Burden Of Antimicrobial Resistance Research Articles

Antimicrobial resistance in <em>Staphylococcus aureus</em>, Enterobacterales, and <em>Pseudomonas</em> spp. clinical isolates at a Teaching Hospital in Sri Lanka

Background: Antimicrobial resistance (AMR) is a signifi-cant global health issue in the 21st century, posing a serious threat to human health.Objectives: This study was to determine the burden and predictors of AMR and multidrug resistance (MDR) among bacterial pathogens isolated from specimens submitted to the diagnostic laboratory of a hospital in Sri Lanka.Methodology: This retrospective study used laboratory records of 1,204 clinical specimens submitted for bacterial culture submitted to the diagnostic laboratory of Neville Fernando Teaching Hospital in Sri Lanka for bacterial culture and sensitivity testing between October 2021 and May 2024. Records from specimens positive for Enterobacteriaceae, Staphylococcus aureus, or Pseudomonas spp. isolates were included for analysis.Results: Number of samples which yielded Gram negative Enterobacterales was 758 (62.95%). Of these 499 (65.83%) were ESBL and 59 (7.78%) were carba-penemase producers. Among the 214 participants, Staphylococcus aureus was isolated from 206 (96.26%) participants. This included 74 (35.92%) participants who were colonized with Methicillin Resistant Staphylococcus aureus (MRSA) isolates and Methicillin Sensitive Staphylococcus aureus (MSSA) 132 (64.07%). Among Pseudomonas spp. isolates, 29.48% were resistant to one or more aminoglycosides, 29.48% were resistant to a fluoroquinolone and only 8.54% were resistant to carbapenems.Conclusion: This study shows that there is a high level of microbial resistance in Sri Lanka. The high levels of extended-spectrum cephalosporin resistance and multi-drug resistance (MDR) among Enterobacterales observed in this study are of concern. However, the relatively low levels of methicillin-resistant Staphylococcus aureus (MRSA) and MDR S. aureus, as well as the very low levels of carbapenem resistance among Pseudomonas spp. isolates, are encouraging.

Comparative assessment of microbiome and resistome of influent and effluent of sewage treatment plant and common effluent treatment plant located in Delhi, India using shotgun approach

Antimicrobial resistance (AMR) is a significant threat that demands surveillance to identify and analyze trends of the emerging antibiotic resistance genes (ARGs) and potential microbial carriers. The influent of the wastewater treatment plants (WWTPs) reflects the microbes derived from the population and effluent being the source of dissemination of potential pathogenic microbes and AMR. The present study aimed to monitor microbial communities and antibiotic resistance genes in WWTPs employing a whole metagenome shotgun sequencing approach. The samples were collected from a sewage treatment plant (STP) and a common effluent treatment plant (CETP) in Delhi, India. The results showed the influent of STP to be rich in Bifidobacterium, Bacteroides, Escherichia, Arcobacter, and Pseudomonas residents of gut microbiota and known to cause diseases in humans and animals; whereas the CETP sample was abundant in Aeromonas, Escherichia, and Shewanella known to be involved in the degradation of different compounds. Interestingly, the effluent samples from both STPs and CETP were rich in microbial diversity, comprising organic and xenobiotic compound degrading and disease-causing bacteria, indicating the effluent being the source of dissemination of concerning bacteria to the environment. The functional profile at both sites displayed similarity with an abundance of housekeeping function genes as analyzed by Clusters of Orthologous Genes (COG), KEGG Orthology (KO), and subsystem databases. Resistome profiling by MEGARes showed the dominance of ARGs corresponding to beta-lactams having relative abundance ranging from 16% to 34% in all the metagenome datasets, followed by tetracycline (8%–16%), aminoglycosides (7%–9%), multi-drug (5%–9%), and rifampin (3%–9%). Also, AMR genes oxa, ant3-DPRIME, and rpoB, which are of clinical importance were predominantly and most prevalently present in all the samples. The presence of AMR in effluents from both types of treatment plants indicates that wastewater from both sources contributes to the spread of pathogenic bacteria and resistance genes, increasing the environmental AMR burden and therefore requires tertiary treatment before discharge. This work will facilitate further research towards the identification of suitable biomarkers for monitoring antibiotic resistance.

