Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations.

OBJECTIVES: Carriage of Clostridioides difficile by different species of animals has led to speculation that animals could represent a reservoir of this pathogen for human infections. The objective of this study was to compare C. difficile isolates from humans, dogs, and cattle from a restricted geographic area. METHODS: C. difficile isolates from 36 dogs and 15 dairy calves underwent whole genome sequencing, and phenotypic assays assessing growth and virulence were performed. Genomes of animal-derived isolates were compared to 29 genomes of isolates from a pediatric population as well as 44 reference genomes. RESULTS: Growth rates and relative cytotoxicity of isolates were significantly higher and lower, respectively, in bovine-derived isolates compared to pediatric- and canine-derived isolates. Analysis of core genes showed clustering by host species, though in a few cases, human strains co-clustered with canine or bovine strains, suggesting possible interspecies transmission. Geographic differences (e.g., farm, litter) were small compared to differences between species. In an analysis of accessory genes, the total number of genes in each genome varied between host species, with 6.7% of functional orthologs differentially present/absent between host species and bovine-derived strains having the lowest number of genes. Canine-derived isolates were most likely to be non-toxigenic and more likely to carry phages. A targeted study of episomes identified in local pediatric strains showed sharing of a methicillin-resistance plasmid with dogs, and historic sharing of a wide range of episomes across hosts. Bovine-derived isolates harbored the widest variety of antibiotic-resistance genes, followed by canine CONCLUSIONS: While C. difficile isolates mostly clustered by host species, occasional co-clustering of canine and pediatric-derived isolates suggests the possibility of interspecies transmission. The presence of a pool of resistance genes in animal-derived isolates with the potential to appear in humans given sufficient pressure from antibiotic use warrants concern.

The role of veterinarians and feed-store vendors in the prescription and use of antibiotics on small dairy farms in rural Peru.

This study aimed to describe and compare the role of veterinarians and feed-store vendors in the use of antibiotics on small dairy farms in Cajamarca, Peru, a major dairy-producing center characterized by small, rural farms with poor, mostly uneducated farmers. We used a purposive sampling strategy to recruit 12 veterinarians into 2 focus group discussions and supplemented these data with 8 semi-structured interviews with feed-store vendors. Participants reported that inappropriate antibiotic usage was widespread among their clients, which may prevent the efficient use of drugs on farms where animal disease can be devastating to the livelihood of the farmer. Participants also identified many barriers to appropriate prescribing and use, including availability of drugs, competition from other prescribers, economic constraints and habits of farmers, and limited farmer knowledge of drugs and disease. Veterinarians expressed mistrust toward nonprofessional prescribers, whereas feed-store vendors felt that veterinarians were important partners in promoting the health of their clients' animals.

Carbapenem prescribing at a veterinary teaching hospital before an outbreak of carbapenem-resistant Escherichia coli.

OBJECTIVES: Carbapenems are a critically important class of antimicrobials used to treat infections caused by multi-drug-resistant bacteria. Following an outbreak of a carbapenemase (NDM-5)-producing strain of Escherichia coli at our veterinary institution, we opted to describe the use of carbapenems in our institution and the role that drug contraindications in patients may have played when culture and susceptibility testing identified alternative drug options. MATERIALS AND METHODS: Medical record reviews of all cases where a carbapenem was prescribed were performed, and indications for use, timing of prescribing relative to culture and susceptibility reports, and alternative possible antimicrobial treatments were extracted. Contraindications to alternative antimicrobials were also documented. RESULTS: Carbapenems were prescribed infrequently: from 2013 to 2018, they accounted for 0.47% of all antimicrobial prescriptions and were administered to 108 of 56,776 (0.2%) patients seen at our institution. They were prescribed empirically in slightly more than half of the patients (57.6%). Among cases where a carbapenem was prescribed after culture and susceptibility results were available, alternative antimicrobials could have been used in 68.3% of cases. CLINICAL SIGNIFICANCE: Variability in use of these drugs within an institution highlights the need to develop well-defined use guidelines, including when to use these drugs empirically and how to safely de-escalate or choose alternative drugs guided by culture and susceptibility results.

The use of antibiotics on small dairy farms in rural Peru.

