Antimicrobial Resistance & Infection Control

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 Carbapenem-resistant bacteria are a major global public health threat, classified as critical priority pathogens by the WHO. In Indonesia, despite a national antimicrobial resistance control programme established by the Ministry of Health in 2015, resistance rates continue to rise, including increasing carbapenem resistance among clinically important bacteria. Strengthening approaches to directly interrupt transmission is essential, yet transmission pathways remain poorly understood with limited research and policy guidance within the Indonesian context. Methods and analysis The INTERCEPT study is a UK-Indonesia multidisciplinary collaboration aiming to identify transmission routes of carbapenem-resistant bacteria across healthcare and community settings, and the mechanisms of resistance gene transfer between bacteria and mobile genetic elementss. We will conduct genomic surveillance of hospital inpatients, healthcare workers, hospital environments, and surrounding communities, including wastewater systems, combined with genomic analyses and mathematical transmission modelling. A cohort of patients with bloodstream infections will be recruited to evaluate resistant bacteria, treatment practices, and clinical outcomes. Qualitative research will explore behavioural and system-level factors influencing transmission and intervention implementation. Findings will inform stakeholder workshops to co-design context-specific interventions, with pilot intervention over 9 months with pre- and post-intervention assessment to guide scalable strategies to reduce AMR transmission. Discussion The INTERCEPT study addresses carbapenem resistance in Indonesia using an integrated approach combining microbiological surveillance, genomics, modelling, and qualitative methods. Strengths include cross-sectoral analysis (patients, workers, environment) and participatory intervention design. Limitations include geographic scope restricted to Central Java, Indonesia.

Background We examined whether two key housing quality indicators, energy efficiency and household overcrowding, were associated with lower respiratory tract infection (LRTI) hospital admissions in infants. Methods We used a cohort of all singleton births in Scotland 2010-2012, created through linked vital statistics and health data. LRTI admissions were characterised in hospital records. Overcrowding (defined using the national room standard) and median postcode-level energy efficiency were defined using maternal Census and postcode-level Energy Performance Certificate data linked to the cohort, respectively. We used logistic regression to model the odds of at least one infant LRTI admission. Results The cohort included 136,123 infants of whom 4.0% had at least one LRTI admission. Overcrowding was more common among infants of younger mothers and those in rented housing. Energy efficiency was lower among infants of older mothers, living in owner occupied homes, in less deprived areas. Compared with infants living in homes with excess rooms (under-occupied housing), those whose homes were below, or met, the minimum room standard had higher odds of LRTI admission (adjusted odds ratio 1.07, 95% CI 0.98-1.17; 1.10, 95% CI 1.03-1.17, respectively). Postcode-level energy efficiency was not associated with LRTI admission odds. Conclusion Overcrowding was more common in socioeconomically disadvantaged households and associated with increased risk of LRTI admission in infancy. Lower energy efficiency was associated with factors commonly linked to socioeconomic advantage and was not associated with LRTI admissions. Improving access to housing with adequate living space may reduce the burden of LRTIs in early life.

Occupational ocular injuries are a preventable yet neglected public health problem, particularly in low- and middle-income countries. Maintenance workers are exposed to diverse ocular hazards daily, yet compliance with protective measures is consistently poor. A descriptive cross-sectional study was conducted among 85 maintenance workers at the Maintenance and Essential Services Organization (MESO) of Kwame Nkrumah University of Science and Technology (KNUST), Ghana, recruited through stratified convenience sampling across seven occupational sections. A structured questionnaire assessed knowledge of ocular hazards and protective equipment, attitudes toward ocular safety, and safety practices. Data were analyzed using IBM SPSS version 26 (IBM Corp., Armonk, NY, USA); chi-square and Fishers exact tests assessed associations (p < 0.05). Participants were predominantly male (84/85, 98.8%), with a mean age of 44.5 {+/-} 10.4 years. Overall knowledge was good (mean 9.40 {+/-} 1.59 out of 11), but attitude and practice scores were average (2.78 {+/-} 0.92 and 3.27 {+/-} 0.93, respectively). Most workers correctly identified goggles and face shields as protective, but only about half recognized that ordinary sunglasses and spectacles offer inadequate protection. Although 97.6% (83/85) recognized the need for ocular protection, only 7.1% (6/85) reported consistent protective eyewear use, and fewer than half (45.9%, 39/85) had received formal ocular safety training. Routine general protective equipment use was significantly associated with ocular protection use (Fishers exact test, p = 0.011). Sand and dust particles were the leading causes of injury and only 25% (5/20) of injured workers sought formal care. Workers demonstrated good knowledge but poor attitudes and practices toward ocular safety, suggesting that knowledge alone does not translate into protective behaviour even within a relatively well-resourced institutional setting. Findings suggest that limited access to task-appropriate protective eyewear may represent an important institutional barrier. Institutional PPE supply and section-specific safety training are essential to bridge this knowledge-practice gap.