Antimicrobial resistance burden in India and Germany in 2022: A systematic analysis along with One Health perspective

Globally increasing antibiotic resistance has been linked to the extensive use of antibiotics in medical, veterinary, and agricultural Practices. This study aims to investigate the correlations of antimicrobial-resistant of various pathogens in three compartments: humans, animals and the environment in India and Germany. A systematic search was carried out in Medline via PubMed, Google Scholar, and science direct, including studies published in 2022. Out of 532 papers, 24 were considered for meta-analysis. Our findings reveals that in India, β-lactam is highly resistant in animals. Quinolone, on the other hand, was highly resistant in humans. In the environmental sectors, aminoglycosides and β-lactams is resistant. While in Germany, β-lactam resistance is high across all three sectors. However, E. coli was the most frequent and resistant pathogen in both countries, with significant resistance to β-lactams and cephalosporins across all compartments. These results underscore the critical need for monitoring antibiotic resistance patterns and developing targeted antibiotic regimens. A One Health-based intervention strategy is essential to mitigate the spread of AMR and improve health outcomes globally.

Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations

Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.

Systematic Review and Meta-analysis on Antimicrobial Resistance and Drug Resistance in Saudi Arabia

This meta-analysis of 25 studies reveals that antimicrobial resistance (AMR) is a substantial problem in Saudi Arabia. The incidence rates for MRSA, Enterobacteriaceae that produce ESBLs, Enterobacteriaceae that are carbapenems resistant, Pseudomonas aeruginosa, and Acinetobacter baumannii were shown to have high levels of resistance. The rates for such bacteria were 38.7%, 26.4%, and 15.2% respectively suggesting an imminent need for improvement in surveillance measures & interventions to reduce the burden of AMR (Antimicrobial Resistance). In this regard, effective infection control programs with targeted or global policies must be implemented simultaneously while promoting antibiotic stewardship every single time preserving its efficacy efficiently alongside it. Additionally associated risk factors including prior usage of antibiotic medicines, prolonged hospital stays plus healthcare related infections increased the detection rate further highlighting this pressing concern which needs immediate attention from authorities concerned.Forest plots had been created through research data collected using appropriate statistical procedures showing confidence intervals (CIs). The conclusion suggests implementation of better policies/control proposals focusing on attainable objectives can put forth countermeasures geared towards diminishing AMR ensuring timely adequate treatments are being administered without underlying potential risks posed by resistant microbes while preserving existing viability of antibiotics properly.

Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population

Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population

Antimicrobial use, residues and resistance in fish production in Africa: systematic review and meta-analysis

In low- and middle-income countries, data on antimicrobial use (AMU) and antimicrobial resistance (AMR) in aquaculture are scarce. Therefore, summarizing documented data on AMU, antimicrobial residue (AR), and AMR in aquaculture in Africa is key to understanding the risk to public health. Google Scholar, PubMed, African Journals online, and Medline were searched for articles published in English and French following the PRISMA guidelines. A structured search string was used with strict inclusion and exclusion criteria to retrieve and screen the articles. The pooled prevalence and 95% confidence intervals were calculated for each pathogen–antimicrobial pair using random effects models. Among the 113 full-text articles reviewed, 41 met the eligibility criteria. The majority of the articles reported AMR (35; 85.4%), while a few were on AMU (3; 7.3%) and AR (3; 7.3%) in fish. The articles originated from West Africa (23; 56.1%), North Africa (8; 19.7%), and East Africa (7; 17.1%). Concerning the antimicrobial agents used in fish farming, tetracycline was the most common antimicrobial class used, which justified the high prevalence of residues (up to 56.7%) observed in fish. For AMR, a total of 69 antimicrobial agents were tested against 24 types of bacteria isolated. Bacteria were resistant to all classes of antimicrobial agents and exhibited high levels of multidrug resistance. Escherichia coli, Salmonella spp., and Staphylococcus spp. were reported in 16, 10, and 8 studies, respectively, with multidrug resistance rates of 43.1% [95% CI (32.0–55.0)], 40.3% [95% CI (24.1–58.1)] and 31.3% [95% CI (17.5–49.4)], respectively. This review highlights the high multidrug resistance rate of bacteria from aquaculture to commonly used antimicrobial agents, such as tetracycline, ampicillin, cotrimoxazole, gentamicin, and amoxicillin, in Africa. These findings also highlighted the lack of data on AMU and residue in the aquaculture sector, and additional efforts should be made to fill these gaps and mitigate the burden of AMR on public health in Africa.

