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Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production

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A special issue of Veterinary Sciences (ISSN 2306-7381). This special issue belongs to the section "Veterinary Food Safety and Zoonosis".

Deadline for manuscript submissions: closed (25 July 2026) | Viewed by 21141

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Editors

Dr. Nikolaos D. Andritsos

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Department of Food Science and Technology, School of Agricultural Sciences, University of Patras, GR-30100 Agrinio, Greece
Interests: food safety; food microbiology; culture-dependent methods; foodborne pathogens; Listeria monocytogenes; Campylobacter; antibiotic resistance; antimicrobial susceptibility testing
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Dr. Antonia Mataragka

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Department of Food Science and Technology, School of Agricultural Sciences, University of Patras, GR-30100 Agrinio, Greece
Interests: molecular microbiology; animal science; animal-originated food; zoonotic diseases; PCR

Prof. Dr. John A. Ikonomopoulos

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Laboratory of Anatomy and Physiology of Farm Animals, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, GR-11855 Athens, Greece
Interests: veterinary microbiology; animal science; zoonotic diseases

Special Issue Information

Dear Colleagues,

Animal-originated food products (e.g., meat, dairy, egg products) rich in protein and nutrients form the baseline of a well-balanced human diet. Nevertheless, livestock producers in primary animal production are struggling to maintain high yields of the respective food commodities (e.g., meat, milk, eggs), as bacterial diseases in animal production remain a significant challenge worldwide affecting production performance, profitability and animal welfare. In an effort to control pathogenic bacteria in primary animal food production, antimicrobials are widely used and administered in farm animals in the form of antibiotic treatment or through feed and/or water supplementation. However, it is well-known that antimicrobial misuse may confer resistance in animal and human bacterial pathogens, thus posing a significant threat for public health in the context of the One Health approach through the consumption of food. This Special Issue focuses on the detection and presence of pathogenic bacteria in the primary animal production environment, as well as on the acquired antimicrobial resistance phenotypes and/or genotypes of those pathogens. Furthermore, the occurrence of bacterial pathogens in foods of animal origin, along with their screening for antimicrobial resistance, is also of interest for this Special Issue.

Dr. Nikolaos D. Andritsos
Dr. Antonia Mataragka
Prof. Dr. John A. Ikonomopoulos
Guest Editors

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Keywords

animal production
animal-originated food
antimicrobial resistance
antibiotic susceptibility
bacterial pathogens
veterinary microbiology
zoonotic diseases

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Published Papers (7 papers)

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Research

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20 pages, 2025 KB

Open AccessArticle

Prevalence, Toxigenicity and Antimicrobial Resistance of Staphylococcus aureus from Animal-Derived Food Products in the Kostanay Region, Kazakhstan: A Genotypic–Phenotypic Concordance Study

by Bakhit Baimenov, Kalamkas Malikzada, Alma Dossova, Zhanaidar Bermukhametov, Pavel Shevchenko, Albina Gabitova, Oxana Tomaruk, Aliya Yskak, Gulzhan Chuzhebayeva and Raushan Rychshanova

Vet. Sci. 2026, 13(7), 687; https://doi.org/10.3390/vetsci13070687 - 15 Jul 2026

Viewed by 577

Abstract

Staphylococcus aureus is a leading cause of foodborne illness in animal-derived food products, yet comprehensive data on its antimicrobial resistance and toxigenic potential from Central Asia remain scarce. We examined 711 food samples (meat, milk, and dairy products) from the Kostanay region of Kazakhstan (2024–2025). Isolates were identified by MALDI-TOF mass spectrometry; antimicrobial susceptibility was assessed by disk diffusion (EUCAST v.16.0); enterotoxin production (types A–E) by ELISA; and resistance and toxin genes by PCR. Concordance between methods was evaluated using Cohen’s kappa coefficient. S. aureus was recovered from 11.8% of samples (84/711), with raw cow’s milk carrying the highest contamination risk (OR = 2.75; 95% CI: 1.74–4.38). High resistance to ampicillin (52.4%) and benzylpenicillin (50.0%) was found; 20.2% of strains were multidrug-resistant. Among the 17 cefoxitin-resistant isolates, only 4 harbored mecA, suggesting that 13 isolates (15.5%) should be interpreted as cefoxitin-resistant, mecA-negative isolates with a putative BORSA-like phenotype rather than as confirmed MRSA. Staphylococcal enterotoxins A–E were detected in 26.2% of isolates, and egc-cluster genes seg and sei were present in 9.5% each. The strongest genotype–phenotype concordance was observed for aph(3′)/kanamycin (κ = 0.65) and blaZ/benzylpenicillin (κ = 0.64). These results underscore the need for combined molecular and phenotypic surveillance for regional food safety monitoring. Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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17 pages, 1263 KB

