productive coughs. Data were collected using a structured questionnaire on sociodemographic characteristics, antibiotic-seeking pathways, and use patterns. Results: Most participants were male (65.0%) and employed (67.0%), with 68.3% earning below Ksh 10,000 (approximately USD 80) monthly and 35.8% having basic education. A history of smoking (37.3%), tuberculosis (32.0%), or other comorbidities (29.8%) was common. Among 347 (86.7%) antibiotic users, 46.4% obtained antibiotics through general practitioners (GP) only, 31.4% via both GP and over-the-counter (OTC) sources, 15.3% from OTC only, and 6.9% through self-medication. Females were more likely to self-medicate (13.3% vs. 3.2%) and had higher odds of antibiotic use (cOR: 2.00; 95% CI: 1.04-4.10). Tuberculosis history was linked to greater GP reliance (61.7% vs. 37.4%). Low-income participants mainly used GP-only sources, while higher-income earners favored GP plus OTC routes (RRR: 2.67; 95% CI: 1.41-5.05). Empirical use was common (71.1%), dominated by Amoxicillin (90.8%), with multiple antibiotic use reported by 67.2% of the participants. Conclusion: Antibiotic use among adults with productive coughs in Nairobi was widespread and largely empirical, dominated by Amoxicillin and Amoxicillin/Clavulanic acid. Self-medication, unregulated antibiotic access, and inappropriate use highlight the urgent need for stricter prescription enforcement and strengthened stewardship programs to promote rational antibiotic use and curb AMR.

WHO recommends bedaquiline-pretomanid-linezolid- (BPaL) and BPaL-moxifloxacin (BPaLM) for treatment of rifampicin-resistant tuberculosis, informed by the TB-PRACTECAL results. However, clinical explanatory data of these drugs exposure and Mycobacterium tuberculosis clearance rates and toxicity relationships remain understudied. We therefore investigated the relationship between the patients exposure to anti-TB drugs in TB-PRACTECAL trial investigational regimens and their treatment outcomes. PRACTECAL-PKPD was a prospective pharmacokinetics and pharmacodynamics study nested in TB-PRACTECAL. Patients with rifampicin-resistant pulmonary tuberculosis were enrolled from Belarus and South Africa. The first objective was to develop drug exposure metrics for bedaquiline, pretomanid, linezolid, moxifloxacin and clofazimine. The efficacy objectives were to establish an exposure-response model for each drug and regimen to both bactericidal activity and long-term treatment outcomes. The safety objective was to investigate the exposure-toxicity relationship of each drug. Antimicrobial exposure did not correlate with the speed of sputum bacterial clearance, however there was a 20% increased bacillary killing rate with BPaLM compared to the standard of care arm whilst BPaL and BPaL-clofazimine (BPaLC) displayed a 15% decreased bacillary killing rate compared to the standard of care arm. Linezolid plasma exposure was higher amongst patients with anaemia or neutropenia compared to those without. No other exposure-toxicity relationships were identified for all other drugs. Absence of correlation between drug exposure and bacillary clearance suggest that the dosages used achieve saturation of bacillary killing, while remaining safe.

Background Antibiotic use is prevalent in hospitals, driving the emergence of drug-resistant pathogens. We investigated the contextual influences on antibiotic prescribing behaviour across hospitals in high, middle, and low-income countries in Asia with an aim to provide actionable insights to improve prescribing behaviour. Methods We conducted a large qualitative study across ten institutions in Singapore, Nepal, and Thailand. Semi-structured interviews and ethnographic observations involving physicians, nurses, pharmacists, and management staff were conducted. Data were analysed thematically using QSR NVivo 14. Findings A total of 194 interviews were conducted amongst physicians (54{middle dot}1%), nurses (19{middle dot}6%), pharmacists (12{middle dot}4%), and management staff (13{middle dot}9%). Structural factors such as limited microbiology laboratory capabilities, concerns about antibiotic quality, weak infection prevention and control policies, and the lack of relevant, updated guidelines were prominent drivers for prolonged and broad-spectrum antibiotics prescriptions. Where these system supports were in place, prescribing decisions were less defensive and more targeted, although prescriber responsibility and concerns about immediate patient deterioration continued to influence practice. Across settings, clinicians tended to prioritise short-term perceived benefits of antibiotic treatment over the longer-term risks of antimicrobial resistance.