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.

The global dissemination of antimicrobial resistance is increasingly driven by bacterial clones combining antimicrobial resistance with enhanced virulence and environmental adaptability. Escherichia coli sequence type 131 (ST131) has historically been regarded as a major disseminator of the extended-spectrum {beta}-lactamase (ESBL) blaCTX-M-15. However, the emergence of E. coli ST1193 carrying blaCTX-M-15 may represent an ongoing shift in the epidemiology of this resistance determinant. Here, we investigated the prevalence, genomic characteristics, virulence and antimicrobial resistance potential of ST1193 in comparison with ST131. A total of 1,136 E. coli isolates were recovered from touristic and non-touristic environments, hospital-associated samples, and aircraft toilets in Guadeloupe. Isolates were whole-genome sequenced and analysed for antimicrobial resistance and virulence determinants. Additionally, publicly available genomic data comprising 1,215 blaCTX-M-15-positive ST131 and ST1193 isolates were analysed to assess temporal and geographical trends. ST1193 was significantly associated with aircraft-associated samples and exhibited a higher antimicrobial resistance gene burden than ST131, while maintaining a comparable virulence factor content. Analysis of publicly available genomes revealed similar temporal emergence patterns for blaCTX-M-15-positive ST1193 and ST131, with ST1193 showing a more recent distribution and a higher number of deposited isolates in recent years, consistent with a potential ongoing clonal replacement. Comparative genomic analysis identified numerous virulence and adaptation-associated genes shared between both sequence types, while ST1193 additionally carried distinct determinants, including components of the transmissible locus of stress tolerance. Furthermore, quinolone resistance-associated mutations were strongly linked to blaCTX-M-15 carriage, particularly among ST1193 isolates. Together, these findings identify E. coli ST1193 as an emerging high-risk clone with substantial potential for blaCTX-M-15 dissemination. Its association with aircraft-associated samples further highlights the potential role of air travel in long-distance transmission and underscores the need to reconsider current surveillance strategies focused predominantly on ST131.

Rationale. Guidelines disagree on antibacterial treatment for adults with community-acquired pneumonia and a positive respiratory viral test, particularly hospitalized patients and outpatients with comorbidities. Objectives. To estimate associations between antibacterial treatment selected for community-acquired pneumonia and outcomes in adults with virus-positive, imaging-evaluated nonsevere pneumonia. Methods. We conducted a retrospective multicenter study using Epic Cosmos data from 2016-2025. Hospitalized patients treated empirically by 24 hours were compared by continuation during hours 24-48; outpatients were compared by prescription at emergency-department discharge. Analyses were stratified by guideline-defined comorbidity and used propensity-score overlap weighting with source-cluster bootstrap confidence intervals. Exploratory analyses assessed respiratory virus, antiviral treatment, antibacterial class, and outpatient timing. Measurements and Main Results. The cohort included 376,320 adults: 275,604 inpatients and 100,716 outpatients. Inpatients who continued treatment had higher 30-day adverse-event risk without guideline comorbidity (adjusted risk difference, 1.70 percentage points; 95% confidence interval, 0.80-2.39) and with guideline comorbidity (2.56; 1.88-3.14), and longer post-landmark stay (adjusted mean ratios, 1.14 and 1.08). Exploratory class-specific analyses showed the largest adverse-event and mortality associations with broad therapy targeting resistant staphylococci or Pseudomonas; macrolide-containing and other atypical coverage showed no consistent adverse signal. Outpatient prescribing was associated with lower risks, but care-transition and residual confounding remained. Conclusions. Continued inpatient therapy after the empiric period showed no evidence of benefit and was associated with worse observed outcomes. Outpatient associations favored prescribing but remained vulnerable to care-transition and residual confounding.

