Search Results (76)

Pseudomonas aeruginosa is a notable opportunistic pathogen in the ESKAPE group due to its multidrug resistance (MDR) and its ability to cause severe healthcare-associated infections. Horizontal gene transfer (HGT) facilitates the dissemination of antibiotic resistance genes (ARGs) through mobile genetic elements (MGEs). A comprehensive genomic analysis of ARGs associated with these elements is essential to understand multidrug resistance in P. aeruginosa. Here, we analyzed 10,412 publicly available P. aeruginosa genome assemblies defined by the Genome Taxonomy Database (GTDB, release 226) species cluster, which provides standardized prokaryotic genome taxonomy. We identified plasmids, prophages, integrative and conjugative elements (ICEs), and integrative and mobilizable elements (IMEs) carrying ARGs. A group of highly prevalent ARG families was identified in P. aeruginosa, comprising mexD, fosA, catB7, blaPAO, and aph(3′)-IIb, each of which was detected in over 96% of the genome assemblies. In contrast, 313 ARG families were found in fewer than 20% of the genomes. Many ARGs were located on plasmids, with certain pairs co-occurring frequently, such as aph(3″)-Ib and aph(6)-Id, CmlA9 and aadA6, or aac(6′)-Ib3 and aph(3′)-XV, which were associated with specific plasmids. Some of these plasmids closely resembled plasmids from E. coli and K. pneumoniae. Moreover, other MGEs displayed distinct ARG cargo enrichment: mexD on IMEs, aph(3′)-IIb on prophages, and sul1, fosA, and catB7 on ICEs. Our study provides a high-resolution map of the P. aeruginosa MGE resistome and highlights the potential roles of MGEs in disseminating different resistance genes. Our results emphasize the significance of ICE- and plasmid-associated ARG dissemination, particularly sul1, which may be linked to class 1 integrons. They also suggest that interspecies plasmid exchange may contribute to the evolution of MDR in P. aeruginosa. Full article

The dissemination of antibiotic resistance genes (ARGs) in riverine ecosystems poses a pressing public health threat, while the mechanisms governing the assembly of the gut resistome in wild fish remain poorly elucidated. This study aimed to elucidate the distributional patterns of ARGs across multiple environmental compartments and to identify factors associated with their variation, particularly the contributions of mobile genetic elements (MGEs) and metal resistance genes (MRGs) to gut resistome variation. Metagenomic sequencing was conducted on 60 samples, comprising water, sediment, and gut contents from three wild fish species (Megalobrama terminalis, Aristichthys nobilis, and Coilia nasus) with distinct feeding habits, collected from four reaches of the Qiantang River basin. A total of 305 ARG subtypes belonging to 23 classes were identified. ARG composition differed significantly across environmental media and host species (permutational multivariate analysis of variance, PERMANOVA; p < 0.01), with host species identity as the primary structuring factor. Variance partitioning analysis (VPA) revealed that MGEs independently explained the largest fraction of ARG variation in A. nobilis (33.8%, p = 0.006), whereas MRGs dominated in C. nasus (33.3%, p = 0.005); in M. terminalis, MGEs and MRGs together accounted for 47.9% of the variation. Metagenomic assembly recovered 2622 ARG-carrying contigs, of which 28.3% (743) were predicted as plasmid sequences; physical co-localization among ARGs, MGEs, and MRGs was detected on both chromosomes and plasmids. Metagenomic binning validated the physical co-localization of ARG-MGE-MRG modules in genera such as Morganella and Burkholderia at the genome level, while plasmid-borne high-risk ARGs were identified in Aeromonas. Risk ranking further revealed significant enrichment of Rank II potentially high-risk ARGs (e.g., mcr-7.1, blaZ) in fish guts, carried by potential pathogens. These findings suggest that horizontal gene transfer involving MGEs and co-selection related to MRGs are closely associated with the fish gut resistome composition in a manner dependent on host ecology, providing a scientific basis for shifting riverine resistance management from concentration-based control toward the interruption of dissemination pathways. Full article

