Search Results (237)

Objectives: Increasing antimicrobial resistance among foodborne pathogens, particularly extended-spectrum β-lactamase (ESBL) and plasmid-mediated AmpC β-lactamase (pAmpC) production, has become a major public health concern worldwide. This study aimed to determine the presence of Salmonella Enteritidis, Salmonella Typhimurium, and Escherichia coli O157:H7 in bovine carcasses and to evaluate their antibiotic resistance profiles together with ESBL and pAmpC resistance characteristics. Methods: A total of 300 bovine carcasses were examined for the presence of Salmonella spp. and E. coli O157:H7 using culture-based isolation methods following ISO 6579-1 and FDA guidelines, respectively. The isolates were confirmed by molecular methods, and stx1, stx2, eae, and hly were investigated in E. coli O157:H7 isolates. Antimicrobial susceptibility testing was performed according to EUCAST guidelines. ESBL and pAmpC production were determined phenotypically and subsequently characterized by molecular methods. Results: A total of 25 Salmonella spp. (32% S. Enteritidis and 68% S. Typhimurium) and 20 E. coli O157:H7 isolates were recovered from different bovine carcasses. stx2 was the most frequently detected virulence gene. Of the 31 phenotypically ESBL-positive isolates, 29 carried at least one ESBL-associated gene. The predominant ESBL gene was bla_CTX-M (79.3%), followed by bla_TEM and bla_SHV (37.9%). Among CTX-M gene groups, CTX-M-25 was the most prevalent (94.4%). Phenotypic pAmpC production was detected in 13 isolates, while 17 isolates carried at least one pAmpC-associated gene, with FOX identified as the predominant gene group. All isolates were resistant to pefloxacin, followed by gentamicin (93.3%) and cefoxitin (55.5%). Multidrug resistance was detected in 34 (75.6%) isolates. Conclusions: The detection of ESBL-producing, pAmpC-positive, and multidrug-resistant Salmonella spp. and Escherichia coli O157:H7 isolates in bovine carcasses indicates the presence of antimicrobial-resistant foodborne pathogens in the beef production chain. These findings highlight the need for continued monitoring of antimicrobial resistance and effective control measures at the slaughterhouse level. Full article

Background/Objectives: Antimicrobial resistance is a major public health concern requiring integrated surveillance across human, animal, and environmental sectors. Enterococcus spp. are widely distributed opportunistic bacteria with the capacity to acquire and disseminate resistance and virulence determinants. This study aimed to characterize species distribution, phenotypic antimicrobial resistance, resistance genes, and virulence-associated traits in Enterococcus spp. from One Health sources. Methods: Enterococci were recovered from 66 samples collected in Lisbon, Portugal, between late 2022 and early 2024, including healthy and sick humans, healthy and sick animals, canteen food, surface water, and public transport surfaces. RAPD-PCR was used to assess genetic diversity among 90 isolates and select 74 representative enterococci. Species identification, resistance gene screening, and virulence gene detection were performed by PCR. Antimicrobial susceptibility was assessed by disk diffusion against 12 antibiotics using CLSI criteria. Vancomycin resistance was further evaluated by agar dilution and Etest when applicable. Results: Enterococcus faecalis predominated, representing 63/74 isolates (85.1%), followed by Enterococcus faecium (5/74, 6.8%) and other Enterococcus spp. (6/74, 8.1%). Antibiotic resistance was detected across all One Health sectors. Sick Human isolates showed higher resistance than Healthy Human isolates. E. faecium showed higher resistance than E. faecalis, and all E. faecium isolates across sectors were multidrug-resistant. Rifampicin and quinupristin-dalfopristin resistance were frequent (except in E. faecalis), while linezolid resistance was not detected. Resistance and virulence determinants were distributed across sectors. Conclusions: Enterococci from human, animal, and environmental sources carried antimicrobial resistance and virulence-associated traits. These findings support integrated One Health surveillance to monitor resistant enterococci across interconnected reservoirs. Full article