Objectives Emergency department (ED) crowding is recognised as an important public health concern internationally, and is driven principally by exit block, the shortage of inpatient beds for patients requiring admission. This study aimed to evaluate whether a complex intervention targeting hospital occupancy improved ED patient flow, and quantified the change in attendances. Methods A controlled interrupted time series using weekly, publicly reported Public Health Scotland data from 1 January 2022 to 1 February 2026. The multi-component intervention focused on reducing hospital occupancy and included additional adult social care funding; engagement with regional social care providers; accelerated implementation of the Discharge without Delay programme; re-evaluation of whole-hospital escalation thresholds and response; resource and data supporting inpatient department reductions in length of stay; and additional investment in remote clinical assessment. The intervention commenced at a large tertiary ED on 01 February 2025. Primary outcomes were the proportions of attendances spending [&ge;]4, [&ge;]8 and [&ge;]12 hours in the ED. The secondary outcome was attendance volume. Segmented regression was fitted with a contemporaneous control series, seasonal terms and autoregressive moving average errors. Long waits were additionally illustrated as potentially avoided deaths. Results The analysis covered 161 pre-intervention and 52 post-intervention weeks. Relative to pre-intervention levels, the proportion of attendances waiting over 4 hours fell by 10.4% (95% CI 1.6 to 19.2%), by 16.4% (95%CI 1.3 to 31.5%) over 8 hours and by 24.3% (95%CI 2.6 to 46.1%) over 12 hours. Using established associations between long ED waits and excess mortality, by one-year the intervention was potentially associated with 54 fewer excess deaths (95%CI 19 to 93). Attendances rose by 3.8% (95%CI 1.3 to 6.4%) against the counterfactual. Conclusions A complex intervention targeting hospital occupancy was associated with a reduction in long ED waits despite rising attendances. Interventions addressing hospital occupancy can meaningfully improve ED crowding.

Background Severe acute respiratory infections (SARI) strain healthcare systems. Sentinel surveillance remains central to SARI monitoring, but routinely collected hospital discharge data offer a scalable, population-wide complement. In Finland, national registers now enable register-based surveillance, yet SARI case definitions remain unevaluated. Aim To evaluate whether routinely collected electronic health records can support register-based SARI surveillance and establish a national case definition. Methods We conducted a retrospective register-based study linking inpatient discharge data from the Finnish Care Register for Health Care (Hilmo) and laboratory-confirmed pathogen notifications from the National Infectious Diseases Register (NIDR). Admissions were aggregated into hospitalisation episodes using generic and pathogen-specific respiratory ICD-10 codes and linked to laboratory-confirmed respiratory pathogens within an admission-centred window. We assessed the impact of diagnostic coding position, laboratory linkage windows and alternative case definitions on age distribution, seasonality and epidemic trend detection. Results We included 145,435 respiratory hospitalisation episodes. Laboratory confirmations clustered around admission, and a -7-to-+3-day window was selected; 51,498 (35.4%) had a linked laboratory confirmation. Specific primary-position diagnoses preserved clear seasonality and age distributions consistent with SARI epidemiology, whereas secondary-position diagnoses showed attenuated seasonality. A combined case definition incorporating specific primary diagnoses and laboratory-supported syndromic episodes produced stable epidemic curves while improving sensitivity over laboratory confirmation alone. Conclusion National discharge and laboratory registers can support robust SARI surveillance in Finland when case definitions are carefully designed. A combined register-based definition balances specificity, sensitivity and feasibility, complementing sentinel surveillance and integrated respiratory monitoring. Keywords Severe acute respiratory infection (SARI); surveillance; electronic health records; ICD-10; case definition; Finland

Background: While critical care pharmacists (CCPs) are broadly associated with improvements in outcomes for critically ill patients, operationalizing staffing in the intensive care unit (ICU) requires further study. The purpose of this evaluation was to determine the relationship of a CCP on interprofessional rounds for weekday admissions of ICU patients on patient-centered outcomes. Methods: This post-hoc analysis of the Optimizing Pharmacist-Team Integration for ICU Patient Management (OPTIM) study included adults admitted to an ICU on a weekday in the multicenter observational study. The primary outcome was in-hospital mortality. The primary exposure was level of comprehensive medication management (CMM) during the first 24 hours of ICU stay. A secondary exposure was pharmacist-to-patient ratio. Multivariable generalized estimating equations (GEE) were used to estimate associations between mortality and patient, ICU, and institution variables. Fine-Gray sub-distribution hazards regression estimated hazard of discharge alive (HDA) from the ICU and hospital and hazard of extubation alive. Results: 21,835 patients met inclusion criteria, and 76.1% of patients had CMM delivered on interprofessional rounds. Patients who had no CMM on the first ICU day had an increased risk of mortality of 23% (Odds Ratio (OR) 1.23, 95% Confidence Interval (CI) 1.04-1.46, p=0.02) compared to those who received CMM on interprofessional rounds. Patients with no CMM also had decreased HDA from the ICU and hospital and decreased hazard of extubation alive. No difference was seen in any outcomes when comparing other levels of CMM (CMM delivered outside of interprofessional rounds or abbreviated CMM) compared to CMM delivered on rounds. Conclusions: Absence of pharmacist CMM on the first day of ICU stay for patients with weekday admission was associated with an increased risk of in-hospital mortality, but no difference was seen in other levels of CMM: this signal supports further investigation in prospective analysis.

