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Antibiotics
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Antimicrobial Resistance in Veterinary Science, 2nd Edition
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Antimicrobial Resistance in Veterinary Science, 2nd Edition

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

Deadline for manuscript submissions: 15 June 2026 | Viewed by 13588

Special Issue Editor

Dr. Nahla O. Eltai

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Guest Editor
Biomedical Research Centre, Microbiology Department, Qatar University, Doha 2713, Qatar
Interests: AMR, bacteria, molecular diagnostic techniques, alternative to antimicrobial agents, epidemiology, sequencing, molecular typing, implementation of new techniques to mitigate air pathogens
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The success of our initial Special Issue, "Antimicrobial Resistance in Veterinary Science," comprising 13 publications, has led us to publish a follow-up edition on the same theme. Building upon the momentum generated by our 2023 publication, for this second volume, we invite researchers to contribute manuscripts exploring antimicrobial resistance in a broad spectrum of veterinary animals, encompassing food animals, wild species, and domestic companions.

We actively encourage submissions of interdisciplinary endeavours and collaborative research spanning multiple centres. Original research articles employing various study designs, literature reviews, and meta-analyses are all welcome.

This Special Issue seeks contributions covering various topics, including epidemiological studies, phenotypic and genotypic resistance profiling, and diagnostic methodologies tailored to animal-centric antimicrobial resistance detection. Moreover, we are interested in exploring the role of animals in disseminating resistant bacteria and the potential utilization of artificial intelligence in resistance detection in animals. Additionally, we welcome studies focusing on the surveillance of AMR in animals.

Through this Special Issue, our predominant objective is to consistently accumulate insights into the veterinary sector's involvement in the spread of antibiotic-resistant bacteria, aligning with the fundamental principles of One Health, which underscores the interconnectedness of human health, animal welfare, and environmental wellbeing.

Dr. Nahla O. Eltai
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

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

  • AMR
  • veterinary animals
  • farm animals
  • food animals
  • wild animals
  • resistance

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Related Special Issue

Published Papers (7 papers)