Background/Objectives: Antimicrobial resistance (AMR) in Staphylococcus spp. associated with poultry production is an emerging concern with implications for animal and public health. This study aimed to characterize antimicrobial susceptibility patterns and detect targeted methicillin resistance determinants in Staphylococcus isolates recovered from broiler chickens affected by bacterial chondronecrosis with osteomyelitis (BCO). Methods: A total of 200 bacterial isolates were evaluated, of which 167 were confirmed as Staphylococcus spp. Species identification was performed using presumptive phenotypic characterization followed by 16S rRNA gene sequencing. Antimicrobial susceptibility was assessed using disk diffusion, while presumptive methicillin-resistant phenotypes were evaluated using oxacillin screening and CHROMagar MRSA. Targeted molecular detection of mecA and mecC was performed by PCR. Results: The isolates demonstrated substantial species diversity, with S. aureus as the predominant species. Antimicrobial resistance was mainly observed against β-lactam antibiotics, particularly penicillin (33.5%), whereas high susceptibility was retained for non-β-lactam agents, including ciprofloxacin, tetracycline, trimethoprim–sulfamethoxazole, and azithromycin. A targeted PCR detected mecA in 7.2% of isolates, while mecC was not detected. The detection of mecA in oxacillin-susceptible isolates suggested genotype–phenotype discordance. Conclusions: BCO-associated Staphylococcus spp. from broiler chickens showed diverse species distribution, penicillin-dominant resistance, and targeted mecA detection across multiple species, supporting the use of combined phenotypic and molecular approaches for methicillin resistance surveillance. Full article

Background and Aims: Helicobacter pylori is a major cause of chronic gastritis and peptic ulcer disease. The increasing global spread of antibiotic-resistant strains, particularly against amoxicillin and clarithromycin, poses a significant challenge to eradication therapies. Moreover, treatment-related adverse effects, often linked to antibiotic-induced intestinal dysbiosis, frequently lead to a poor patient compliance; this, in turn, promotes the persistence of resistant bacterial populations. Probiotics may mitigate these effects and improve treatment adherence. This study aimed to assess the genomic safety of new probiotics intended for adjuvant use in H. pylori eradication regimens. Methods: Whole-genome sequencing was performed on three probiotic strains: one of Lactobacillus acidophilus, and two of Bifidobacterium animalis subsp. lactis. Genomes were compared with corresponding wild-type reference strains to identify genetic variations and detect mobile genetic elements. Results: Comparative genomic analysis revealed differences between selected and wild-type strains. Importantly, no plasmids or transposons were identified, suggesting a reduced theoretical risk of horizontal transfer of antimicrobial resistance determinants. Genomic findings were consistent with in vitro phenotypic observations. Conclusions: Whole-genome sequencing provided a robust assessment of the safety profile of these strains. The absence of transferable resistance elements supports their potential use as probiotic candidates to improve tolerability and adherence to H. pylori eradication therapies, contributing to more effective treatment outcomes. Full article

Background/Objectives: Klebsiella (K.) pneumoniae is a significant pathogen in both humans and animals. However, data on its occurrence in animals in Germany remain limited. This study aimed to investigate the antimicrobial resistance (AMR) phenotypes, AMR genes, and virulence traits of animal-derived K. pneumoniae isolates from Germany. Methods: A total of 59 K. pneumoniae isolates obtained in 2023 from dogs, cats, horses, cattle, and chickens across 11 German federal states were analysed. Phenotypic antimicrobial susceptibility testing (AST) was performed, and whole-genome sequencing (WGS) was used for genomic characterisation, including detection of AMR genes, virulence-associated genes, sequence types (STs), and plasmid replicons. Results: Most isolates (78%) were susceptible to all tested antibiotics, while three isolates were classified as multidrug-resistant (MDR). Resistance was most frequently observed for piperacillin (n = 8) and trimethoprim/sulfamethoxazole (n = 4). Carbapenem resistance was detected in two isolates (one from a dog and one from a cat), and phenotypic colistin resistance in one dog isolate. WGS identified 96 AMR genes across isolates, with 20–42 AMR determinants per isolate, conferring resistance to β-lactams, aminoglycosides, fluoroquinolones, sulfonamides, tetracyclines, trimethoprim, and fosfomycin. Ten extended-spectrum β-lactamase (ESBL)-producing isolates carried genes including bla_CTX-M-15, bla_SHV-2, bla_SHV-27, bla_SHV-42, bla_SHV-106, and bla_TEM-158. Although fosA was detected in all isolates, only three exhibited phenotypic resistance to fosfomycin. A total of 52 STs were identified, including high-risk clones. One hypervirulent isolate (ST60) carrying hypervirulence-associated genes rmpA and iroB was detected. Plasmid replicons were present in 70% of isolates, while plasmid-associated AMR genes were identified in nine isolates. Conclusions: This study demonstrates the genomic diversity of K. pneumoniae identified in companion animals and highlights the presence of AMR and virulence determinants relevant to a One Health context. Full article

Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6′)-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome–mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings. Full article

Background/Objectives: Freshwater microalgae–bacteria consortia are increasingly utilized in wastewater treatment and biomass production. However, bacteria associated with the algal phycosphere may act as environmental reservoirs of multidrug-resistant (MDR) phenotypes and antibiotic resistance genes (ARGs), including resistance to last-resort antibiotics such as colistin. Methods: An axenic culture of the freshwater microalga Pectinodesmus pectinatus was established using a NaClO-based cleaning protocol. Three phycosphere-associated bacterial strains (Chryseobacterium sp., Pseudomonas monteilii, and Stenotrophomonas pavanii) were isolated and identified by 16S rRNA gene analysis. Antimicrobial susceptibility testing was performed using broth microdilution against 16 antibiotics. Whole-genome sequencing of the most resistant isolate, S. pavanii, was conducted using Oxford Nanopore technology, followed by genome annotation and in silico resistome analysis using CARD, AMRFinderPlus, and ResFinder. Results: Among the three isolates, S. pavanii exhibited the broadest resistance profile, including high minimum inhibitory concentrations (MICs) to multiple β-lactams and colistin (MIC ≥ 16 μg/mL). No plasmid-borne mcr genes were detected. Instead, the genome encoded multiple chromosomal determinants potentially associated with polymyxin non-susceptibility, including lipid A and lipopolysaccharide modification pathways (e.g., arn genes and eptA), outer-membrane maintenance and LPS transport systems, multidrug efflux pumps, and regulatory elements. Integration of genomic and phenotypic data suggested that the observed colistin non-susceptibility may be associated with intrinsic chromosomal determinants inferred from whole-genome analysis. Conclusions: This study demonstrates that the P. pectinatus phycosphere can harbor multidrug-resistant (MDR) bacteria, including strains exhibiting colistin non-susceptibility potentially associated with a repertoire of intrinsic chromosomal resistance mechanisms inferred from genomic analysis. Therefore, freshwater microalgae-based systems should be considered potential environmental reservoirs contributing to the dissemination of antimicrobial resistance. Full article

Antimicrobial resistance (AMR) represents one of the most urgent global health threats, significantly impacting patient outcomes, healthcare systems, and economic sustainability. Rapid and accurate antimicrobial susceptibility testing (AST) are essential to guide targeted therapy, reduce inappropriate antimicrobial use, and support antimicrobial stewardship programs. However, conventional phenotypic AST methods, including broth microdilution, disk diffusion, agar dilution, and gradient strip tests, remain labor-intensive and require prolonged turnaround times, often delaying optimal therapeutic decisions. Although automated commercial platforms such as VITEK 2, BD Phoenix, MicroScan WalkAway, and Sensititre ARIS have improved laboratory workflow and standardization, they still rely on culture-based approaches and typically require 16–36 h to generate minimum inhibitory concentration (MIC) results. In recent years, several innovative rapid phenotypic AST technologies have emerged, aiming to significantly shorten the time to susceptibility results while maintaining high accuracy. This review provides an overview of currently available rapid automated phenotypic platforms for MIC determination, including VITEK^® Reveal™, ASTar, FASTinov^®AST, QuickMIC^®, and the Accelerate Pheno^® system. These systems employ advanced technologies such as volatile organic compound detection, flow cytometry, microfluidics, real-time imaging, and morphokinetic cellular analysis to deliver susceptibility results within a few hours directly from positive blood cultures. We summarize their technical principles, antibiotics and pathogens included, performances, and current limitations. Overall, the implementation of rapid phenotypic AST tools has the potential to substantially improve clinical decisions, optimize antimicrobial therapy, and contribute to fight AMR. Full article

