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Search Results (840)

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Keywords = genes for AMR

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15 pages, 280 KB  
Article
Antimicrobial Resistance and Species Dynamics of Enterococcus faecalis and Enterococcus faecium in Breeding Hens: Phenotypic and Genotypic Characterization
by Alejandro Fenollar, María A. Ferrús, Pablo Catalá-Gregori, Vicente Tallá-Ferrer, Miguel García-Ferrús and Ana Isabel Jiménez-Belenguer
Vet. Sci. 2026, 13(8), 795; https://doi.org/10.3390/vetsci13080795 - 9 Aug 2026
Viewed by 163
Abstract
Enterococcus faecalis and Enterococcus faecium are commensal bacteria of poultry but also important opportunistic pathogens and key indicators for antimicrobial resistance (AMR) surveillance within a One Health framework. However, data on the occurrence and antimicrobial resistance of enterococci in breeding hens remain limited [...] Read more.
Enterococcus faecalis and Enterococcus faecium are commensal bacteria of poultry but also important opportunistic pathogens and key indicators for antimicrobial resistance (AMR) surveillance within a One Health framework. However, data on the occurrence and antimicrobial resistance of enterococci in breeding hens remain limited despite their critical role in the poultry production pyramid. This study evaluated the prevalence, antimicrobial resistance profiles, and resistance genes of Enterococcus faecalis and Enterococcus faecium isolated from two commercial breeding hen farms in eastern Spain. A total of 330 isolates were obtained from different production stages and sample types. Species identification was performed by multiplex PCR, antimicrobial susceptibility was assessed using disk diffusion according to Clinical and Laboratory Standards Institute (CLSI) guidelines, and resistance genes (erm and tet) were detected by PCR. A significant age-related shift from E. faecalis in early production stages to E. faecium in adult hens was observed. High resistance rates were detected for tetracycline (up to 95.2%) and erythromycin, whereas resistance to critically important antimicrobials such as vancomycin, aminoglycosides, and ampicillin was rare or absent. Significant differences between farms were identified in both antimicrobial resistance levels and the prevalence of multidrug resistance. The most prevalent resistance genes were ermB, tetL, and tetM, frequently co-occurring. This study shows that breeding hens constitute a relevant reservoir of AMR within poultry production systems. Species dynamics and resistance patterns appear to be influenced by age and farm-related factors. These findings underscore the need for continuous AMR surveillance integrating phenotypic and genotypic approaches from a One Health perspective. Full article
(This article belongs to the Section Veterinary Food Safety and Zoonosis)
15 pages, 1128 KB  
Article
Antimicrobial Resistance and Selected Virulence-Associated Genes Escherichia coli Pathotypes in Free-Living Cats from Southern Spain
by Gómez-Gascón Lidia, Romero-Salmoral Antonio, Huerta Lorenzo Belén, Galán-Relaño Ángela, Marco-Fuertes Ana, Mena-Rodríguez Mª Ángeles, Molina Guillén Eva and Rafael J. Astorga Márquez
Animals 2026, 16(15), 2435; https://doi.org/10.3390/ani16152435 - 6 Aug 2026
Viewed by 206
Abstract
Stray cats may act as reservoirs of antimicrobial-resistant and potentially pathogenic bacteria, representing a potential public health concern within a One Health framework. This study investigated the occurrence of antimicrobial resistance (AMR), multidrug resistance (MDR), and virulence-associated traits in commensal Escherichia coli isolated [...] Read more.
Stray cats may act as reservoirs of antimicrobial-resistant and potentially pathogenic bacteria, representing a potential public health concern within a One Health framework. This study investigated the occurrence of antimicrobial resistance (AMR), multidrug resistance (MDR), and virulence-associated traits in commensal Escherichia coli isolated from free-living cat colonies in southern Spain. A total of 169 rectal swabs were collected from cats belonging to feline colonies and shelters in Benalmádena (Málaga, Spain). Bacterial isolation and identification were performed using selective culture media, conventional biochemical tests, and MALDI-TOF mass spectrometry. Antimicrobial susceptibility was determined by minimum inhibitory concentration (MIC) testing against 15 antimicrobial agents, and isolates were screened for selected virulence-associated genes associated with major diarrheagenic E. coli pathotypes. A total of 68 E. coli isolates (40.2%) were recovered. The highest resistance frequencies were observed for sulfamethoxazole (25.0%) and ampicillin (20.6%), whereas all isolates showed high susceptibility rates to most of the antimicrobials tested, including azithromycin (100%), as well as gentamicin, amikacin, cefotaxime, ceftazidime, meropenem, colistin, chloramphenicol and tigecycline (98.5%). Six isolates (8.8%) were classified as multidrug-resistant. In addition, six isolates (8.8%) were identified as atypical enteropathogenic E. coli (aEPEC), although none exhibited a multidrug resistance phenotype. These findings demonstrate the presence of both AMR and virulence-associated traits among commensal E. coli circulating in free-living cats. The inclusion of feline colonies or shelters in AMR surveillance programmes may contribute valuable information for integrated One Health monitoring strategies. Full article
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27 pages, 1718 KB  
Article
Molecular Characteristics and Factors Associated with Antimicrobial Resistance in Campylobacter Isolates from Small-Scale Chicken Farms in Southern Thailand
by Nguyen Thi My Nhan, Doan Hoang Phu, Phitchayapak Wintachai and Thotsapol Thomrongsuwannakij
Antibiotics 2026, 15(8), 756; https://doi.org/10.3390/antibiotics15080756 - 5 Aug 2026
Viewed by 301
Abstract
Background/Objectives: Campylobacter spp. are leading causes of foodborne gastroenteritis, and small-scale poultry farms are important reservoirs of antimicrobial resistance (AMR). This study investigated the prevalence of Campylobacter spp., AMR profiles, virulence genes, and associated risk factors of Campylobacter isolates in small-scale chicken [...] Read more.