Very little is known about the use of antibiotics on small dairy farms in lower/middle-income countries. The use of these drugs can have profound impacts on animal health, farmer income and public health. A survey of 156 farmers was conducted in Cajamarca, a major dairy-producing center in the highlands of Peru characterized by small farms (<15 cows) to assess patterns and determinants of antibiotic use and farmers' knowledge of antibiotics. The reported incidence of disease on these farms was relatively low (0.571 episodes of disease per cow-year), but more than 83% of the reported episodes were treated with antibiotics. The most commonly used antibiotics were oxytetracycline, penicillin and trimethoprim-sulfamethoxazole drugs; antiparasitic drugs were also used to treat what were likely bacterial infections. An increased incidence of treated disease was significantly associated with smaller farm size, lower farmer income, the previous use of the Californian Mastitis test on the farm and antibiotic knowledge. Farmers' knowledge of antibiotics was assessed with a series of questions on antibiotics, resulting in a "knowledge score". Increased knowledge was significantly associated with the use of antibiotics for preventative reasons, the purchase of antibiotics from feed-stores, the experience of complications in animals after having administered antibiotics, the number of workers on the farm and the educational level of the farmer. Overall, antibiotics appeared to be used infrequently, most likely because therapeutic interventions were sought only when the animal had reached an advanced stage of clinical disease. Few farmers were able to define an antibiotic, but many farmers understood that the use of antibiotics carried inherent risks to their animals and potentially to the consumers of dairy products from treated animals. The results of this study are useful for understanding the patterns of antibiotic use and associated management, demographic and knowledge factors of farmers on small dairy farms in rural Peru.

Antibiotic residues in milk from small dairy farms in rural Peru.

The use of antibiotics in livestock can pose a public health threat, especially if antibiotic residues remain in the food product. Understanding how often and why farmers sell products with antibiotic residues is critical to improving the quality of these products. To understand how often milk with antibiotic residues is sold on small farms in a major dairy-producing region of Peru and identify factors associated with selling milk with antibiotic residues, we tested milk samples for antibiotic residues from every provider on three routes of commercial milk companies and from bulk tanks of farmers currently treating cows with antibiotics. We also asked farmers if they sold milk from treated cows and examined factors associated with the tendency to do so. The prevalence of milk contamination with antibiotic residues on commercial routes was low (0-4.2%); however, 33/36 farmers treating their animals with antibiotics sold milk that tested positive for antibiotic residues. The self-reported sale of milk from treated cows had a sensitivity, specificity, and positive and negative predictive values of 75.8%, 100%, 100% and 27.2%, respectively (with testing of milk for residues as the gold standard). Finally, 69/156 randomly selected farmers reported selling milk from treated cows, and farmers' knowledge of antibiotics and the milk purchaser were significantly associated with a farmer's tendency to report doing so. Educating farmers on the risks associated with antibiotics and enforcement of penalties for selling contaminated milk by milk companies are needed to improve milk quality.

Comparison of two methods for collecting antibiotic use data on small dairy farms.

Antibiotics are commonly used in animal agriculture; they can improve animal health and productivity, but their use may also represent a public health threat. Very little is known about antibiotic use on small farms in lower/middle income countries. To understand antibiotic use on these farms and promote the judicious use of these drugs, pharmacoepidemiologic data are necessary. However, acquiring such data can be difficult, as farmers are often illiterate (and therefore cannot participate in written surveys or keep treatment records), antibiotics can be obtained over-the-counter (in which case no prescriptions are generated) and monitoring and surveillance systems for drug use are often non-existent. The goal of this study was to compare two methods of acquiring pharmacoepidemiologic data pertaining to antibiotics that are well-adapted to farms in lower-middle income countries: self-report and the collection of discarded drug packaging. A convenience sample of 20 farmers in Cajamarca, Peru, participated in the study. Farmers placed discarded antibiotic packaging in bins for six months. At the end of the six-month period, farmers were interviewed and asked to recall the antibiotic usage that occurred on their farm over the past month and past six months; these self-reported data were quantitatively and qualitatively compared to the bin contents collected in the last month and previous six months. We found that the agreement between the bins and self-report was relatively poor for both the quantity and types of antibiotics used. The bins appeared to perform better than self-report when bottles and mLs of antibiotics were measured, while self-report appeared to perform better for intra-mammary infusions. The bins also appeared to perform better when data pertaining to an extended time period (six months) were collected. The results of this study will provide guidance to investigators seeking to collect pharmacoepidemiologic data in similar environments.