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Research

19 pages, 3240 KB  
Article
Cost Analysis of the Belgian National Antimicrobial Resistance Monitoring in Livestock: Effects on Sampling Design and Statistical Performance
by Maria Eleni Filippitzi, Adrien de Fraipont, Mickaël Cargnel, Céline Guillaume and Jean Baptiste Hanon
Antibiotics 2026, 15(2), 172; https://doi.org/10.3390/antibiotics15020172 - 5 Feb 2026
Viewed by 607
Abstract
Background/Objectives: As part of the European Union’s harmonized monitoring framework, Belgium conducts antimicrobial resistance (AMR) monitoring in commensal bacteria from livestock. The aim of this study was to conduct a cost analysis of the national AMR monitoring in livestock, and to explore sampling [...] Read more.
Background/Objectives: As part of the European Union’s harmonized monitoring framework, Belgium conducts antimicrobial resistance (AMR) monitoring in commensal bacteria from livestock. The aim of this study was to conduct a cost analysis of the national AMR monitoring in livestock, and to explore sampling size scenarios in relation to their associated costs and statistical performance (power and confidence) of monitoring. Methods: To our knowledge, this is the first published cost evaluation using unit cost aggregation of a national AMR monitoring program in animals. Results: The testing of the different sample size scenarios showed that if the sample size increases, the costs increase linearly. A sample size increase of 10 samples/isolates (e.g., from 170 to 180) can increase the yearly total costs per animal species by 5.2%. Moreover, the testing of the different scenarios showed that if the sample size increases, the power and the confidence level also increase, providing a higher level of trust in the results of the monitoring program. The highest total monitoring costs per animal category were estimated for fattening pigs, broilers and veal calves (over 18% of total costs each, using 2024 data). Among the various monitoring activities, antimicrobial susceptibility testing emerged as the costliest component, representing 50.2% of the total monitoring costs. Conclusions: The approach presented allows it to be used by other countries aiming to estimate the cost of their national AMR monitoring in animals or other similar activities. This economic and scenario testing analysis can be used to suggest informed suggestions to improve AMR monitoring in animals. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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27 pages, 3694 KB  
Article
Whole-Genome Sequence Analysis of Colistin-Resistant, mcr-Harboring Escherichia coli Isolated from a Swine Slaughterhouse in Thailand
by Ratchadaporn Boripun, Pakpoom Tadee, Ravisa Warin, Naparat Suttidate, Doan Hoang Phu, Hidenori Kabeya, Chaithep Poolkhet, Sumalee Boonmar, Suchawadee Tesakul, Yanika Klainiem and Nuttapong Pavana
Antibiotics 2026, 15(2), 135; https://doi.org/10.3390/antibiotics15020135 - 29 Jan 2026
Viewed by 808
Abstract
The emergence of colistin-resistant Escherichia coli (E. coli) in livestock poses a major public health concern due to its zoonotic potential and multidrug resistance (MDR). The study aimed to detect mobilized colistin resistance genes (mcr-1 to mcr-9) in E. [...] Read more.
The emergence of colistin-resistant Escherichia coli (E. coli) in livestock poses a major public health concern due to its zoonotic potential and multidrug resistance (MDR). The study aimed to detect mobilized colistin resistance genes (mcr-1 to mcr-9) in E. coli isolates, along with characterizing their antimicrobial susceptibility, resistance genes, virulence genes, and whole genome sequencing. We investigated E. coli contamination in a swine slaughterhouse in Nakhon Si Thammarat Province, Thailand. A total of 200 fecal samples were collected and screened for E. coli using selective media supplemented with colistin. A total of 200 fecal samples were collected from a swine slaughterhouse and screened for E. coli using selective media supplemented with colistin. Presumptive E. coli isolates were confirmed by PCR, followed by molecular detection of mcr-1 to mcr-9 genes. Antimicrobial susceptibility testing was performed using the disk diffusion method. Selected isolates were further analyzed for additional antimicrobial resistance genes and virulence associated genes by PCR. Whole genome sequencing was conducted on representative isolates exhibiting high levels of antimicrobial resistance. Our results showed that out of 200 fecal samples, 124 presumptive E. coli isolates were recovered from a swine slaughterhouse using selective media containing colistin. PCR confirmation identified 112 isolates (90.32%) as E. coli. Molecular detection of mobilized colistin resistance (mcr) genes (82 isolates, 73.21%) demonstrated that mcr-1 (50.89%) was the most prevalent, followed by mcr-9 (25.89%) and mcr-3 (24.11%). Overall, the 82 mcr E. coli isolates showed the highest level of resistance to ampicillin (97.56%), followed by tetracycline (95.12%), piperacillin (73.17%), and chloramphenicol (65.85%). For non-mcr E. coli isolates, the