Quantitative risk model to estimate the level of antimicrobial residues that can be transferred to soil via manure, due to oral treatments of pigs

Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland

Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.

Tetracycline removal from soil by phosphate-modified biochar: Performance and bacterial community evolution

Since the remediation performance of soil tetracycline pollution by original biochar is not ideal, many modified methods have been proposed to improve its performance. Considering the cost, complex modification process and environmental friendliness, many modified biochar are difficult to be used in soil environments. In this work, biochar derived from corn stover was modified using phosphate to increase the adsorption ability of soil tetracycline and alleviate the negative effects caused by tetracycline. The results showed that pyrolysis temperatures and anion types of phosphate (PO43-, HPO42-, H2PO4-) played important roles in the performance of modified biochar. Compared with original biochar, phosphate modified biochar not only improved the adsorption capacity, but also changed the adsorption behavior of tetracycline. Via SEM, BET and FTIR techniques, the intrinsic reasons for the increase of adsorption capacity were explained by the change of morphological structures as well as functional groups of the modified biochar. K3PO4 and high temperature (800 °C) maximally improved the surface morphology, increased the pore structure, changed the surface functional groups of biochar, and then increased the adsorption capacity of tetracycline (124.51 mg/g). Subsequently, the optimal material (K3PO4-800) was selected and applied for tetracycline contaminated soil remediation. Compared to the soil without remediation, K3PO4-800 modified biochar effectively reduced the effective concentration of tetracycline in soil, and improved soil K and P nutrition, and reshaped microbial communities. Our study showed that K3PO4-800 modified biochar was not only a good tetracycline resistant material, but also a good soil amendment.

Residues of veterinary antibiotics in manures from pig and chicken farms in a context of antimicrobial use reduction by implementation of health and welfare plans

The use of antibiotics in food-producing animals can induce the presence of residual substances in manure, which are then released into the environment and may contribute to soil and groundwater contamination. During the on-farm implementation of strategies to improve animal health and welfare in chicken and pig farms, the consequences of antibiotic use were evaluated in terms of the occurrence and levels of antibiotic residues in manure. A set of 35 broiler farms from Cyprus, Greece, the Netherlands and 40 pig farms from France and Italy provided a total of 350 manure samples. The primary objective was to develop a specific LC/MS/MS method capable of quantifying antibiotic residues in both types of manure. The method was able to detect fifteen antibiotics belonging to nine classes, with validated limits of quantification of 10-20 μg/kg, and accuracies ranging from 81% to 138%. With the exception of amoxicillin, which was never detected in any manure, all antibiotics used were detected in manure from treated animals with typical concentrations ranging from 10 to 99198 μg/kg for both chickens and pigs. The occurrence of residual antibiotics was higher in chicken than in pig manure, especially for fluoroquinolones and doxycycline which were detected in 89% and 100% of the chicken manure, respectively, and in 28% of the pig manure. The impact of the health plans on the antibiotic load manure was assessed by measuring for each farm the ratio of the sum of all antibiotic concentrations measured after and before the implementation of the plan. The results showed that, in addition to the frequency of treatments, the class of antibiotic used is an important factor to consider as it strongly influences the stability/instability of the compounds, i.e. their ability to persist in the manure of food-producing animals.

Impact of fertilization with pig or calf slurry on antibiotic residues and resistance genes in the soil

Antibiotic residues and antibiotic resistance genes can enter the environment via fertilization with calf and pig manure. In a longitudinal study, nine antibiotic resistance genes (tet(B), tet(L), tet(M), tet(O), tet(Q), tet(W), erm(B), erm(F) and sul2) and 56 antibiotic residues were investigated in 288 soil samples and 8 corresponding slurry samples from 6 pig farms and 2 veal farms using qPCR and LC-MS/MS, respectively. A significant increase in gene copy number of tet(M), erm(B), erm(F) and sul2 was observed in all the soil layers between sampling times prior to (T1) and 2-3 weeks after fertilization (T3). Tet(B), tet(Q) and tet(L) were least abundant in the soil among the genes tested. From 7 classes of antibiotics, 20 residues were detected in soil and slurry using an optimized and validated extraction method. Flumequine was detected in all soil samples in concentrations below 100 μg/kg despite being detected in only half of the corresponding slurry samples. Doxycycline, oxytetracycline, lincomycin and sulfadiazine were also frequently detected in concentrations ranging from 0.1 μg/kg to 500 μg/kg and from 2 μg/kg and 9480 μg/kg in soil and slurry, respectively. Furthermore a positive association between the presence of antibiotic residues (total antibiotic load) and antibiotic resistance genes in soil was found. One possible explanation for this is a simultaneous introduction of antibiotic residues and resistance genes upon application of animal slurry.

Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries

Livestock feces with antimicrobial resistant bacteria reaches the farm floor, manure pit, farm land and wider environment by run off and aerosolization. Little research has been done on the role of dust in the spread of antimicrobial resistance (AMR) in farms. Concentrations and potential determinants of antimicrobial resistance genes (ARGs) in farm dust are at present not known. Therefore in this study absolute ARG levels, representing the levels people and animals might be exposed to, and relative abundances of ARGs, representing the levels in the bacterial population, were quantified in airborne farm dust using qPCR. Four ARGs were determined in 947 freshly settled farm dust samples, captured with electrostatic dustfall collectors (EDCs), from 174 poultry (broiler) and 159 pig farms across nine European countries. By using linear mixed modeling, associations with fecal ARG levels, antimicrobial use (AMU) and farm and animal related parameters were determined. Results show similar relative abundances in farm dust as in feces and a significant positive association (ranging between 0.21 and 0.82) between the two reservoirs. AMU in pigs was positively associated with ARG abundances in dust from the same stable. Higher biosecurity standards were associated with lower relative ARG abundances in poultry and higher relative ARG abundances in pigs. Lower absolute ARG levels in dust were driven by, among others, summer season and certain bedding materials for poultry, and lower animal density and summer season for pigs. This study indicates different pathways that contribute to shaping the dust resistome in livestock farms, related to dust generation, or affecting the bacterial microbiome. Farm dust is a large reservoir of ARGs from which transmission to bacteria in other reservoirs can possibly occur. The identified determinants of ARG abundances in farm dust can guide future research and potentially farm management policy.

Clostridioides difficile infection and One Health: An Equine Perspective

Clostridioides (Clostridium) difficile presents a significant health risk to humans and animals. The complexity of the bacterial–host interaction affecting pathogenesis and disease development creates an ongoing challenge for epidemiological studies, control strategies and prevention planning. The recent emergence of human disease caused by strains of C. difficile found in animals adds to mounting evidence that C. difficile infection (CDI) may be a zoonosis. In equine populations, C. difficile is a known cause of diarrhoea and gastrointestinal inflammation, with considerable mortality and morbidity. This has a significant impact on both the well‐being of the animal and, in the case of performance and production animals, it may have an adverse economic impact on relevant industries. While C. difficile is regularly isolated from horses, many questions remain regarding the impact of asymptomatic carriage as well as optimization of diagnosis, testing and treatment. This review provides an overview of our understanding of equine CDI while also identifying knowledge gaps and the need for a holistic One Health approach to a complicated issue.

Emergency vaccine immunization protects hamsters against acute leptospirosis

Leptospirosis, caused by pathogenic Leptospira, is a global critical zoonotic disease in terms of mortality and morbidity. Vaccines are often used to prevent leptospirosis. However, few studies have reported the therapeutic effect of a vaccine against Leptospira infection. This study demonstrates the efficacy of the emergency vaccine immunization against acute leptospirosis in hamsters. Treatment with a whole-cell vaccine (Leptospira interrogans serovar Lai) at 24 h post-infection improved the survival rate of hamsters with lower leptospiral burden and minor pathological damage to organs. The vaccine also protected against multiple Leptospira serotypes acute infection. However, the protective effect of the vaccines was lost when beginning treatment at 36 h or 48 h post-infection. These results indicated that vaccines could treat acute leptospirosis in hamsters, but only if immunization is within 24 h after infection.