Objectives: To better define the clinical features of Acinetobacter spp. infection in Northern Thailand, including a comparison of hospital- and community-acquired infections (HAIs and CAIs). Methods: A prospective clinical study of Acinetobacter spp. infections at two Northern Thailand hospitals from 2019 to 2022, collecting data on sample sources, patient demographics, comorbidities, antimicrobial resistance profiles, and outcomes. Results: Of 129 enrolled patients, 81.4% had Acinetobacter spp. isolated from a respiratory sample. A significant minority (25.6%) of infections were CAIs, 33.3% of which were admitted to ITU within 24 hours of admission. Compared to HAIs, CAIs were significantly more likely to be caused by blood (15.2%, p=0.0258), wound (21.2%, p=0.0120), or urine infections (12.1%, p=0.0370). Acinetobacter spp. HAIs mainly occurred after admission to ITU (87.7%, p<0.0001) and were more likely to be multidrug-resistant than CAIs (76.3% vs. 34.4%, p<0.0001). Overall, the median length of hospital stay was 27 days and there was a 27.1% in-hospital mortality, which was increased in patients with CVA/brain (p=0.005), and multidrug-resistant (p=0.010) or carbapenem-resistant infections (p=0.003). Conclusions: These data define the clinical profile of Acinetobacter spp. infections in Northern Thailand, confirming their high mortality and demonstrating CAIs are a significant proportion of all cases.

Urinary tract infection (UTI) is one of the most common community-acquired bacterial infections mainly caused by extraintestinal pathogenic Escherichia coli (ExPEC) strains. The high-risk Escherichia coli ST131 clone is a major global cause of this disease. The lineage rapid dissemination is associated to multidrug resistance (MDR), production of extended-spectrum beta-lactamase (ESBL), and multiple virulence-associated genes. Although we lack information about ExPEC high-risk clones in Latin America, we recently reported an increase in ST131 dissemination in Rio de Janeiro from 2015 to 2019. The present study aims to characterize virulence and resistance molecular and phenotypic features that may contribute to dissemination of E. coli ST131 in Rio de Janeiro, Brazil. We assessed a 133 E. coli ST131 strains collection obtained from urine of outpatients with suspected UTI, in 2019. We determined antimicrobial susceptibility, fluoroquinolones resistance genes, virulence factors associated genes and biofilm production of all strains and analyzed the frequencies by each clade or subclade. A higher incidence of women (92%) and elderly (65%) subjects was observed. Overall resistance to first- and second-line treatment for UTI antimicrobials ampicillin, ciprofloxacin and sulfamethoxazole-trimethoprim was detected in high rates (40%), with a major impact of subclade C2 strains that were resistant to almost all antimicrobials tested, 52% carry ESBL and 66% of strains harbor the aac(6)-Ib-cr ciprpofloxacin resistance gene. Clade B and subclade C2 showed higher virulence scores among the other clades. They present unique virulence profiles characterized by the presence of papGIII, sfa/focDE, and especially ibeA genes in clade B, and the afa/DrBC, papGII, hlyA, cnf1 genes in subclade C2. Over 50% of our strains are biofilm producers, characterized by weak (24%) and strong producers (32%). ESBL and MDR strains harbor mainly papA, papGII, hlyA, cnf1 and kpsMTII genes that plays a key role in ST131 colonization. Subclade C1 is the major biofilm producer (78%), despite its lower virulence score. We also detected higher incidence of papA (27%), hlyA (19%) genes and the RPAI(malX) marker (84%) in biofilm producer strains with a statistical association of sfa/focDE gene (9%). We can infer that Clade C strains might be responsible for ST131 dissemination and persistence in Rio de Janeiro.