Background/Objectives: Campylobacter spp. are leading causes of foodborne gastroenteritis, and small-scale poultry farms are important reservoirs of antimicrobial resistance (AMR). This study investigated the prevalence of Campylobacter spp., AMR profiles, virulence genes, and associated risk factors of Campylobacter isolates in small-scale chicken farms in southern Thailand. Methods: Cloacal swab samples were collected from 10 randomly selected birds at three time points across 12 farms. Isolates were identified by multiplex PCR. Antimicrobial susceptibility was determined by agar dilution. Resistance-associated genes (gyrA, 23S rRNA A2075G/A2074C, cmeABC, tet(O)) and virulence genes (flaA, flhA, cadF, cdtABC) were detected using PCR. Risk factors were analyzed using logistic regression. Results: Of 358 cloacal samples, 151 were positive for Campylobacter spp. (overall weighted prevalence: 53.56%). A total of 153 isolates were recovered from positive samples of 142 C. jejuni (weighted prevalence: 50.04%) and positive samples of 11 C. coli (crude prevalence: 3.07%), as two samples contained mixed infections of both species. For C. jejuni, weighted resistance was high for CIP (91.44%), NAL (90.10%), and TET (64.22%), while erythromycin resistance was absent (0.00%), and MDR was low (0.70%). For C. coli, resistance reported as crude proportions was 81.82% for CIP, 72.73% for NAL, 45.45% for TET, 0.00% for ERY, and 9.09% for MDR. The gyrA Thr-86-Ile mutation was associated with quinolone and fluoroquinolone resistance, and the A2074C mutation with tylosin resistance. The cmeABC operon was found in all isolates. The cdt virulence cluster was present in all C. jejuni, but largely absent in C. coli. Multivariable modelling showed that prevalence was associated with larger flock size, inadequate manure management, and overall antimicrobial use, whereas AMR was associated with farm location, owner age, and specifically tetracycline use. Conclusions: High prevalence and molecular diversity of Campylobacter highlight the need for improved antimicrobial stewardship and biosecurity in small-scale poultry systems. Full article
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17 pages, 2819 KB  
Article
Genomic Insights into the Population Structure and Antimicrobial Resistance of the Most Prevalent Human-Associated Non-Typhoidal Salmonella Serotypes in Romania
by Mihaela Oprea, Laura-Ioana Popa, Daniela Cristea, Sorin Dinu, Andreea Ghiță, Catherine Ragimbeau, Lavinia-Cipriana Rusu and Codruța-Romanița Usein
Microorganisms 2026, 14(8), 1716; https://doi.org/10.3390/microorganisms14081716 - 5 Aug 2026
Viewed by 248
Abstract
This study aimed to identify circulating lineages of the most prevalent human-associated Salmonella serotypes identified through routine surveillance in Romania between 2023 and 2025 and assess their role in the spread of antimicrobial resistance (AMR). A total of 271 isolates (217 S. Enteritidis, [...] Read more.