Open AccessArticle

Serotyping and Antibiotic Resistance Profiles of Salmonella spp. and Listeria monocytogenes Strains Isolated from Pet Food and Feed Samples: A One Health Perspective

by Nikolaos D. Andritsos, Antonia Mataragka, Nikolaos Tzimotoudis, Anastasia-Spyridoula Chatzopoulou, Maria Kotsikori and John Ikonomopoulos

Vet. Sci. 2025, 12(9), 844; https://doi.org/10.3390/vetsci12090844 - 1 Sep 2025

Cited by 2 | Viewed by 3053

Abstract

Foodborne pathogenic bacteria, like Salmonella spp. and Listeria monocytogenes, can be detected in the primary food production environment. On the other hand, and in the current context of One Health, antimicrobial resistance (AMR) is gaining increased attention worldwide, as it poses significant threat to public health. The purpose of this study was to confirm the presence of Salmonella spp. and L. monocytogenes in pet food and feed samples, by means of biochemical and/or serological testing of the microbial isolates, and then to screen for AMR against a panel of selected antibiotics. Serotyping of the isolates with multiplex polymerase chain reaction revealed the presence of three of the most common clinical Salmonella serovars (S. Enteritidis, S. Typhimurium, S. Thompson) and the major epidemiologically important L. monocytogenes serotypes (1/2a, 1/2b, 1/2c, 4b) in 15 and 9 confirmed isolates of the pathogens, respectively. Strains of Salmonella spp. showed resistance to tetracycline (n = 3) and combined AMR to tetracycline with either ampicillin (n = 2) or trimethoprim-sulfamethoxazole (n = 3), without any multidrug resistance (MDR) being recorded whatsoever. AMR in L. monocytogenes was documented in 55.5% of the bacterial strains (n = 5) tested against ciprofloxacin, meropenem, penicillin, trimethoprim-sulfamethoxazole, and tetracycline. Alarmingly, one strain of L. monocytogenes was MDR to the latter five antibiotics and deemed resistant in three antibiotic groups (carbapenems, penicillins, tetracyclines), after exhibiting minimum inhibitory concentrations (MICs) to meropenem (MIC = 4 μg/mL), penicillin (MIC = 4 μg/mL), and tetracycline (MIC = 48 μg/mL). To the best of our knowledge, finding an MDR L. monocytogenes in pet food is something reported for the first time herein. The results presented in this study highlight the presence of important foodborne bacterial pathogens, such as Salmonella spp. and L. monocytogenes, with increased AMR to antibiotics and possible MDR at the primary production and at the farm level, due to the misuse of pharmacological substances used to treat zoonotic diseases, probably resulting in detection of resistant strains of these pathogenic bacteria in animal-originated food products (e.g., meat, milk, eggs). Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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21 pages, 2528 KB

Open AccessArticle

Escherichia coli Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS)

by Theodora Skarlatoudi, Glykeria-Myrto Anagnostou, Vasileios Theodorakis, Loulouda Bosnea and Marios Mataragas

Vet. Sci. 2025, 12(8), 744; https://doi.org/10.3390/vetsci12080744 - 8 Aug 2025

Cited by 3 | Viewed by 1887

Abstract

The objective of this work was to deliver a comprehensive genetic characterization of a collection of E. coli strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Shigella spp. and Salmonella spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the E. coli strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic E. coli strains is particularly alarming for cheese production in artisan dairies. Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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21 pages, 2325 KB

Open AccessArticle

Comparative Genomic Analysis and Antimicrobial Resistance Profile of Enterococcus Strains Isolated from Raw Sheep Milk

by Anagnostou Glykeria-Myrto, Skarlatoudi Theodora, Theodorakis Vasileios, Bosnea Loulouda and Mataragas Marios