PurposeAntibiotic use (ABU) is a major driver of antimicrobial resistance (AMR), but ABU patterns are poorly understood in low-income countries where the burden of AMR is great and ABU is insufficiently regulated. Here, we report ABU from ten sites ranging from rural villages to small cities in Madagascar, a country with high AMR levels, and present results from modeling to identify factors that may be associated with ABU in this setting. MethodsWe conducted surveys of 290 individuals from ten sites in the SAVA Region of northeast Madagascar to gather data on sociodemographic characteristics, agricultural and animal husbandry practices, recent antibiotic use, the antibiotics that participants recalled using in their lifetimes, and the sources of their antibiotics. Using these data, we conducted statistical analyses with a mixed-effects logistic model to determine which characteristics were associated with recent antibiotic use. ResultsNearly all respondents (N=283, 97.6%) reported ABU in their lifetimes, with amoxicillin being the most widely reported antibiotic (N=255, 90.1% of those reporting ABU). All recalled antibiotics were classified as frontline drugs except for ciprofloxacin. Most respondents who reported antibiotic use also reported obtaining antibiotics without prescriptions from local stores (N=273, 96.5%), while only 52.3% (N=148) reported obtaining antibiotics through a prescriptive route, such as from a health clinic or private doctor. Of the 127 individuals (44.9%) who reported recent ABU, men were found to be significantly less likely to have recently taken antibiotics than women. ConclusionsOur findings provide new insights into ABU in agricultural settings in low-income countries, which have historically been understudied in AMR and pharmacoepidemiologic research. Knowledge of ABU patterns supports understanding of AMR dynamics and AMR control efforts in these contexts, such as interventions on inappropriate antibiotic dispensing. Key pointsO_LIAntibiotic use (ABU) in Madagascar is largely unstudied despite its role in antimicrobial resistance (AMR), which Madagascar faces a high burden of. C_LIO_LIABU was widespread among livestock owners in northeast Madagascar, with the majority of study participants reporting ABU in their lifetimes and most people reporting ABU also having taken antibiotics in the previous three months. C_LIO_LIMost respondents reported obtaining their antibiotics from non-pharmaceutical stores, indicating high levels of unregulated ABU, though more than half also reported sourcing their antibiotics through prescriptive means (like doctors and health clinics). C_LIO_LIMen were less likely than women to have taken antibiotics in the previous three months. C_LIO_LIThese findings support the development of interventions to mitigate the burden of AMR in Madagascar and similar contexts while underscoring the need for more comprehensive research on the drivers and patterns of ABU. C_LI Plain language summaryIn this study, we provide basic information on antibiotic use (ABU) patterns in Madagascar, a country that experiences high levels of resistance but has been particularly understudied in AMR and pharmacological research. We surveyed 290 farmers with livestock from ten sites across northeast Madagascar about their ABU and found that nearly all study participants (N=283, 97.6%) have used antibiotics in their lifetimes, while a little under half of those who reported ABU also reported using antibiotics in the previous three months (N=127, 44.9%). The most used antibiotic was amoxicillin (N=255, 90.1%). Most people obtained their antibiotics from sources that do not require prescriptions, like general stores, indicating that most ABU is unregulated. Through modeling, we also found that men were less likely than women to have taken antibiotics in the previous three months (OR=0.50, CI 0.30-0.82). These findings help us better understand the dynamics of ABU in low-income countries, which have historically been understudied in AMR and pharmacological research. They also support efforts to mitigate the burden of AMR by revealing ABU dynamics that may contribute to the emergence and spread of AMR, as well as identifying targets for intervention to curb inappropriate ABU.

Background: In Rwanda, genomic surveillance identified a dominant multidrug-resistant tuberculosis (MDR-TB) strain, the R3clone, responsible for approximately 70% of rifampicin-resistant TB cases. Its presence beyond Rwanda remains unexplored. Methods: Unique genetic signatures of the R3clone were defined using whole-genome sequencing of MDR-TB isolates from Rwanda. We developed a targeted qPCR assay detecting a clone-specific single-nucleotide polymorphism. With these tools, we screened isolates from neighbouring countries and public genomic repositories. Results: We identified 375 R3clone isolates, including 264 from historical Rwandan collections (1991-2021), 49 from recent Rwandan diagnostic routine (2021-2024), 25 from historical Burundi isolates (2002-2013), and 37 among public repositories from several countries. The R3clone-specific qPCR showed 100% specificity in distinguishing the R3clone from other MTBC (sub-)lineages. Transmission analysis revealed cross-border transmission of the R3clone within the Great Lakes Region. Conclusion: This study comprehensively assesses cross-border transmission of a dominant MDR-TB strain, highlighting the need for coordinated international surveillance.