Healthcare-associated infections and antimicrobial resistance in Canadian acute care hospitals, 2018-2022.

Healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) continue to contribute to excess morbidity and mortality among Canadians. This report describes epidemiologic and laboratory characteristics and trends of HAIs and AMR from 2018 to 2022 (Candida auris, 2012-2022) using surveillance and laboratory data submitted by hospitals to the Canadian Nosocomial Infection Surveillance Program (CNISP) and by provincial and territorial laboratories to the National Microbiology Laboratory. Data collected from 88 Canadian sentinel acute care hospitals between January 1, 2018, and December 31, 2022, for Clostridioides difficile infections (CDIs), carbapenemase-producing Enterobacterales (CPE) infections, methicillin-resistant Staphylococcus aureus (MRSA) bloodstream infections (BSIs) and vancomycin-resistant Enterococcus (VRE) BSIs. Candida auris (C. auris) surveillance was initiated in 2019 by CNISP and in 2017 (retrospectively to 2012) by the National Microbiology Laboratory. Trend analysis for case counts, rates, outcomes, molecular characterization and AMR profiles are presented. From 2018 to 2022, decreased rates per 10,000 patient days were observed for CDIs (7% decrease; 5.42-5.02) and MRSA BSIs (2.9% decrease; 1.04-1.01). Infection rates for VRE BSIs increased by 5.9% (0.34-0.36). Infection rates for CPE remained low but increased by 133% (0.06-0.14). Forty-three C. auris isolates were identified in Canada from 2012 to 2022, with the majority in Western and Central Canada (98%). From 2018 to 2022, the incidence of MRSA BSIs and CDIs decreased and VRE BSI and CPE infections increased in the Canadian acute care hospitals participating in a national sentinel network (CNISP). Few C. auris isolates were identified from 2012 to 2022. Reporting standardized surveillance data to inform the application of infection prevention and control practices in acute care hospitals is critical to help decrease the burden of HAIs and AMR in Canada.

Dental antibiotic policies, stewardship, and implementation in India: A policy document analysis.

Dental antibiotic stewardship is crucial in low- and middle-income countries where the burden of antimicrobial resistance (AMR) is high and antibiotic misuse is common. Given that India is the most populous country, the largest antibiotic consumer and has a large dental prescriber population, this study investigated the extent to which current Indian policy and practice for dental antibiotic prescribing and stewardship aligns with the global policy and best practice. The READ approach was used to identify and extract data and synthesize the findings. Policy documents on dental antimicrobial stewardship were identified using a systematic search strategy involving nine medical and grey literature databases (Medline, Global Health, Web of Science, Cochrane, CINAHL, Eldis, Global Index Medicus, Proquest and Opengrey), targeted websites (government organizations and dental regulatory bodies) and contact with experts. Framework analysis was used to code extracted data into themes related to dental antimicrobial stewardship. Of the 3039 records screened, 25 documents were included in the final analysis. The analysis showed a lack of guidelines or toolkits for appropriate antibiotic prescribing in dentistry in India. The treatment guidelines for antimicrobial use in common syndromes published by the Indian Council of Medical Research had no section or content for dental practitioners. Furthermore, the undergraduate dental curriculum developed by the Dental Council of India (DCI), included little content on appropriate antibiotic prescribing and no mention of AMR or stewardship. There were no educational resources either for dental practitioners or patients in the documents. This document analysis showed that there was little or no mention of dental antibiotic prescribing guidelines in key policy documents such as the National Action Plan on AMR. In addition, contradictory and subjective information provided in some policy documents could encourage dentists and other health professionals such as general practitioners to prescribe antibiotics for common dental conditions for which they are contra-indicated. There is an urgent need to develop relevant guidelines and include these in Indian policy documents on AMR particularly the National Action Plan on AMR.

Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community

The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC’s NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.

Opportunities to Enhance Diagnostic Testing and Antimicrobial Stewardship: A Qualitative Multinational Survey of Healthcare Professionals.

Antimicrobial resistance (AMR) is a global public health challenge. Global efforts to decrease AMR through antimicrobial stewardship (AMS) initiatives include education and optimising the use of diagnostic technologies and antibiotics. Despite this, economic and societal challenges hinder AMS efforts. The objective of this study was to obtain insights from healthcare professionals (HCPs) on current challenges and identify opportunities for optimising diagnostic test utilisation and AMS efforts. Three hundred HCPs from six countries (representing varied gross national incomes per capita, healthcare system structure, and AMR rates) were surveyed between November 2022 through January 2023. A targeted literature review and expert interviews were conducted to inform survey development. Descriptive statistics were used to summarise survey responses. These findings suggest that the greatest challenges to diagnostic test utilisation were economic in nature; many HCPs reported that AMS initiatives were lacking investment (32.3%) and resourcing (40.3%). High resistance rates were considered the greatest barriers to appropriate antimicrobial use (52.0%). Most HCPs found local and national guidelines to be very useful (≥ 51.0%), but areas for improvement were noted. The importance of AMS initiatives was confirmed; diagnostic practices were acknowledged to have a positive impact on decreasing AMR (70.3%) and improving patient outcomes (81.0%). AMS initiatives, including diagnostic technology utilisation, are pivotal to decreasing AMR rates. Interpretation of these survey results suggests that while HCPs consider diagnostic practices to be important in AMS efforts, several barriers to successful implementation still exist including patient/institutional costs, turnaround time of test results, resourcing, AMR burden, and education. While some barriers differ by country, these survey results highlight areas of opportunities in all countries for improved use of diagnostic technologies and broader AMS efforts, as perceived by HCPs. Greater investment, resourcing, education, and updated guidelines offer opportunities to further strengthen global AMS efforts.

Point Prevalence Survey of Antimicrobial Prescription and Consumption in a Nigerian Tertiary Hospital: A Gateway to the Antimicrobial Stewardship Program

Background: Antimicrobial stewardship is an important action plan for curbing the rising trend of antimicrobial resistance (AMR). Surveillance of antimicrobial use and consumption is needed as baseline data and for monitoring the impact of antimicrobial stewardship interventions. The survey was done to understand the burden of AMR, in view of establishing an antimicrobial stewardship program in our hospital. Methods: A point prevalence survey (PPS) of antimicrobial use and consumption was conducted on all inpatients admitted before 8.00 am on the days of the survey using a standardized questionnaire. The collected data were entered online into the Global PPS web-based application (www.global-pps.com), for analysis. Result: Of the 178 patients admitted during the survey period, 50.6% were on one or more antimicrobial agents. All the patients in adult intensive care units were on antibiotics (100%), followed by neonatal intensive care units (83.3%), with the least being adult medical wards (39.4%). Beta-lactam antibiotics were the most frequently prescribed antimicrobial for various infections, especially skin and soft tissue infections, 41.3%, which were the most common diagnoses treated with antibiotics. The infection was mostly community-acquired (81.6%), of which 94.9% were treated empirically. There was no written guideline in existence. Conclusion: The present study revealed a poor prescribing habit because of a high rate of empirical treatment. The need for antimicrobial stewardship cannot be overemphasized as it will help streamline and improve the prescribing pattern.

Designing, piloting and evaluating (through a matched pre- and post-implementation survey) a targeted e-learning resource on antimicrobial resistance for public health professionals.