This study aimed to identify circulating lineages of the most prevalent human-associated Salmonella serotypes identified through routine surveillance in Romania between 2023 and 2025 and assess their role in the spread of antimicrobial resistance (AMR). A total of 271 isolates (217 S. Enteritidis, 28 monophasic S. Typhimurium, and 26 S. Typhimurium) were investigated using Illumina short-read sequencing. The isolates were assigned to 9 MLST sequence types (STs) and 109 core genome MLST complex types. The predominant STs were ST11 (96% in S. Enteritidis), ST19 (77% in S. Typhimurium), and ST34 (79% in monophasic S. Typhimurium). Overall, 148 isolates carried at least one AMR determinant, including 28 acquired genes and 6 gene mutations, conferring resistance to ten antimicrobial classes. Four percent of all isolates were predicted to be multidrug-resistant, often associated with determinants conferring tolerances to biocides and/or heavy metals. The most prevalent resistance markers were GyrA_D87Y in S. Enteritidis ST11 (94/217) and blaTEM-1 in S. Typhimurium ST19 (7/26). Among monophasic S. Typhimurium ST34 isolates, the co-occurrence of blaTEM-1, aph(3”)-Ib, aph(6)-Id, sul2, and tet(B) genes was common (17/28). The 43 predicted AMR plasmids were not shared across serotypes, except among those carrying the qnrB19 gene. These results provide a genomic baseline for AMR surveillance in Romania and strengthen the human surveillance component of national One Health efforts to control resistant Salmonella. Full article
(This article belongs to the Special Issue Genomic Insights into Microbial Pathogens)
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17 pages, 791 KB  
Article
Baseline Investigation of Non-Wild-Type Bacterial Indicators and Antibiotic Resistance Genes in Urban Wastewater from Patras, Greece
by Zoi Anastopoulou, Konstantina Charalambous, Angelos Padouvas, Rafail Fokas, Kalypso-Angeliki Koukouvini, Maria Athanasiou, Nikolaos Giormezis, Despoina Gkentzi and Apostolos Vantarakis
Microorganisms 2026, 14(8), 1714; https://doi.org/10.3390/microorganisms14081714 - 4 Aug 2026
Viewed by 204
Abstract
Antimicrobial resistance (AMR) is a major public health concern, and wastewater monitoring can complement clinical surveillance by capturing resistance signals at the population level. This exploratory study assessed selected antibiotic-resistant bacteria and antimicrobial resistance genes (ARGs) in untreated influent wastewater from the municipal [...] Read more.
Antimicrobial resistance (AMR) is a major public health concern, and wastewater monitoring can complement clinical surveillance by capturing resistance signals at the population level. This exploratory study assessed selected antibiotic-resistant bacteria and antimicrobial resistance genes (ARGs) in untreated influent wastewater from the municipal wastewater treatment plant of Patras, Greece. Escherichia coli, Pseudomonas aeruginosa, and Enterococcus spp. were isolated using culture-based methods, tested for antimicrobial susceptibility by disk diffusion and Etest according to EUCAST epidemiological cut-off values, and screened by real-time PCR for intI1, sul1, qnrS1, blaTEM, blaVIM, vanA, and ermB. Among 16 E. coli isolates, non-wild-type (non-WT) profiles were detected on 14/16 for meropenem and 15/16 for ciprofloxacin, whereas only 1/16 was non-WT for ampicillin. All 13 P. aeruginosa isolates were wild type (WT) for meropenem but non-WT for ciprofloxacin, while all 17 Enterococcus spp. isolates were WT for vancomycin and ampicillin. Molecular screening showed that blaTEM was the most frequently detected gene in E. coli, while intI1 and sul1 were detected in subsets of P. aeruginosa isolates. No targeted ARGs were detected in Enterococcus spp. These findings provide preliminary, site-specific baseline information on selected AMR phenotypes and genetic determinants in wastewater-derived bacterial isolates from Patras. Full article
(This article belongs to the Special Issue Epidemiology of Foodborne and Waterborne Diseases)
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15 pages, 1674 KB  
Perspective
The Role of Migratory Birds in the Dissemination of Antimicrobial Resistance: A One Health Perspective
by Ahmad Ali, Mohammad Adil, Bilal Ahmad, Muhammad Ilyas, Rakhshanda Rani, Uzair Alam, He Hongsu, Zhang Hui and Sun Zhihua
Vet. Sci. 2026, 13(8), 782; https://doi.org/10.3390/vetsci13080782 - 4 Aug 2026
Viewed by 302
Abstract
Antimicrobial resistance (AMR) is a major One Health challenge driven by antimicrobial misuse in human medicine, veterinary practice, animal production, and polluted environments. Migratory birds move among wetlands, farms, wastewater-affected habitats, landfills, and coastal ecosystems and may acquire and redistribute antimicrobial-resistant bacteria (ARB) [...] Read more.