Vet. Sci. 2025, 12(8), 685; https://doi.org/10.3390/vetsci12080685 - 23 Jul 2025

Cited by 2 | Viewed by 2462

Abstract

The role of Enterococcus spp. in food is debated since this group of lactic acid bacteria contains opportunistic pathogenic strains, some of which exhibit a multidrug-resistant profile. In livestock farms, the use of antibiotics is the most common practice to deal with mastitis-causing bacteria. However, the heavy usage and/or misuse of antibiotics has led to the emergence of antibiotic resistance. This study aimed to genetically and phenotypically characterize Enterococcus strains isolated from raw sheep milk. Samples were collected over one year from the bulk tank of a dairy sheep farm and cultured on selective media. Isolates were purified and analyzed by whole-genome sequencing and antimicrobial susceptibility testing. The isolates were divided into clusters and the corresponding species were identified along with their genes related to virulence and antibiotic resistance. The pan-, core- and accessory-genomes of the strains were determined. Finally, the antibiotic-resistant profile of selected strains was examined and associated with their genomic characterization. These findings contribute to a better understanding of Enterococci epidemiology, providing comprehensive profiles of their virulence and resistance genes. The presence of antibiotic-resistant bacteria in raw sheep milk destined for the production of cheese should raise awareness. Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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42 pages, 2279 KB

Open AccessEditor’s ChoiceReview

From Farm to Fork: Antimicrobial-Resistant Bacterial Pathogens in Livestock Production and the Food Chain

by Ayman Elbehiry and Eman Marzouk

Vet. Sci. 2025, 12(9), 862; https://doi.org/10.3390/vetsci12090862 - 4 Sep 2025

Cited by 45 | Viewed by 6816

Abstract

Antimicrobial resistance (AMR) in livestock production systems has emerged as a major global health concern, threatening not only animal welfare and agricultural productivity but also food safety and public health. The widespread, and often poorly regulated, use of antimicrobials for growth promotion, prophylaxis, and metaphylaxis has accelerated the emergence and dissemination of resistant bacteria and resistance genes. These elements circulate across interconnected animal, environmental, and human ecosystems, driven by mobile genetic elements and amplified through the food production chain. It is estimated that more than two-thirds of medically important antimicrobials are used in animals, and AMR could cause millions of human deaths annually by mid-century if unchecked. In some livestock systems, multidrug-resistant E. coli prevalence already exceeds half of isolates, particularly in poultry and swine in low- and middle-income countries (LMICs). This narrative review provides a comprehensive overview of the molecular epidemiology, ecological drivers, and One Health implications of AMR in food-producing animals. We highlight key zoonotic and foodborne bacterial pathogens—including Escherichia coli, Salmonella enterica, and Staphylococcus aureus—as well as underappreciated reservoirs in commensal microbiota and livestock environments. Diagnostic platforms spanning phenotypic assays, PCR, MALDI-TOF MS, whole-genome sequencing, and CRISPR-based tools are examined for their roles in AMR detection, surveillance, and resistance gene characterization. We also evaluate current antimicrobial stewardship practices, global and regional surveillance initiatives, and policy frameworks, identifying critical implementation gaps, especially in low- and middle-income countries. Emerging sectors such as aquaculture and insect farming are considered for their potential role as future AMR hotspots. Finally, we outline future directions including real-time genomic surveillance, AI-assisted resistance prediction, and integrated One Health data platforms as essential innovations to combat AMR. Mitigating the threat of AMR in animal agriculture will require coordinated scientific, regulatory, and cross-sectoral responses to ensure the long-term efficacy of antimicrobial agents for both human and veterinary medicine. Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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Other

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11 pages, 1315 KB

Open AccessBrief Report

Co-Occurrence of an NDM-1-Carrying SGI1 Variant and a Novel GIflu-1 Resistance Island in a Seafood-Derived Vibrio fluvialis

by Ming Liu, Wenhui Zhang, Wanyu Zhang, Patrick Butaye, Zhiqiang Wang and Ruichao Li

