Infection Control & Hospital Epidemiology

BackgroundThe hospital environment is increasingly recognized as a critical reservoir for antimicrobial-resistant (AMR) bacteria. In sub-Saharan Africa, maternity wards represent high-risk settings where environmental contamination poses a direct threat to vulnerable mothers and neonates. Despite this, there is a significant lack of data integrating phenotypic resistance with whole-genome sequencing (WGS) to understand antimicrobial resistance (AMR) in these settings. This study characterized the AMR patterns and genomic features of ESBL-producing Escherichia coli and Klebsiella spp. isolated from maternity ward surfaces in Yaounde, Cameroon. MethodsA cross-sectional environmental study was conducted across four maternity wards. Isolates were identified via standard microbiological methods, and antimicrobial susceptibility testing against 13 antibiotics was performed following EUCAST 2024 guidelines. Short-read WGS was utilized to identify sequence types (STs), plasmid incompatibility groups, antibiotic resistance genes (ARGs), and virulence factors. Plasmid-ARG association networks were constructed to visualize resistance dynamics. ResultsNineteen ESBL-producing Enterobacterales were identified, comprising 15 E. coli and four Klebsiella isolates. High levels of multidrug resistance were observed against ciprofloxacin, penicillins, and third-generation cephalosporins. While the isolates remained sensitive to colistin and imipenem, alarming resistance to meropenem was detected. Genomic analysis revealed the presence of globally disseminated high-risk lineages, including E. coli ST131, ST1193, and ST410, alongside Klebsiella ST1324 and ST489. Critical resistance determinants, including ESBLs, AmpC enzymes, and carbapenemases (NDM and OXA-48-like), are frequently associated with epidemic plasmids such as IncF, IncA/C2, and IncL/M. Additionally, the isolates harboured virulence factors characteristic of extraintestinal pathogenic Enterobacterales. ConclusionsThe widespread presence of high-risk carbapenemase-producing clones on maternity ward surfaces identifies the hospital environment as a significant AMR reservoir in Yaounde. These findings highlight the urgent need for reinforced infection prevention and control (IPC) measures, robust antimicrobial stewardship, and the integration of genomic surveillance to safeguard highly susceptible maternal and neonatal populations from life-threatening infections.

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.

Conventional air filtration relies on passive mechanical capture without pathogen inactivation, where viral reduction must be balanced with airflow and energy performance. We developed an Ablative Polymer Coated (APC) filtration system that converts passive filters into active pathogen-reducing surfaces while maintaining low airflow resistance. Unlike conventional approaches requiring denser, higher-resistance media, this strategy enhances biological performance at the filter surface without equivalent aerodynamic penalties. The coating incorporates benzalkonium chloride within a polyvinyl acetate/acrylate matrix for controlled ablative exposure. Performance was evaluated using transmission electron microscopy (TEM), aerosol challenge testing, and HVAC-scale filtration. Ablative exposure caused progressive structural disruption of MS2 bacteriophage, the SARS-CoV-2 simulant. In aerosol challenge testing, coated media achieved up to 99.997% viral filtration efficiency under respiratory airflow conditions. In HVAC (Heating, Ventilation, and Air Conditioning)-scale testing, coated filters achieved >85% viral filtration efficiency with minimal pressure-drop increase. Computational fluid dynamics modeling confirmed uniform airflow distribution without significant turbulence generation. Energy analysis suggested coated filters may reduce energy demand relative to conventional higher-resistance configurations while improving biological performance. These findings support ablative polymer-coated media as a strategy for reducing airborne viral burden without aerodynamic penalties of higher-efficiency passive filtration, suggesting an approach that complements rather than depends solely on tighter filter design.

