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Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives

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A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Antibiotics in Animal Health".

Deadline for manuscript submissions: 30 April 2026 | Viewed by 8858

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Prof. Dr. Pedro A. Jiménez Gómez

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Guest Editor

Microbiology Area, Department of Health and Pharmaceutical Sciences, School of Pharmacy, CEU San Pablo University, Madrid, Spain
Interests: antibiotic resistance; One Health; environmental microbiology

Prof. Dr. Marina Robas Mora

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Guest Editor

Special Issue Information

Dear Colleagues,

Antibiotic resistance represents a global challenge threatening public health, food safety, and environmental sustainability. The complex interplay between the clinical, environmental, and veterinary domains requires an integrated approach to understanding and mitigating the transmission of resistance mechanisms.

This Special Issue will focus on the study and prevention of antibiotic resistance transmission from a One Health perspective. Emphasizing a holistic approach, this Special Issue will uncover the pathways by which resistance mechanisms spread, particularly from non-pathogenic environmental strains to potentially human-pathogenic strains. This knowledge is critical in designing innovative interventions and policies aimed at controlling the dissemination of resistance across ecosystems.

Aims and Scope:

This Special Issue aligns with the journal's mission to advance knowledge in antibiotic resistance. Our aim is to collect high-quality original research and review articles that address key aspects of antibiotic resistance transmission and prevention. Submissions that offer interdisciplinary insights into the One Health paradigm are particularly welcome.

Suggested themes and article types for submission:

The mechanisms behind antibiotic resistance emergence and spread in natural environments;
The role of environmental reservoirs in transmitting resistance to human pathogens;
The surveillance and detection of resistance genes in clinical, environmental, and veterinary settings;
Strategies for mitigating the spread of resistance in integrated ecosystems;
Case studies showcasing successful One Health interventions;
Policy and education frameworks to support One Health approaches to resistance prevention;
New methods and techniques advancing knowledge in, and evaluating the impact of, human activities in relation to the expression of antibiotic resistance in microbial communities.

We look forward to receiving your contributions and engaging in meaningful discussions on this pressing issue.

Prof. Dr. Pedro A. Jiménez Gómez
Prof. Dr. Marina Robas Mora
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

antibiotic resistance
One Health
environmental microbiology
zoonotic pathogens
antimicrobial stewardship
resistance mechanisms
horizontal gene transfer
integrated surveillance
microbial ecology
public health

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Published Papers (8 papers)

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Research

16 pages, 1227 KB

Open AccessArticle

Antimicrobial Resistance Profiles of Gram-Negative Bacteria Isolated from Saker Falcons (Falco cherrug) in Western Romania

by Daiana-Ionela Cocoș, Oana-Maria Boldura, Eugenia Dumitrescu, Răzvan-Tudor Pătrînjan, Florin Muselin, Diana Brezovan, Janos Degi and Romeo Teodor Cristina

Antibiotics 2026, 15(4), 400; https://doi.org/10.3390/antibiotics15040400 - 15 Apr 2026

Viewed by 277

Abstract

Background/Objectives: The Saker Falcon (Falco cherrug) is an endangered raptor species of ecological and conservation relevance. Despite its status, data regarding its microbiota and the prevalence of antimicrobial resistance (AMR) remain scarce, especially in Eastern Europe. This single-facility study aims to investigate the phenotypic and genotypic AMR profiles of Gram-negative bacteria isolated from captive Saker Falcons in Western Romania. Methods: Freshly voided fecal droppings were collected non-invasively from 40 clinically healthy Saker Falcons. Bacterial identification was performed using selective media and the VITEK^® 2 system. Antimicrobial susceptibility testing (AST) was conducted on a representative subset of 12 isolates. Selected resistance-associated genes were screened by conventional PCR. Results: Escherichia coli was the most prevalent 60% (n = 24/40), followed by Hafnia alvei 10% (n = 4/40) and Pseudomonas spp. 10% (n = 4/40). AST revealed phenotypic resistance among Enterobacteriaceae primarily to ampicillin 20% (n = 2/10), tetracycline 20% (n = 2/10), fluoroquinolones and sulfonamides 10% (n = 1/10), while susceptibility to imipenem 90% (n = 9/10) and gentamicin 90% (n = 9/10) remained high. The targeted resistance-associated genes were detected in selected phenotypically resistant isolates. PCR screening detected blaZ and ampC in 62.5% (n = 5/8) of tested isolates, blaOXA-61 in 37.5% (n = 3/8), blaOXA-51 in 25% (n = 2/8), tetK in 37.5% (n = 3/8), and gyrA in 12.5% (n = 1/8). The isolate used as the negative control, pansusceptible in AST, was confirmed negative for all targeted genes. Conclusions: This single-facility study provides baseline data on AMR traits in Gram-negative bacteria associated with Saker Falcons in Western Romania. Given the limited scale and isolate-based design of the study, the findings should be interpreted cautiously, but they support further investigation of wildlife-associated AMR within a One Health context. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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15 pages, 2750 KB

