Search Results (21)

Background: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored. Methods: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal. Results: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin. Conclusions: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies. Full article

Enterotoxigenic Escherichia coli (ETEC)-induced neonatal calf diarrhea (NCD) causes significant economic losses to the cattle industry; therefore, understanding its antibiotic resistance is crucial for developing targeted prevention and treatment strategies. However, reports on antibiotic resistance in bovine ETEC are currently limited. This study conducted whole-genome sequencing (WGS) and antimicrobial susceptibility testing on ETEC F5- and F5-F41-positive strains isolated from neonatal calf diarrhea samples in Inner Mongolia, China. The results showed that both ETEC F5- and ETEC F5-F41-positive strains are multidrug-resistant, containing ceftriaxone (CRO), ceftazidime (CAZ)) and ciprofloxacin (CIP), which are listed as the highest priority critically important antimicrobial (HP-CIAs) by the World Health Organization (WHO). Combined analysis using the Comprehensive Antibiotic Resistance Database (CARD) and ResFinder 4.1 predictive analysis revealed that the chromosomes and plasmids of the 2 ETEC-positive strains contained 11 classes of antibiotic resistance genes, with the top 3 categories in terms of the number of resistance genes being aminoglycosides, β-lactamases, and chloramphenicols. In addition, various bacterial efflux pumps, including RND, MFS, SMR, and the ABC efflux pump family, were detected. A total of 74 antimicrobial resistance genes were identified in the 2 strains, belonging to 5 categories of drug resistance mechanisms; the antimicrobial resistance phenotype was consistent with the genotype. This study provides a reference for the prevention and treatment of diarrhea caused by ETEC. Full article

High-risk clones represent a major concern, as they are very efficient vehicles for mobile genetic elements carrying antimicrobial resistance genes and therefore promote their spread, especially if they confer resistance to cefotaxime, ciprofloxacin, and fosfomycin, included within the highest-priority, critically important antimicrobial agents (HPCIA). Between February 2022 and April 2024, 138 pork samples were obtained from 46 butcher shops in La Plata, Buenos Aires, Argentina. A total of 102 HPCIA-resistant E. coli were isolated. Eighty-five HPCIA-resistant E. coli were selected for whole-genome sequencing. Of these, 27 belonged to 9 clones described as high risk: ST101 (n = 5), ST10 (n = 4), ST48 (n = 4), ST744 (n = 4), ST23 (n = 3), ST58 (n = 2), ST88 (n = 2), ST117 (n = 2), and ST410 (n = 1). Twelve of them were third-generation cephalosporin-resistant. Resistance was mediated by bla_CTX-M-55 (n = 7), bla_CTX-M-14 (n = 4), bla_CTX-M-8 (n = 1), and bla_CMY-2 (n = 1). This study highlights the importance of food products and the food production chain as reservoirs of high-risk clones and resistance genes of epidemiological relevance to public health. Full article

Antimicrobial resistance (AMR) is a growing global health threat, with wild birds increasingly recognized as potential reservoirs of resistant pathogens and as sentinels of environmental AMR. This study investigated the occurrence and AMR profiles of Gram-negative bacteria isolated from wild birds that died at the Wildlife Rescue Center in Vanzago, Lombardy, in 2024. Cloacal swabs were collected from 112 birds representing various ecological categories. A total of 157 Gram-negative bacteria were isolated and identified, including clinically relevant genera and species, such as Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Salmonella spp., Pseudomonas aeruginosa, and Acinetobacter baumannii. Antimicrobial susceptibility testing revealed resistance to first-line and critically important antimicrobials, including those exclusively authorized for human use. Notably, a phenotype compatible with Extended-Spectrum Beta-Lactamase (ESBL) production was detected in four out of ten (40%) K. pneumoniae isolates. In addition, 20 out of the 157 (12.7%) isolated bacteria phenotypically exhibited a resistance profile indicative of AmpC beta-lactamase (AmpC) production, including Enterobacter spp. and P. aeruginosa. Resistance patterns were particularly interesting in birds with carnivorous, scavenging, or migratory-associated behaviors. These findings highlight the role of wild birds in the ecology and dissemination of antimicrobial-resistant bacteria (ARB) and highlight the need for wildlife-based AMR monitoring programs as part of a One Health approach. Full article