This study aimed to clarify aerosol exposure risks throughout the workflow of a Biosafety Level 2 (BSL-2) polymerase chain reaction (PCR) laboratory, validate the suitability of the {Phi}X174 bacteriophage as an indicator virus, and provide evidence for biosafety control measures. The {Phi}X174 bacteriophage was used to simulate viral samples, and a concentration-bacteriophage plaque standard curve was constructed (R2=0.998). Five operational steps in a simulated PCR laboratory were quantitatively monitored for aerosol concentration using double-layer agar plates, with blank controls used to eliminate interference. Statistical analysis was employed to identify risk differences. Sample homogenization ((5.67 {+/-} 1.23) x 104 plaque-forming units (PFU)/m3) and nucleic acid extraction ((3.45 {+/-} 0.89) x 104 PFU/m3) were identified as high-/very high-risk steps. The viral load in the samples was strongly positively correlated with the aerosol concentration (r = 0.926, P <0.001), with aerosol levels linearly decreasing with increasing distance in high-risk steps. The {Phi}X174 bacteriophage demonstrated high detection sensitivity (101 PFU/ml) and demonstrated safety compatibility with BSL-2 laboratories. Aerosol risks in PCR laboratories exhibit step-specific differentiation, and {Phi}X174 serves as an ideal indicator virus. Proposed strategies such as equipment upgrades and personal protective equipment (PPE) grading can reduce exposure risks.

BackgroundIn long-term care facilities (LTCFs), close-contact identification often relies on staff recall and monitoring records because residents may be unable to self-report reliably. How these different record-generation processes relate to proximity-based sensor measurements in routine LTCF workflow remain unclear, and how such differences may influence contact-based decision-making in outbreak response is not well understood. MethodsWe conducted a five-day observational study in a Japanese LTCF using ultra-wideband (UWB) indoor positioning. Twenty-seven participants wore UWB tags, including 16 residents and 11 staff members; 10 staff members completed questionnaires. We compared UWB-derived proximity with questionnaire-derived contacts from staff self-report and monitoring-based proxy records, and assessed directional discrepancies under multiple distance-time thresholds. ResultsQuestionnaire-based records and UWB-derived proximity showed different patterns of discrepancy across contact types. Within this facility, resident-related monitoring-based proxy records showed relatively small directional discrepancies, whereas staff self-reports tended to identify additional resident-staff contacts under the baseline threshold ([&le;]1.0 m for [&ge;]15 min). Several alternative thresholds were associated with discrepancies closer to zero than the baseline, although the apparent ranking varied by summary metric. ConclusionsIn this single-facility observational study, different contact-list generation processes were associated with different patterns of discrepancy relative to a proximity-based operational measure. These findings support interpretation in terms of workflow-specific contact-list generation rather than a single universally optimal threshold and may help inform facility-level review of contact identification practices in LTCFs. These findings support aligning contact identification strategies with facility-specific workflows to improve the feasibility and effectiveness of IPC practices in LTCFs.

ObjectiveLeukemic and hematopoietic cell transplant patients have one of the highest incidences of C. difficile infection (CDI). While CDI patients are considered the primary source of transmission, asymptomatic colonized patients (AC) can progress to CDI or contribute to in-unit transmission. We aim to quantify the roles of CDI and AC patients in C. difficile importation and transmission within oncological units. DesignProspective cohort study SettingTwo leukemia and HCT transplant units in a large tertiary care hospital in the US MethodsWe developed a stochastic, individual-based network model to simulate C. difficile acquisition and transmission. Data from cultures and nucleic acid amplification testing (NAAT) obtained at admission and weekly, and toxin enzyme immunoassay (EIA) tests used for CDI diagnosis were used to calibrate the model. Healthcare worker room assignments informed the network structure. Key parameters were estimated via particle filtering. ResultsThe model reproduced observed weekly test counts and transmission pairs. AC patients were the primary source of new colonizations: 51% were due to importation (of those, 88% were admitted as AC), and 49% were due to transmission (AC was the source in 92% of transmissions). Sensitivity analysis showed that these findings were most influenced by the colonization rate and rates of environmental contamination and cleaning. ConclusionsThese findings reinforce the role of AC, particularly via admission importation, in sustaining C. difficile transmission in high-risk hospital settings. Infection control focused on CDI effectively reduced onward transmission, as indicated by CDIs low contribution to new colonizations.

