Antibiotic resistance genes in swine manure slurry as affected by pit additives and facility disinfectants

Lysine and valine weaken antibiotic resistance in Salmonella Typhimurium induced by disinfectant stress

Disinfectants are widely used in food production and environmental sanitation to prevent illness, but bacteria resistance to these disinfectants and co-resistance to antibiotics pose a threat to public health. This study investigated the impact of commonly used disinfectants on the resistance of Salmonella Typhimurium (ST) to disinfectants and antibiotics, and explored the metabolic mechanisms underlying the resistance changes. The results showed that subinhibitory concentrations of disinfectants had a minor impact on the resistance of ST to four disinfectants. However, chlorine-containing disinfectants stress enhanced bacteria resistance to ampicillin, while quaternary ammonium compounds stress increased resistance to tetracycline and gentamicin. Untargeted metabolomics analysis revealed significant changes in glutathione metabolism and lysine and valine degradation pathways after disinfectant exposure. Specifically, ST activated lysine decarboxylation, leading to a significant decrease in lysine levels after benzalkonium chloride exposure, while valine and leucine degradation pathways were activated by sodium hypochlorite stress. The addition of downregulated L-lysine and L-valine increased the sensitivity of ST to antibiotics, providing further evidence for the findings of metabolomics. This study provides guidance for the proper use of disinfectants in food processing and establishes a strategy based on metabolomics to control antibiotic-resistant bacteria.

Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents

Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.

Role of infrastructure and operation in disease prevalence in dairy farms: groundwork for disease prevention-based antibiotic stewardship

Attempts at regulating misuse of antibiotics in the dairy industry have been ineffective, especially in low- and middle-income countries, who also typically have high burden of preventable infectious disease, we propose a disease prevention-based approach to minimize the need and in turn consumption of antibiotics in dairy farms. Since the immediate environment of the animals is key to disease prevalence, we targeted the infrastructure- and operation-related factors in dairy farms and their link with prevalence of most common diseases and symptoms. We conducted four focused group discussions and a cross-sectional survey in 378 dairy farms to investigate disease prevalence and associated infrastructural (housing system, and manger shape), and operational (waste management, feed management, and type of cleaning agent) parameters. The most common diseases (Mastitis and secondary infections related to Foot-and-mouth disease) and symptoms (fever and diarrhoea) in the focus area were linked with the infrastructural and operational factors on the dairy farm with higher disease prevalence reported in dairy farms, where the animals were exposed to variations in diurnal temperatures or were hard to clean. We further used ML classifiers - Neural Network (NN), k-Nearest Neighbour (kNN), Support Vector Machine (SVM), Decision Tree (DT), and Random Forest (RF) - to corroborate the relationship between infrastructure and operations of the dairy farms and disease prevalence- The DT classifier on randomly sampled data could predict the prevalence of the two most common diseases (accuracy = 92%, F1-score = 0.919) Our results open new avenues for cost-effective interventions such as use of curve-edged mangers, use of rubber mats on floors, not reusing leftover feed etc. in dairy farms to prevent the most common diseases and symptoms in dairy farms and reduce the need and consumption of antibiotics.

Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing

Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, bla_TEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and bla_TEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and bla_TEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.

Occurrence and prevalence of antibiotic resistance genes in apple orchard after continual application of anaerobic fermentation residues of pig manure

Fermented organic fertilizers made from pig manure contaminated with antibiotics are widely used in fruit tree production. However, their effects on the residual antibiotics and the spread of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in apple orchards are still largely unknown. In the present study, we detected 100 ARGs and 10 MGEs that were transferred from pig manure to an apple orchard. Compared with the original pig manure, significantly greater concentrations of tetracycline, chlortetracycline, oxytetracycline, sulfadiazine, and salfamethyldiazine were observed in anaerobic fermentation residues of the pig manure. The total relative abundance levels of ARGs on the apple pericarp surface, in the orchard soil treated with biogas slurry, and in the orchard soil treated with biogas residue were 122.5, 5.2, 1.4 times higher than those in pristine soil, respectively, which were primarily attributed to the increase in the relative abundance of some ARG subtypes, including blaCTX-M, blaTEM, ermC, sul2, tetO, vgaB, and vgb. Long-term biogas slurry and biogas residue applications to orchard soil enriched bioaccumulation of 10 ARGs and 1 MGEs on the apple pericarp surface with 67.98 the highest factor. This research indicates that the application of anaerobic fermentation residues of pig manure promoted the spread of ARGs in the soil and fruits and increased the level of ARG pollution in the orchard. Results of this study highlight the importance of assessing the ecological safety of organic fertilizers from the perspective of ARGs and indicate that efforts should be devoted to further reducing ARG levels in pig manure before its application to farmland.