highest resistance percentage was observed for ampicillin (96.67%), followed by piperacillin (80%) and tetracycline (73.33%). Among the isolates, 75% exhibited MDR phenotypes, showing 22 distinct resistance profiles. The most common MDR pattern was AMP-PIP-TE-C-S (12.5%). Additional antimicrobial resistance genes, including aadA, ampC, and blaTEM, were detected in over 60% of a subset of 30 tested isolates. The virulence gene analysis revealed that eae (74.10%), associated with enteropathogenic E. coli (EPEC), was the predominant pathotype. Whole genome sequencing of five selected isolates confirmed the presence of multiple antimicrobial resistance and virulence determinants. In conclusion, this study reveals a high prevalence of MDR E. coli harboring colistin resistance genes (mcr-1 to mcr-9) in a swine slaughterhouse in southern Thailand. The findings highlight the potential risk of zoonotic transmission of antimicrobial resistant E. coli through the food production chain and emphasize the importance of continuous genomic surveillance and prudent antimicrobial use in livestock production systems. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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19 pages, 1992 KB  
Article
Antimicrobial Use and Epidemiological Resistance Profiles of Commensal Escherichia coli from Swine Farms in Córdoba, Argentina
by Nicolás Javier Litterio, María del Pilar Zarazaga, Augusto Matías Lorenzutti, Juan Pablo Vico, Martín Alejandro Himelfarb, Mariano Guillermo Tinti, Ana Paola Zogbi, Sonia Rubio-Langre and Manuel Ignacio San Andrés Larrea
Antibiotics 2026, 15(1), 86; https://doi.org/10.3390/antibiotics15010086 - 15 Jan 2026
Viewed by 635
Abstract
Background/Objectives: The expansion of intensive swine production in Córdoba, Argentina, underscores the need to assess the risks associated with antimicrobial (AM) use, whose extensive application has driven antimicrobial resistance, a major global threat within the One Health framework. This study aimed to characterize [...] Read more.
Background/Objectives: The expansion of intensive swine production in Córdoba, Argentina, underscores the need to assess the risks associated with antimicrobial (AM) use, whose extensive application has driven antimicrobial resistance, a major global threat within the One Health framework. This study aimed to characterize AM use practices and evaluate the epidemiological resistance profiles (non-wild-type phenotypes, NWT) of commensal Escherichia coli of fecal origin from swine farms, using epidemiological cut-off values (ECOFFs) as a surveillance criterion. Methods: An observational cross-sectional study was conducted in 19 farrow-to-finish farms in Córdoba during 2023. Information on AM use (prophylaxis, metaphylaxis, treatment) across production categories was collected. A total of 437 E. coli isolates were obtained from fecal samples, and minimum inhibitory concentrations (MICs) were determined for 10 AMs of critical importance for human and animal health. NWT phenotypes were classified according to EUCAST ECOFFs, and multidrug resistance (MDR) was assessed. Results: AM use was frequent and predominantly prophylactic (89.5% of farms), mainly through mass medication (66.3%), with macrolides and amoxicillin being the most commonly administered AMs. NWT proportions were extremely high (90–92%) for ampicillin, tetracyclines, and chloramphenicol and substantial for ciprofloxacin (50.6%), sulfamethoxazole (68.2%), and trimethoprim (44.9%). Extended-spectrum β-lactamase (ESBL)-producing phenotypes were detected. Alarmingly, 92% of isolates were classified as MDR E. coli, with homogeneous distribution across production categories. Conclusions: Findings reveal intensive and largely empirical AM use that has consolidated a stable intestinal resistome in the swine population. High MDR levels, even in categories with limited direct AM exposure or involving banned compounds, suggest that co-selection and horizontal gene transfer are key drivers of resistance. This scenario highlights the urgent need to strengthen integrated surveillance and promote prudent AM use strategies under the One Health approach to preserve therapeutic efficacy. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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16 pages, 1354 KB  
Article
A Snapshot of Antimicrobial Resistance in Semi-Wild Oryx: Baseline Data from Qatar
by Asma Mushahidur Rahman, Salma E. Ahmed, Shayma A. Osman, Radhia A. Al-Haddad, Abdallah Almiski, Ristha Kamar, Hana Abdelrahman, Issmat I. Kassem, Andrea Dogliero and Nahla O. Eltai
Antibiotics 2025, 14(3), 248; https://doi.org/10.3390/antibiotics14030248 - 1 Mar 2025
Cited by 3 | Viewed by 2421
Abstract
Background/Objectives: The spread of antimicrobial resistance (AMR) is a growing global health concern. Wild animals can play an important role in the amplification and dissemination of AMR and in conservation efforts aiming at controlling diseases in vulnerable wild animal populations. These animals [...] Read more.
