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PubMed2026

Environmental antibiotic contamination and AMR: Integrating pathways, impacts, and artificial intelligence-driven mitigation.

The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance (AMR). Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of AMR, and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.

Anti-Bacterial Agents↗

PubMed2026

Optimizing a culture-enriched hybrid metagenomics pipeline to assess the AMR footprint of livestock manure in anaerobic digestate.

The role of environmental samples from livestock production systems, including manure and anaerobic digestate, as reservoirs of antimicrobial resistance genes (ARGs) is likely underestimated because conventional metagenomic approaches can overlook low-abundance ARGs and often lack the resolution to associate these genes with their microbial hosts and co-localized mobile genetic elements (MGEs). We evaluated whether culture-enriched metagenomics (CEMG), with and without antibiotic selection, enhances ARG detection in anaerobic digestate and improves the resolution of ARG-MGE-host associations using hybrid short- and long-read metagenomic assembly. CEMG increased ARG recovery; mean ARG abundance rose from 15.4 counts per million (CPM) in metagenomic fresh digestate (FD) to 124 CPM in CEMG without antibiotics and 160 CPM in antibiotic-selective CEMG. In FD, only 9 unique ARGs were detected, whereas CEMG recovered 112, including ARGs of clinical importance, such as glycopeptide resistance, beta-lactamase genes, and the cfr 23S rRNA methyltransferase conferring cross-resistance to multiple antibiotic classes. Antibiotic selection induced targeted, class-specific shifts in ARG profiles, with ARGs associated with tetracycline resistance consistently enriched across treatments. Hybrid metagenomic assembly resolved the genomic context of 784 ARGs, of which 59.3% were co-localized with at least one class of MGEs, predominantly plasmids and integrative conjugative elements/integrative mobilizable elements. Biocide and metal resistance genes frequently co-occurred with ARGs on the same contigs. Together, these findings demonstrate that antibiotic-selective culture enrichment enhances resistome surveillance by improving detection of low-abundance ARGs, while hybrid assembly provides critical genomic context for assessing their mobility and host associations.IMPORTANCELivestock manure and its byproducts, such as anaerobic digestate, are recognized as important environmental reservoirs of antimicrobial resistance genes (ARGs) and resistant bacteria, yet current metagenomic approaches may underestimate this risk by failing to detect low-abundance but clinically relevant ARGs. Here, we show that integrating culture enrichment with hybrid metagenomics improves ARG recovery and reveals ARG co-localization with mobile genetic elements and putative bacterial hosts. This approach captures a cultivable and condition-responsive fraction of the resistome that is not readily accessible through direct metagenomic sequencing alone, providing a more informative framework for environmental AMR surveillance.

anaerobic digestion↗

PubMed2026

Editorial: Antimicrobial resistance (AMR) in foodborne pathogens.

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One Health↗

PubMed2025

Utility of Plasma Cell-free Chromatin Immunoprecipitation to Detect Cardiac Allograft Rejection.

BACKGROUND: Antibody-mediated rejection (AMR) remains the major risk factor for allograft loss across all solid organ transplantation. Unfortunately, its diagnosis relies on biopsy, an invasive gold standard that often sample unaffected allograft tissue leading to missed diagnosis. Plasma donor-derived cell-free DNA (dd-cfDNA) is noninvasive biomarker that has high sensitivity but low specificity for AMR diagnosis. This proof-of-concept study assessed the utility of cell-free chromatin immunoprecipitation (cfChIP) as a surrogate for gene expression to detect cardiac AMR and the associated pathobiology. METHODS: The discovery GRAfT multicenter cohort of heart transplant patients (NCT02423070) identified AMR, acute cellular rejection (ACR), and stable controls based on biopsy and ddcfDNA results. Plasma cfChIP-sequencing was performed to identify peaks, associated genes and pathobiological pathways. Plasma from an external cohort (GTD, NCT01985412) was also analyzed to verify pathways identified. Digital droplet PCR (ddPCR) assays targeting differential regions were constructed to test the diagnostic performance of cfDNA to detect AMR/ACR from stable controls (rejection-specific assays) or AMR from ACR (AMR-specific assays). RESULTS: The cohort included 21 AMR, 28 ACR, and 45 stable controls from GRAfT and GTD, and 23 healthy controls. cfChIP detected expected active genes, including housekeeping genes and gene targets of transplant immunosuppressive drugs but not inactive genes. Unsupervised clustering of the discovery GRAfT cohort assigned 95% of samples correctly as AMR, ACR or stable control. Differential analysis identified pathobiological pathways of AMR such as neutrophil degranulation and complement activation. The pathways were consistent in GTD samples. Rejection-specific assays detected AMR/ACR from controls with AUC of 0.78 - 0.95. AMR-specific assays detected AMR from ACR with AUC of 0.71 - 0.85, sensitivities of 0.73 - 0.94 and specificities of 0.73 - 0.80. CONCLUSION: This study provides valuable preliminary data supporting the use of cfChIP to detect AMR and the associated pathobiological pathways.