Antimicrobial resistance (AMR) is a major One Health challenge driven by antimicrobial misuse in human medicine, veterinary practice, animal production, and polluted environments. Migratory birds move among wetlands, farms, wastewater-affected habitats, landfills, and coastal ecosystems and may acquire and redistribute antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs) across ecological and political boundaries. This perspective synthesizes evidence on exposure sources, bacterial reservoirs, resistance determinants, cross-species interfaces, and surveillance priorities while explicitly distinguishing four claims: detection or carriage, persistence in individual birds, redistribution along migratory routes, and onward transmission to recipient hosts or environments. Published studies report multidrug-resistant Escherichia coli, Klebsiella pneumoniae, Salmonella spp., Enterococcus spp., and Campylobacter spp., with determinants including blaCTX-M, blaTEM, blaNDM, mcr, tet, sul, and qnr genes. The eight evidence groups summarized here constitute an illustrative, non-comprehensive selection; they are predominantly observational surveys or screenings, and none reconstructs a complete source–bird–destination–recipient transmission chain. Taxon-specific ecology modifies exposure: gulls and storks frequently exploit refuse and wastewater, waterfowl and shorebirds connect aquatic habitats, whereas passerines often reflect more local point-source contamination. Current evidence therefore supports migratory birds primarily as mobile sentinels and opportunistic carriers of anthropogenic AMR, while acknowledging possible natural or ancestral resistance in avian-associated microbiota. Future surveillance should combine longitudinal sampling, baseline cohorts such as pre-migratory nestlings, paired bird–water–soil–sediment sampling, whole-genome sequencing, plasmid profiling, telemetry, environmental DNA, wastewater-based epidemiology, and interoperable veterinary reporting. Practical mitigation requires antimicrobial stewardship, wastewater and landfill control, farm biosecurity, and coordinated veterinary, environmental, and public-health action. Full article
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56 pages, 2904 KB  
Review
Functional Liposomal Nanocarriers for the Treatment of Antimicrobial-Resistant and Biofilm-Associated Ocular Infections
by Paula Stefana Pintilei, Roya Binaymotlagh, Farid Hajareh Haghighi, Laura Chronopoulou and Cleofe Palocci
Macromol 2026, 6(3), 56; https://doi.org/10.3390/macromol6030056 - 31 Jul 2026
Viewed by 400
Abstract
Nanomedicine-based liposomal delivery systems are gaining increasing attention as advanced therapeutic platforms for managing ocular infections associated with antimicrobial resistance (AMR) and biofilm formation. The primary objective of this review is to critically evaluate the potential of liposomal drug delivery systems for improving [...] Read more.
Nanomedicine-based liposomal delivery systems are gaining increasing attention as advanced therapeutic platforms for managing ocular infections associated with antimicrobial resistance (AMR) and biofilm formation. The primary objective of this review is to critically evaluate the potential of liposomal drug delivery systems for improving the treatment of antimicrobial-resistant and biofilm-associated ocular infections by integrating current knowledge on antimicrobial resistance mechanisms, biofilm-targeted therapeutic strategies, and advances in liposomal formulations, while also identifying the major limitations, translational challenges, and knowledge gaps in this rapidly evolving field. Traditional ocular antimicrobial treatments are frequently limited by poor drug penetration, short precorneal residence time, low bioavailability, systemic side effects, and inadequate activity against resistant microorganisms and biofilm-embedded pathogens. This review provides a comprehensive overview of different liposomal systems, including conventional, cationic, polyethylene glycol (PEG)-modified, deformable, and stimulus-responsive liposomes, and discusses their advantages in ophthalmic drug delivery, such as enhanced corneal permeation, prolonged drug retention, controlled release, improved biocompatibility, and reduced ocular toxicity. The review further examines the mechanisms through which liposomes help overcome AMR, including improved epithelial transport, membrane disruption, intracellular drug delivery, efflux pump evasion, and enhanced antimicrobial efficacy. In addition, liposomal approaches targeting ocular biofilms are explored, focusing on improved biofilm penetration and the delivery of anti-biofilm agents such as antibiotics, enzymes, quorum-sensing inhibitors, and antimicrobial peptides. Current evidence from in vitro and in vivo ocular infection models is summarized together with disease-specific applications in keratitis, endophthalmitis, and contact lens-related infections. The article also compares liposomes with other ocular nanocarriers and addresses important considerations related to safety, stability, sterilization, large-scale production, and regulatory translation. In addition to highlighting recent advances, this review critically discusses the current limitations of liposomal formulations, the major barriers to clinical translation, and the key knowledge gaps that should be addressed to facilitate the future development and successful clinical application of these systems. Finally, emerging directions including ligand-targeted and stimulus-responsive liposomes, AI-driven formulation development, personalized nanotherapy, and gene therapy combinations are discussed as promising future strategies for combating resistant ocular infections. Full article
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24 pages, 5140 KB  
Article
Phenotypic and Genomic Divergence in Biofilm Formation in STEC and Non-STEC Escherichia coli: The Impact of Genomic Plasticity on the Virulence and Persistence of Bovine Isolates
by Vinicius Silva Castro, Emmanuel W. Bumunang, Xianqin Yang, Yuri Duarte Porto, Eduardo Eustáquio de Souza Figueiredo and Kim Stanford
Pathogens 2026, 15(8), 807; https://doi.org/10.3390/pathogens15080807 - 31 Jul 2026
Viewed by 287
Abstract
Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of global relevance whose persistence in food processing environments is frequently mediated by biofilm formation. The acquisition of stx prophages and associated regulatory mutations can impose adaptive restrictions on this phenotype. This study analyzed [...] Read more.
Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of global relevance whose persistence in food processing environments is frequently mediated by biofilm formation. The acquisition of stx prophages and associated regulatory mutations can impose adaptive restrictions on this phenotype. This study analyzed 216 whole-genome sequences (WGS) to investigate the genomic determinants of biofilm formation in a diverse collection of E. coli isolates (STEC and non-STEC) isolated from cattle feedlots. Genomes were characterized for serogroup, MLST, stx subtyping, integrity of the mlrA and rpoS regulators, single nucleotide polymorphisms (SNPs) in the csg/bcs operons, antimicrobial resistance (AMR) genes, and plasmid replicons. The biofilm phenotype was quantitatively evaluated using a crystal violet assay at 15 °C for 96 h. Results demonstrated higher biofilm forming ability among non-STEC isolates compared to STEC strains, with strains simultaneously carrying both stx1 and stx2 exhibiting the lowest prevalence of biofilm formation (3.3%). Although the rpoS mutation did not show a significant overall association (p = 0.354) with biofilm formation, it was universally present across all O157:H7 isolates, and likely enhanced mlrA disruption toward csgD repression. In addition, stx-positive isolates accumulated significantly more SNPs in the curli (csg) and cellulose (bcs) structural genes. Exploratory gene-level association tests and multiple correspondence analysis further indicated that stx status was associated with broader differences in non-stx accessory gene composition. In addition, there was no statistical association between AMR classes and biofilm-forming capacity. Furthermore, STEC strains demonstrated a lower frequency of resistance to aminoglycosides, phenicols, and tetracyclines. Finally, the plasmid replicons IncX1 and IncFII(pSE11) were present and associated with biofilm-positive isolates. In conclusion, biofilm suppression in STEC suggests a multifactorial and evolutionary phage-induced regulatory trade-off, whereas biofilm persistence in non-STEC strains is independently driven by mobile genetic elements and potential accessory determinants. Full article
(This article belongs to the Section Bacterial Pathogens)
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25 pages, 1714 KB  
Review
Raw Milk as a Vehicle for Antimicrobial-Resistant Pathogens: Emerging Public Health Risks from a One Health Perspective
by Koycho Koev
Microbiol. Res. 2026, 17(8), 149; https://doi.org/10.3390/microbiolres17080149 - 30 Jul 2026
Viewed by 260
Abstract
Raw-milk and raw dairy products remain a high-sensitivity One Health interface because they bypass a major microbial control step and may carry viable foodborne pathogens, bacteria exhibiting antimicrobial resistance (AMR), and AMR genes from dairy animals, farm environments, milking equipment, handlers, storage systems, [...] Read more.
Raw-milk and raw dairy products remain a high-sensitivity One Health interface because they bypass a major microbial control step and may carry viable foodborne pathogens, bacteria exhibiting antimicrobial resistance (AMR), and AMR genes from dairy animals, farm environments, milking equipment, handlers, storage systems, and informal or direct-sale chains. This narrative review synthesizes verified scientific evidence on raw milk as a potential vehicle pathway for resistant foodborne pathogens, clinically relevant opportunistic bacteria, indicator organisms, and AMR determinants, and evaluates AMR-related emerging public health risks through a One Health perspective. The review integrates evidence from outbreak investigations, raw milk and raw dairy surveillance, culture-based antimicrobial susceptibility testing, polymerase chain reaction (PCR), whole-genome sequencing (WGS), metagenomics, metaproteomics, risk assessment, and the consumer-risk literature. The synthesis shows that raw-milk-associated AMR evidence should be interpreted by inference level rather than by a single organism or global prevalence estimate. Public health concern becomes stronger when detection or occurrence is supported by viable recovery, plausible consumer exposure, transmission linkage, infection or colonization evidence, source-attribution data, or quantified burden estimates. Evidence is strongest for exposure pathways involving Campylobacter, extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, methicillin-resistant Staphylococcus aureus (MRSA), Salmonella, Listeria, Enterococcus, Yersinia, and raw-milk resistomes, although causal strength differs across organism groups and study designs. The review distinguishes detection or occurrence, viable recovery, potential exposure, transmission, infection or colonization, source attribution, and attributable AMR burden. One Health control requires mastitis prevention, prudent antimicrobial use, milking hygiene, environmental monitoring, pasteurization or equivalent exposure barriers, WGS-supported outbreak investigation, integrated surveillance, and targeted risk communication. Full article
(This article belongs to the Section Medical and Veterinary Microbiology)
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19 pages, 1554 KB  
Article
Transcriptome-Integrated Metabolic Modeling Identifies Candidate Metabolic Adjuvants in Antibiotic-Resistant Pseudomonas aeruginosa
by Ceyda Kula, Rabia Cankul Kerek and Kazim Yalcin Arga
Antibiotics 2026, 15(8), 730; https://doi.org/10.3390/antibiotics15080730 - 28 Jul 2026
Viewed by 379
Abstract
Background/Objectives: Antimicrobial resistance (AMR) poses a major global health challenge, particularly in opportunistic pathogens such as Pseudomonas aeruginosa. This study aimed to identify metabolic adaptations associated with antibiotic resistance by integrating transcriptomic data from drug-resistant clinical isolates with a genome-scale metabolic model [...] Read more.