Background: General illness-related sick leave among teachers represents a relevant public health and workforce management issue. However, long-term population-based evidence describing its distribution and associated factors in Latin American urban educational systems remains limited. This study aimed to characterize the occurrence, distribution, duration, and sociodemographic, occupational, temporal, and territorial factors associated with general illness-related sick leave among public school teachers in Bogota between 2010 and 2025. Methods: A retrospective cohort study was conducted using integrated administrative databases from the Bogota District Department of Education. The primary outcome was the occurrence of at least one general illness-related sick leave episode in a teacher-month observation. Descriptive analyses were performed to characterize sociodemographic and occupational patterns. A multivariable logistic regression model was used to estimate associations. Month and year were included as temporal fixed effects to account for seasonal patterns, academic-calendar effects, pandemic-related disruption, and secular changes. Results: The cohort included 59,697 unique teachers, contributing 537,025 teacher-year observations from teachers with an active employment record between January 1, 2010, and July 31, 2025. Overall, 41.59% of teacher-year observations included at least one general illness-related sick leave episode, and 83.26% of teachers had at least one episode at any time during follow-up. Respiratory diseases accounted for the largest share of episodes, followed by musculoskeletal and infectious diseases. Mean duration varied substantially by diagnostic category, ranging from short respiratory and infectious episodes to longer absences related to neoplasms, circulatory diseases, injuries, and mental health conditions. In the multivariable teacher-month model, sick leave occurrence was associated with age, sex, occupational role, teaching area, contract type, locality, calendar month, and calendar year. Lower odds were observed among male teachers, principals, and teachers with provisional contracts, while temporal and territorial variation was observed across months, years, and localities. Conclusions: General illness-related sick leave among public school teachers in Bogota showed consistent sociodemographic, occupational, temporal, and territorial patterns. Respiratory and musculoskeletal conditions accounted for the largest share of episodes, while chronic, neoplastic, injury-related, circulatory, and mental health conditions were associated with longer durations. These findings provide population-level evidence to inform occupational health surveillance, seasonal preparedness, and workforce planning strategies within urban educational systems.

Introduction: Antimicrobial resistance poses a major global health threat, yet evidence on its economic impact in low- and middle-income countries remains limited. This study estimated the economic burden of infections caused by ESBL-producing Escherichia coli (E. coli), a key resistant pathogen, in Laos. Methods: A prospective cost-of-illness study was conducted among patients with laboratory-confirmed infections in Setthathirath hospital in Vientiane, Laos, collecting cost data through repeated interviews and medical records. Descriptive analyses and econometric modeling approaches, including inverse probability weighting (IPW) and instrumental variable (IV) analyses, were used to estimate out-of-pocket expenditures, public expenditures, total cost of illness, and length of stay, accounting for potential confounding. Results: ESBL-producing E. coli was consistently associated with higher economic burden across all analyses. The unadjusted per-patient cost was US$ 689.0 for ESBL-producing E. coli, compared with US$ 489.4 for non-ESBL-producing E. coli and US$ 537.6 for non-E. coli. The association remained statistically significant for out-of-pocket cost after IPW-adjustment (US$156.2; 95% CI, 14.3 to 298.1; P = 0.03), while other outcomes were not statistically significant. Instrumental variable analyses showed consistent directional effects but with wide confidence intervals and no statistically significant differences. Conclusions: Findings suggest that ESBL-producing E. coli may be associated with increased economic burden in Laos; however, this association was not consistently statistically robust across analytical approaches. These findings suggest a potential economic impact of ESBL infection, although uncertainty remains regarding the magnitude of the effect. Strengthening antimicrobial stewardship, infection prevention and control, and improved diagnostic capacity remain essential to mitigate the potential AMR burden.