Background/Objectives: The spread of antimicrobial resistance (AMR) is a growing global health concern. Wild animals can play an important role in the amplification and dissemination of AMR and in conservation efforts aiming at controlling diseases in vulnerable wild animal populations. These animals can serve as reservoirs for antibiotic resistance genes and are key in the spread of AMR across ecosystems and hosts. Therefore, monitoring AMR in wild animals is crucial in tackling the spread of resistance in the environment and human population. This study investigated the phenotypic and genotypic resistance of Escherichia coli (E. coli) isolated from semi-wild oryx (Oryx leucoryx) in Qatar. Methods: One hundred fecal samples were collected from oryx in diverse natural reserves across Qatar. A selective agar medium was used to isolate E. coli, and the identity of the isolates was further confirmed using the VITEK® 2 Compact system. The Kirby–Bauer disk diffusion method was used to test antibiotic susceptibility. Genetic resistance determinants were identified through polymerase chain reaction (PCR) analyses and sequencing using the Oxford Nanopore Technology (ONT). Results: The results revealed that 18% (n = 18) of the samples harbored E. coli with resistance to a single antibiotic, 28% (n = 28) were resistant to at least one antibiotic, and 2% (n = 2) were multidrug-resistant (MDR). No resistance was observed against colistin. tetA and tetB encode tetracycline resistance were the most frequently detected genes (57.7%). Whole genome sequencing (WGS) was used to expand on AMR gene-PCR analyses and analyze the resistome of 12E. coli isolates. WGS identified several important antibiotic resistance determinates, including blaCTX-M-encoding Extended Spectrum Beta-Lactamase (ESBL) resistance, soxR associated with tetracycline target alteration, and mdtE, emrB, AcrE, mdtF, and marA related to ciprofloxacin efflux pump resistance. Conclusions: This study provides essential information regarding AMR in Qatari semi-wild animals, which will guide conservation strategies and wildlife health management in a world experiencing increasing antibiotic-resistant infections. Furthermore, these findings can inform policies to mitigate AMR spread, improve ecosystems, and enhance public and environmental health while paving the way for future research on AMR dynamics in wildlife. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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11 pages, 1019 KB  
Article
Multidrug-Resistant Escherichia coli in Broiler and Indigenous Farm Environments in Klang Valley, Malaysia
by Yuvaneswary Veloo, Syahidiah Syed Abu Thahir, Rafiza Shaharudin and Sakshaleni Rajendiran
Antibiotics 2025, 14(3), 246; https://doi.org/10.3390/antibiotics14030246 - 28 Feb 2025
Cited by 2 | Viewed by 3145
Abstract
Background/Objectives: The global health threat posed by antimicrobial resistance (AMR) is a cause for serious concern. Poultry farming in Asia, particularly with indiscriminate use, has been identified as a major contributor to AMR, resulting in the emergence of multidrug-resistant (MDR) bacteria, particularly Escherichia [...] Read more.
Background/Objectives: The global health threat posed by antimicrobial resistance (AMR) is a cause for serious concern. Poultry farming in Asia, particularly with indiscriminate use, has been identified as a major contributor to AMR, resulting in the emergence of multidrug-resistant (MDR) bacteria, particularly Escherichia coli (E. coli). Considering the environment’s role in harboring pathogens, this study aimed to determine the distribution of MDR E. coli in the environments of broiler and indigenous farms in Klang Valley, Malaysia. Methods: Soil and effluent samples were collected from 30 poultry (19 broiler and 11 indigenous) farms. Selective chromogenic E. coli agar plates were used for the isolation of bacteria. The VITEX® 2 system was employed for identification and susceptibility testing. Results: A total of 117 E. coli isolates were recovered. The isolates were highly resistant to ampicillin (76.1%), followed by trimethoprim-sulfamethoxazole (47.9%), and ampicillin-sulbactam (46.2%). AMR rates were higher in broiler farms (91.3%) than in indigenous farms (64.6%) (p < 0.05). The high multiple antibiotic resistance index in the environment of broiler farms (0.22) implies a higher risk of contamination compared to indigenous farms (0.10). Conclusions: The elevated levels of AMR observed in broiler farms underscore the need for collaborative efforts across sectors to address this issue. As AMR is a global One Health issue, monitoring AMR in the environment is essential to complement existing health programs. Implementing best practices, biosecurity, hygiene, continuous monitoring, and food safety management systems is crucial to reduce antimicrobial use and curb the rise of MDR bacteria. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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11 pages, 1938 KB  
Article
Novel Variants of SCCmec Type IX Identified in Clonal Complex 398 Livestock-Associated Methicillin-Resistant Staphylococcus aureus from Pork Production Systems in Korea
by Gi Yong Lee, Soo In Lee, Hoon Je Seong and Soo-Jin Yang