Background: Short food supply chains are commonly perceived as more sustainable and safer alternatives to conventional production systems, often linked to organic, free-range livestock practices. Materials and methods: This study investigates, for the first time, the distribution of antimicrobial resistance genes (ARGs) and characterizes the microbial communities’ composition, using 16S rRNA sequencing and real-time PCR, respectively. Eleven fecal, 76 slaughterhouse surface, 11 cecal, and 11 carcass samples, from 11 poultry farms belonging to the same short food chain, were analyzed in the study. Results: While cleaning and disinfection procedures appeared to reduce the bacterial load on slaughterhouse surfaces, diverse and potentially resistant bacteria, including genera such as Staphylococcus and Streptococcus, persisted both before and after slaughter. ARGs conferring resistance to high-priority critically important antimicrobials (HPCIAs), such as fluoroquinolones and third-generation cephalosporins, were frequently detected on carcasses, with qnrS (76.15%, 95%CI 68.02-84.28%) and bla_CMY2 (57.8%, 95%CI 48.38-67.22%) being the most prevalent. The slaughtering process emerged as a critical step for ARG dissemination via intestinal bacteria, such as genus Lactobacillus. Additionally, the detection of mcr genes and bla_NDM on carcasses but not in the bird gut samples suggests possible anthropogenic contamination. Discussion: These findings highlight that the evisceration process, slaughterhouse environment, and personnel are all contributing factors in ARG spread and underscore the need for enhanced hygiene protocols and reduced gut ARG carriage in domestic birds to mitigate the risk for the consumer. Full article

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

Background/Objectives: While antibiotic usage in farm animals has been systematically monitored and reduced in many countries, including Germany, data on companion animals such as dogs and cats remain scarce. To address this gap, a study was conducted in Germany to analyze patterns of antibiotic use in dogs and cats. Methods: Antibiotic usage data were obtained from debevet, a cloud-based veterinary practice management software based in Berlin, Germany. Practices with fewer than 100 patients were excluded, and data from 2018 to 2022 were analyzed. Results: The analysis included 477,310 consultations of 78,381 dogs and 241,532 consultations of 55,729 cats across 133 veterinary practices. Antibiotics were used in 12.9% of dog consultations and 22.5% of cat consultations, with substantial variation across practices. Aminopenicillins, particularly amoxicillin, were the most commonly used antibiotics, while the highest-priority critically important antibiotics (HPCIAs) accounted for 12.4% of treatments. Follow-up treatments led to changes in antibiotic substances in 9.3% of cases, often within the first two days. Indications varied by species, with respiratory issues more frequent in cats and orthopedic problems in dogs. Body weight and breed characteristics influenced the likelihood of antibiotic treatment, with short-nosed breeds showing higher odds. Conclusions: The routine data analysis provided valuable insights into antibiotic use in dogs and cats, enabling tracking trends across species and indications over time. While some specific information was missing, the invoicing data’s completeness, the cost-effectiveness of their use, and their unbiased nature make them a robust tool for monitoring and informing legislative changes. Full article

Background/Objectives: Antimicrobial resistance (AMR) is a global public health threat, with antimicrobial use (AMU) in livestock recognized as a significant driver. This study examines farm-level AMU and AMR as well as the relationship between AMU and AMR on broiler farms in Indonesia. Methods: Data were collected from 19 farms in West Java between 2019 and 2021 to examine AMU in depth across four to five successive production cycles. The correlation between AMU and AMR in commensal Escherichia coli (E. coli) was investigated. AMU was recorded as treatment days per 30-day production cycle, and antimicrobial susceptibility was assessed using epidemiological cut-off (ECOFF) values to differentiate wildtype (WT) and non-wildtype (NWT) E. coli. Results: The average AMU was 12 treatment days per 30-day production cycle, with a wide range of 4 to 22 days. On average, E. coli isolates from each farm exhibited NWT phenotypes, reflecting AMR levels, for 6 out of 14 antimicrobials tested. This included notable levels for the highest priority critically important antimicrobials (HPCIAs) ciprofloxacin (93%) and nalidixic acid (64%). A significant correlation (Spearman ρ = 0.67, p < 0.05) was observed between the total farm-level AMU and the number of antimicrobials for which NWT E. coli isolates were found. However, no significant correlation was found between AMU and AMR for the five most frequently used antimicrobials, likely due to a high baseline prevalence of NWT E. coli isolates and relatively few independent observations. Conclusions: These findings highlight the urgent need to reduce AMU in general, specifically the use of (HP)CIAs, to mitigate AMR on Indonesian broiler farms. Full article