Open AccessArticle

Prospective Study of the Relative Abundance of Antimicrobial Resistance Genes in Escherichia coli O157:H7 Obtained from Chicken Carcasses from Local Markets in Lima, Peru

by Daniel Desposorio-Vicente and Oscar Nolasco

Antibiotics 2026, 15(2), 191; https://doi.org/10.3390/antibiotics15020191 - 9 Feb 2026

Viewed by 741

Abstract

Objective: This study addresses antimicrobial resistance (AMR), a growing public health threat, by evaluating the role of chicken carcasses as possible vehicle for the spread of Escherichia coli O157:H7 and antimicrobial resistance genes (ARGs), with the aim of analyzing the association between bacterial load and the relative abundance of ARGs in samples obtained from an open and an enclosed market in Lima, Peru. Methods: SYBR Green qPCR was used to analyze 28 chicken carcasses from two local markets in the Lima metropolitan area (Enclosed market n = 13, and Open Market n = 15), detecting Escherichia coli O157:H7 and ARGs like bla_CTX-M, bla_TEM, and strA. Results: The bacterial load was higher in the enclosed market (5.062 log CFU/mL) than in the open market (3.875 log CFU/mL). E. coli O157:H7 was detected in 76.9% and 86.6% of samples, with average loads of 1.676 and 1.251 log CFU/mL, respectively. The relative abundance of bla_CTX-M and bla_TEM showed greater dispersion in the open market, whereas strA was more homogeneous in both markets. Significant positive correlation was found between E. coli load and ARGs abundance, stronger in the enclosed market (r = 0.904–0.945) and moderate to high in the open market (r = 0.794–0.920). Conclusions: The results demonstrate a significant correlation between E. coli O157:H7 load and ARGs, highlighting the need for a comprehensive approach within the framework of the “OneHealth” initiative. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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22 pages, 10038 KB

Open AccessArticle

Genomic Evidence Supporting a One Health Perspective on Staphylococcus aureus Bovine Mastitis

by Gabriele Meroni, Valerio Massimo Sora, Giulia Laterza, Alessio Soggiu, Piera Anna Martino, Francesca Zaghen, Luigi Bonizzi, Luciana Colombo and Alfonso Zecconi

Antibiotics 2026, 15(1), 98; https://doi.org/10.3390/antibiotics15010098 - 18 Jan 2026

Cited by 1 | Viewed by 752

Abstract

Background/Objectives: Staphylococcus aureus is a multifaceted pathogen responsible for diseases in humans and in several animal species, including dairy cows. This study aimed to characterize and compare the genetic diversity, lineage distribution, and antimicrobial resistance profiles of S. aureus isolates from bovine milk with human-derived reference genomes to investigate host adaptation and inter-species transmission. Methods: Genomic analyses were performed on S. aureus isolates from quarter milk samples of dairy cows together with human-derived sequences from public databases. Whole-genome sequencing and multi-locus sequence typing (MLST) were used to determine sequence type (ST) distribution, and the presence of key antibiotic resistance genes and mobile genetic elements (MGEs) was assessed. Comparative genomics was applied to evaluate gene content, phylogenetic relationships, and lineage–host associations. Results: The dataset encompassed bovine-adapted lineages (CC97, CC133, CC151) and human-associated lineages (CC1, CC5, CC8, CC30, CC45), as well as livestock-associated ST398 in bovine samples and human-adapted ST5 and ST6 in animals. ST8 was the only ST shared between animal and human isolates and showed differing resistance profiles, with animal ST8 carrying resistance determinants absent from human ST8. Bovine-adapted strains were characterized by recurrent loss of human-associated virulence genes and acquisition of bovine-associated mobile genetic elements, and blaZ and mecA were rarely detected in bovine-adapted CC97 but were frequently present in human CC5 and CC8. Overall, animal isolates carried fewer resistance genes than human isolates. Conclusions: S. aureus from dairy cows and humans displayed substantial genetic diversity, with evidence of host-associated lineages and dynamic changes in gene and mobile element content. These findings support the need for integrated One Health surveillance to track shared and host-adapted lineages and their antibiotic resistance determinants. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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22 pages, 1313 KB