Presence of Antibiotic Residues and Antibiotic Resistant Bacteria in Cattle Manure Intended for Fertilization of Agricultural Fields: A One Health Perspective

Antibiotic resistant bacteria and antibiotic residues can enter the environment when using animal manure as fertilizer. Twenty-five mixed beef cattle farmyard manure samples and 9 mixed fattening calf slurry samples from different farms across Belgium were investigated for the presence of 69 antibiotic residues, antibiotic resistant Escherichia coli and Salmonella spp. Doxycycline, oxytetracycline, ciprofloxacin, enrofloxacin, flumequine and lincomycin were detected in all fattening calf slurry samples with mean concentrations of 2776, 4078, 48, 31, 536 and 36 µg/kg manure, respectively. Sulfadiazine was detected at a mean concentration of 10,895 µg/kg. Further, antibiotic residues were found in only 4 of the 25 beef cattle farmyard manure samples. Oxytetracycline was detected twice below 500 µg/kg. Paromomycin, ciprofloxacin and enrofloxacin were detected in a concentration below 100 µg/kg. Of E. coli isolates, 88% and 23% from fattening calf slurry and beef cattle farmyard manure, respectively, were resistant to at least one of the antibiotics tested. Multi-drug resistance was observed at a maximum of 10 and 7 antibiotics, respectively. The occurrence of antibiotic resistant E. coli and antibiotic residues is shown to be higher in fattening calf slurry than in beef cattle farmyard manure used for agricultural field fertilization.

Triple-hurdle model analysis of the factors influencing biogas digester building, use and processing by Chinese pig farmers

Because of the pollution associated with pig manure, pig farmers are being encouraged to adopt environmentally friendly manure management solutions such as biogas digesters. However, as the correlations and influencing factors associated with the different manure disposal stages remain unclear, these solutions have failed to positively change farmer disposal behaviors. Therefore, this paper constructed a triple-hurdle model to empirically analyze the pig farmer manure disposal behaviors and the associated relationships under the belief that the three stage biogas digester decisions were driven by structurally different processes. This paper adds to the literature in three ways: (1) it provides a dynamic framework that identifies pig farmer manure disposal behaviors; (2) it applies a recently developed econometric method that corrects for conditional correlations between error terms; and (3) proves that certain factors might have opposite impacts in different behavior stages. It was found that cultivated land area and farm income ratio had statistically significant positive impacts on biogas digesters construction behavior but a negative influence on the farmers' use of the biogas digesters. Farmers who joined a cooperative were found to be statistically more likely to be biogas digester users, and the unconditional expected share of the actual treated manure was significantly higher. This study can assist policymakers in formulating and implementing strategies to encourage greater biogas digestor use by pig farmers.

Farm dust resistomes and bacterial microbiomes in European poultry and pig farms

BACKGROUND

Livestock farms are a reservoir of antimicrobial resistant bacteria from feces. Airborne dust-bound bacteria can spread across the barn and to the outdoor environment. Therefore, exposure to farm dust may be of concern for animals, farmers and neighboring residents. Although dust is a potential route of transmission, little is known about the resistome and bacterial microbiome of farm dust.

OBJECTIVES

We describe the resistome and bacterial microbiome of pig and poultry farm dust and their relation with animal feces resistomes and bacterial microbiomes, and on-farm antimicrobial usage (AMU). In addition, the relation between dust and farmers' stool resistomes was explored.

METHODS

In the EFFORT-study, resistomes and bacterial microbiomes of indoor farm dust collected on Electrostatic Dust fall Collectors (EDCs), and animal feces of 35 conventional broiler and 44 farrow-to-finish pig farms from nine European countries were determined by shotgun metagenomic analysis. The analysis also included 79 stool samples from farmers working or living at 12 broiler and 19 pig farms and 46 human controls. Relative abundance of and variation in resistome and bacterial composition of farm dust was described and compared to animal feces and farmers' stool.

RESULTS

The farm dust resistome contained a large variety of antimicrobial resistance genes (ARGs); more than the animal fecal resistome. For both poultry and pigs, composition of dust resistomes finds (partly) its origin in animal feces as dust resistomes correlated significantly with fecal resistomes. The dust bacterial microbiome also correlated significantly with the dust resistome composition. A positive association between AMU in animals on the farm and the total abundance of the dust resistome was found. Occupational exposure to pig farm dust or animal feces may contribute to farmers' resistomes, however no major shifts in farmers resistome towards feces or dust resistomes were found in this study.

CONCLUSION

Poultry and pig farm dust resistomes are rich and abundant and associated with the fecal resistome of the animals and the dust bacterial microbiome.