Allograft rejection↗

PubMed1992

On-scene helicopter transport of patients with multiple injuries--comparison of a German and an American system.

Hospital-based helicopter services from a German (GER) and an American (AMR) university-affiliated trauma center were reviewed. All patients with multiple injuries transported via helicopter from the scene to the trauma centers during a 1-year period were included. The patients were comparable regarding mechanism of injury, age, flight times, mean ISS, ISS distribution, and number of severe injuries per body region (patients with AIS score > 3 for head, thorax, and abdomen). Overall mortality was 21 of 221 (9.5%) for GER and 21 of 186 (11.3%) for AMR (NS). Survivor-based TRISS analysis yielded Z statistics of +2.459 for GER (p < 0.025) and +1.049 for AMR (NS). M statistics were 0.89 for GER, 0.874 for AMR; the W statistic +1.35 for GER. There were nine unexpected survivors (Ps < 0.50) for GER and six for AMR. There was a significantly higher (p < 0.01) number of early deaths (< 6 hours) in AMR (12; ISS = 56) than in GER (four; ISS = 64). Analysis of the prehospital data demonstrated significant differences in the mean volume of IV fluids infused: 1800 mL, GER; 825 mL, AMR (p < 0.05); rate of intubation: 82 of 221 (37.1%) GER; 24 of 186 (13.4%) AMR (p < 0.001); and thoracic decompressions: 20 of 221 (9.1%) GER; 1 of 186 (0.5%) AMR (p < 0.001). Prehospital care in the GER system is directed on scene by a trauma surgeon member of the flight crew compared with a nurse/paramedic team with remote medical control in the AMR system.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

PubMed2026

Comparative genomics of ESKAPE pathogen species: Integrating pan-genome architecture, antimicrobial resistance, and virulence factor repertoires.

BACKGROUND: ESKAPE pathogens are major causes of hospital-acquired infections and are characterized by extensive antimicrobial resistance (AMR) and diverse virulence mechanisms. Although species-specific pan-genome studies have revealed substantial genomic diversity, the relationships among genome plasticity, resistance burden, and virulence remain incompletely understood across the ESKAPE complex. METHODS: We analyzed 120 high-quality genomes representing six single-species ESKAPE groups (20 genomes per species). Genome quality was assessed using CheckM2. Species-specific pan-genomes were constructed with Roary, AMR genes were identified using AMRFinderPlus, and virulence factors were detected against the VFDB database using DIAMOND. AMR genes were mapped to core and accessory genome compartments through integration of Prokka annotations and Roary outputs. Statistical associations were evaluated using Fisher's exact tests and correlation analyses, with false discovery rate correction applied within each test family. Core-genome maximum-likelihood phylogenies were reconstructed to provide an evolutionary framework. RESULTS: Pan-genome sizes ranged from 4720 to 17,272 genes, with Enterobacter and Pseudomonas possessing the largest accessory genomes. Multidrug resistance (MDR; resistance to ≥3 antimicrobial classes) was detected in 93.3% of strains. After false discovery rate correction, AMR genes remained significantly enriched in the accessory genomes of Enterobacter, Enterococcus, Klebsiella, and Staphylococcus, whereas Acinetobacter and Pseudomonas did not show significant enrichment in either genome compartment. Within-species analyses identified significant positive associations between accessory genome size and AMR class burden in Staphylococcus, Enterococcus, and Enterobacter, whereas the moderate Pearson correlation observed in Pseudomonas was not significant after FDR correction. Virulence factor repertoires varied markedly among species, with Pseudomonas exhibiting the highest burden and Enterococcus the lowest. CONCLUSIONS: ESKAPE pathogens display distinct patterns of resistance and virulence. Accessory genome expansion was associated with higher AMR burden in several species, whereas other species showed no significant association between accessory genome size and AMR burden and no significant enrichment of AMR genes in either genome compartment, highlighting the species-specific nature of AMR evolution.