BackgroundMicroplastics and nanoplastics (MNP) are an increasingly recognized component of airborne particulate matter, yet their impact on respiratory health is unclear. This study aimed to develop a job exposure matrix (JEM) for occupational exposure to airborne MNP (PlastiXJEM(R)) and examine its association with respiratory outcomes in the Lifelines cohort. MethodsFour experts scored occupational airborne MNP exposure levels (none, low, high) for all ISCO-08 occupations based on documented sources and published evidence. After consensus, the PlastiXJEM(R) was applied to baseline current or last-held jobs of 136,928 adult Lifelines participants. Cross-sectional and longitudinal associations with lung function, respiratory symptoms, and asthma were assessed using linear and logistic regression models adjusted for age, sex, smoking, height, BMI, and co-exposure to organic dust, gasses and fumes, pesticides, metals, solvents and silica. ResultsHigh exposure was associated with lower FEV (-43 ml; 95% CI:-61;-25), lower FVC (-47 ml(-69;-26)), lower FEV1%FVC (-0.26 % (-0.51;-0.00) and higher odds of airway obstruction, respiratory symptoms and asthma (e.g. dyspnea OR=1.58; 1.34-1.87). Low exposure was associated with lower FEV1 and FVC in women only. Associations were attenuated after adjustment for socio-economic status but remained for FEV, airway obstruction and dyspnea. MNP exposure was not associated with accelerated lung function decline or with the development of airway obstruction, respiratory symptoms, or asthma. ConclusionOccupational exposure to airborne MNP is associated with lower lung function and a higher prevalence of respiratory symptoms in this cohort. These findings warrant further investigation with complete occupational histories.

Background: Conjugative plasmids encoding New Delhi metallo-beta-lactamase (blaNDM) pose a threat for the spread of carbapenem resistance among healthcare acquired pathogens. Plasmid-associated outbreaks of blaNDM-producing bacteria can involve multiple bacterial species and persist over long time periods, making their detection and control difficult. We systematically studied the genomic epidemiology of blaNDM-encoding plasmids detected within a single hospital system over a five-year period. Methods: blaNDM-producing isolates were collected from clinical cultures as part of the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT) genomic sequencing active surveillance program, or during infection prevention and control (IP&C) investigations. Isolates were identified as blaNDM producers by polymerase chain reaction (PCR); the presence of plasmid-encoded blaNDM genes was confirmed by sequencing on both Illumina and Oxford Nanopore platforms. Plasmids were clustered using Pling and bacterial relatedness of host isolates was evaluated with split kmer analysis. Electronic health record data were used to identify shared unit-level spatiotemporal exposures and epidemiologic links within both plasmid and host clusters. Results: We identified 61 blaNDM-producing isolates collected from 54 patients sampled between November 2020 and July 2025. Isolates belonged to 15 Enterobacterales species; Enterobacter hormaechei was the most frequently sampled species (n=23, 37%), and blaNDM-5 was the most frequently observed blaNDM allele (n=36, 59%). We observed six clusters of genetically similar blaNDM-encoding plasmids each containing 2-28 isolates, and eight singleton plasmids. The two largest plasmid clusters consisted of a highly conserved 46 kb IncX3 family blaNDM-5-encoding plasmid (n=28 plasmids, 9 species) and a more variable 98-201 kb IncC family blaNDM-1-encoding plasmid (n=12 plasmids, 6 species). Epidemiologic investigation paired with whole genome sequencing identified spatiotemporal associations between shared patient exposures and putative plasmid and bacterial transmission clusters, suggesting that unit-level exposures contribute to plasmid dissemination. Finally, analysis of publicly available sequences showed that the most prevalent plasmids detected, IncX3(blaNDM-5) and IncC(blaNDM-1), also demonstrated high global prevalence. Conclusions: This study demonstrates the diversity of blaNDM carrying plasmids within a single hospital system and their capacity to cause prolonged, multispecies outbreaks. Integrating whole genome sequencing with epidemiologic data identified unit-level spatiotemporal overlap as a likely contributor to plasmid dissemination in the hospital.

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.