Background/Objectives: Antimicrobial resistance (AMR) poses a major global health challenge, particularly in opportunistic pathogens such as Pseudomonas aeruginosa. This study aimed to identify metabolic adaptations associated with antibiotic resistance by integrating transcriptomic data from drug-resistant clinical isolates with a genome-scale metabolic model (GEM) of P. aeruginosa under four antibiotic treatments: ceftazidime (CAZ), ciprofloxacin (CIP), meropenem (MEM), and tobramycin (TOB). Methods: Transcriptomic data from 414 clinical isolates were integrated with the iPau21 genome-scale metabolic model (GEM) of P. aeruginosa. Differential gene expression analysis was performed using DESeq2, and differentially expressed genes (DEGs) were identified using a false discovery rate (FDR)-adjusted p-value < 0.05 and a fold-change threshold of ≥2 or ≤0.5. Reporter metabolites (RMs) were identified using the Reporter Metabolite algorithm with an FDR-adjusted p-value < 0.05. Pathway enrichment analysis was performed to characterize condition-specific metabolic alterations, and pathway significance was determined using the Benjamini–Hochberg procedure with an adjusted p-value < 0.05. Results: The analysis revealed predominantly antibiotic-specific transcriptional responses, with limited overlap in DEGs across treatment conditions. Reporter metabolite and pathway enrichment analyses identified distinct metabolic adaptations associated with biofilm formation, virulence, and stress response pathways. Several metabolites, including propionic acid, acetic acid, L-inositol, glutamine, glutarate, fumarate, and melatonin, were computationally prioritized candidate metabolites for future metabolite-based adjuvant strategies aimed at enhancing antibiotic efficacy. Conclusions: This systems biology approach provides a comprehensive framework for identifying metabolic vulnerabilities associated with AMR in P. aeruginosa. The identified metabolites represent candidate antibiotic adjuvant molecules generated through computational prioritization and should be regarded as hypotheses for future experimental validation rather than validated therapeutic interventions. These findings provide a foundation for future studies exploring metabolism-based strategies to improve antibiotic efficacy and combat antimicrobial resistance. Full article
(This article belongs to the Special Issue Advances in Antimicrobial Action and Resistance)
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19 pages, 451 KB  
Review
Novel Therapeutic Approaches and Alternatives to Antibiotic Therapy for Drug-Resistant Intra-Abdominal Infections
by Elena-Adelina Toma, Octavian Enciu, Irina-Mihaela Matache, Andrei Ludovic Porosnicu, Valentin Calu, Adrian Miron, Maliya Delawan, Mohamad Bydon and Mircea Ioan Popa
Antibiotics 2026, 15(8), 727; https://doi.org/10.3390/antibiotics15080727 - 27 Jul 2026
Viewed by 399
Abstract
Antimicrobial resistance (AMR) among pathogens involved in intra-abdominal infections (IAIs) represents a critical and escalating clinical challenge. The interconnected nature of antimicrobial resistance, spanning human medicine, veterinary practice, agricultural use and environmental reservoirs, has required coordinated international responses based on the ‘One Health’ [...] Read more.
Antimicrobial resistance (AMR) among pathogens involved in intra-abdominal infections (IAIs) represents a critical and escalating clinical challenge. The interconnected nature of antimicrobial resistance, spanning human medicine, veterinary practice, agricultural use and environmental reservoirs, has required coordinated international responses based on the ‘One Health’ principle. This study presents an update on efforts underway worldwide to develop new antibiotics, novel combined antimicrobial agents, and alternatives to classic therapies for IAIs. New antibiotics or compounds with antibacterial activity are currently in various stages of clinical trials, including several fluoroquinolones, beta-lactamase inhibitors, and polymyxin analogues. To reduce the risk of bacterial resistance, various additions to antimicrobial treatments are being explored, such as nanoparticles (NPs), antimicrobial peptides (AMPs), bacteriophages, the CRISPR/Cas system, and probiotics. Each modality offers distinct mechanisms that circumvent established resistance pathways, including multi-target membrane disruption, sequence-specific gene editing, and microbiome restoration. Current preclinical and clinical evidence is synthesized, and key translational barriers, including delivery challenges, safety concerns, regulatory complexity, and the need for IAI-specific pharmacokinetic data are critically examined. In conclusion, the convergence of novel antibiotic agents and non-traditional antimicrobial strategies reviewed herein provides the foundation for a new paradigm in the management of drug-resistant IAIs. The transition from a monotherapy-centric approach to an integrated, multi-modal treatment framework, guided by rapid diagnostics and informed by antimicrobial stewardship, will be essential to preserve therapeutic efficacy against AMR threats of the coming decades. Full article
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23 pages, 4848 KB  
Article
Integrated Genomics and Phenotypic Analysis of Pediococcus pentosaceus BGI-N8 and Pediococcus acidilactici BGI-N9: Partial Evidence Suggesting In Vitro Probiotic Properties to Glycolipid Metabolism Regulation Potential
by Jiayi Ma, Zhihui Ma, Xinyu Yang, Yuanyuan Yao, Benliang Wei, Jielei Zhu, Qiang Luo, Haifeng Zhang, Liang Xiao, Yiyi Zhong and Yuanqiang Zou
Microorganisms 2026, 14(8), 1614; https://doi.org/10.3390/microorganisms14081614 - 24 Jul 2026
Viewed by 337
Abstract
Dietary interventions using probiotics actively regulate metabolism in obesity and type 2 diabetes. This study aimed to characterize two novel co-isolated strains, P. pentosaceus BGI-N8 and P. acidilactici BGI-N9, using an integrated genome–phenotype approach. Whole-genome sequencing established their preliminary safety and functional genotypes, [...] Read more.