Virulence Factors↗

PubMed2026

Comparative genomic analysis of Streptococcus parasuis and Streptococcus suis reveals mobile element-associated enrichment of antimicrobial resistance and lack of detectable same-MGE colocalization with virulence-associated genes within stable species boundaries.

Streptococcus suis is a major porcine pathogen and a zoonotic agent that causes meningitis and septicemia in humans. Streptococcus parasuis, a recently recognized close relative, remains poorly characterized with regard to its clinical significance and genomic features. In this study, we generated a single-contig closed genome assembly with genome-wide DNA methylation profiles for S. parasuis strain A1, isolated from a diseased pig in Xinjiang, China, and complemented in silico genomic predictions with isolate-level experimental validation of antimicrobial resistance (AMR) genotypes, virulence genotypes, and phenotypic susceptibility for this reference strain. Using this high-quality genome as a reference anchor, we performed comparative genomic analyses across 195 streptococcal genomes, comprising 15 S. parasuis and 180 S. suis strains, to distinguish genome-level co-occurrence of resistance and virulence determinants from their physical colocalization on the same mobile genetic element (MGE).Species boundaries remained clearly delineated at the genomic level, with a median interspecies average nucleotide identity (ANI) of approximately 86.0%, compared with intraspecies ANI medians of 97.5% for S. parasuis and 96.2% for S. suis. Pangenome analysis identified 12,693 gene clusters, of which 1086 were core clusters, and functional annotation revealed significant differences in accessory gene repertoires between the two species. Within this stable genomic framework, S. parasuis genomes carried a higher AMR gene burden; strain A1 harbored 10 AMR genes, multiple virulence-associated genes, three genomic islands, and eight prophage regions. For strain A1, PCR validation confirmed six AMR genes and six virulence genes, and disk diffusion testing demonstrated a multidrug-resistant phenotype consistent with the genotypic profile.Among 235 predicted mobile elements, 19 harbored AMR genes and seven carried Virulence Factor Database (VFDB) homologs, but none carried both categories simultaneously. This finding reflects a lack of detectable same-MGE colocalization under the applied annotation and assembly framework; it should not be interpreted as evidence of biological physical decoupling. Under a random-placement model, the expected number of co-carrying regions was only 0.57, and the probability of observing zero co-carrying regions was P = 0.55. This negative result should be interpreted with caution, given the limited number of cargo-bearing regions and the predominantly draft status of most genomes. Furthermore, the A1 genome contained multiple restriction-modification systems, showed depletion of several methylation motif families in mobile regions, and had limited CRISPR spacer matching evidence, suggesting prior exposure to the relevant sequence space. None of the genomes met our predefined criteria for whole-genome convergence.Collectively, our results support a model in which S. parasuis accumulates AMR-related genes in a modular fashion via mobile elements within stable species boundaries, with no detectable same-MGE colocalization of AMR and virulence determinants under our analytical pipeline. These findings imply that AMR surveillance strategies for this species should prioritize tracking mobile genetic elements rather than inferring wholesale genomic convergence toward S. suis.

Streptococcus suis↗

PubMed2025

WHO global gonococcal antimicrobial surveillance programmes, 2019-22: a retrospective observational study.