To understand the utility of healthcare facility-level wastewater surveillance (WWS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is important to correlate wastewater SARS-CoV-2 RNA detection with the number of clinical infections. WWS for SARS-CoV-2 was performed at three skilled nursing facilities (SNFs) over 25 weeks. Electronegative membrane filtration (enMF) and Nanotrap(R) Magnetic Virus Particles (NP) virus concentration methods were compared. Extracts were tested by droplet digital polymerase chain reaction. Spearman's correlations ({rho}) between wastewater virus RNA concentrations and infection counts were calculated. From split wastewater samples, enMF recovered higher SARS-CoV-2 RNA concentrations than NP. Combining data from all facilities, the median concentrations were 53.0 versus 38.6 gc/100 mL for enMF and NP, respectively (p=0.001). Using enMF, correlations were moderate to strong at SNF A ({rho} ranged 0.67 to 0.86, all p-values <0.001). Weak to moderate correlations can be explained by the sampled manhole not representing the entire facility (SNF B, {rho} ranged 0.47 to 0.72, p-values ranged <0.001 to 0.12) and longitudinal data gaps from summer heat and equipment maintenance (SNF C, {rho} ranged 0.14 to 0.59, p-values ranged 0.52 to <0.01). WWS can be a valuable tool for tracking dynamics of SARS-CoV-2 infections in healthcare facilities.

ObjectivesRising temperatures are a major climate-related hazard for U.S. workers, increasing heat-related illness and a broad range of occupational injuries through indirect pathways often overlooked in economic evaluations. We examined the association between temperature and occupational injury and illness and quantified heat-attributable injuries (including illnesses) and costs in New York State. MethodsWe conducted a time-stratified case-crossover study of 591,257 workers compensation (WC) claims during the warm season (2016-2024). Daily maximum temperature was linked to injury date and county and modeled using natural cubic splines, with effect modification by industry and worker characteristics. ResultsInjury risk increased with temperature, becoming statistically significant at approximately 78{degrees}F. Relative to 65{degrees}F, injury odds increased to 1.06 (95% CI: 1.01-1.10) at 80{degrees}F, 1.12 (1.07-1.18) at 90{degrees}F, and 1.17 (1.11-1.23) at 95{degrees}F. Overall, 5.0% of claims (2,322 annually) were attributable to heat. At temperatures [&ge;]80{degrees}F, an estimated 1,729 excess injuries occurred annually, generating approximately $46 million in WC costs. An estimated $3.2 million to $36.1 million in medical expenditures were associated with incomplete claims, likely borne outside the WC system. ConclusionsThese findings demonstrate substantial economic costs not fully captured within WC and support workplace heat protections as a cost-containment strategy that can reduce health care spending and strengthen workforce resilience.

BackgroundLivestock production systems in peri-urban areas are associated with high levels of interaction between humans, animals, and the environment, which may contribute to the dissemination of antimicrobial resistant bacteria. However, genomic characterization of resistant bacteria in the interconnected systems of humans, animals, and the environment in low- and middle-income countries like Cameroon is very limited. MethodsThis study was undertaken to investigate the ESBL-producing E. coli and K. pneumoniae in the peri-urban pig production systems in Yaounde, Cameroon, through the application of the One Health genomic approach. A total of 338 samples were collected from humans, pigs, and the environment. Enterobacterales were isolated using standard microbiological procedures, followed by antimicrobial susceptibility testing of the isolated bacteria using the Kirby-Bauer disk diffusion method based on the EUCAST breakpoints. Ten multidrug-resistant Enterobacterales with similar resistance profiles were sequenced to identify their sequence types, resistance determinants, plasmid replicons, and virulence determinants. ResultsEnterobacterales were found in 187 samples, comprising 38 human, 98 pig, and 51 environmental samples. E. coli (166 isolates) was the most prevalent species, followed by K. pneumoniae (100 isolates). Whole-genome sequencing revealed eight E. coli and two K. quasipneumoniae isolates from human, pig, wastewater, and farm environmental samples. The E. coli isolates represented seven sequence types, including the globally successful ST410 lineage. Notably, E. coli ST3580 was found in human and environmental samples from the Afanoyoa farm in different sampling months, while K. quasipneumoniae ST1535 was found in human and pig samples from the Etoudi farm in different months. All genomes encoded ESBL genes, with blaCTX-M-15 being the most prevalent, accompanied by other resistance genes to various antibiotic classes and several plasmid incompatibility groups. ConclusionsThese results show the circulation of genetically diverse ESBL-producing E. coli and K. pneumoniae in human, animal, and environmental reservoirs in peri-urban pig farming systems and the potential for cross-reservoir persistence of particular lineages. Improved One Health antimicrobial resistance surveillance and stewardship are critical to address antimicrobial resistance in rapidly urbanizing environments.