Listeria monocytogenes is a ubiquitous Gram-positive bacterium responsible for listeriosis, a foodborne zoonotic disease affecting humans and animals. Although infection in immunocompetent individuals is often asymptomatic or limited to mild self-limiting gastroenteritis, Listeria monocytogenes may cause severe invasive disease in vulnerable groups, including pregnant women, neonates, elderly individuals, and immunocompromised patients. Although the incidence of listeriosis is relatively low compared with many other foodborne pathogens, the high hospitalization and mortality rates associated with clinical cases make this bacterium a major concern for food safety and public health. The evolutionary success of L. monocytogenes reflects the interaction between a conserved core genome and a dynamic accessory genome shaped by horizontal gene transfer (HGT), ecological selection, and expansion of specific clones. Transient intestinal carriage in humans and animals, potentially influenced by gut microbiome composition, creates ecological interfaces where plasmids, transposons, prophages, and integrative conjugative elements contribute to the exchange of antimicrobial resistance determinants, virulence factors, and stress tolerance systems. Virulence diversification is further influenced by the differential distribution of pathogenicity islands such as LIPI-1, LIPI-3, and LIPI-4 across specific clonal lineages. These evolutionary processes occur across interconnected farm, food-production, environmental, and clinical ecosystems consistent with the One Health framework. Advances in whole-genome sequencing have clarified lineage-specific gene flow, expansion of specific clones, and the dynamics of the resistome and mobilome in L. monocytogenes populations. This narrative review aims to synthesize current knowledge on the mobile genetic elements and ecological interfaces that shape horizontal gene transfer in L. monocytogenes. Its novelty lies in integrating antimicrobial resistance, virulence-associated genomic islands, stress adaptation, and gut microbiome-mediated selection within a One Health and metapopulation framework. The main message of this review is that HGT should be interpreted as a context-dependent contributor to L. monocytogenes adaptation, acting together with clonal background, ecological selection, and mobile genetic elements. Full article

Growing resistance to carbapenem antibiotics is a major public health problem as these antibiotics are considered the last line of therapy for infections caused by multidrug-resistant (MDR) Gram-negative bacteria. The rapid emergence and dissemination of carbapenem-resistant bacterial strains are mainly due to horizontal gene transfer (HGT) within or between bacterial cells via the mobilome. The aim of this article is to discuss the role of mobile genetic elements (MGEs) that capture and disseminate resistance determinants of carbapenem antibiotics, as a comprehensive review integrating the combined role of plasmids, transposons and integrons. It attempts to systematically fill the gap by investigating the role of these MGEs in the acquisition, mobilization and dissemination of genes encoding carbapenemases across clinically important bacteria. Various types of plasmids such as IncF and IncH in Klebsiella pneumoniae, IncL/M in Enterobacter cloacae, IncX3 in Escherichia coli and IncA/C₂ in Salmonella enterica carry important genes encoding carbapenemases. The rapid distribution of transposons among bacterial species is one of the main contributing factors in the dissemination of carbapenem-resistant isolates. Transposons including Tn4401 carrying bla_KPC in K. pneumoniae and Tn1721 carrying bla_KPC in E. coli; Tn2006, Tn2007, Tn2008 and Tn2009 carrying bla_OXA-23 in Acinetobacter baumannii; Tn1696 carrying bla_IMP-4 in Pseudomonas aeruginosa; Tn125 carrying bla_NDM in E. coli; and Tn6306 carrying bla_IMI in Raoultella ornithinolytica encode different types of carbapenemases. Integrons mainly belonging to class 1 capture resistance determinants for metallo-carbapenemases such as NDM-, VIM-, SIM- and IMP-type enzymes in P. aeruginosa, A. baumannii, K. pneumoniae and E. coli and can promote the transcription and expression of these determinants. These findings are useful for understanding the genetics of carbapenem resistance and additional knowledge on MGEs may provide avenues for screening of resistance to these antibiotics in clinical settings. Full article

