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Antibiotics
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Antibiotic Resistance in Bacterial Isolates of Animal Origin
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Antibiotic Resistance in Bacterial Isolates of Animal Origin

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

Deadline for manuscript submissions: 31 May 2026 | Viewed by 5616

Special Issue Editors

Dr. Tomasz Jarzembowski

E-Mail Website
Guest Editor
Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdańsk, Dębowa 25, 80-204 Gdańsk, Poland
Interests: biofilm; antibiotic resistance; heterogenic resistance; host-microbiome balance; virulence factor
Dr. Lidia Piechowicz

E-Mail Website
Guest Editor
Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdańsk, Dębowa 25, 80-204 Gdańsk, Poland
Interests: antibiotic-resistance; virulence potential; Staphylococus aureus; bacteriophages

Special Issue Information

Dear Colleagues,

The increasing antibiotic resistance in bacterial isolates from animals is critical threat of  animal health, food safety, and public health. Microorganisms such as Salmonella enterica, Campylobacter jejuni, enterohemorrhagic Escherichia coli, Enterococcus faecalis, and strains of Staphylococcus aureus are commonly detected in farm animals, companion species, and wildlife. The intensive use of antibiotics in agriculture exerts strong selection pressure, driving the emergence and multiplication of resistant strains. Resistance mechanisms commonly include the production of β-lactamases (e.g., extended-spectrum β-lactamases), the alteration of the antibiotic receptor, or the overexpression of the efflux pump, and are based on mutations in the bacterial genome or the acquisition of resistance genes through conjugation, transduction, or transformation processes.

Antibiotic-resistant strains are transmitted from animals to humans in a variety of ways: through the consumption of contaminated meat or other animal food products, through direct contact with animals, or through exposure to the environment. Such  isolates can cause infections in humans that are extremally difficult to treat. This is why addressing antibiotic resistance requires a One Health approach, a strategy that encompasses actions for human health, animal health, and a healthy environment. This includes reducing the non-therapeutic use of antibiotics in farm animals, improving hygiene and biosecurity on farms, promoting the surveillance of antibiotic resistance markers in animal populations, and fostering cooperation between the veterinary and public health sectors. Such integrated measures are essential to slow down the spread of resistance genes and protect both animal welfare and public health.

We are delighted to invite you, as a recognised expert in your field, to share your unique insights and contribute to the current Special Issue with research on the spread of antibiotic resistance in the human environment.

Dr. Tomasz Jarzembowski
Dr. Lidia Piechowicz
Guest Editors

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

  • zoonotic infection
  • resistance genes
  • “one health concept”
  • Salmonella enterica
  • Campylobacter jejuni
  • enterohemorrhagic Escherichia coli
  • Enterococcus faecalis

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Published Papers (6 papers)