A clinical strain of the opportunistic pathogen Serratia rubidaea, a known contaminant of healthcare environments and an emerging cause of invasive infections, is described. The studied isolate, recovered from a nurse’s hand skin swab during routine screening, exhibits a broad profile of antibiotic resistance combined with reduced susceptibility to several disinfectants. Phenotypic susceptibility testing using a tablet-based microdilution and disk diffusion method was employed to determine the minimum inhibitory concentrations (MICs) of antimicrobial agents from different classes, while broth microdilution assays with disinfectants revealed high-level tolerance to widely used agents, including 70% C₂H₅OH, 3% H₂O₂, 0.05% polyhexamethylene guanidine (PHMG) and others. Whole-genome sequencing identified multiple resistance-associated determinants, such as chromosome-encoded class C $\beta$-lactamase (ampC), several efflux systems (sdeXY, macAB, and emrAB) combined with multicopy tolC, and specific transferases (fos and arnT). Shotgun bottom-up HPLC-MS/MS proteomics confirmed baseline expression of these and other stress-tolerance-related proteins under non-inducing conditions. Taken together, these data underscore the importance of surveillance for Serratia spp. in healthcare facilities to detect strains that combine intrinsic or acquired multidrug resistance with robust survival traits such as disinfectant tolerance and biofilm formation. The present study provides a reference-level phenotypic, genomic, and proteomic characterization of a S. rubidaea clinical isolate, contributing to the understanding of the adaptive potential of this resilient opportunistic pathogen in clinical environments. Full article

Hospital wastewater represents a critical hotspot for the dissemination of antibiotic resistance genes (ARGs), serving both as an environmental reservoir and a transmission pathway for multidrug-resistant bacteria into receiving ecosystems. The intense antibiotic selective pressure within healthcare facilities promotes the emergence, persistence and amplification of resistant strains, posing substantial risks to public health and environmental integrity. This study aimed to characterize Escherichia coli (E. coli) isolates recovered from hospital wastewater effluents in multiple cities across Gabon, with emphasis on bacterial loads, antimicrobial resistance patterns and associated genetic determinants. Wastewater samples were aseptically collected from sewer outlets of eleven healthcare facilities distributed across five provinces over a 12-week period, structured into two six-week sampling campaigns to capture temporal variability. A total of 158 bacterial isolates were obtained, among which 49 were confirmed as E. coli. Mean concentrations of presumptive E. coli ranged from 7.1 × 10³ to 1.49 × 10⁹ CFU/mL, indicating substantial microbial contamination of hospital effluents. Antimicrobial susceptibility testing using the Kirby–Bauer disk diffusion method against 19 antibiotics revealed that all isolates exhibited multidrug-resistant phenotypes. Resistance rates were particularly high to β-lactams and third-generation cephalosporins, reaching 90–100% in most facilities, reflecting strong selective pressure and widespread circulation of resistance mechanisms in urban aquatic environments. In contrast, carbapenems and amikacin remained comparatively effective, with resistance levels below 40%, suggesting partial preservation of last-resort therapeutic options. The values of the Multiple Antibiotic Resistance Index (MARI) ranged from 0.21 to 0.84, indicating selection pressure on different classes of antibiotics. Phylogenetic analysis showed a predominance of phylogroup A, traditionally considered commensal but increasingly associated with the spread of resistance. Groups B2, D/E and F proved to be the most resistant. These groups showed marked resistance to first-line antibiotics. The blaCTX-M-1 was the most prevalent resistance determinant (66.6%), occurring twice as frequently as blaSHV (33.3%), a finding that confirms the significant circulation of extended-spectrum β-lactamase-producing E. coli. Overall, these findings highlight hospital wastewater as a major reservoir and dissemination source of multidrug-resistant E. coli, underscoring the urgent need for improved wastewater treatment, strengthened antimicrobial stewardship and integrated One Health-based surveillance strategies. Full article

Background/Objectives: Glyphosate-based formulations are globally pervasive pollutants increasingly recognized as potential contributors to antimicrobial resistance (AMR) in environmental microbiomes. Although glyphosate is designed to inhibit plant 5-enolpyruvylshikimate-3-phosphate synthase, it also affects microbial metabolism, stress response, and genetic exchange. This review synthesizes the pathways through which glyphosate, its metabolite aminomethylphosphonic acid (AMPA), and commercial mixtures influence resistance-associated phenotypes and the dissemination of antibiotic resistance (ABR). Methods: A critical synthesis of the literature was conducted to evaluate the mechanistic and ecological interactions between glyphosate exposure and bacterial resistance in soil, aquatic, and host-associated microbiomes. Results: Experimental evidence showed that sublethal glyphosate exposure induced oxidative stress, altered membrane permeability, activated multidrug efflux pumps, and promoted tolerance phenotypes that could modify antibiotic susceptibility. It also enhances mutation rates and horizontal gene transfer processes associated with the emergence of resistance under controlled conditions. At the community level, glyphosate exposure is associated with microbiome restructuring and enrichment of resistance determinants, often without major shifts in overall diversity of the microbiome. These effects have been reported at environmentally relevant concentrations, although the evidence remains largely derived from laboratory and mesocosm studies. Conclusions: Glyphosate acts as both a biochemical modulator of resistance-related phenotypes and an environmental selective pressure that shapes microbial communities. Its widespread use and environmental persistence position it as a context-dependent contributor to the emergence and dissemination of AMR through interacting mechanistic and ecological pathways. Integrating AMR endpoints into pesticide risk assessments and surveillance frameworks is warranted, in addition to expanded field-based validation. Full article