Open AccessArticle

Antimicrobial Resistance in Bacterial Strains of Agricultural Interest: Predictions Based on Genomic Data

by Eloísa Pajuelo, Manuel Medina-Rodríguez, Noris J. Flores-Duarte, Bouchra Doukkali, Jennifer Mesa-Marín, Ignacio D. Rodríguez-Llorente and Salvadora Navarro-Torre

Antibiotics 2026, 15(1), 14; https://doi.org/10.3390/antibiotics15010014 - 20 Dec 2025

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Abstract

Background: Plant growth promoting bacteria (PGPB) are non-pathogenic bacteria that enhance plant growth through several mechanisms such as nutrient mobilization, phytohormones production, defense against phytopathogens, and alleviation of plant stress. Hence, these bacteria are used as ecologic biofertilizers to diminish the use of agrochemicals. Nevertheless, some PGPR strains can harbor antibiotic resistance determinants and the possibility of spreading them upon releasing these bacteria is an environmental concern. Objectives: The objectives of this work are as follows: (1) evaluating the antibiotic resistance in a collection of PGPB, and (2) prospecting antibiotic resistance genes in the genomes of PGPB in order to predict the risk for antibiotic resistance dissemination. Methods: The resistance towards 12 antibiotics in a collection of 20 PGPB (10 Gram-positive and 10 Gram-negative strains) has been evaluated using disk diffusion in agar, broth microdilution, and agar dilution tests. In addition, the whole genomes of six strains have been sequenced in order to find the correlation between the resistance levels and AMR genes by using bioinformatic tools. Results: The results indicated a wide range of halo diameters, but in general Gram-negatives showed higher resistance compared to Gram-positives. The four most resistant strains and the two more susceptible strains were selected for further analysis and sequencing the whole genomes. The resistant strains were identified as Achromobacter spanius N6, Leclercia adecarboxylata H17, Priestia aryabhattai strain MHA1, and Bacillus cereus N25. The susceptible strains were identified as Pantoea sp. S3 and Priestia megaterium MS4. Mining antibiotic resistance genes in the genomes confirmed the existence of resistance determinants responsible for the phenotypic behavior, indicating the potential of genomics for predicting antibiotic resistance in PGPB. However, there was not an exact correspondence between the presence of the genes and the level of resistance, suggesting the existence of additional regulatory mechanisms. Conclusions: The information obtained by genomics must be complemented experimentally by tests for antibiotic resistance determination. In this regard, it is necessary to develop a global antibiotic resistance database for PGPB, due to the difficulty of interpretation of the antibiotic susceptibility tests after comparing the experimental results with those tabulated for clinical species. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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12 pages, 348 KB

Open AccessArticle

Plasma and Muscle Pharmacokinetics of Ceftriaxone in Nile Tilapia (Oreochromis niloticus) After Different Administration Routes

by Pedro Marín, Orhan Corum, Duygu Durna Corum, Elena Badillo, María Teresa Yuste, Onder Yildirim, Ertugrul Terzi, Ruby C. Gonzales, Dan M. Arriesgado, Victor R. Navarro and Kamil Uney

Antibiotics 2025, 14(12), 1253; https://doi.org/10.3390/antibiotics14121253 - 11 Dec 2025