Dietary interventions using probiotics actively regulate metabolism in obesity and type 2 diabetes. This study aimed to characterize two novel co-isolated strains, P. pentosaceus BGI-N8 and P. acidilactici BGI-N9, using an integrated genome–phenotype approach. Whole-genome sequencing established their preliminary safety and functional genotypes, followed by in vitro assays measuring gastrointestinal tolerance, adhesion, and metabolic enzyme activity. Genomic analysis revealed that both strains achieved genome-based safety levels, and no high-confidence transferable AMR determinants and canonical virulence factors were identified. Functional annotation showed that BGI-N8 and BGI-N9 contain essential genes for gastrointestinal adaptation, including F0F1-ATPase, the dltA-D operon, and the opp transport system. Phenotypically, BGI-N9 exhibited superior acid resistance (79.3% survival at pH 2.0), while both strains showed robust auto-aggregation (>70%) and high adhesion to HT-29 cells (ranged from 5.4 to 5.9 adherent bacteria per cell). Furthermore, the strains displayed inhibitory activity against selected indicator pathogens (88.6–97.6% inhibition). Notably, BGI-N8 and BGI-N9 showed comparable α-glucosidase inhibitory activities, with inhibition rates of 44.53% and 39.94%, respectively, Both strains also exhibited comparable cholesterol-removal capacities under the tested conditions, with removal rates of 68.76% and 74.49%. Overall, these genomic and phenotypic results supported the potentials of BGI-N8 and BGI-N9 as candidate probiotic strains with distinct complementary strengths in glycolipid regulation, providing a theoretical basis for their synergistic application. Further mechanistic, safety, and in vivo studies are required to validate their metabolic-health-related relevance. Full article
(This article belongs to the Special Issue Genomics of Microorganisms from Traditional Fermented Products)
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28 pages, 2629 KB  
Article
Global Genomic Analysis of Bovine-Associated Klebsiella pneumoniae Reveals Genetic Diversity and Resistance–Virulence Profiles
by Meihui Tian, Yaqian Liang, Jia Lu, Weidi Shi, Yang Zhao, Weize Gan, Shuan Jia, Chencheng Xiao, Tianyi Zhao and Hui Zhang
Biology 2026, 15(14), 1215; https://doi.org/10.3390/biology15141215 - 22 Jul 2026
Viewed by 371
Abstract
Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and [...] Read more.