BACKGROUND: Gonorrhoea and gonococcal antimicrobial resistance (AMR) remain global public health concerns, and enhanced quality-assured global surveillance of gonococcal AMR is imperative to inform management guidelines and public health policies. We aimed to describe the results of surveillance of gonococcal AMR conducted globally by WHO and discuss the actions needed to retain our ability to treat gonorrhoea. METHODS: In this retrospective observational study, we present gonococcal AMR data reported to WHO by 77 countries between Jan 1, 2019, and Dec 31, 2022. Gonococcal isolates were tested for minimum inhibitory concentrations of one to four key antimicrobials (ceftriaxone, cefixime, azithromycin, and ciprofloxacin) in each country. We used breakpoints for resistance and decreased susceptibility to antimicrobials from the European Committee on Antimicrobial Susceptibility Testing or Clinical Laboratory and Standards Institute. FINDINGS: 29 (39%) of 75 participating countries reported at least one isolate with resistance or decreased susceptibility to ceftriaxone, 28 (50%) of 56 reported resistance or decreased susceptibility to cefixime, 58 (88%) of 66 reported resistance to azithromycin, and 74 (99%) of 75 reported resistance to ciprofloxacin. Globally, azithromycin resistance is increasing, as is resistance or decreased susceptibility to ceftriaxone and cefixime, especially in the WHO Western Pacific region. Resistance to ciprofloxacin remained very high globally. Since 2017-18, the numbers of reporting countries, examined isolates, and resistant isolates have increased. However, surveillance levels remain inadequate in central America and the Caribbean, eastern Europe, and the WHO African, Eastern Mediterranean, and South-East Asia regions. INTERPRETATION: Global AMR surveillance conducted by WHO is expanding and, in selected countries, improving through standardisation and quality assurance, as well as implementation of extragenital sampling, test of cure, and whole-genome sequencing. This approach provides evidence-based data for management guidelines and public health policies. Improvements in prevention, early diagnosis, treatment of patients and their contacts, surveillance (of infection rates, AMR, treatment failures, and antimicrobial use), and antimicrobial stewardship are essential. WHO supports this work through several global action plans on AMR, new global gonorrhoea treatment recommendations, surveillance, and research. FUNDING: None.

Neisseria gonorrhoeae↗

PubMed2025

Transmission of extended spectrum β-lactamase-producing Escherichia coli and antimicrobial resistance gene flow across One Health compartments in eastern Africa: a whole-genome sequence analysis from a prospective cohort study.

BACKGROUND: The One Health paradigm considers interdependence of human, animal, and environmental health. However, there is little evidence from high-income countries to support the importance of a One Health approach to addressing spread of antimicrobial resistance (AMR). Given AMR is a global threat, understanding how the close interactions of humans with animals and the environment in low-income settings affect the spread of AMR is important. We aimed to investigate diversity and transmission of extended spectrum β-lactamase (ESBL)-producing Escherichia coli across household-linked One Health compartments using genomic data. METHODS: We sequenced whole genomes of ESBL-producing E coli isolates from humans, animals, and the environment from a prospective, longitudinal cohort study conducted in Malawi (April 29, 2019, to Dec 3, 2020) and Uganda (July 16, 2020, to Aug 6, 2021). In the cohort study, 259 households were enrolled at baseline in Malawi and 92 in Uganda from a mix of urban, peri-urban, and rural areas. Households were followed up at months 1, 3, and 6 in Malawi and at months 1, 2, and 4 in Uganda. Samples collected at each visit included human and animal stool, environmental samples from hand-contact areas, food, and water, and broader environmental samples such as river water. Samples were cultured in buffered peptone water and then ESBL chromogenic agar to isolate ESBL-producing E coli. ESBL-producing E coli isolates underwent whole-genome sequencing. We performed phylogenetic analyses, and in-silico multi-locus sequence typing, characterised AMR determinants and linked genotypes with sample location, ecological source, and other covariates. We performed fine-scale single nucleotide polymorphism (SNP) and network analysis to infer strain and plasmid transmission across ecological compartments. The primary outcome was colonisation with ESBL-producing E coli. Secondary outcomes were genomic clusters and ESBL genomic determinants within and between One Health compartments. FINDINGS: We found high diversity of ESBL-producing E coli, with 170 sequence types and 166 genomic clusters identified from 2344 genomes, including 1814 genomes from Malawi (907 human, 221 animal, and 686 environmental) and 530 genomes from Uganda (380 human, 147 animal, and three environmental). Sequence type (ST)131 dominated in Malawi (209 [11·5%] of 1814 genomes), and ST10 dominated in Uganda (45 [8·5%] of 530 genomes). Common ESBL genes blaCTX-M-15 (1604 [68·4%] of 2344 genomes) and blaCTX-M-27 (336 [14·3%] of 2344 genomes) were carried on a complex network of 55 and 30 different plasmids. This diversity of plasmids presented multiple pathways for dissemination and revealed high force of selection. Phylogenetic analyses revealed common intermixing of isolates between humans, animals, and the environment. SNP transmission analysis revealed ecologically overlapping clusters, suggesting ESBL-producing E coli co-circulation both within and between compartments with frequent spillover events. Applying a five-SNP threshold, we inferred 463 human-environment transmission events, 146 human-animal events, and 142 animal-environment events. INTERPRETATION: Our work suggests that a One Health approach is crucial to addressing AMR in eastern Africa. Improving water, sanitation, and hygiene systems will create a safer environment, reduce spillovers of AMR bacteria between compartments, and eventually reduce AMR reservoirs in the environment and in animals. FUNDING: Medical Research Council, National Institute for Health and Care Research, and Wellcome Trust.