Viewed by 915

Abstract

Background/Objectives: The aim of this study was to determine the plasma and muscle pharmacokinetics of ceftriaxone (25 mg/kg) in tilapia after different administration routes. Methods: Two hundred and sixteen fish maintained at 30 ± 1.5 °C were divided equally into three treatment groups: intravascular (IV), intraperitoneal (IP), and intramuscular (IM). Ceftriaxone concentrations were quantified using high-performance liquid chromatography, and pharmacokinetic parameters were calculated by non-compartmental analysis. Results: The plasma total body clearance, volume of distribution at steady state, and elimination half-life (t_1/2λz) were 0.22 L/h/kg, 0.85 L/kg, and 5.27 h, respectively. The t_1/2λz values were comparable among the IV, IP, and IM injection groups. The peak plasma concentration was 37.71 ± 3.12 µg/mL and 40.51 ± 2.77 µg/mL following IP and IM injection, respectively. The bioavailability was 67.04% for IP and 101.48% for IM. The peak muscle concentration was 9.49 ± 0.75 µg/g for IV, 5.71 ± 0.85 µg/g for IP, and 12.24 ± 2.41 µg/g for IM injection. The AUC_{0–∞muscle}/AUC_{0–∞plasma} ratio was 0.23, 0.18, and 0.30 for the IV, IP, and IM groups, respectively. The AUC_muscle/AUC_plasma indicates the ratio of drug penetration into the muscle, and a value less than 1 indicates that ceftriaxone penetrates into muscle tissue at a low ratio. Conclusions: These results indicate that ceftriaxone is well absorbed after IP and IM injections and passes into muscle tissue at a low tissue penetration. Ceftriaxone can be administered via IP and IM injection in Nile tilapia; nevertheless, its therapeutic efficacy requires evaluation. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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17 pages, 1595 KB

Open AccessArticle

Gut Resistome and Hearing Loss in Young Adults: A Preliminary Study on the Interplay Between Microbial Resistance and Auditory Health

by Julia Almazán-Catalán, Paula Carpizo-Zaragoza, Diana Penalba-Iglesias, María Luisa Sánchez, Daniel González-Reguero, Sara Bueno, Marina Robas-Mora, Gregorio Varela-Moreiras, Teresa Partearroyo and Pedro Jiménez-Gómez

Antibiotics 2025, 14(12), 1241; https://doi.org/10.3390/antibiotics14121241 - 8 Dec 2025

Viewed by 703

Abstract

Background: Hearing loss (HL) affects more than 1.5 billion people worldwide and represents a major global health concern. Recent evidence suggests that alterations in gut microbial composition and antimicrobial resistance (AMR) may be linked to inflammatory and metabolic pathways that could influence auditory physiology. Objectives: This study aimed to explore the relationship between auditory function and the antimicrobial resistance in the gut microbiome of young adults. Methods: Fecal and auditory data were collected from young adults. Auditory function was assessed through pure-tone audiometry, and participants were classified according to the presence or absence of HL based on the American Speech-Language-Hearing Association (ASHA) criteria. Bacterial resistance was analyzed under aerobic and anaerobic conditions using disk diffusion and E-test methods to determine minimum inhibitory concentrations (MICs) for a panel of antibiotics. Gut microbiota composition was further characterized using quantitative polymerase chain reaction (qPCR) to quantify 15 key microbial taxa. Results: Overall, 40.9% of participants presented some degree of HL, with mild or slight HL being more frequent in women (53.3%) than in men (14.3%). Participants with HL exhibited significantly higher MICs for nalidixic acid, amoxicillin, and ciprofloxacin, as well as trends toward increased MIC variability for several other agents. Principal component analysis demonstrated distinct clustering of individuals without HL and greater dispersion among those with HL, suggesting higher interindividual variability in resistance profiles. These findings suggest potential associations between antimicrobial resistance and auditory function, possibly mediated through gut microbiome alterations. qPCR analyses demonstrated that Faecalibacterium prausnitzii abundance was significantly higher in individuals with HL and in those exhibiting greater resistance to amoxicillin. Conclusions: These findings provide preliminary evidence connecting the gut resistome with auditory function, supporting the emerging concept of a gut–ear–brain axis and underscoring the need for further research into microbiome-related mechanisms underlying HL. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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12 pages, 606 KB

Open AccessArticle

High Prevalence of Antimicrobial Resistance Genes in Rabbit Farms from Sumy Region, Ukraine

by Sara Gomes-Gonçalves, Jaqueline T. Bento, Ana Machado, Yevheniia Dudnyk, Oksana Shkromada, Halyna Rebenko, Adriano A. Bordalo and João R. Mesquita