Background/Objectives: The emergence of antimicrobial-resistant (AMR) pathogens in aquaculture ecosystems poses a significant risk to both food security and human health. Shewanella species are recognized as significant AMR reservoirs, yet their prevalence and resistance mechanisms within a shrimp-related ecosystem remain poorly characterized. This study aimed to perform a genotypic and phenotypic characterization of S. algae VK101, isolated from wild-caught black tiger shrimp (Penaeus monodon) broodstock. Methods: A complete 5.21 Mb genome was generated using a hybrid Illumina and Oxford Nanopore sequencing approach. Antimicrobial susceptibility was evaluated for 21 antibiotics via Minimum Inhibitory Concentration (MIC) testing. Comparative pangenomics and genome-wide association studies (GWAS) across 125 S. algae genomes were conducted to identify novel resistance determinants. Results: MIC analysis revealed that VK101 was resistant to ampicillin (>16 µg/mL) and colistin (8 µg/mL), while showing intermediate susceptibility to imipenem and ciprofloxacin. In silico analysis identified 205 antimicrobial resistance genes (ARGs), including a perfect hit for the fluoroquinolone resistance gene qnrA3. Notably, no mcr genes were detected. Although VK101 exhibited moderate resistance (8 µg/mL), GWAS across the broader S. algae population linked a specific lptA mutation (K140N) to high-level resistance (64 µg/mL). Other GWAS-identified genes (e.g., czcA, ampC, and oprM) likely represent indirect associations driven by genetic linkage or clade-specific markers rather than direct causal factors. Conclusions: These findings highlighted the presence of multidrug-resistant S. algae in wild-caught P. monodon broodstock, reflecting the occurrence of antimicrobial resistance in aquatic environments. Colistin resistance in these isolates was primarily mediated by chromosomal variants rather than mobile mcr elements, indicating the need for integrated genomic surveillance within the aquaculture value chain. Full article

Background/Objectives: Staphylococcus aureus (S. aureus) intramammary infection remains a major global dairy problem due to its contagious nature, its ability to persist and colonize teat/skin and mucosal niches, and the often-limited bacteriological cure achieved with antimicrobial therapy. Beyond udder health, it is relevant to public health because it can enter raw milk chains and serve as a reservoir for antimicrobial resistance determinants that may circulate between dairy animals and humans. Methods: We assessed S. aureus’ ecology in raw ewe milk from 75 sheep farms in Epirus (Greece) by sampling clinically healthy controls (group A) and clinical mastitis cases pre-treatment (group B), followed by resampling at the first post-withdrawal milking after penicillin/streptomycin treatment (group C1—therapeutic protocol 1), oxytetracycline treatment (group C2—therapeutic protocol 2), or enrofloxacin treatment (group C3—therapeutic protocol 3). Results: S. aureus detection was high and comparable across groups (A 23.0%, B 22.0–30.0%, C 20.0–22.0%), and paired analyses showed no significant pre–post shifts in detection/burden within therapeutic protocols (all p > 0.05). Nevertheless, persistence remained evident. The chromosomal gene mecA was detected in S. aureus strains in all groups, ranging from 13.6% in controls to 54.5% post-withdrawal in group C1, and was also present in the pre-treatment group. In paired sampling animals, mecA was mostly stable, with rare emergence or loss. Across antibiotic classes, within-animal resistance transitions were generally uncommon and non-significant (p > 0.05); β-lactam resistance was fully stable (p = 1.00). Descriptively, resistance to protein synthesis inhibitors tended to decline after therapy in protocol 1 and protocol 3, while protocol 3 showed post-treatment gains in fluoroquinolone resistance. By contrast, virulence-associated phenotype traits shifted after therapy: enterotoxigenicity increased post-withdrawal (especially in the C3 group), Staphylococcal Enterotoxin A (SEA) and Staphylococcal Enterotoxin B (SEB) appeared only post-therapy, Staphylococcal Enterotoxin D (SED) increased significantly in paired isolates (p = 0.002), and strong biofilm adherence increased (in C3, p = 1.5 × 10⁻⁵). Conclusions: The detection of S. aureus after therapy suggests that one possibility is that antimicrobial exposure may select for, or otherwise reshape, the residual intramammary population, rather than reliably eliminating it—an outcome that remains clinically relevant for udder health. Moreover, the persistence of mecA/methicillin-resistant Staphylococcus aureus (MRSA)-compatible profiles indicates that milk released to the food chain after withdrawal compliance may still harbor S. aureus with enhanced preservation capacity and significant food safety relevance. Full article