Humans↗

PubMed2026

Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.

BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results. METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus. FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%. INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation. FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.

Humans↗

PubMed2026

Novel potential treatment options for infections caused by multi-drug and extensively drug-resistant Neisseria gonorrhoeae strains.

INTRODUCTION: Neisseria gonorrhoeae has evolved antimicrobial resistance (AMR) since antimicrobial treatment of gonorrhea was introduced. The AMR development is driven by the bacterium's high capacity for genetic adaptation, antimicrobial overuse and misuse, and insufficient surveillance. Novel therapeutic options are urgently needed. AREAS COVERED: This review summarizes novel gonorrhea treatment options, with special emphasis on the novel oral antimicrobials zoliflodacin and gepotidacin that obtained US FDA-approval for treatment of uncomplicated urogenital gonorrhea in December 2025. It also highlights compounds in early clinical or preclinical development that have demonstrated promising in vitro activity against N. gonorrhoeae. EXPERT OPINION: Zoliflodacin and gepotidacin have the potential to optimize gonorrhea management as oral alternatives to current injectable ceftriaxone. Their successful long-term use will depend on optimized use strategies, including indications, evidence-based approved dosing, adherence, surveillance, and population-specific considerations. Public-health agencies and clinicians will need to balance broad clinical access with antimicrobial stewardship measures to delay the AMR emergence. Looking ahead, gonorrhea management will hopefully shift from empirical, syndromic treatment toward etiology-guided and AMR-informed therapy, driven by advances in rapid point-of-care testing and whole-genome sequencing technologies. Continuous phenotypic and genomic surveillance remains essential to detect early AMR signals, transmission of AMR strains, and inform treatment guidelines.

AMR↗

PubMed2026

Evaluation of Oxford nanopore sequencing for antimicrobial resistance surveillance in Salmonella: comparison with phenotypic antimicrobial susceptibility in a large-scale study.