Vet. Sci. 2026, 13(7), 639; https://doi.org/10.3390/vetsci13070639 - 30 Jun 2026

Viewed by 329

Abstract

Vibrio fluvialis is an important zoonotic pathogen that poses a growing threat to both public health and aquaculture, particularly to shrimp and fish farming. In this study, we report that a seafood-associated V. fluvialis strain, 10M-VF, possesses two genomic islands, SGI1-VfNDM1 and GIflu-1, in addition to hemolysins and type VI secretion systems (T6SSs). SGI1-VfNDM1 is a new member of the Salmonella genomic island 1 (SGI1) and harbors several antibiotic resistance genes. A potential transferable region, ISCR1-trpF-ble_MBL-bla_NDM-1, was observed in SGI1-VfNDM1, suggesting that ISCR1 may have mediated the integration of bla_NDM-1 into this island. Additionally, GIflu-1 represents a novel resistance island. Other GIflu variants carrying resistance genes in Vibrio all possess ISCR2, but their resistance regions vary. This indicates that ISCR2 may contribute to the integration of antibiotic resistance genes into GIflu islands. Notably, not every GIflu variant carries drug resistance genes. To the best of our knowledge, GIflu-1 is a previously unreported resistance island, and no previous report has documented the co-existence of two distinct resistance genomic islands in a single Vibrio isolate. The emergence of such resistance islands in a seafood-borne pathogen raises concerns for the maintenance and potential dissemination of clinically important resistance genes in aquatic food systems and underscores the need for ongoing surveillance of resistance determinants in seafood-borne Vibrio populations from a One Health perspective. Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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13 pages, 708 KB

Open AccessProject Report

Evaluation of Antimicrobial Usage Supply Chain and Monitoring in the Livestock and Poultry Sector of Pakistan

by Muhammad Farooq Tahir, Riasat Wasee Ullah, Jing Wang, Kinzang Dukpa, Muhammad Usman Zaheer, Sami Ullah Khan Bahadur, Usman Talib, Javaria Alam, Muhammad Akram, Mo Salman and Hamid Irshad

Vet. Sci. 2025, 12(3), 215; https://doi.org/10.3390/vetsci12030215 - 1 Mar 2025

Cited by 4 | Viewed by 4180

Abstract

Irrational use of antimicrobials in humans, livestock, and poultry is often cited as the key driver of the accelerated emergence of antimicrobial resistance (AMR) in humans and animals. In Pakistan, the use of antimicrobials in livestock and poultry is not well-regulated, owing to limited and/or ineffective implementation of existing legislations and lack of coordination amongst the key stakeholders. To gather data and information pertinent to the supply chain mapping and the usage of antibiotics in the livestock and poultry sectors of Pakistan, a national workshop for selected influential stakeholders was held in Islamabad, Pakistan during March 2020 to map the supply chain and the usage of antibiotics in the country. Participants from all relevant organizations identified the supply chain and discussed the status, challenges, and the way forward to enhance data collection and monitoring of antimicrobial usage (AMU) in livestock and poultry sectors to contain the emergence of AMR. The pre-workshop questionnaire was designed to gather relevant information on AMU and its distribution among diverse markets and users from the workshop participants, utilizing open-ended questions. A chart depicting the relative magnitude of an antimicrobial use (AMU) supply chain was constructed to illustrate the flow of antimicrobials from import and production to end-use at the farm level. This chart was shared with participants to gather their professional opinions and potential corrections. It also presented a list of agencies and their roles in regulating AMU, along with the types of AMU data available at each level. Specific recommendations were made at the end of the workshop to review and update legislation to cover the entire AMU supply chain, enhance regulations to restrict the use of antimicrobial growth promoters, build an integrated national AMU database system, and raise awareness about the responsible use of antimicrobials in the livestock and poultry sectors. It was concluded that the AMU supply chain in the veterinary sector of Pakistan is fragmented and is co-regulated by various federal and provincial stakeholders. There are some drugs, such as antibiotic growth promoters, which are not regulated at all. The approach and findings from this study can serve as a model to validate the use and management of antibiotics in other, similar countries currently grappling with serious antimicrobial resistance (AMR) crises. Full article

(This article belongs to the Special Issue Occurrence and Antimicrobial Resistance of Bacterial Pathogens in Primary Animal Food Production)

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