Companion animal ownership has evolved to new exotic animals, including small mammals, posing a new public health challenge, especially due to the ability of some of these new species to harbour zoonotic bacteria, such as Salmonella, and spread their antimicrobial resistances (AMR) to other bacteria through the environment they share. Therefore, the objective of the present pilot study was to evaluate the current epidemiological AMR situation in commensal Escherichia coli and Salmonella spp., in non-traditional companion animal small mammals in the Valencia region. For this purpose, 72 rectal swabs of nine different species of small mammals were taken to assess the antimicrobial susceptibility against 28 antibiotics. A total of one Salmonella enterica serovar Telelkebir 13,23:d:e,n,z₁₅ and twenty commensal E. coli strains were isolated. For E. coli strains, a high prevalence of AMR (85%) and MDR (82.6%) was observed, although neither of them had access outside the household. The highest AMR were observed in quinolones, one of the highest priority critically important antimicrobials (HPCIAs) in human medicine. However, no AMR were found for Salmonella. In conclusion, the results showed that small mammals’ commensal E. coli poses a public health risk due to the high AMR found, and the ability of this bacterium to transmit its resistance genes to other bacteria. For this reason, this pilot study highlighted the need to establish programmes to control AMR trends in the growing population of new companion animals, as they could disseminate AMR to humans and animals through their shared environment. Full article

Between June and September 2023, a total of 80 meat samples from pork and chicken meat were collected from 16 retail markets in La Plata, Argentina. Eighty-four highest priority critically important antimicrobial-resistant Escherichia coli and two Salmonella spp. were isolated. Resistance to ciprofloxacin and cefotaxime was observed in 65 and 49 E. coli isolates, respectively. Seventy-five E. coli isolates were multidrug resistant. Fourteen E. coli isolates from chicken meat showed resistance to three of the HPCIA. Resistance to third-generation cephalosporin was associated with bla_CTX-M. It is 15 times more likely to find HPCIA-resistant E. coli in chicken meat than in pork. Full article

Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) are plasmid-encoded genes that threaten the clinical utility of colistin (COL), one of the highest-priority critically important antibiotics (HP-CIAs) used to treat infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. For more than six decades, COL has been used largely unregulated in the poultry sector in low- and middle-income countries (LMICs), and this has led to the development/spread of mcr gene-containing bacteria (MGCB). The prevalence rates of mcr-positive organisms from the poultry sector in LMICs between January 1970 and May 2023 range between 0.51% and 58.8%. Through horizontal gene transfer, conjugative plasmids possessing insertion sequences (ISs) (especially ISApl1), transposons (predominantly Tn6330), and integrons have enhanced the spread of mcr-1, mcr-2, mcr-3, mcr-4, mcr-5, mcr-7, mcr-8, mcr-9, and mcr-10 in the poultry sector in LMICs. These genes are harboured by Escherichia, Klebsiella, Proteus, Salmonella, Cronobacter, Citrobacter, Enterobacter, Shigella, Providencia, Aeromonas, Raoultella, Pseudomonas, and Acinetobacter species, belonging to diverse clones. The mcr-1, mcr-3, and mcr-10 genes have also been integrated into the chromosomes of these bacteria and are mobilizable by ISs and integrative conjugative elements. These bacteria often coexpress mcr with virulence genes and other genes conferring resistance to HP-CIAs, such as extended-spectrum cephalosporins, carbapenems, fosfomycin, fluoroquinolone, and tigecycline. The transmission routes and dynamics of MGCB from the poultry sector in LMICs within the One Health triad include contact with poultry birds, feed/drinking water, manure, poultry farmers and their farm workwear, farming equipment, the consumption and sale of contaminated poultry meat/egg and associated products, etc. The use of pre/probiotics and other non-antimicrobial alternatives in the raising of birds, the judicious use of non-critically important antibiotics for therapy, the banning of nontherapeutic COL use, improved vaccination, biosecurity, hand hygiene and sanitization, the development of rapid diagnostic test kits, and the intensified surveillance of mcr genes, among others, could effectively control the spread of MGCB from the poultry sector in LMICs. Full article

Antimicrobial usage in both human and veterinary medicine is considered one of the main drivers of antimicrobial resistance; its reduction poses a serious challenge. To analyse the associations between usage and resistance, data from monitoring systems and classification of all antimicrobial substances are crucial. In this analysis, we investigated longitudinal data collected between 2013 and 2020 within the Veterinary Consumption of Antibiotics project from pig farms in Germany, including all antimicrobial classes, but focusing on critically important antimicrobials: third- and fourth-generation cephalosporins, fluoroquinolones, macrolides, and polymyxins. Analysing the treatment frequency, we found that a reduction in antimicrobial use in all types of pig production has occurred over time, accompanied by a rising percentage of farms without any usage. The lists of the World Health Organisation, World Organisation for Animal Health, and European Medicine Agency classify different antimicrobial substances as critically important. The vast differences between the respective weighted treatment frequencies allocated to the antimicrobials of main interest reflect the huge impact of the three categorisation systems. We concluded that, with the aim of creating national treatment guidelines supporting veterinarians to make treatment decisions, the list of the European Medicine Agency is the most suitable. Full article