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Research

15 pages, 721 KB  
Article
Genetic Characterization of Carbapenem-Resistant Acinetobacter spp. Isolated from Diseased Companion Animals in Japan
by Saki Harada, Mari Matsuda, Yuta Hosoi, Taimu Toyama, Michiko Kawanishi and Hideto Sekiguchi
Antibiotics 2026, 15(4), 329; https://doi.org/10.3390/antibiotics15040329 - 24 Mar 2026
Viewed by 476
Abstract
Background/Objectives: Carbapenem-resistant Acinetobacter spp. represent an emerging concern in human medicine; however, their epidemiology and genetic backgrounds in companion animals in Japan remain unclear. This study aimed to determine the prevalence of carbapenem resistance among Acinetobacter spp. isolated from diseased dogs and cats [...] Read more.
Background/Objectives: Carbapenem-resistant Acinetobacter spp. represent an emerging concern in human medicine; however, their epidemiology and genetic backgrounds in companion animals in Japan remain unclear. This study aimed to determine the prevalence of carbapenem resistance among Acinetobacter spp. isolated from diseased dogs and cats and elucidate the underlying genetic mechanisms. Methods: In this surveillance study conducted as part of the Japanese Veterinary Antimicrobial Resistance Monitoring (JVARM) program, 139 isolates were collected from diseased companion animals across Japan (84 from dogs and 55 from cats) during 2020, 2021 and 2023. Antimicrobial susceptibility testing was performed for seven antimicrobials and carbapenem-resistant isolates (meropenem MIC ≥ 8 μg/mL) underwent whole-genome sequencing to identify resistance genes, genomic contexts, and associated mobile genetic elements. Results: Resistance rates to all tested antimicrobials were below 20%. Meropenem resistance was detected in three isolates: one from a dog and two from cats. These resistant strains were identified as A. radioresistens, A. proteolyticus, and A. johnsonii, all harboring carbapenemase genes. The A. radioresistens isolate carried chromosomal blaOXA-23, the A. proteolyticus isolate carried blaOXA-58, and the A. johnsonii isolate possessed a plasmid containing blaNDM-1 and blaOXA-58. This represents the first report of blaNDM-1-harboring Acinetobacter isolate from companion animals in Japan. Conclusions: Carbapenem-resistant Acinetobacter spp. remain rare in companion animals in Japan; however, insertion sequence mobility may promote resistance gene dissemination. As carbapenems are not approved for veterinary use in Japan, strict antimicrobial stewardship and appropriate hygiene management are essential. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Bacterial Isolates of Animal Origin)
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17 pages, 2551 KB  
Article
Antimicrobial-Resistant E. coli in Goats in Qatar: Nationwide Evidence of MDR and ESBL Occurrence
by Nahla O. Eltai, Cut Salsabila Fatin, Shayma A. Osman, Hebah A. Al Khatib, Abdullah A. Shaito, Asmaa A. Al Thani, Gheyath K. Nasrallah and Hadi M. Yassine
Antibiotics 2026, 15(4), 325; https://doi.org/10.3390/antibiotics15040325 - 24 Mar 2026
Viewed by 588
Abstract
Background/Objectives: Data on antimicrobial resistance (AMR) in goat-derived E. coli within the Gulf Cooperation Council (GCC) region remain limited, and are largely restricted to studies conducted in Saudi Arabia and the UAE, with no published reports from Qatar. This study provides the [...] Read more.
Background/Objectives: Data on antimicrobial resistance (AMR) in goat-derived E. coli within the Gulf Cooperation Council (GCC) region remain limited, and are largely restricted to studies conducted in Saudi Arabia and the UAE, with no published reports from Qatar. This study provides the first baseline characterization of AMR and extended-spectrum β-lactamase (ESBL) profiles of E. coli isolated from goats in Qatar. Methods: A total of 280 fecal samples were collected from goats across nine locations in Qatar (140 healthy and 140 diseased goats; 12 samples did not yield E. coli cultures). A selective agar medium was used to isolate E. coli, and the isolates were subsequently confirmed using the VITEK® 2 Compact system. Antimicrobial susceptibility testing was performed to determine resistance profiles, and PCR assays were used to detect ESBL-associated genes. Results: 268 E. coli isolates were recovered from 280 samples. AMR analysis revealed a high prevalence of tetracycline resistance among E. coli isolates (53%), consistently observed across all nine sampling locations. Ampicillin resistance was also widespread. AMR was detected in isolates from both healthy and diseased goats; however, gentamicin resistance was found exclusively in the isolates from diseased animals. Overall, 44 isolates (16%) were classified as multidrug resistant (MDR), while nine isolates (3%) demonstrated ESBL production based on cefotaxime resistance. MDR and ESBL-producing E. coli were detected across all nine locations and in both healthy and diseased animals, with MDR strains occurring more frequently than ESBL producers. PCR analysis identified ESBL-associated genes, namely, blaCTX-M in nine isolates and blaTEM in three isolates. Conclusions: Goats in Qatar harbor multidrug-resistant and ESBL-producing E. coli, highlighting their role as AMR reservoirs within a One Health framework. The high resistance rates to commonly used antibiotics, particularly tetracycline and ampicillin, across health statuses and geographic locations suggest potential influences of local management practices and environmental factors. The detection of ESBL genes, notably blaCTX-M and blaTEM, underscores the need for prudent antimicrobial use and the implementation of integrated One Health surveillance programs to mitigate potential public health risks and to support national AMR surveillance and antimicrobial stewardship efforts across the region. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Bacterial Isolates of Animal Origin)