Antimicrobial resistance (AMR) is a significant global public health threat and key priority for the public health, especially health protection, workforce to lead by example. There is a paucity of learning resources on this for public health professionals (PHPs) in the UK. This project aimed to develop and disseminate a tailored interactive learning resource and evaluate impact on self-reported intention to change behaviour. Learning objectives were agreed, content developed by the multi-disciplinary team and piloted by PHPs in 2022 alongside a matched pre- and post-implementation evaluation survey. Questions were mapped to the capability-opportunity-motivation-behaviour change model. Before and after responses were calculated to compare change in self-reported knowledge, understanding and behaviour. Significance of change in binary responses was estimated. The resource was delivered using an interactive, user-friendly and cost-free internal platform. Thirty-one PHPs completed the pilot e-learning and survey. Perceived and actual knowledge increased in parallel. Actual knowledge on AMR burden increased from 6.45 to 35.48% (P = 0.004). Self-reported confidence to explain AMR to others improved by 0.71 (95% CI; 0.38-1.04: P = 0.0001) Likert points on a five-point scale. Motivation to advocate for antimicrobial stewardship (AMS) in day-to-day work, improved by 0.71 (95% CI; 0.34-1.08: P < 0.00001) Likert points. Case scenarios were well-received as an effective way to apply theory to practice. Ensuring a well-informed and confident public health workforce is vital for reducing the AMR threat and advocating for AMS with the public and partner organizations. This targeted e-learning module is an effective additional learning medium in contributing to PHPs knowledge, understanding and self-reported intention to change behaviours.

Investigating the feasibility and potential of combining industry AMR monitoring systems: a comparison with WHO GLASS

Background Efforts to estimate the global burden of antimicrobial resistance (AMR) have highlighted gaps in existing surveillance systems. Data gathered from hospital networks globally by pharmaceutical industries to monitor antibiotic efficacy in different bacteria represent an additional source to track the temporal evolution of AMR. Here, we analysed available industry monitoring systems to assess to which extent combining them could help fill the gaps in our current understanding of AMR levels and trends. Methods We analysed six industry monitoring systems (ATLAS, GEARS, SIDERO-WT, KEYSTONE, DREAM, and SOAR) obtained from the Vivli platform and reviewed their respective isolates collection and analysis protocols. Using the R software, we designed a pipeline to harmonise and combine these into a single dataset. We assessed the reliability of resistance estimates from these sources by comparing the combined dataset to the publicly available subset of WHO GLASS for shared bacteria-antibiotic-country-year combinations. Results Combined, the industry monitoring systems cover 18 years (4 years for GLASS), 85 countries (71), 412 bacterial species (8), and 75 antibiotics (25). Although all industry systems followed a similar centralised testing approach, the criteria for isolate collection were unclear (patients selection, associated sampling periods…). For E.coli, K. pneumoniae and S. aureus, at least 65% of comparable resistance proportions were within 0.1 of the corresponding estimate in GLASS. We did not identify systemic bias towards resistance in industry systems compared to GLASS. Conclusions Combining industry monitoring systems can substantially strengthen our knowledge of global AMR burden across bacterial species and countries. High agreement values for available comparisons with GLASS suggest that data for other bacteria-antibiotic-country-year combinations only present in industry systems could complement GLASS, particularly for Priority Pathogens currently not covered. This valuable information on resistance levels could help clinicians and stakeholders prioritize testing and select appropriate antibiotics in settings with limited surveillance data.

Infection prevention and control compliance during COVID-19 pandemic era: assessment of 26 regional referral hospitals in Tanzania

BackgroundInfection prevention and control (IPC) implementation at referral hospitals (RHs) in Tanzania is still inadequate, regardless of ongoing IPC capacity-building initiatives. This continues to challenge the quality of healthcare service provision as poor IPC implementation fuels healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) problems. The study aimed to describe the implementation of IPC practices in 26 Regional RHs’ functional units in 2021.MethodsThe study involved secondary data from an assessment conducted using the National IPC Standard checklist for hospitals to all functional units at 26 regional RHs in 2021. Data were analysed in STATA version 15.0 to compute the weighted median with interquartile range (IQR) for each functional unit score.ResultsThe overall weighted median IPC compliance with 26 regional RHs in 2021 was 50 (41–60), whereby the lowest and highest scores were 24 and 72%, respectively. The highest-performing unit was the intensive care unit (ICU) for adults 71.4% (46.4–78.6), and lowest performing functional units were the mortuary, Central Sterilization and Supply Department, and blood transfusion [47.4% (36.8–57.9), 47.4% (40–50), and 47.6% (38.1–61.9)], respectively.ConclusionImplementation of IPC practices in 26 RHs in Tanzania is inadequate. We recommend that RHs need to strengthen IPC practices implementation in each functional unit in order to reach the required target of at least 80% score. This will enhance the reduction of the burden of HAIs and AMR, and increase the energy and morale of healthcare workers in preparedness and response to emerging and remerging diseases.