Macrococcus is a genus of Gram-positive cocci in the Staphylococcaceae family and a close phylogenetic relative of Staphylococcus. It is not a significant human pathogen but is known to widely colonize different environments, including animal skin and food products. Phylogenetically, Macrococcus is distinct from yet closely related to Staphylococcus, particularly the sciuri group. The species is effectively identified through such molecular markers as hsp60 and 16S rDNA. A key biochemical feature is an identified FAD-dependent oleate hydratase in Macrococcus equipercicus (M. equipercicus). Critically, Macrococcus carries various mobile antibiotic-resistance genes, especially against β-lactams (e.g., mecB, mecD) and macrolides (e.g., mef(F), msr(G)); these genes are located on plasmids, SCCmec-like elements, or resistance islands (e.g., McRI_mecD), which facilitates their horizontal transfer. Surveillance confirms the widespread presence of methicillin-resistant Macrococcus, often with a multidrug-resistant phenotype, in food animals and their products. Although its own pathogenicity is low, Macrococcus acts as a reservoir and transmission platform for resistance genes: through horizontal gene transfer, it can potentially confer resistance to pathogenic Staphylococcus, thereby posing a threat to animal and public health. This review summarizes the basic biological characteristics and drug resistance-related research progress of the genus Macrococcus; it aims to provide a reference for subsequent studies as well as to establish technical support and a theoretical basis for the epidemiological investigation, drug-resistant strain identification, and clinical drug-resistance risk prevention and control of Macrococcus. Full article

Antimicrobial resistance (AMR) has emerged as one of the most significant global health challenges affecting both human and veterinary medicine. The growing prevalence of resistant bacterial strains in livestock and companion animals not only compromises treatment efficacy but also poses serious public health risks through potential zoonotic transmission. Recent molecular and genomic studies have shown the widespread dissemination of resistance genes across different ecological compartments, emphasizing the need for integrated monitoring systems. Antimicrobial stewardship programs and evidence-based interventions are therefore essential in veterinary medicine to mitigate these trends. This is particularly important because the emergence of multidrug-resistant (MDR) pathogens is increasingly associated with mobile genetic elements, such as plasmids, transposons, and integrons, which facilitate horizontal gene transfer within and across bacterial species. Full article

Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa’s one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human–animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5–83.7%) and 94% (95% CI: 85–98%), with significant heterogeneity (I² = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human–animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates. Full article

This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (bla_CTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four bla_CTX-M subtypes were identified. bla_CTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the bla_CTX-M gene, and 96.29% of strains successfully transferred the bla_CTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of bla_CTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework. Full article

Antimicrobial resistance (AMR) represents a global health crisis, driven largely by the mobility of resistance determinants through mobile genetic elements (MGEs). These include plasmids, integrons, insertion sequences, transposons, integrative and conjugative elements (ICEs), and prophages, which together facilitate horizontal gene transfer (HGT) across bacterial species and ecosystems. This review aims to provide a comprehensive synthesis of current knowledge on the types, mechanisms, ecological drivers, and impacts of MGEs in the dissemination of antibiotic resistance genes (ARGs). Methods involved critical evaluation of recent genomic, epidemiological, and ecological studies, alongside case studies of clinically significant resistance outbreaks. Findings highlight how MGEs function as hubs for ARG capture, recombination, and stabilization, enabling the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens. We also explored their interactions with ecological pressures such as antibiotics, heavy metals, and biocides, as well as their role in One Health transmission pathways. The significance of this study lies in linking molecular insights with applied strategies, including genomic surveillance, MGE-targeted inhibitors, phage therapy, and CRISPR-based interventions. Understanding MGEs is essential for designing effective interventions to mitigate AMR and protect global health. Full article