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9 pages, 221 KB  
Article
Comparison of a Single-Shot Antibiotic Protocol Compared to a Conventional 5-Day Antibiotic Protocol in Equine Diagnostic Laparotomy Regarding Pre- and Postoperative Colonization with Multi-Drug-Resistant Indicator Pathogens
by Sabita Diana Stöckle, Dania Annika Kannapin, Roswitha Merle, Antina Lübke-Becker and Heidrun Gehlen
Antibiotics 2026, 15(1), 106; https://doi.org/10.3390/antibiotics15010106 - 21 Jan 2026
Viewed by 613
Abstract
Objective: The emergence and spread of multi-drug-resistant (MDR) bacteria pose a growing threat in veterinary medicine, particularly in equine hospitals. This study investigated the colonization and infection dynamics of horses undergoing emergency laparotomy with two distinct antibiotic protocols (single-shot versus 5-day protocol) during [...] Read more.
Objective: The emergence and spread of multi-drug-resistant (MDR) bacteria pose a growing threat in veterinary medicine, particularly in equine hospitals. This study investigated the colonization and infection dynamics of horses undergoing emergency laparotomy with two distinct antibiotic protocols (single-shot versus 5-day protocol) during hospitalization. Methods: Nasal swabs and fecal samples were collected from 67 horses undergoing emergency laparotomy at clinic admission as well as on postoperative days 3 and 10. These were screened for multi-drug-resistant indicator pathogens. As multi-drug-resistant indicator pathogens, methicillin-resistant Staphylococcus aureus (MRSA), extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-E), and bacteria belonging to the Acinetobacter baumannii complex were defined. Results: Preoperatively, 6.2% of horses tested positive for MRSA and 13% for ESBL-E. An increase in colonization was observed on day 3 postoperatively, with 62.1% of nasal swabs and 86.4% of fecal samples testing positive for MDR organisms. On day 10, 53.4% of nasal swabs and 62.5% of fecal samples tested positive for indicator pathogens. Surgical site infection developed in five horses, two of which tested positive for MRSA in both nasal and wound samples during hospitalization, supporting the potential role of nasal carriage as a source of infection. Furthermore, all horses tested positive for ESBL-E during at least one time-point during hospitalization, and Enterobacterales (MDR in two surgical site infections (SSI)) were involved in all surgical site infections. No significant differences were observed between the two antibiotic treatment groups regarding colonization rates with indicator pathogens during hospitalization. However, the results indicate that hospitalization itself contributes to increased colonization with resistant bacteria. A clear limitation of the study is the restricted number of sampled horses and the lack of environmental contamination data. Non-sampled hospitalized horses with and without antibiotic treatment may have acted as reservoirs for MDR bacteria. Conclusion: The findings emphasize the need for routine environmental monitoring and strict adherence to hygiene protocols in equine clinics to reduce the risk of nosocomial transmission. Ongoing surveillance and infection control strategies are essential to mitigate the spread of MDR pathogens in veterinary settings. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Bacterial Isolates of Animal Origin)
31 pages, 7576 KB  
Article
Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats
by Julio David Soto-López, Omar Velásquez-González, Manuel A. Barrios-Izás, Moncef Belhassen-García, Juan Luis Muñoz-Bellido, Pedro Fernández-Soto and Antonio Muro
Antibiotics 2026, 15(1), 51; https://doi.org/10.3390/antibiotics15010051 - 3 Jan 2026
Viewed by 1261
Abstract
Background/Objectives: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear. Methods: [...] Read more.
Background/Objectives: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear. Methods: To characterize ARG diversity in wildlife exposed to contrasting levels of human influence, we analyzed homologs of resistance mechanisms from the Comprehensive Antibiotic Resistance Database in shotgun metagenomes of bat guano. Samples were collected from a colony exposed to continuous anthropogenic activity in Spain (Salamanca) and from a wild, non-impacted bat community in China (Guangdong). Metagenomic analyses revealed marked differences in taxonomic and resistome composition between sites. Results: Salamanca samples contained numerous hospital-associated genera (e.g., Mycobacterium, Staphylococcus, Corynebacterium), while Guangdong was dominated by Lactococcus, Aeromonas, and Stenotrophomonas. β-lactamases and MurA transferase homologs were the most abundant ARGs in both datasets, yet Salamanca exhibited higher richness and functional diversity (median Shannon index = 1.5; Simpson = 0.8) than Guangdong (Shannon = 1.1; Simpson = 0.66). Salamanca also showed enrichment of clinically relevant ARGs, including qacG, emrR, bacA, and acrB, conferring resistance to antibiotics critical for human medicine. In contrast, Guangdong exhibited a more restricted resistome dominated by β-lactamase and MurA homologs. Beta diversity analysis confirmed significant compositional differences between resistomes (PERMANOVA, R2 = 0.019, F = 1.33, p = 0.001), indicating ecological rather than stochastic structuring. Conclusions: These findings suggest that anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, potentially increasing their role as reservoirs of antimicrobial resistance. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Bacterial Isolates of Animal Origin)