Clinical Features, Diagnostics, Etiology, and Outcomes of Hospitalized Solid Organ Recipients With Community-Acquired Pneumonia: A Retrospective Cohort Analysis

BackgroundCommunity-acquired pneumonia (CAP) is a leading cause of morbidity and mortality worldwide. Limited evidence is available on the most effective diagnostic approaches, management strategies, and long-term outcomes for CAP in patients who have undergone solid organ transplantation. Research QuestionWhat is the acute and long-term morbidity and mortality after CAP in organ transplant recipients? Study Design and MethodsWe retrospectively analysed hospitalisations for CAP in solid organ recipients at the largest German transplant centre. The study included patients admitted between 1 January 2010 and 31 May 2021. The reported outcomes are in-hospital and 1-year mortality, risk of cardiovascular events during hospitalisation and at one year, admission to the intensive care unit, and risk of pneumonia with P. aeruginosa. Multivariable binary logistic regression using stepwise forward selection was performed to determine predictive factors for pneumonia with P. aeruginosa. ResultsWe analysed data from 403 hospitalisations of 333 solid organ recipients. In over 60% of cases, patients had multiple comorbidities, with cardiovascular and chronic kidney disease being the most prevalent. More than half of the patients required oxygen supplementation after admission. In-hospital mortality (13.2%) and the death rate at one year post-event (24.6%) were higher than data reported from immunocompetent patients. We also observed high rates of acute cardiovascular events and events occurring one year after admission. Early blood cultures and bronchoscopy in the first 24 hours significantly increased the odds of establishing an aetiology. In our low-resistance setting, the burden of antimicrobial resistance was driven by bacteria from chronically colonised patients, mostly lung transplant recipients. InterpretationThis comprehensive analysis highlights the high morbidity associated with CAP after transplantation. It also emphasises the need for prospective multicenter studies to guide evidence-based practices and improve outcomes for these vulnerable patients.

Burden of Antimicrobial Resistance in Japan: A Systematic Literature Review and Meta-Analysis.

Antimicrobial resistance (AMR) is one of the most serious public health challenges worldwide, including in Japan. However, there is limited evidence assessing the AMR burden in Japan. Thus, this systematic literature review (SLR) and meta-analysis (MA) were conducted to assess the clinical and economic burden of AMR in Japan. Comprehensive literature searches were performed on EMBASE, MEDLINE, the Cochrane Library, and ICHUSHI between 2012 and 2022 following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. MA estimated a pooled effect between the two comparative arms (AMR vs. non-AMR). The results were reported in measures of odds ratios (ORs) for in-hospital mortality and in standardized mean differences (SMDs) for length of stay (LOS) and direct medical costs. Literature searches identified 1256 de-duplicated records, of which 56 observational studies(English, n = 35; Japanese, n = 21) were included. Of note, twenty-two studies (39.3%) compared the AMR group with non-AMR group. In the SLR, in-hospital mortality, LOS, and direct medical costs were higher in the AMR group compared to the non-AMR group. Eight studies were selected for the MA. In the AMR group, the pooled estimate showed a statistically higher in-hospital mortality [random effect (RE)-OR 2.25, 95% CI 1.34-3.79; I2 = 89%; τ2 = 0.2257, p < 0.01], LOS (RE-SMD 0.37, 95% CI - 0.09-0.84; I2 = 99%; τ2 = 0.3600, p < 0.01), and direct medical cost (RE-SMD 0.53, 95% CI 0.43-0.62; I2 = 0.0%; τ2 = 0.0, p = 0.88) versus the non-AMR group. Our study presents an overview of the clinical and economic burden of AMR in Japan. Patients with AMR infections experience significantly higher in-hospital mortality, LOS, and direct medical costs compared with patients without AMR infections.