UNLABELLED: Salmonella is a major zoonotic foodborne pathogen, and antimicrobial resistance (AMR) in Salmonella presents a significant public health challenge. Compared with conventional antimicrobial susceptibility testing (AST), whole-genome sequencing (WGS) provides a more rapid and comprehensive approach to AMR characterization, thereby informing antimicrobial selection and supporting public health surveillance. In this study, Oxford Nanopore Technology (ONT)-based WGS was performed on 1,490 Salmonella isolates collected through nationwide surveillance in Taiwan in 2025. Genotypic resistance inferred from WGS data was compared with phenotypic AST results to assess the performance of ONT-WGS. Overall, WGS-inferred resistance showed high concordance with phenotypic resistance for most antimicrobials. However, major genotype-phenotype discordance was observed, attributed to four categories: (i) breakpoint-dependent classification, (ii) reduced or absent phenotypic expression of resistance genes, (iii) minimum inhibitory concentration (MIC) modulation by ramAp, and (iv) absence of known AMR determinants. Notable discrepancies included tigecycline resistance without known genetic determinants, nalidixic acid resistance linked to ramAp-mediated MIC elevation, and a high prevalence of colistin resistance (35.7%) in S. Enteritidis, with most resistant isolates lacking identifiable AMR determinants. Additionally, a significant proportion of ESBL- and AmpC-producing isolates were classified as susceptible or intermediate to cefotaxime and ceftazidime under CLSI criteria, highlighting the potential for misclassification and treatment failure. These findings demonstrate that ONT-WGS enables accurate and comprehensive AMR characterization by directly identifying resistance determinants and avoiding potential misclassification associated with breakpoint-based AST interpretations. When interpreted appropriately, WGS can support better antimicrobial selection and serve as a valuable alternative to conventional susceptibility testing. IMPORTANCE: Accurate prediction of antimicrobial resistance is essential for appropriate therapy and effective surveillance of Salmonella. However, discordance between genotype-based predictions and phenotypic antimicrobial susceptibility testing (AST) can complicate clinical interpretation. In this nationwide study of 1,490 Salmonella isolates, we show that Oxford Nanopore Technology-based whole-genome sequencing (ONT-WGS) provides rapid and comprehensive detection of antimicrobial resistance determinants with high concordance to phenotypic AST. We further identify four major mechanisms underlying genotype-phenotype discordance, including breakpoint-dependent classification, reduced or absent phenotypic expression of resistance genes, minimum inhibitory concentration (MIC) modulation by ramAp, and the absence of known AMR determinants. These findings demonstrate how WGS can complement conventional AST, improve interpretation of challenging susceptibility results, and strengthen genomic surveillance of emerging antimicrobial-resistant Salmonella.

Microbial Sensitivity Tests↗

PubMed2026

A comprehensive review of AI innovations for tackling antimicrobial resistance.

Antimicrobial resistance (AMR) represents a major global public health concern, rendering available antimicrobials ineffective and leading to infections that are difficult to treat. Artificial intelligence (AI) has been increasingly applied across the AMR continuum, including resistance prediction, rapid diagnostics, new antimicrobial discovery, drug repurposing, antimicrobial surveillance, and clinical decision support. In this review, we aim to highlight recent developments in the use of artificial intelligence (AI) to address antimicrobial resistance (AMR). In addition, we review computational methods that help interpret genomic, phenomic, clinical, and epidemiological data to support the development of treatment strategies and novel antimicrobial agents. The key issues addressed include data quality, model interpretability, external validation, regulatory requirements, privacy, and fairness. While AI is not a complete solution to AMR, it can certainly strengthen the global AMR response by complementing key areas of AMR such as antimicrobial stewardship, infection prevention, laboratory diagnostics, and global surveillance.

Antimicrobial resistance (AMR)↗

PubMed2026

Antimicrobial Resistance Phenotypes and Genotypes of Cecal Digesta Escherichia coli of Pullets Fed Omega-3 Fatty Acids or Yeast Bioactives (Glycobolites).

Antimicrobial resistance (AMR) is a significant threat to poultry production and food safety. In laying hens, commensal Escherichia coli can serve as a reservoir of AMR and virulence genes. Although omega-3 fatty acids (N-3 FAs), yeast bioactives (YB), and spacing allowance (SA) influence gut health and immunity, their combined effects on AMR profiles of gut bacteria remain unclear. A total of 2,832 chicks were raised in enriched cages under high (HSA, 348 cm2/bird) or low (LSA, 284 cm2/bird) SA and fed a control diet (C), C+3% N-3 FA, or C+0.05% YB. At 4, 16, and 35 weeks of age (woa), cecal contents were cultured on ChromoCult agar to isolate E. coli. Susceptibilities of isolates to 14 antibiotics were determined. Of the 428 isolates, 35.7% were resistant to at least one antimicrobial, and overall, AMR prevalence decreased with age (P < 0.05). At each of 4 and 16 woa, N-3 FA-fed birds showed the lowest prevalance of ampicillin-resistant (P < 0.05). The prevalence of streptomycin resistance was higher in N-3 FA than in YB-fed birds at 16 woa (P = 0.02) but lower than in control-fed birds. Whole-genome sequencing and analysis of 237 selected isolates identified 19 antimicrobial resistance genes (ARGs) and 29 plasmids, with the distribution of 15 (78.9%) ARGs and 19 (65.5%) plasmid replicons affected by either diet, SA, or age (P < 0.05). Several virulence genes were identified in sequenced E. coli isolates, with the prevalence of those encoding fimbriae, pili, protectin, and toxins being higher in younger pullets (P < 0.05). Overall, isolates of phylogroups A and B1 were predominant; however, at 4 woa, phylogroup D isolates were most prevalent, depending on diet and SA (P < 0.05). Isolates of serotype O23:H16, ST2 were the most prevalent. Of the 237 sequenced isolates, 13 were related to human extraintestinal pathogenic Escherichia coli (ExPEC) strains. Overall, these findings suggest that N-3 FA YB and SA modulate AMR and virulence genotypes of E. coli in laying hens, highlighting their potential use of these agents in mitigating AMR.

