Fecal cultivable aerobic microbiota of dairy cows and calves acting as reservoir of clinically relevant antimicrobial resistance genes

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Evaluación de la administración de medicamentos veterinarios en hatos lecheros de quince municipios de Cundinamarca, Colombia

Objetivo Evaluar el conocimiento en el uso de Medicamentos de Uso Veterinario (MUV) de los productores ganaderos y personal involucrado en Bogotá y municipios aledaños. Métodos Se realizó un estudio de corte transversal a través de entrevistas a operarios y productores ganaderos de una muestra de 30 hatos lecheros localizados en 15 municipios cerca de Bogotá, Cundinamarca. Resultados Se identificó la implementación de prácticas para la administración de MUV, incluyendo parámetros que influencian su administración y conocimientos en las personas que los prescriben y administran. Se encontró que los medicamentos de mayor frecuencia fueron los antimicrobianos con 60,7%, entre los cuales se destaca el uso de penicilina y oxitetraciclina. Los MUV inyectables (parenterales) fueron las formas más frecuentes de aplicación con un 64,7%. Se identificaron 251 MUV en los hatos lecheros, de los cuales el 81,3% están compuestos por principios activos que requieren tiempo de retiro en leche y carne. Se destaca el rol del mayordomo en el cuidado animal a nivel diagnóstico y administración del tratamiento. Conclusión El presente estudio sugiere que el uso de MUV es implementado empíricamente en producciones lecheras y podría contribuir a mediano y largo plazo a la emergencia de cepas con resistencia a MUV.

A Review of Current Bacterial Resistance to Antibiotics in Food Animals

The overuse of antibiotics in food animals has led to the development of bacterial resistance and the widespread of resistant bacteria in the world. Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in food animals are currently considered emerging contaminants, which are a serious threat to public health globally. The current situation of ARB and ARGs from food animal farms, manure, and the wastewater was firstly covered in this review. Potential risks to public health were also highlighted, as well as strategies (including novel technologies, alternatives, and administration) to fight against bacterial resistance. This review can provide an avenue for further research, development, and application of novel antibacterial agents to reduce the adverse effects of antibiotic resistance in food animal farms.

Invited Review: Antimicrobial Use and Antimicrobial Resistance in Pathogens Associated with Diarrhea and Pneumonia in Dairy Calves

Antimicrobial use (AMU) is the major driver of antimicrobial resistance (AMR) among bacteria in dairy herds. There have been numerous studies on AMU and AMR in dairy cows; however, studies on AMU and AMR in dairy calves are limited. A comprehensive overview of the current state of knowledge of AMU and AMR among pathogens in dairy calves is important for the development of scientifically supported and applicable measures to curb antimicrobial use and the increasing risk of AMR. Therefore, we performed a systematic review of research on AMU and AMR in dairy calves. A total of 75 publications were included, of which 19 studies reported AMU data for dairy calves and 68 described AMR profiles of the four most prevalent bacteria that are associated with calf diarrhea and calf pneumonia. Large variation in AMU was found among herds across different regions. There seems to be a positive association between exposure to antimicrobials and occurrence of resistance. Most AMU was accounted for by treatment of diseases, while a small proportion of AMU was prophylactic. AMU was more common in treating calf diarrhea than in treating pneumonia, and the resistance rates in bacteria associated with diarrhea were higher than those in pathogens related to pneumonia. Organic farms used significantly fewer antimicrobials to treat calf disease; however, the antimicrobial resistance rates of bacteria associated with calf diarrhea and pneumonia on both types of farms were comparable. Feeding waste or pasteurized milk was associated with a higher risk of AMR in pathogens. Altogether, this review summarizes AMU and AMR data for dairy calves and suggests areas for future research, providing evidence for the design of antimicrobial use stewardship programs in dairy calf farming.

Tracking antibiotic resistance genes (ARGs) during earthworm conversion of cow dung in northern China

Using cow dung to breed earthworms poses a risk of environmental transmission of antibiotic resistance genes (ARGs). The purpose of this study was to address the occurrence, persistence and environmental fate of ARGs during earthworm conversion of cow dung. The results showed that ARGs persisted through the whole process. Notably, earthworm conversion effectively reduced some ARGs in cow dung, but a definite concentration of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). We found that tet-ARGs were the most abundant in 15 earthworm farms (10^-6~10^-1 copies/16S copies) and some high-risk ARGs (i.e., bla_ampC, bla_OXA-1 and bla_TEM-1) were even prevalent in these farms. Interestingly, although ARGs differ widely in cow dung (10^-10~10^-1 copies/16S copies), the ARGs levels were comparable in vermicompost samples from different farms (10^-8~10^-2 copies/16S copies). Notably, earthworm conversion effectively reduced some ARGs in cow dung, but significant level of ARGs still remained in earthworms and vermicompost (up to 10^-1 and 10^-2 copies/16S copies, respectively). Nevertheless, the concentrations of some heavy metals (Cu, Zn and Ni), the abundance of mobile genetic elements (MGEs) and total nitrogen content were confirmed to be correlated to the enrichment of some ARGs. Overall, this study demonstrated the high prevalence of ARGs contamination in earthworm farms, and also highlighted the dissemination risk of ARGs during the earthworm conversion of cow dung.