Campylobacter jejuni is a major zoonotic pathogen that circulates among birds, livestock, humans, and environmental reservoirs, yet the genomic mechanisms that enable persistence and transmission across divergent hosts remain incompletely understood. Here, we sequenced 61 C. jejuni isolates recovered from multiple host-associated sources in Shenzhen, China, from 2016 to 2023, and analyzed them together with 312 dereplicated publicly available high-quality reference genomes. Phylogenomic analyses resolved three major clades, including one avian-restricted clade and two clades showing frequent cross-host occurrence. Human-associated isolates displayed lower coding density than mammal-associated isolates and significantly higher proteome-level carbon and nitrogen demands than avian-associated isolates. Comparative genomic analyses further revealed strong host-associated divergence in chromosome-encoded, plasmid-encoded, and horizontally acquired gene repertoires. In human-derived isolates, 11 dataset-specific human-unique KEGG genes and 48 human-unique virulence-associated genes were identified, and human-associated strains showed the strongest multidrug-resistance signal across both chromosome-encoded and mobile-gene compartments. Resistance-associated functions enriched in human-associated genomes included antibiotic inactivation, efflux-mediated resistance, target protection/replacement/alteration, reduced permeability, and nutrient-acquisition-associated resistance. By contrast, core host-interaction loci remained under strong purifying selection, indicating that major human-associated traits were linked more closely to mobile gene acquisition than to extensive mutation-driven diversification. Together, these findings support a proposed genome-partition framework of host adaptation in C. jejuni, in which relatively stable chromosomal backgrounds are complemented by rapid plasmid- and horizontal-transfer-mediated acquisition of high-impact accessory genes. Full article

Background/Objectives: Antimicrobial agents have revolutionized disease management in humans and animals; however, their misuse and overuse have accelerated the emergence and spread of antimicrobial resistance (AMR) and antimicrobial resistance genes (ARGs). Dairy farms are recognized as potential hotspots for ARG dissemination, particularly through Escherichia coli, which acts as a reservoir and vector of ARGs, enabling their horizontal transfer via plasmids and other mobile genetic elements. This study aimed to characterize the genomic diversity, ARG profiles, plasmid content, and phylogenetic relationships of E. coli isolated from dairy farm environments and milk using whole-genome sequencing. Methods: A total of 31 E. coli isolates recovered from soil, effluent, cow dung, and milk samples underwent deoxyribonucleic acid extraction, library preparation, and sequencing on the Illumina MiSeq platform, followed by comprehensive bioinformatic analysis. Results: The E. coli isolates exhibited 20 distinct sequence types, including one novel sequence type. Plasmids were detected in 71% of the isolates, with the IncF plasmid family being the most predominant. Furthermore, 12 ARG groups were identified, with β-lactam resistance genes detected in 67.7% of isolates. Notably, blaCTX-M genes were identified in all phenotypically confirmed extended-spectrum β-lactamase-producing isolates. Additional ARGs, including those conferring resistance to tetracyclines (tet(A), tetX4), quinolones (qnrS1), aminoglycosides (aph, aad, ant), and folate pathway inhibitors (dfr and sul), were widely distributed throughout the samples. Phylogenetic analysis revealed clustering of isolates from different sample types, particularly among ST58 isolates, suggesting cross-environmental transmission. Conclusions: This study demonstrates that E. coli from dairy farm environments harbor diverse ARGs and plasmids, confirming their role as reservoirs of AMR. These findings underscore the importance of prudent antimicrobial use, routine genomic surveillance, and enhanced biosecurity measures to limit cross-environmental transmission. Full article

Antimicrobial resistance (AMR) constitutes one of the most severe and pressing threats to global public health, food security, and environmental integrity. This review synthesizes current evidence across interconnected One Health domains—humans, animals, food, and the environment—to delineate the scope, mechanisms, and drivers of AMR transmission. Our analysis reveals three principal findings. First, the scope of AMR is alarmingly extensive, with antibiotic-resistant bacteria (ARB) and genes (ARGs) now pervasive across all four ecological compartments, transcending traditional clinical boundaries. Second, this widespread distribution is critically facilitated by horizontal gene transfer mechanisms, particularly via mobile genetic elements such as plasmids, which enable ARGs to disseminate rapidly between diverse bacterial populations across different ecosystems. Third, we identify multiple interconnected drivers that actively promote this cross-ecosystem spread, encompassing both evolutionary and transmission drivers. By characterizing these critical transmission pathways and underlying drivers, this review provides an integrated framework to identify critical transmission risks and inform integrated strategies for mitigating antimicrobial resistance across One Health domains. Full article