Introduction Antibiotic use drives antimicrobial resistance, and optimizing prescribing in skilled nursing facilities (SNFs) - which care for medically complex residents in congregate settings characterized by frequent care transitions and diagnostic uncertainty - presents unique challenges. Antimicrobial stewardship (AMS) in SNFs has therefore become a focus of quality improvement efforts by federal and state health agencies. We aimed to identify factors that facilitate and hinder AMS implementation in SNFs. Methods A qualitative study of AMS implementation was conducted in Southern Arizona SNFs randomly sampled to represent urban/suburban, border, and rural regions. Semi-structured interviews were conducted with administrators, clinicians, and nonclinical staff within participating facilities. Interview transcripts were analyzed using constant comparative analysis, with both directed and emergent coding, facilitated by NVivo 12 software. Findings From 04/13/2019 through 12/13/2019, 57 interviews were conducted with 9 administrators, 38 clinical providers, and 10 nonclinical staff across 6 urban/suburban, 2 border, and 2 rural facilities. Analysis identified two thematic categories: "influencer themes," which describe specific barriers and facilitators to AMS implementation, and "system themes," which characterize SNFs as complex adaptive systems shaped by interacting staff roles, care transition challenges, and differing perceptions of AMS practices within the same facility. Key facilitators included effective internal communication, ongoing AMS education, and clinician AMS champions. Primary barriers included poor interfacility communication during care transitions, limited access to diagnostic resources, enculturated prescribing norms, and tension between immediate infection control priorities and long-term AMS goals. Conclusions Findings suggest that AMS implementation in Arizona SNFs is best understood as a systems-level process emerging from interactions among staff roles, organizational workflows, and care transitions, rather than solely from individual prescribing decisions. Recognizing SNFs as complex adaptive systems highlights the importance of communication structures, local champions, and feedback mechanisms. It underscores the need for coordination strategies within and across SNFs to sustain AMS interventions.

Background: With the emergence of drug-resistant strains and an unprecedented threat to control initiatives, tuberculosis remains to be a major public health risk in Ethiopia. Resistance to rifampicin (RR) is an important indicator, since RR is an acceptable surrogate for multidrug-resistant TB (MDR-TB). Over 95% of RR is based on mutations in an 81base pair segment of the rpoB gene, detected using rapid molecular assays. Despite this, detailed molecular epidemiological information is scarce. This study characterized the specific rpoB gene mutation patterns among patients in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted in 753 Mycobacterium tuberculosis complex (MTBC) clinical samples, corroborated as positive for MTBC from 2020 to 2024; respective probe mutation patterns were generated by the Xpert MTB/RIF platform. Demographic and clinical variables were also assessed for detecting the potential risk factors. Results: The overall RR-TB rate was 2.3% (17/753). Molecular analysis showed a distinct pattern of mutation, with codon 526 mutations being the most frequent, occurring in 54.3% of the resistance mechanisms. This was followed by those at codons 531 (21.7%) and 533 (15.2%). Most significant was the fact that 100% of RR-TB was observed among treatment-naive patients, providing unequivocal evidence that primary transmission is the exclusive cause of resistance in this population. Moreover, there were no statistically significant correlations between RR-TB and demographic factors, including sex, age, or HIV co-infection. Conclusion: The study demonstrates a steady, low-grade epidemic of RR-TB in Addis Ababa, dominated by a virulent bacterial strain with a distinctive mutation at codon 526. These observations highlight the imperative necessity for a strategic shift from a reactive, clinically-oriented model to proactive public health measures. To effectively break the chains of transmission, we recommend the universal application of drug susceptibility testing, enhanced and socially-directed contact tracing, and integrating molecular surveillance into the TB control program.

ObjectiveTo evaluate the diagnostic performance of FeverPAIN and Centor with point-of-care test (POCT) results for Group A Streptococcus (GAS) among children and adults presenting with sore throat in community pharmacies. MethodsCross-sectional analysis of patients aged six years and over with sore throat presenting to community pharmacies across Wales delivering the Sore Throat Test and Treat (STTT) service from November 2018 to September 2024. Patients who scored FeverPAIN [&ge;]2 or Centor [&ge;]3 and were able to undergo POCT were eligible for analysis. We described GAS positivity by age group and assessed diagnostic performance of FeverPAIN at the National Institute for Health and Care Excellence (NICE) antibiotic threshold ([&ge;]4), reporting sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under receiver operating characteristic curve (AUROC) with 95% confidence intervals (CI). We estimated potential overtreatment and undertreatment if antibiotics were supplied based on FeverPAIN alone. ResultsAmong 73,617 eligible patients, 37.0% (n=27,220) tested POCT-positive for GAS. Positivity was highest in children aged 6-10 years (47.0%: 5,339/11,371). FeverPAIN was used in 92.5% (n=68,099) of assessments. At the NICE-recommended threshold for antibiotic treatment (FeverPAIN [&ge;]4), sensitivity was 55.0% (95% CI: 54.4-55.6%) and specificity 77.0% (95% CI: 76.6-77.4%). PPV was 57.6% (95% CI: 57.0-58.2%) and NPV 75.1% (95% CI: 74.7-75.5%). Overall AUROC was 0.70 (95% CI: 0.70-0.71), with the lowest AUROC of 0.69 (95% CI: 0.68-0.70) observed among children aged 6-10 years. Using FeverPAIN alone would undertreat 44% and overtreat 23% of patients based on POCT results. ConclusionsFeverPAIN alone showed limited diagnostic performance for identifying GAS, with more pronounced discordance observed among children. Incorporating POCTs within community pharmacy sore throat pathways may support more targeted antibiotic prescribing. Our findings support a re-evaluation of the role of POCTs within community pharmacy sore throat pathways.