Bovine-associated Klebsiella pneumoniae is an important bacterial species linking animal health, microbial ecology, and One Health-oriented antimicrobial resistance research. In this study, we performed a global genomic analysis of 1291 publicly available bovine-associated K. pneumoniae genomes collected from 18 countries between 2005 and 2024 using data retrieved from NCBI. MLST, core-genome phylogenetic analysis, pangenome analysis, CARD, VFDB, and PlasmidFinder were used to characterize sequence types, genomic diversity, antimicrobial resistance-associated genes, virulence-associated genes, and plasmid replicons. A total of 256 sequence types were identified, among which ST107 was the most common. Core-genome phylogenetic analysis revealed multiple genomic lineages, while pangenome analysis identified 46,325 gene clusters, including 1967 core genes and 40,595 cloud genes, indicating an open pangenome structure and substantial accessory gene diversity. Virulence-associated genes were unevenly distributed, with yagZ/ecpA being the most frequently detected determinant. In total, 138 antimicrobial resistance-associated genes or potential resistance determinants were detected across 16 antimicrobial categories, including clinically important β-lactamase- and carbapenemase-associated genes. IncF-family plasmid replicons, particularly IncFIB(K)_1_Kpn3, were frequently detected, suggesting widespread plasmid replicon-associated genomic backgrounds; however, physical co-localization between resistance genes and specific plasmid backbones could not be confirmed. Overall, this study reveals the genetic diversity, resistance-associated gene reservoir potential, heterogeneity of virulence-associated genes, and plasmid replicon backgrounds of bovine-associated K. pneumoniae. Importantly, the genome-predicted AMR potential identified in this study should not be interpreted as confirmed phenotypic resistance without further experimental validation. These findings provide genomic insights for risk surveillance, candidate control-target screening, and microbiota-oriented intervention research. Full article
(This article belongs to the Section Microbiology)
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12 pages, 481 KB  
Article
Characterization of CRISPR Loci and Antimicrobial Resistance in Foodborne Listeria monocytogenes Isolates
by Yufan Wu, Xiaoqiang Huang, Qiang Gu, Yun Li, Yuan Zhou, Lu Sun and Xiang Wang
Microorganisms 2026, 14(7), 1592; https://doi.org/10.3390/microorganisms14071592 - 21 Jul 2026
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Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) are widespread in bacterial and archaeal genomes as an adaptive immune system against invading mobile genetic elements. This study investigated the distribution of CRISPR loci and their potential association with antimicrobial resistance (AMR) in 40 foodborne [...] Read more.
Clustered regularly interspaced short palindromic repeats (CRISPR) are widespread in bacterial and archaeal genomes as an adaptive immune system against invading mobile genetic elements. This study investigated the distribution of CRISPR loci and their potential association with antimicrobial resistance (AMR) in 40 foodborne Listeria monocytogenes isolates. CRISPR analysis showed that 18 isolates harbored CRISPR Locus 1, five carried Locus 2, and five possessed both loci. Antimicrobial susceptibility testing against seven antimicrobial agents indicated that most isolates were highly susceptible to the tested agents. Specifically, all isolates were susceptible to gentamicin, ampicillin, penicillin, and tetracycline, whereas resistance was observed in a small subset of isolates: four were resistant to chloramphenicol, five to levofloxacin, and four to ciprofloxacin. Statistical analysis showed no statistically significant association between the presence of CRISPR loci and antimicrobial susceptibility phenotypes. These findings provide baseline information on CRISPR locus distribution and antimicrobial susceptibility profiles in foodborne L. monocytogenes isolates. Further studies based on larger isolate collections, whole-genome sequencing, and characterization of associated cas genes are needed to clarify the potential role of CRISPR-Cas systems in AMR evolution in this species. Full article
(This article belongs to the Special Issue Advanced Antimicrobial Susceptibility Testing and Detection)
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15 pages, 1134 KB  
Article
Antimicrobial Resistance Patterns of Cutaneous Samples in Companion Animals in North-Western Italy from 2013 to 2024
by Sara Crimi, Davide Danieli, Graziana Gambino, Michela Amadori, Cristina Vercelli and Giovanni Re
Pets 2026, 3(3), 31; https://doi.org/10.3390/pets3030031 - 16 Jul 2026
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Abstract
Skin diseases are among the most frequently diagnosed conditions in companion animals and have historically been treated empirically with antibiotics, contributing to the emergence and persistence of antimicrobial resistance (AMR). In recent years, greater awareness of AMR has led to a reduction in [...] Read more.
Skin diseases are among the most frequently diagnosed conditions in companion animals and have historically been treated empirically with antibiotics, contributing to the emergence and persistence of antimicrobial resistance (AMR). In recent years, greater awareness of AMR has led to a reduction in antibiotic use in veterinary medicine, particularly in dermatology. To assess AMR trends in skin infections and evaluate the use of diagnostic tools to guide antimicrobial prescriptions, we conducted a retrospective study of medical records from a veterinary hospital in northwestern Italy between 2013 and 2024. A total of 447 antimicrobial susceptibility tests from dogs and cats with clinical signs of skin disease were analyzed. Of these, 391 yielded positive bacterial cultures, and 56 were negative. Most positive samples came from dogs (83.4%), with cats accounting for 16.6%. The most frequently isolated bacterial families were Staphylococcaceae, Enterobacteriaceae, and Pseudomonadaceae. Amoxicillin-clavulanic acid was prescribed in 36.6% of patients, fluoroquinolones in 25.9%, while 17% received only detergent–disinfectant products. Among first-line drugs, ampicillin showed the lowest susceptibility, with resistance exceeding 60%, whereas imipenem (used as an indicator of carbapenemase production but avoided in veterinary medicine) retained high activity, with susceptibility rates of 77.2% in dogs and 90.3% in cats. These findings are clinically relevant, but continuous AMR surveillance remains essential within a One Health framework to limit the spread of resistant bacteria and resistance genes to cohabiting humans. Full article
(This article belongs to the Special Issue Pathology in Companion Animals—From Diagnostics to Treatment)
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