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14 pages, 1352 KB  
Article
First Detection of Critical Carbapenemase Genes (NDM, OXA-48, VIM) in Avian Campylobacter spp. Isolates in Tunisia: A Zoonotic and Public Health Concern
by Manel Gharbi, Mohammed Abdo Saghir Abbas, Chadlia Hamdi, Safa Hamrouni and Abderrazak Maaroufi
Antibiotics 2025, 14(12), 1236; https://doi.org/10.3390/antibiotics14121236 - 8 Dec 2025
Cited by 1 | Viewed by 855
Abstract
Background/Objectives: The global emergence of carbapenem resistance is a major public health concern. Campylobacter jejuni and Campylobacter coli, key zoonotic agents causing human campylobacteriosis, are mainly isolated from poultry, their primary host. Their increasing resistance in animals and humans highlights the [...] Read more.
Background/Objectives: The global emergence of carbapenem resistance is a major public health concern. Campylobacter jejuni and Campylobacter coli, key zoonotic agents causing human campylobacteriosis, are mainly isolated from poultry, their primary host. Their increasing resistance in animals and humans highlights the risk of gene transfer. This study investigates the molecular mechanisms of carbapenem resistance in 287 avian Campylobacter spp. isolates from Tunisia within a One Health approach. Methods: Antibiotic susceptibility of 287 carbapenem-resistant isolates, including 147 C. jejuni and 140 C. coli, was determined according to CLSI. All isolates were screened by PCR for genes encoding the most reported carbapenemases, including VIM, IMP, NDM and OXA-48. Eleven multidrug-resistant (MDR)/carbapenem-resistant C. coli isolates were selected to determine their clonal lineage by Multilocus sequence typing (MLST). Results: All isolates were susceptible to imipenem, but resistance to meropenem and ertapenem were observed in 60.71% and 35.71% of C. coli isolates, respectively, versus 13.6% in C. jejuni for each antibiotic. The blaVIM, blaNDM and blaOXA-48 genes were detected in 15, 8, and 19 of the 20 C. jejuni isolates, respectively. However, for C. coli, 53, 12, and 15 isolates harbored blaVIM, blaNDM and blaOXA-48 genes, respectively. The eleven (MDR)/carbapenem-resistant C. coli isolates belonged to a unique ST sequence type ST13450. Conclusions: We report for the first time the emergence of blaVIM, blaNDM, and blaOXA-48 genes in Campylobacter spp. isolates of poultry origin highlighting possible horizontal transfer of these genes to pathogenic Gram-negative bacteria of the poultry’s microbiota. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Bacterial Isolates of Animal Origin)
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23 pages, 763 KB  
Article
Characterization of Staphylococcus aureus CC1 and CC1660 of Human and Equine Origin
by Johanna Jahnen, Christiane Cuny, Wolfgang Witte, Ralf Ehricht, Stefan Monecke, Dennis Hanke, Tanja Ahrens, Marta Leal, Sofia S. Costa, Isabel Couto, Stefan Schwarz and Andrea T. Feßler
Antibiotics 2025, 14(11), 1082; https://doi.org/10.3390/antibiotics14111082 - 27 Oct 2025
Viewed by 1269
Abstract
Background/Objectives: Staphylococcus aureus isolates from humans and horses of the equine-associated clonal complexes (CCs) CC1 and CC1660 were comparatively investigated for their genomic relationships. Methods: A total of 91 S. aureus isolates (64 human, 27 equine) were subjected to whole-genome sequencing [...] Read more.
Background/Objectives: Staphylococcus aureus isolates from humans and horses of the equine-associated clonal complexes (CCs) CC1 and CC1660 were comparatively investigated for their genomic relationships. Methods: A total of 91 S. aureus isolates (64 human, 27 equine) were subjected to whole-genome sequencing (WGS), sequence analysis, and antimicrobial susceptibility testing. Results: WGS confirmed 75 CC1 and 16 CC1660 isolates, comprising nine sequence types (STs) in CC1 and four STs in CC1660. Ten spa types were present in CC1 and five in CC1660. In the arcC gene of three CC1 isolates, a 285 bp deletion was detected, and a nucleotide deletion causing a premature stop codon was found in one CC1660 isolate. Core genome (cg) MLST revealed a minimum difference of 1398/1492 alleles between the two CCs. All CC1 isolates harbored agr group III and capsule type 8 alleles, whereas all CC1660 isolates had agr group II and capsule type 5 alleles. Antimicrobial susceptibility testing revealed 18 phenotypic and 19 genotypic resistance patterns. All isolates were susceptible to vancomycin, linezolid and quinupristin–dalfopristin. Several virulence genes were detected in different combinations. The equine leukocidin genes lukP/lukQ were found in 22 isolates from horses and 38 isolates from humans, of which 35 had confirmed contact with horses. No Panton–Valentine leukocidin genes were found. Three human CC1660 isolates carried the toxic shock syndrome toxin-1 gene tst-1. Conclusions: The analysis of the 91 isolates might suggest intra- and interspecies transmission among and between humans and horses, which should be monitored in the future. Full article
(This article belongs to the Special Issue Antibiotic Resistance in Bacterial Isolates of Animal Origin)
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