BackgroundPseudomonas aeruginosa is a major cause of healthcare-associated infections in paediatric settings, where its persistence in moist environments such as hospital water and wastewater systems poses a particular risk to neonates and immunocompromised children. AimThe aim of this study was to showcase the long-term survival and transmission of P. aeruginosa in a large tertiary childrens hospital in England which is crucial to develop strategies for water-safe care. MethodsEnvironmental P. aeruginosa isolates were collected from taps, sinks, showers, and baths in augmented care areas of a 330-bed tertiary childrens hospital built to NHS water-safety standards. Clinical isolates were classified as invasive (blood, cerebrospinal fluid, and bronchoalveolar lavage) or non-invasive (respiratory, urine, ear, abdominal, and rectal surveillance). Variable number tandem repeat (VNTR) profiles and metadata were extracted from PDF reports, de-identified, deduplicated, and curated using Python and R. FindingsThis retrospective study analysed nine-locus VNTR profiles of 457 P. aeruginosa isolates submitted to the UK Health Security Agency from a large tertiary childrens hospital, identifying 56 isolate clusters (each with [&ge;]2 isolates), of which 19 (34%) contained at least one invasive isolate. The most persistent cluster (Cluster 1, n=20) spanned from July 2016 to September 2024, containing environmental and clinical (invasive and non-invasive) isolates. ConclusionThese findings demonstrate long-term persistence of certain genotypes and temporal overlap between environmental and clinical isolates, highlighting the difficulty in detecting and eradicating P. aeruginosa in hospital water and wastewater systems and reinforcing the need for continuous rigorous water system controls.

Wastewater genomic surveillance provides an opportunity to detect human and animal influenza A virus (IAV). We aimed to implement an IAV genomic surveillance framework agnostic to subtype, which enables recovery of IAV from multiple hosts and estimation of proportions across subtypes. We conducted IAV genomic surveillance in wastewater during the 2024-2025 flu season at multiple sites in California and compared these data with available human clinical IAV sequences and test positivity. We applied a custom whole-genome, multi-host IAV probe enrichment panel and adapted our custom expectation-maximization (EM) algorithm to deconvolute IAV mixtures in wastewater and infer subtype relative abundances. Absolute IAV concentrations were quantified using RT-PCR-based assays. H5N1 wastewater and clinical sequences were further characterized by constructing a whole-genome maximum-likelihood phylogenetic tree. Finally, we performed variant analysis to examine amino acid substitutions detected in wastewater. Our IAV probe enrichment method and EM algorithm successfully enriched all eight segments of three circulating IAV subtypes and accurately estimated subclade relative abundances for mixed IAV samples. Seasonal human H1N1pdm09 and H3N2 were detected throughout the study period from both wastewater and clinical sequencing data, with H1N1 subclades 6B.1A.5a.2a.1 and 6B.1A.5a.2a co-circulating, and H3N2 dominated by subclade 3C.2a1b.2a.2a.3a.1. Wastewater surveillance consistently detected H5N1 clade 2.3.4.4b across three monitored wastewater sites, while clinical H5N1 detections, from anywhere in CA, were sporadic and rare. Whole-genome phylogenetic analysis revealed that wastewater H5N1 sequences clustered with reference sequences associated with dairy cow and avian infections, while all human clinical H5N1 sequences clustered exclusively with reference sequences associated with dairy cow infections. Amino acid substitutions were identified across viral segments, and no mutations associated with mammalian adaptation were observed from wastewater samples.