Antimicrobial resistance (AMR) is a growing global public health threat that complicates the treatment and control of bacterial infections. Shigella spp., a leading cause of bacterial diarrhea worldwide, has increasingly exhibited resistance to multiple antimicrobial agents that are commonly recommended therapy for severe shigellosis. Although conventional antimicrobial susceptibility testing (AST) remains the reference standard, it is time-consuming and provides limited insight into the genetic mechanisms underlying resistance. Whole-genome sequencing (WGS) has emerged as a complementary approach for AMR detection by enabling direct identification of resistance genetic determinants encoded in bacterial genomes. Machine learning (ML) methods applied to genomic features such as k-mers have shown promise for predicting resistance phenotypes from WGS data; however, applications to Shigella remain limited. In this study, we developed and evaluated an interpretable ML framework for predicting ciprofloxacin resistance using k-mer features derived from WGS data of 1,424 Shigella isolates collected in Ontario, Canada, between 2018 and 2025. K-mers were extracted from known gene targets associated with ciprofloxacin resistance, including chromosomal quinoline resistance-determining regions (QRDRs: gyrA and parC) and plasmid-mediated determinants (qnr). Supervised ML approaches were trained and compared. We evaluated the influence of k-mer lengths (k=11, 15, 21 and 31) on predictive performance and model interpretability; and compared models based on chromosomal determinants alone and models incorporating both chromosomal and plasmid-mediated determinants. Randon Forest classifier achieved the most consistent performance across models. Inclusion of plasmid-mediated determinants improved predictive accuracy relative to chromosomal-only models. Although differences across k-mer lengths were modest, k = 11 produced the highest area under the receiver operating characteristic curve (AUC) and the lowest Brier score. SHAP analyses localized high-impact features within QRDRs of gyrA and parC, supporting biological interpretability. These findings demonstrate that biologically-informed k-mer-based ML models can accurately and transparently predict ciprofloxacin resistance in Shigella, supporting their potential integration into genomic AMR surveillance and digital public health frameworks. Author summaryIn this study, we used genome sequencing data to develop machine learning models that predict ciprofloxacin resistance for Shigella directly from bacterial DNA. We focused on small DNA fragments (k-mers) derived from known resistance genes and mutations. Among the approaches tested, a Random Forest model showed the most consistent performance. Combining chromosomal mutations with plasmid-mediated resistance genes improved prediction accuracy and helped identify key genetic regions associated with resistance. These findings demonstrate that machine learning applied to genomic data can accurately and interpretable predict antibiotic resistance, supporting its potential use in genomic surveillance and public health monitoring.

Background: Antimicrobial resistance (AMR) is a growing global health concern driven largely by inappropriate antimicrobial use. Antimicrobial stewardship programs (ASPs), guided by the Centers for Disease Control and Prevention (CDC) core elements, are essential for optimizing antimicrobial use. However, adherence to these practices and the barriers faced by healthcare workers remain inadequately explored, particularly in resource-limited settings. Objective To assess adherence to the CDC antimicrobial stewardship checklist and identify barriers affecting stewardship practices among healthcare workers at a tertiary care hospital in Uttarakhand, India. Methods A quantitative cross sectional descriptive study was conducted among 355 healthcare workers, including nursing officers and physicians. Data were collected using a sociodemographic questionnaire, the CDC antimicrobial stewardship checklist, and a self-structured barrier assessment tool (test retest reliability r = 0.78). Descriptive and inferential statistics were applied using SPSS version 23.0, with a significance level set at p < 0.05. Results The overall adherence to the CDC antimicrobial stewardship checklist was 52.3%, indicating moderate compliance. Higher adherence was observed in action-oriented interventions, while lower adherence was noted in domains such as accountability, pharmacy expertise, reporting, and education. Major barriers identified included lack of antimicrobial supply (89.0%), shortage of key personnel (88.5%), delays in laboratory reports (85.1%), lack of training (83.9%), and inadequate administrative support (79.2%). Significant associations were found between perceived barriers and factors such as working area, designation, qualification, and work experience (p < 0.05), whereas age and gender showed no significant association. Conclusion Adherence to antimicrobial stewardship practices was moderate, with notable gaps in organizational and educational components. Multiple systemic, resource-related, and behavioral barriers hinder effective implementation. Targeted interventions focusing on strengthening infrastructure, workforce capacity, training, and administrative support are essential to improve stewardship practices in tertiary care settings. Keywords: Antimicrobial resistance, Antimicrobial stewardship program, Barriers, CDC Checklist