Antibiotics 2025, 14(3), 217; https://doi.org/10.3390/antibiotics14030217 - 21 Feb 2025
Cited by 4 | Viewed by 1899
Abstract
Background/Objectives: The occurrence of novel variants of staphylococcal cassette chromosome mec (SCCmec) in livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has frequently been reported, posing significant zoonotic concern worldwide. In this study, the occurrence of novel types of SCCmec IX elements [...] Read more.
Background/Objectives: The occurrence of novel variants of staphylococcal cassette chromosome mec (SCCmec) in livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has frequently been reported, posing significant zoonotic concern worldwide. In this study, the occurrence of novel types of SCCmec IX elements was identified in two clonal complex (CC) 398 LA-MRSA strains derived from a pig farm and a slaughterhouse in Korea. Methods: Whole-genome sequence analysis of the two CC398 MRSA-SCCmec IX strains, designated KF1A-1172 and JS1E-122, revealed that these strains are most closely related to previously characterized strains of CC398 LA-MRSA carrying SCCmec V isolated from pig farms in Korea. Results: Further structural analysis of the SCCmec IX in KF1A-1172 and JS1E-122 revealed the presence of multiple ccr gene complexes (ccrA5B3, ccrAB3, and a truncated ccrA1), including ccrA1B1 genes for SCCmec type IX. In addition, the pseudo-SCC (ΨSCC) elements, genes associated with the type 1 restriction–modification (RM) system, and zinc resistance gene czrC, were identified in the SCCmec IX. Conclusions: These findings suggest that the multiple recombination events of elements derived from various SCCmec types contributed to the emergence of the novel SCCmec IX variant. The identification of these novel SCCmec IX types in CC398 LA-MRSA also suggests that epidemiological diversification of SCCmec IX in CC398 LA-MRSA is an ongoing event, necessitating continued surveillance on the emergence of novel SCCmec variants. This study is the first to report the complete genome sequences of CC398 MRSA carrying SCCmec IX in Korea. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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13 pages, 1354 KB  
Article
National-Level Consumption of Antimicrobials in the Veterinary Sector in Uganda: A Report on Analysis of Import Data for 2021
by Marion Murungi, Patrick Vudriko, Helen Byomire Ndagije, Diana Nakitto Kesi, Allan Serwanga, Kalidi Rajab, Leonard Manirakiza, John Paul Waswa, Hassan Kasujja, Mark Barigye, Ddembe Kaweesi, Harriet Akello, Juliet Namugambe, Reuben Kiggundu and Niranjan Konduri
Antibiotics 2025, 14(2), 150; https://doi.org/10.3390/antibiotics14020150 - 4 Feb 2025
Cited by 5 | Viewed by 3143
Abstract
Background: Antimicrobials are crucial for animal health and food security. However, their overuse in animals can lead to the emergence of resistant microorganisms. Antimicrobial resistance (AMR) poses a global public health threat that impacts both animal and human health. The objective of this [...] Read more.
Background: Antimicrobials are crucial for animal health and food security. However, their overuse in animals can lead to the emergence of resistant microorganisms. Antimicrobial resistance (AMR) poses a global public health threat that impacts both animal and human health. The objective of this study was to estimate the antimicrobial consumption (AMC) of veterinary antimicrobials at the national level using import data from January to December 2021, available from the Uganda National Drug Authority (NDA). Methods: The World Organization for Animal Health (WOAH) methodology was applied using the Anatomical Therapeutic Chemical classification codes for veterinary medicines. Results: Approximately 88,387.37 kg (88.39 tonnes) of veterinary antimicrobials were consumed in 2021. Parenteral veterinary antimicrobials accounted for 63.8% (56,375.65 kg) and oral veterinary antibacterials accounted for 36.2% (32,011.71 kg). Tetracyclines were the single most consumed veterinary antimicrobial class, accounting for 62.7% of total consumption. Oxytetracycline was the most consumed antibacterial (58.4%), followed by sulphadiazine + trimethoprim (11.1%), penicillin g/dihydrostreptomycin (7.4%), penicillin G procaine + dihydrostreptomycin (6.8%), and tetracycline (3.5%), respectively. Out of all imported veterinary antimicrobials, 76% belonged to the World Health Organization (WHO)’s Highly Important Antimicrobials (HIA) category, 16% to the Critically Important (CIA), and 9% to the Highest Priority Critically Important (HPCIA) categories. Imported colistin accounted for 0.1% of total veterinary consumption. Conclusions: This study contributes to understanding antimicrobial consumption in Uganda’s livestock sector and, for the NDA, leaves in place a system for routine surveillance at a national level. We recommend strict regulatory oversight on the importation and use of colistin and macrolides to address AMR. Full article
(This article belongs to the Special Issue Antimicrobial Resistance in Veterinary Science, 2nd Edition)
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