BackgroundAn upsurge in Streptococcus pyogenes infections 2022-2023 highlighted potential benefits of point-of-care tests (POCT) to support clinical pathways, prevent outbreaks, and optimise antibiotic use. ObjectivesWe conducted a pilot research study in a west London paediatric emergency department (ED) to determine whether a molecular POCT had potential to alter management in children who were also having a conventional throat swab taken for culture. MethodsChildren <16 years presenting to ED who had a throat swab requested by a clinician were invited to have a second swab taken for research purposes only. Clinical management was unaffected by the research swab result, which was processed using a molecular POCT that was not approved for use in the host NHS Trust. ResultsPrevalence of streptococcal infection was low during the study (May 2023-June 2025); swab positivity in symptomatic children was 12.8% (6/47). Overall, 38/49 (77.6%) participants who had throat swabs received antibiotics. Of those children recommended to receive antibiotics, 29/38 (76.3%) had a negative POCT. Mean time to reporting of positive throat swab culture results was 3.67 days (range 3-5 days) leading to occasional delay in treatment, although POCT identified positive results within minutes. ConclusionAntibiotic use was frequent and could be avoided or stopped by use of a rule out POCT in over three-quarters of children in the ED, if suspicion of S. pyogenes is the main driver for prescribing. POCT were easy to process and produced immediate results compared with culture, in theory enabling timely decision-making and avoiding treatment delay.

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.

BackgroundThe rise of antimicrobial resistance (AMR) in the Lake Chad Basin poses a significant threat to global health. While Escherichia coli and Klebsiella pneumoniae are primary concerns for the WHO, Proteus species have emerged as important clinical pathogens and potential reservoirs for genetic resistance. This study aimed to analyze the molecular diversity and horizontal gene transfer (HGT) potential of ESBL-producing Proteus species in the region. MethodsA regional surveillance was conducted with 1,500 clinical samples from Borno, Adamawa, Bauchi, Gombe, Taraba, and Yobe states. Proteus isolates were identified biochemically, and antibiotic susceptibility was assessed using the Kirby-Bauer method. Resistance genes (blaTEM, blaSHV, blaCTX-M) were identified via PCR, and HGT was evaluated through conjugation assays. ResultsA total of 144 Proteus isolates were identified, with a prevalence of 9.6%. P. mirabilis was the dominant species (90.97%). Phenotypic screening indicated that 69.44% produced extended-spectrum beta-lactamases (ESBL), with high resistance rates observed for Cefotaxime (80.56%) and Ampicillin (84.72%). Alarmingly, resistance to Ertapenem reached 54.86%. Molecular analysis showed blaTEM as the predominant gene (81.69%), and the conjugation assay revealed a high HGT rate of 76.92%, confirming blaTEM acquisition by E. coli. ConclusionThese results indicate that Proteus species in North-Eastern Nigeria are significant reservoirs for genetic resistance, facilitating the spread of ESBL markers. The high frequency of HGT raises concerns about the effectiveness of beta-lactam therapies in sub-Saharan Africa, underscoring the need to include Proteus in the GLASS framework and promote regional antimicrobial stewardship efforts. Current UnderstandingAntimicrobial resistance (AMR) in Enterobacteriaceae, particularly with Escherichia coli and Klebsiella pneumoniae, is a significant global issue highlighted by the World Health Organizations Global Antimicrobial Resistance and Use Surveillance System (WHO GLASS). While Proteus species are recognized as opportunistic pathogens, their role as genetic reservoirs in sub-Saharan Africa, especially in the Lake Chad Basin, remains inadequately defined in surveillance data. Study ContributionThis study identifies Proteus species as a critical "Genetic Hub" for the transmission of extended-spectrum beta-lactamases (ESBL) in North-Eastern Nigeria, revealing a high horizontal gene transfer (HGT) rate of 76.92% for the blaTEM genotype to E. coli. It also shows a concerning 54.86% resistance rate to Ertapenem, underscoring the urgent need to include Proteus in regional stewardship and global surveillance efforts.