The indiscriminate usage and overuse of antimicrobials in pets or companion animals are underlying causes of antimicrobial resistance (AMR). Despite the multi-faceted global challenge presented by antimicrobial resistance, very few studies have appraised pet practitioners’ factors, such as written policy on antimicrobials, dose rate prescribed, use of critically important antimicrobials, and antimicrobial prescription in clean surgical procedures, which can contribute to AMR. In the present study, an online cross-sectional survey among randomly selected pet practitioners (n = 104) of various Indian provinces and union territories was conducted using a questionnaire comprising 33 closed-ended questions on different parameters, viz., the dosage regimen and level of compliance towards guidelines of the World Health Organization (WHO), other relevant veterinary associations, and their opinion while prescribing antimicrobials. Almost every practitioner of the 104 respondents had revealed the difficulties with owner compliance; i.e., incomplete course of the antibiotics, inappropriate follow-ups, and improper care of the sick animals. The majority of practitioners (95%) reported self-prescription of antimicrobials by the owner before presenting the pet(s) to the veterinary clinic, whereas more than half of the respondents (64%) revealed unavailability of antibiogram facilities. Furthermore, a large number (76%) of practitioners stated empirical treatment based on their experience as the main criteria for antimicrobial choice in the absence of timely results from the laboratory. Although non-necessitated use of antimicrobials in clean surgical procedures has been claimed, surprisingly, the majority of pet practitioners (97%) reported their use to reduce the post-operative complications. The use of the highest priority, critically important antimicrobials (HPCIA) listed by the WHO for humans, particularly quinolones and third-generation cephalosporin, also has been reported for different infections. The treatment durations were nearly as per the recommended guidelines issued by the Danish Small Animal Veterinary Association (DSAVA) for different ailments. Analysis using chi-square tests exhibited a significant correlation between less experienced veterinarians (less than 5 years) and prescription of antimicrobials restricted for critically important infections in human medicine. However, there seems to be no association between the experience of the practitioner and the further studied parameters, namely, antimicrobial regimen prescription, weighing the animals before prescription, dose rate calculation, and antimicrobial selection and use after clean surgical operations. The findings suggest periodic awareness campaigns among practitioners regarding the implementation of the official guidelines, the need for systematic surveillance of AMR, awareness among pet owners about antimicrobial resistance, and the importance of rational use of antimicrobials on their pets. Full article

To minimize the use of third- and fourth-generation cephalosporins and fluoroquinolones, the 2018 amendment to the regulations of veterinary pharmacies (TÄHAV) introduced legal restrictions in Germany. In an online survey among German veterinarians, we investigated the influence of these requirements on the use of antibiotics in the treatment of dogs and cats and the development of resistance rates. It was found that, on average, between 21% and 30% of daily treated dogs and cats received antimicrobial therapy. The TÄHAV amendment led to a less frequent use of highest priority critically important antimicrobials (HPCIA) in 79% (240/303) of respondents and less antimicrobial use in general in 36% (108/303). As a result of these legal changes, 63% (190/303) of participants requested antimicrobial susceptibility testing (AST) more frequently. Participants consulted ASTs particularly frequently for treatment of otitis externa with 63% (190/303), cystitis with 55% (168/303), wounds with 44% (132/303), and pyoderma with 29% (88/303). Veterinarians also noted an increased loss of antimicrobial efficacy, especially when treating these diseases. The results of our survey confirm that the TÄHAV amendment is having a positive impact on prudent antibiotic use, with participants performing more ASTs, using HPCIA less frequently, and choosing alternative antimicrobials for therapy. Full article

The quantification of antimicrobial usage (AMU) in food-producing animals can help identify AMU risk factors, thereby enhancing appropriate stewardship policies and strategies for a more rational use. AMU in a sample of 34 farms in the Province of Trento (north-eastern Italy) from 2018 to 2020 was expressed as defined daily doses for animals per population correction unit according to European Surveillance of Veterinary Antimicrobial Consumption guidelines (DDDvet) and according to Italian guidelines (DDDAit). A retrospective analysis was carried out to test the effects of several husbandry practices on AMU. Overall, the average AMU ranged between 6.5 DDDAit in 2018 and 5.2 DDDAit in 2020 (corresponding to 9 and 7 DDDvet, respectively), showing a significant trend of decrement (−21.3%). Usage of the highest priority critically important antimicrobials (HPCIA) was reduced by 83% from 2018 to 2020. Quarantine management, available space, water supply, animals’ cleanliness and somatic cell count had no significant association with AMU. Rather, farms with straw-bedded cubicles had lower AMU levels than those with mattresses and concrete floors (p < 0.05). In conclusion, this study evidenced a decrement in AMU, particularly regarding HPCIA, but only a few risk factors due to farm management. Full article