Genome-based machine learning for predicting antimicrobial resistance in Salmonella isolated from chicken

Antimicrobial resistance (AMR) continues to pose a grave threat to public health. The increase in the burden of AMR is fueled by the indiscriminate use of antimicrobial agents in agriculture. The objective of this study was to develop a genome-based machine learning model to predict AMR in Salmonella isolated from chicken meat. Genomic information on 205 Salmonella isolates from chicken meat was combined with data on the AMR phenotype of these isolates to amoxicillin-clavulanic acid, ampicillin, ceftiofur, ceftriaxone, sulfisoxazole, streptomycin, tetracycline, and cefoxitin. Four machine learning algorithms i.e., logit boost, random forest, support vector machine, and extreme gradient boosting were trained on this data to build models. The best-performing model for each antimicrobial was used to predict the AMR phenotypes of a new set of 200 Salmonella isolates also from chicken meat, and the predictions were compared to AMR phenotype predictions from ResFinder. The machine learning models showed high sensitivity (≥0.833), specificity (≥0.833), and balanced accuracy (≥0.866), across all the antimicrobials. The models predicted resistance prevalences ranging from 1% (ceftriaxone) to 65.5% (streptomycin). When the AMR phenotype predictions of the machine learning models were compared to predictions from ResFinder, the predictions from this study were accurate (>95%).

Characterising global antimicrobial resistance research explains why One Health solutions are slow in development: An application of AI-based gap analysis

The global health crisis posed by increasing antimicrobial resistance (AMR) implicitly requires solutions based a One Health approach, yet multisectoral, multidisciplinary research on AMR is rare and huge knowledge gaps exist to guide integrated action. This is partly because a comprehensive survey of past research activity has never performed due to the massive scale and diversity of published information. Here we compiled 254,738 articles on AMR using Artificial Intelligence (AI; i.e., Natural Language Processing, NLP) methods to create a database and information retrieval system for knowledge extraction on research perfomed over the last 20 years. Global maps were created that describe regional, methodological, and sectoral AMR research activities that confirm limited intersectoral research has been performed, which is key to guiding science-informed policy solutions to AMR, especially in low-income countries (LICs). Further, we show greater harmonisation in research methods across sectors and regions is urgently needed. For example, differences in analytical methods used among sectors in AMR research, such as employing culture-based versus genomic methods, results in poor communication between sectors and partially explains why One Health-based solutions are not ensuing. Therefore, our analysis suggest that performing culture-based and genomic AMR analysis in tandem in all sectors is crucial for data integration and holistic One Health solutions. Finally, increased investment in capacity development in LICs should be prioritised as they are places where the AMR burden is often greatest. Our open-access database and AI methodology can be used to further develop, disseminate, and create new tools and practices for AMR knowledge and information sharing.

Assessment of antimicrobial resistance laboratory-based surveillance capacity of hospitals in Zambia: findings and implications for system strengthening

A well-established antimicrobial resistance (AMR) laboratory-based surveillance (LBS) is of utmost importance in a country like Zambia which bears a significant proportion of the world's communicable disease burden. This study assessed the capacity of laboratories in selected hospitals to conduct AMR surveillance in Zambia. This cross-sectional exploratory study was conducted among eight purposively selected hospitals in Zambia between August 2023 and December 2023. Data were collected using the self-scoring Laboratory Assessment of Antibiotic Resistance Testing Capacity (LAARC) tool. Of the assessed facilities, none had full capacity to conduct AMR surveillance with varying capacities ranging from moderate (63% (5/8)) to low (38% (3/8)). Some of the barriers of AMR-LBS were the lack of an electronic laboratory information system (63% (5/8)) and the lack of locally generated antibiograms (75% (6/8)). Quality control for antimicrobial susceptibility testing (AST), pathogen identification and media preparation had the lowest overall score among all of the facilities with a score of 14%, 20% and 44%, respectively. The highest overall scores were in specimen processing (79%), data management (78%), specimen collection, transport and management (71%), and safety (70%). Most facilities had standard operating procedures in place but lacked specimen-specific standard operating procedures. The absence of laboratories with full capacity to conduct AMR surveillance hinders efforts to combat AMR and further complicates the treatment outcomes of infectious diseases. Establishing and strengthening LBS systems are essential in quantifying the burden of AMR and supporting the development of local antibiograms and treatment guidelines.