Antimicrobial resistance↗

PubMed2025

A One Health perspective: Genomic insights into temporal trends of antimicrobial resistance and zoonotic transmission risks in Escherichia coli from human and swine.

Antimicrobial resistance (AMR) poses a significant challenge within the One Health framework. By integrating genomic data from 824 E. coli isolates obtained from 22 swine farms in southwestern China with 8432 publicly available genomes from human and swine sources, this study provides comprehensive insights into the temporal trends and divergence of AMR in human and swine E. coli populations, the risk of AMR transmission from swine to human, and the evolutionary mechanisms underlying the human adaptation of ST2 strains. The results revealed an overall increase in AMR until approximately 2016, followed by a subsequent decline. However, resistance to tetracyclines, quinolones, and phenicols continues to exhibit an upward trend, highlighting the urgency of enhancing regulatory measures targeting these drugs. Horizontal gene transfer play pivotal roles in shaping distinct AMR profiles in human and swine strains. ST2 E. coli was identified as a major carrier of AMR in both human and swine, and also served as the primary reservoir of blaNDM-5 within the human-associated lineage. During evolution, ST2 E. coli underwent significant genetic changes, including the enrichment of blaNDM-5 and remodeling of virulence factors, facilitating its transition from a generalist lineage colonizing both human and swine to a human-adapted lineage.

Humans↗

PubMed2026

Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.

Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.

Metagenomics↗

PubMed2025

Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.

Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.

Microbiome↗

PubMed2026

National Antimicrobial Resistance Monitoring System: Three Decades of Advancing Public Health Through Integrated Surveillance of Antimicrobial Resistance.

Antimicrobial resistance (AMR) occurs when bacteria and other microorganisms adapt in ways that make medicines less effective, causing infections that are harder to treat and more likely to spread. According to the Centers for Disease Control and Prevention (CDC), AMR infections affect millions of Americans each year and contribute to thousands of deaths (CDC, 2019). After three decades of operation, the U.S. National Antimicrobial Resistance Monitoring System (NARMS) stands as a model of sustained, collaborative public health surveillance. What began in 1996 as an effort to track resistance in Salmonella and E. coli O157 has evolved into a One Health surveillance network monitoring AMR across the farm-to-fork continuum. Through a partnership among CDC, the Food and Drug Administration (FDA), the U.S. Department of Agriculture (USDA), state and local health departments, and universities, NARMS has become the backbone of foodborne AMR surveillance in the United States. The past decade has been particularly transformative. NARMS explored new sampling to include companion animals, minor livestock, aquaculture, surface water, and wildlife. Whole-genome sequencing (WGS) revolutionized the program's capabilities, enabling timely identification of emerging pathogens and revealing how resistance genes spread. Near real-time public dashboards make NARMS data accessible to researchers, clinicians, regulators, and policymakers. NARMS data shape decisions about new animal drug approvals, guide stewardship programs, and inform clinical treatment guidelines nationwide. As NARMS enters its fourth decade with a 2026-2030 strategic plan, the program will leverage artificial intelligence and metagenomics while expanding surveillance to fill remaining gaps ensuring this vital system continues to protect the food supply and both human and animal health from AMR.

Antimicrobial Resistance (AMR)↗