Short-Term Benzalkonium Chloride (C12) Exposure Induced the Occurrence of Wide-Spectrum Antibiotic Resistance in Agricultural Soils

Antibiotic resistance genes (ARGs) are global pollutants that pose a potential risk to human health. Benzalkonium chloride (C₁₂) (BC) disinfectants are thought to exert selection pressure on antibiotic resistance. However, evidence of BC-induced changes in antibiotic resistance in the soil environment is lacking. Here, we established short-term soil microcosms to investigate ARG profile dynamics in agricultural soils amended with sulfamethazine (SMZ, 10 mg kg^-1) and gradient concentrations of BC (0-100 mg kg^-1), using high-throughput quantitative PCR and Illumina sequencing. With the increase in BC concentration, the number of ARGs detected in the soil increased, but the normalized ARG abundance decreased. The added SMZ had a limited impact on ARG profiles. Compared to broad-spectrum fungicidal BC, the specificity of SMZ significantly affected the microbial community. Network analysis found that low-medium BC exposure concentrations resulted in the formation of small but strong ARG co-occurrence clusters in the soil, while high BC exposure concentration led to a higher incidence of ARGs. Variation partitioning analysis suggested that BC stress was the major driver shaping the ARG profile. Overall, this study highlighted the emergence and spread of BC-induced ARGs, potentially leading to the antimicrobial resistance problem in agricultural soils.

Antimicrobial Resistance Development Pathways in Surface Waters and Public Health Implications

Human health is threatened by antibiotic-resistant bacteria and their related infections, which cause thousands of human deaths every year worldwide. Surface waters are vulnerable to human activities and natural processes that facilitate the emergence and spread of antibiotic-resistant bacteria in the environment. This study evaluated the pathways and drivers of antimicrobial resistance (AR) in surface waters. We analyzed antibiotic resistance healthcare-associated infection (HAI) data reported to the CDC's National Healthcare Safety Network to determine the number of antimicrobial-resistant pathogens and their isolates detected in healthcare facilities. Ten pathogens and their isolates associated with HAIs tested resistant to the selected antibiotics, indicating the role of healthcare facilities in antimicrobial resistance in the environment. The analyzed data and literature research revealed that healthcare facilities, wastewater, agricultural settings, food, and wildlife populations serve as the major vehicles for AR in surface waters. Antibiotic residues, heavy metals, natural processes, and climate change were identified as the drivers of antimicrobial resistance in the aquatic environment. Food and animal handlers have a higher risk of exposure to resistant pathogens through ingestion and direct contact compared with the general population. The AR threat to public health may grow as pathogens in aquatic systems adjust to antibiotic residues, contaminants, and climate change effects. The unnecessary use of antibiotics increases the risk of AR, and the public should be encouraged to practice antibiotic stewardship to decrease the risk.

A Review on Constructed Treatment Wetlands for Removal of Pollutants in the Agricultural Runoff

Constructed wetland (CW) is a popular sustainable best management practice for treating different wastewaters. While there are many articles on the removal of pollutants from different wastewaters, a comprehensive and critical review on the removal of pollutants other than nutrients that occur in agricultural field runoff and wastewater from animal facilities, including pesticides, insecticides, veterinary medicine, and antimicrobial-resistant genes are currently unavailable. Consequently, this paper summarized recent findings on the occurrence of such pollutants in the agricultural runoff water, their removal by different wetlands (surface flow, subsurface horizontal flow, subsurface vertical flow, and hybrid), and removal mechanisms, and analyzed the factors that affect the removal. The information is then used to highlight the current research gaps and needs for resilient and sustainable treatment systems. Factors, including contaminant property, aeration, type, and design of CWs, hydraulic parameters, substrate medium, and vegetation, impact the removal performance of the CWs. Hydraulic loading of 10–30 cm/d and hydraulic retention of 6–8 days were found to be optimal for the removal of agricultural pollutants from wetlands. The pollutants in agricultural wastewater, excluding nutrients and sediment, and their treatment utilizing different nature-based solutions, such as wetlands, are understudied, implying the need for more of such studies. This study reinforced the notion that wetlands are effective for treating agricultural wastewater (removal > 90%) but several research questions remain unanswered. More long-term research in the actual field utilizing environmentally relevant concentrations to seek actual impacts of weather, plants, substrates, hydrology, and other design parameters, such as aeration and layout of wetland cells on the removal of pollutants, are needed.

Distribution of genetic elements associated with antibiotic resistance in treated and untreated animal husbandry waste and wastewater

Animal breeding for meat production based on swine, cattle, poultry, and aquaculture is an activity that generates several impacts on the environment, among them the spread of antibiotic resistance. There is a worldwide concern related to the massive use of antibiotics, which causes selective pressure on the microbial community, triggering bacteria that contain "antibiotic resistance genes." According to the survey here presented, antibiotic resistance-related genes such as tetracyclines (tet), erythromycin (erm), and sulfonamides (sul), as well as the genetic mobile element interferon (int), are the most reported genetic elements in qualitative and quantitative studies of swine, cattle, poultry, and aquaculture manure/wastewater. It has been observed that biological treatments based on waste composting and anaerobic digestion are effective in ARG removal, particularly for tet, bla, erm, and qnr (quinolone) genes. On the other hand, sul and intI genes were more persistent in such treatments. Tertiary treatments, such advanced oxidative processes, are suitable strategies to improve ARG reduction. In general temperature, hydraulic retention time, and penetration of sunlight are the main operational parameters for ARG reduction in treatments applied to animal waste, and therefore attention should be addressed to optimize their efficacy regarding ARG removal. Despite being reduced, the presence of ARG in treated effluents and in biosolids indicates that there is a potential risk of antibiotic resistance spread in nature, especially through the release of treated livestock waste into the environment.