Background Five-biomarker-defined hypervirulent Klebsiella pneumoniae (hvKp) causes invasive infections, but its burden in bloodstream infections versus classical K. pneumoniae (cKp) is unclear. Methods This retrospective cohort study at a tertiary hospital in Japan included K. pneumoniae bloodstream infection episodes from January 2022-December 2024. hvKp was defined by the presence of all 5 genotypic biomarkers (rmpA, rmpA2, iucA, iroB, and peg-344). The primary outcome was abscess complications, and secondary outcomes were length of stay and antibiotic duration. Whole-genome sequencing was performed for 164 isolates. Results Among the 207 episodes, 28 (14%) were of hvKp. Abscess complication occurred in 17 (61%) hvKp versus 23 (13%) cKp episodes (adjusted odds ratio 10.7; 95% CI, 4.36-26.2). Median length of stay in hvKp versus cKp was 28 versus 14 days (adjusted ratio 1.60; 95% CI, 1.18-2.16) and median antibiotic duration was 43 versus 14 days (adjusted ratio 2.13; 95% CI, 1.64-2.77). These associations were attenuated after adjusting for abscess-related complications. No significant difference in 30-day mortality was observed, although the study was underpowered. Multidrug resistance was less frequent in hvKp strains than in cKp strains (11% vs. 30%; P = .040). Among the sequenced hvKp episodes, abscess rates varied across lineages, from 9 of 10 in ST23 to 1 of 4 in ST412. Conclusions Five biomarker-defined hvKp strains delineated a bloodstream infection subgroup with frequent abscess complications and prolonged care. hvKp and cKp present distinct clinical challenges; diagnostic tools distinguishing these subgroups may aid abscess evaluation and source control.

Aminoglycoside drugs, amikacin, streptomycin, and amikacin liposome inhalation suspension are crucial for treating refractory Mycobacterium avium-intracellulare complex pulmonary disease. In Mycobacterium tuberculosis, cross-resistance occurs between amikacin and kanamycin, but not between amikacin and streptomycin in genetic drug susceptibility testing. However, the occurrence of cross-resistance among aminoglycosides remains unclear in M. avium-intracellulare complex. We aimed to evaluate cross-resistance among aminoglycosides to determine whether streptomycin or kanamycin remains effective after the development of amikacin resistance. This single-center retrospective study included 20 patients with amikacin-resistant M. avium-intracellulare complex harboring rrs mutations. Paired analyses of streptomycin and kanamycin minimum inhibitory concentration values before and after amikacin resistance development were performed. In addition, streptomycin- and kanamycin-resistant strains were generated in vitro and resistance-associated mutations were identified using whole-genome sequencing. No significant increase was observed in streptomycin minimum inhibitory concentration values following amikacin resistance. In contrast, kanamycin values uniformly increased to >256 g/mL after the acquisition of amikacin resistance. Furthermore, amikacin- and kanamycin-resistant isolates shared mutations at position 1408 in the rrs gene, whereas streptomycin-resistant isolates exhibited mutations at position 20 in the rrs gene. These results suggest that amikacin and kanamycin exhibit cross-resistance in M. avium-intracellulare complex, whereas amikacin and streptomycin may not. Two cases in our cohort in which streptomycin treatment was effective after the acquisition of amikacin resistance further support these findings. In conclusion, streptomycin may be a potential therapeutic alternative for amikacin-resistant M. avium-intracellulare complex pulmonary disease. Future studies correlating streptomycin minimum inhibitory concentration values with clinical outcomes are required.