Wastewater systems are increasingly recognized as important environmental reservoirs of antimicrobial resistance (AMR), acting as interfaces where resistant bacteria, antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) converge and potentially disseminate. Wastewater samples were collected from hospital and community sites, including municipal medical centers, household wastewater outlets, and open drainage systems. Genomic DNA was extracted using the ZymoBIOMICS DNA/RNA Miniprep Kit and sequenced on the Oxford Nanopore Technologies MinION MK1D platform using the Native Barcoding Kit (SQK-NBD114.24, V14). Sequencing data were processed through a custom Snakemake workflow integrating quality control, taxonomic profiling, resistome characterization, mobilome analysis, and genome-resolved metagenomics. A total of 489 unique ARGs conferring resistance to 29 antibiotic classes were identified through metagenomic analysis. The resistome was dominated by genes conferring resistance to {beta}-lactams (including cephalosporins and carbapenems), aminoglycosides, tetracyclines, macrolides, and fluoroquinolones. Clinically important resistance determinants, including blaOXA, blaTEM, blaGES, blaCARB, cfxA, tet, qnr, sul, dfrA, erm, msrE, and aminoglycoside-modifying enzyme genes such as aac(3) and ant(3'') were detected across both hospital and community wastewater samples. Resistance mechanisms were predominantly driven by antibiotic inactivation, followed by efflux and target protection. Several priority bacterial pathogens were detected, including Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Integration/excision elements were the predominant category of MGEs, followed by transfer-associated elements and replication/recombination/repair functions. Plasmid analysis further identified diverse incompatibility groups, predominantly IncP6, IncC, IncF, and IncR replicons, supporting the widespread occurrence of plasmid-mediated horizontal gene transfer in both settings. These findings reveal a substantial burden of clinically relevant ARGs, mobile genetic elements, and potential bacterial pathogens in hospital and community wastewater in Conakry. This study provides the first metagenomic baseline for environmental AMR surveillance in Guinea and highlights the urgent need for integrated One Health strategies to mitigate the environmental dissemination of antimicrobial resistance.

Hospital wastewater (WW) and wastewater biofilms (WWB) are increasingly recognized as important reservoirs of carbapenemase-producing Enterobacterales (CPE), yet their long-term ecological dynamics and relationship with contemporaneous clinical isolates remain poorly understood. Here, we performed longitudinal CPE surveillance of WW and WWB over a 17-month period, combining culture-based screening and comparative whole-genome sequencing of environmental isolates with CPE isolates recovered from patients hospitalized in the same hospital building. A total of 42 environmental and 21 clinical CPE isolates were characterized. Environmental CPE populations underwent a marked ecological shift, with blaOXA-48 -producing Citrobacter spp. progressively replaced by blaVIM-4-producing Serratia nevei. In contrast, clinical isolates remained taxonomically diverse throughout the study period, with a range of betalactamases including blaOXA-48, blaVIM-4, and blaNDM, with no comparable temporal replacement. Comparative genomic analyses revealed a strong association between resistance genes and mobile genetic elements (MGEs), with MGE dynamics largely following those of their hosts. blaOXA-48 was predominantly associated with highly conserved IncL/M plasmid backbones shared across environmental and clinical compartments, whereas blaVIM-4 was consistently embedded within conserved class 1 integron-associated genetic contexts on IncHI2A-rep1088 plasmids. In contrast, blaNDM displayed heterogeneous genomic organizations involving multiple plasmid backgrounds and frequent chromosomal integration. Together, our findings show that bacterial hosts and carbapenemase-carrying genetic elements follow distinct ecological trajectories within hospital WW ecosystems. Integrating longitudinal environmental surveillance with comparative genomics provides new insights into the persistence of clinically important carbapenemases across interconnected environmental and clinical reservoirs.

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.

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.

The global prevalence of Extended-spectrum {beta}-lactamase-producing Enterobacterales (ESBL-E) colonization is increasing. However, it is unclear whether ESBL-E persist and if that is associated with an altered gut microbial ecology especially in early life where the developing microbiome may not provide the same colonization resistance as in adults. In this study, we collected longitudinal infant gut microbiome samples at delivery and in the nonclinical home setting in Chicago, Illinois, U.S.A, aiming to disentangle how genetic factors pertaining to the ESBL-E, as well as the surrounding gut ecology, influences persistence in the infant gut microbiome. We observed not only a higher-than-expected prevalence of ESBL-E in healthy infant gut microbiomes, but also a trend of ESBL-E persistence once colonized. Microbial communities showed higher dissimilarity between ESBL-E positive and negative infant gut microbiome at earlier time points. Although dissimilarity decreased over time, we present evidence that ESBL-E persist even when traditional detection methods are negative.