2.Streptococcus pneumoniae is the leading cause of empyema and pneumonia in children, and monitoring of effectiveness of polyvalent pneumococcal vaccines has been essential for controlling invasive pneumococcal disease (IPD) in children and elderly adults. Conventional serotyping of pneumococci has relied on Quellung reaction following laboratory culture, however more recently whole genome sequencing (WGS) has been implemented in many reference laboratories to enhance traditional typing. Pleural fluid samples from cases with empyema are often culture negative, limiting the utility of WGS and requiring polymerase chain reaction (PCR) or 16S rRNA sequencing to detect S. pneumoniae. These molecular methods have limited sensitivity and capacity to characterise pneumococcus in clinical samples, especially in specimens with a low pathogen abundance. This study applied capture-based enrichment (tNGS) to identify and characterise S. pneumoniae directly from pleural fluid samples. A total of 51 pleural fluid samples were subjected to tNGS with a custom probe panel, for 39 known positive fluids collected from IPD cases between 2018-2025 in New South Wales, Australia. tNGS results were benchmarked against molecular-based serotyping. Our tNGS achieved 100% sensitivity and specificity in detecting S. pneumoniae. Serotyping results were concordant with PCR and 95% (37/39) of S. pneumoniae PCR positive pleural fluid cases could be serotyped using tNGS. Standard molecular methods however could only determine serotype in 56% (22/39) of samples. This tNGS enabled 39% improvement in ability to directly identify and serotype IPD-associated serotypes of S. pneumoniae in difficult-to-culture pleural fluids can significantly enhance laboratory surveillance of IPD as well as our understanding of vaccine effectiveness. 3. Impact statementThere is currently a gap in understanding the pneumococcus serotype diversity causing infection within the pleural fluid space. The gold-standard Quellung method to determine serotype relies on culturing the pneumococci first. However, pleural fluids often remain culture-negative, and cases of pneumococcal empyema have been a historical blind spot in pneumococcal surveillance. This study offers a new methodology to close this gap and allow serotyping of previously untypable cases. The study demonstrated a targeted next generation sequencing (tNGS) approach to determine serotype without the need to first culture the bacteria. This novel use of tNGS targets part of the cps gene cluster, which determines serotype. To the best of our knowledge this is the first panel to do so. We have successfully serotyped 95% of pleural fluid S.pneumoniae PCR positive samples, where previously only 56% could be determined using conventional PCR typing methods. This demonstrates for the first time a novel tNGS method capable of determining the full serotype landscape causing pleural fluid infection. This development will enhance the understanding of vaccine effectiveness and contribute to the prevention of invasive pneumococcal disease. 4. Data summarySupplementary data containing reference cpsB genomes are available within this article. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. 1.5 RepositoriesENA project accession number PRJEB111154. All supporting data has been provided within the article or in supplementary data files. One supplementary data file is available with the online version of this article.

BackgroundIn the United States (US), several intravenous (IV) iron products are available for treatment of iron deficiency, including low-molecular-weight iron dextran (LMWID), iron sucrose (IS), ferumoxytol (FM), ferric carboxymaltose (FCM), ferric derisomaltose (FD), and sodium ferric gluconate (FG). However, these IV iron products are associated with rare, but serious, hypersensitivity and anaphylactic reactions. ObjectiveThis study aimed to assess the frequencies of hypersensitivity and anaphylactic reactions and associated downstream medical costs of the six IV iron products in the US. MethodsThis study used data from the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) from January 1, 2014, to June 30, 2024. The lower bound of the 90% confidence interval of the reporting odds ratio (ROR05) was used to identify a likely drug-adverse event (AE) association related to hypersensitivity and anaphylactic reactions. Downstream medical costs were estimated using Agency for Healthcare Research and Quality/Healthcare Cost and Utilization Project data. ResultsSignal strength of a likely drug-AE association for hypersensitivity was highest with FG (ROR05=9.66) and lowest with FCM (2.87). Signal strength for anaphylactic reactions was highest with FM (43.59) and lowest with FCM (6.99). The medical cost per AE was lowest with FCM (US$2,348) and highest with LMWID ($9,593). ConclusionFCM had the lowest signal strength of a likely drug-AE association for hypersensitivity and anaphylaxis and the lowest medical cost per AE in the US patient population, demonstrating its potential value by improving patient safety while lowering overall medical spending. Plain Language SummaryThis study has found that ferric carboxymaltose (FCM) had the lowest signal strength of a likely drug-adverse event (AE) association for hypersensitivity and anaphylaxis, compared to other intravenous iron products. FCM also had the lowest downstream medical cost per AE in the US patient population. These findings suggest that FCM may provide value by improving patient safety while reducing overall medical spending in the real-world setting.

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.