One of the greatest threats to global public health is antimicrobial resistance (AMR), due to the increasing number of infections caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae. Escherichia coli and Klebsiella pneumoniae ESBL-producing bacteria possess resistance mechanisms that inactivate β-lactam antibiotics by hydrolyzing their β-lactam ring, thereby limiting conventional therapeutic options. In response to this problem, the objective of this exploratory in vitro study was to evaluate the antimicrobial activity of Origanum vulgare (oregano) essential oil and its interaction with the antibiotic cefepime using in vitro methods. Antimicrobial susceptibility tests were performed, including determination of the minimum inhibitory concentration by the microdilution method with statistical analysis, and evaluation of the fractional inhibitory concentration index using the checkerboard method. In addition, advanced methods such as MALDI-TOF mass spectrometry for bacterial identification and PCR were employed for the identification of resistance genes. The studied strains exhibited both phenotypic and genotypic resistance. The MIC of the essential oil was 1024 µg/mL for ESBL-producing E. coli and 2048 µg/mL for ESBL-producing K. pneumoniae, whereas the ATCC strains showed higher susceptibility. The FICI values indicated synergism in E. coli (FICI = 0.188) and an additive effect in K. pneumoniae (FICI = 0.563). Oregano essential oil exhibits antimicrobial activity and the ability to potentiate the effect of cefepime, suggesting its potential as a therapeutic adjuvant. Additional studies are required, including a larger number of strains, cytotoxicity analyses, and clinical validation. Full article

Background: Multidrug-resistant (MDR) Escherichia coli in intensive pig production represents a persistent animal health and One Health concern. Here, we integrated quantitative phenotypic susceptibility data with whole-genome sequencing (WGS) to characterize the resistome and its inferred genomic context (chromosomal vs. plasmid-predicted contigs and mobile genetic element (MGE)-proximal regions) in swine-associated MDR E. coli from Hungary. Methods: A total of 203 E. coli isolates from large-scale pig farms were tested by broth microdilution. Based on resistance-oriented screening from an extended-spectrum β-lactamase (ESBL)-screen-positive pool, 116 isolates were subjected to whole-genome sequencing (WGS) as a resistance-enriched subset. Resistance determinants were annotated using the Comprehensive Antibiotic Resistance Database (CARD). Results: Resistance-oriented screening indicated frequent β-lactamase activity and ESBL screening positivity (110/203 and 127/203 isolates, respectively), consistent with strong antimicrobial selection pressure in the source population. Across the full phenotypic panel, 78/203 isolates (38.4%) met the MDR definition (non-susceptible to ≥3 antimicrobial classes), with marked between-farm variation (p < 0.001) but no age-group effect (p = 0.75). Non-β-lactam minimum inhibitory concentration (MIC) distributions showed pronounced, site-dependent high-MIC “tails”, most notably for tetracyclines, trimethoprim–sulfamethoxazole, fluoroquinolones, and colistin. In the WGS cohort (n = 116), we detected 82 distinct resistance determinants (5433 total occurrences), featuring a conserved chromosomal backbone enriched for intrinsic multidrug resistance components and lipid A modification pathways, alongside common plasmid- and MGE-associated acquired ARG modules involving tetracycline (tetA/tetB), sulfonamide/trimethoprim (sul/dfrA), aminoglycoside-modifying enzymes, and phenicol determinants (floR/cat). High-priority mobile determinants were rare but present, including mcr-1 (3/116; plasmid-associated) and plasmid-mediated quinolone resistance qnrB5 (2/116). Conclusions: Importantly, mobility/context inferences are restricted to this ESBL-screen-enriched WGS subset. Swine-associated E. coli from Hungarian large-scale farms harbors complex resistance architectures shaped by co-selection of mobile ARG modules on top of a pervasive chromosomal resistance backbone. Mobility-aware surveillance and stewardship are warranted to mitigate dissemination risks at the animal–environment–human interface. Full article