The rapid spread of antibiotic resistance through plasmid-mediated conjugation remains a primary global health concern. Despite its critical role in horizontal gene transfer, no approved drugs currently target this process, leaving a critical therapeutic gap. Integration Host Factor (IHF), a DNA-binding protein essential for plasmid replication and mobilization, emerges as a promising yet underexplored target for anti-conjugation strategies. This work aimed to develop a predictive computational model and identify small molecules that disrupt IHF function, thereby reducing plasmid transfer and limiting resistance gene dissemination. A curated dataset of 65 compounds with reported anti-plasmid activity was analyzed using a 3D-QSAR model based on algebraic descriptors computed with QuBiLS-MIDAS. The model was validated through leave-one-out cross-validation (Q² = 0.82), Tropsha’s criteria, and Y-scrambling. Representative compounds were selected via pharmacophore clustering and evaluated through molecular docking at both the DNA-binding site and a predicted allosteric pocket of IHF. The most promising complexes underwent 200 ns molecular dynamics simulations to assess stability and interaction patterns. The QSAR model demonstrated strong predictive performance (R² = 0.90). Docking simulations revealed more favorable binding energies at the allosteric site (up to −12.15 kcal/mol) compared to the DNA-binding site. Molecular dynamics confirmed the stability of these interactions, with allosteric complexes showing lower RMSD fluctuations and consistent binding energy profiles. Dynamic cross-correlation analysis revealed that allosteric ligand binding induces conformational changes in key catalytic residues, including Pro65, Pro61, and Leu66. These alterations may compromise DNA recognition and disrupt the initiation of replication. To our knowledge, this is the first computational study proposing allosteric inhibition of IHF as an anti-conjugation strategy. These findings provide a foundation for experimental validation and the development of novel agents to prevent horizontal gene transfer, offering a promising approach to restoring antibiotic efficacy against multidrug-resistant pathogens. Full article

Antimicrobial resistance (AMR) poses a severe threat to global health by limiting treatment options and increasing clinical and economic burdens. This review synthesizes evidence showing that resistance evolution is strongly shaped by antibiotic pressure, leading to the accumulation of adaptive mutations, activation of efflux systems, and widespread dissemination of resistance determinants across clinical, animal, and environmental settings. We highlight recent genomic, metagenomic, and structural findings that elucidate the molecular basis of AMR, with particular emphasis on horizontal gene transfer mediated by mobile genetic elements such as plasmids, integrons, and transposons. Analyses across One Health interfaces reveal extensive sharing of antimicrobial resistance genes among humans, livestock, and environmental reservoirs, identifying Enterobacteriaceae and ESKAPE pathogens as key hubs of resistance dissemination. Special focus is placed on Acinetobacter baumannii, where phylogenetic and three-dimensional structural analyses of class D β-lactamases OXA-23 and OXA-24/40 demonstrate a conserved catalytic framework coupled with substantial sequence and conformational variability. These structural differences likely influence carbapenem specificity and resistance levels. Collectively, the findings underscore how genetic diversity, mobile elements, and structural adaptation converge to drive AMR, reinforcing the need for integrated genomic and structural approaches to guide surveillance and antimicrobial development. Full article

Environmental metagenomics and microbial taxonomy provide essential frameworks to evaluate how population structures shape the evolution of antimicrobial resistance and microbial community dynamics within densely populated environments. To evaluate microbial community composition and pathogenic potential, high-touch surfaces at high-traffic sites on and off campus were analyzed using metagenomics and characterization of 188 bacterial isolates, including antibiotic susceptibility testing, hemolytic assays, and whole-genome sequencing. Off-campus sites showed significantly higher bacterial richness and more complex communities enriched with diverse potential pathogens. Notably, high-risk carbapenemase genes were predominantly identified in these off-campus urban environments. In contrast, on-campus environments harbored less diverse communities dominated by opportunistic, antibiotic-resistant Staphylococcus species, with metagenomic analysis confirming a concentrated enrichment of β-lactam resistance determinants associated with methicillin-resistant staphylococci. Phenotypic profiling revealed extensive antimicrobial resistance, with 84.7% of isolates exhibiting resistance to at least one antibiotic and 35.1% of Staphylococcus showing hemolytic activity. Whole-genome sequencing further revealed that these resistance and pathogenic traits are predominantly localized on mobile plasmids, highlighting a high potential for horizontal gene transfer. These findings indicate that population activities shape distinct microbial communities in closely adjacent environments and highlight the importance of monitoring high-risk resistance determinants in densely populated university settings. Full article