Objectives: To evaluate the sustainability of Lean Healthcare practices after the implementation phase of a national quality improvement programme and to identify organisational factors associated with maintaining results over time. Design: Multicentre cross-sectional study with a mixed-methods approach. Setting: Twelve public and philanthropic hospitals in Brazil participating in Phase 2 of the Lean in Emergency Departments Project. Participants: Key respondents in managerial or leadership roles from participating hospitals (response rate: 75.0%). Outcome measures: Sustainability of Lean practices and organisational readiness, assessed through a structured survey and triangulated with operational indicators collected across successive implementation cycles at hospital level. Results: During one year of structured follow-up, 66.7% of respondents reported maintenance of Lean practices; this decreased to 33.3% after the end of structured follow-up. Although 66.7% considered professionals capable of maintaining results, only 58.3% positively evaluated institutional structure, indicating a discrepancy between individual capacity and organisational readiness. Operational indicators showed heterogeneous behaviour across hospitals, with no consistent pattern of sustained improvement. Qualitative analysis identified professional and managerial turnover, formal governance structures, and continuous monitoring as key factors associated with sustainability. Conclusions: The sustainability of Lean Healthcare practices is more strongly associated with institutional capacity to embed and sustain changes over time than with isolated individual training. Quality improvement programmes should incorporate structured strategies for the post-implementation phase. Keywords: Lean Healthcare; Sustainability; Quality improvement; Hospital flow; Health systems; Organisational factors

Background: Children spend more than 90% of their time indoors, and early childhood education settings (ECEs) are an understudied, high-occupant-density indoor microenvironment where exposure to volatile organic compounds, particulate matter, and other toxicants has been documented. Limited knowledge exists on ECE-specific exposures affecting young children and how they compare to exposures in the home. Methods: This prospective, repeated-measures pilot study targeted enrollment of 44 preschool-aged children and 8 ECE staff across two geographically and sociodemographically distinct ECEs in metropolitan Atlanta, Georgia. Paired silicone wristbands, one home-designated and one ECE-designated, were exchanged between settings across three consecutive days and nights beginning at enrollment to characterize microenvironment-specific exposure. A single spot urine sample was also collected from each child. Continuous indoor air quality monitoring was conducted in two classrooms per site. Caregivers and ECE staff completed structured questionnaires assessing home and ECE environmental characteristics, child respiratory risk, and protocol feasibility and acceptability. Feasibility was evaluated using eight pre-specified indicators spanning recruitment and enrollment, wristband wear duration and loss by microenvironment, urine sample collection completeness, and survey completion by instrument and respondent group. Conclusion: This pilot will establish feasibility and acceptability parameters for a paired, multi-matrix silicone wristband protocol across home and ECE microenvironments. Findings will inform the design, sample size, and power calculations for a subsequent study testing indoor air interventions and pediatric respiratory outcomes in ECEs. Feasibility outcomes are reported in a companion manuscript.

Background: Refractory and macrolide-resistant Mycoplasma pneumoniae pneumonia (MPP) has emerged as a major challenge in pediatric respiratory medicine, amplified by the post-2023 resurgence. However, a systematic overview of the research landscape specific to treatment-refractory and drugresistant disease in children remains lacking. Methods: Research articles and reviews on pediatric refractory or macrolide-resistant MPP published between 2000 and 2025 were retrieved from OpenAlex using Boolean searches. After screening, 2,286 records were quantitatively analyzed for annual output, contributing countries/institutions, thematic clusters, and citation-burst dynamics using Python. Results: Annual publications grew exponentially, with a pronounced surge after 2023 (n=378 in 2025). China produced the highest volume (45.1%) but recorded fewer citations per publication than the US, Japan, and Canada. The literature resolved into four clusters: macrolide resistance/molecular basis, epidemiology, etiology/co-infection, and refractory disease management. Burst analysis showed an evolution from earlier fronts like 23S rRNA mutations and azithromycin to recent emerging trends like pandemic-related co-circulation, genotype surveillance, and co-infection. Conclusions: Research on pediatric refractory and resistant MPP is expanding rapidly, shifting in emphasis from etiologic descriptions toward resistance mechanisms and clinical management. Standardizing the treatment of macrolide-unresponsive disease and post-pandemic epidemiological surveillance represent the principal directions for future work. Keywords: Mycoplasma pneumoniae; children; macrolide resistance; refractory pneumonia; bibliometric analysis; research trends