Antibiotics 2025, 14(9), 907; https://doi.org/10.3390/antibiotics14090907 - 8 Sep 2025

Cited by 1 | Viewed by 1166

Abstract

Background/Objectives: Antimicrobial resistance (AMR) poses a significant threat to public health, food security, and sustainable livestock production. Despite increasing concern, AMR remains poorly studied in cuniculture, particularly in regions where rabbit farming is predominantly small-scale and household-based. This study aimed to assess the prevalence and diversity of antimicrobial resistance genes (ARGs) in rabbit farms in northeastern Ukraine. Methods: A total of 100 fecal samples were collected from clinically healthy rabbits housed in two farms and one vivarium. DNA was extracted and analyzed using real-time PCR targeting 21 ARGs associated with resistance to major antibiotic classes, including tetracyclines, sulfonamides, β-lactams, macrolides, quinolones, carbapenems, and multidrug efflux systems. Results: A diverse and widespread resistome was identified. The most prevalent genes included sul1 (96%), blaTEM (95%), tetM (94%), and ermB (93%). AcrB (78%) and qnrS/oqxB (approximately 67%) were also frequently detected. Carbapenemase genes (blaKPC, blaNDM, blaVIM) were identified in 6% of samples, despite limited veterinary use of carbapenems. Notably, 96% of samples harbored ARGs from three or more antibiotic classes, indicating a high potential for multidrug resistance. Conclusions: The findings demonstrate a high prevalence and diversity of ARGs in rabbit farming systems in northeastern Ukraine. The presence of clinically significant resistance genes, including those conferring carbapenem resistance, underscores the urgent need for targeted AMR surveillance and improved antibiotic stewardship in cuniculture, particularly in regions with minimal regulatory oversight of antimicrobial use. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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20 pages, 1681 KB

Open AccessArticle

Effective Control of Salmonella Enteritidis in Poultry by Dietary Supplementation with Microencapsulated Essential Oils

by Heitor Leocádio de Souza Rodrigues, Valdinete Pereira Benevides, Isis Mari Miyashiro Kolososki, Mauro M. S. Saraiva, Nayla Pádua Del Bianco Gontijo Souki, Tarley Araújo Barros, André Luis Costa Rabelo, Viviane Amorim Ferreira, Melissa Freitas Feitosa Dix, Adriana Maria Almeida, Cesar Augusto Roque-Borda and Angelo Berchieri Junior

Antibiotics 2025, 14(6), 552; https://doi.org/10.3390/antibiotics14060552 - 29 May 2025

Cited by 6 | Viewed by 2713

Abstract

Background/Objectives: Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is a major pathogen associated with poultry products, and the rise of antimicrobial-resistant strains has intensified the need for effective natural control strategies. Essential oils (EOs) are recognized for their antimicrobial potential, but their volatility, instability, and risk of toxicity at high concentrations limit their practical application. Therefore, the objective of this study was to evaluate the antimicrobial efficacy of EOs in broilers infected with S. Enteritidis and to characterize potential synergistic or antagonistic interactions between the oils. Methods: To achieve this, the oils were first assessed through Minimum Inhibitory Concentration (MIC), Minimum Bactericidal Concentration (MBC), and Fractional Inhibitory Concentration (FIC) assays, and the most effective ones against S. Enteritidis were selected. These selected oils were then microencapsulated and incorporated into the broiler feed for the in vivo assay. Results: The encapsulated formulation retained key bioactive compounds and significantly reduced bacterial shedding and intestinal colonization when administered to broilers experimentally infected with S. Enteritidis. Broilers receiving the optimized half-dose supplementation exhibited a 36% reduction in fecal shedding and a 4 log₁₀ decrease in cecal bacterial counts compared to untreated controls. A transient reduction in liver colonization was also observed, while feed intake remained unaffected. Conclusions: These findings demonstrate that microencapsulated EOs can serve as an effective natural strategy to control S. Enteritidis in poultry. The results support the broader application of lipid-based encapsulation technologies for improving the functional performance of phytobiotics in animal production. Full article

(This article belongs to the Special Issue Antibiotic Resistance in a One Health Context: Bridging Environmental, Agricultural, Nutritional, Veterinary, and Clinical Perspectives)

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