The fate of antibiotics during phosphate recovery processes - A critical review

The principles of circular economy encourage the recovery of phosphorus from nutrient-rich waste streams such as animal manure, domestic wastewater, and urine to supplement existing sources of raw phosphorus. However, these waste streams also contain a wide variety of contaminants of emerging concern including antibiotics, and the recovery of phosphorus from these waste streams results in the co-occurrence of antibiotics with the recovered phosphorus products. This paper provides a comprehensive overview of the fate of environmentally relevant antibiotics in three major existing and upcoming phosphorus recovery processes: precipitation-, membrane-, and adsorption-based treatment. In general, the co-occurrence of antibiotics in recovered phosphorus increases with the presence of dissolved organic matter (DOM) and cations due to π-π interaction and cationic bridge formation, respectively. Additionally, antibiotics display pH-based speciation resulting in electrostatic interactions with recovered phosphorus at pH > 7.0. Furthermore, this critical review establishes a new metric, the relative antibiotic-to‑phosphorus (RAP), defined as the ratio of the concentration of antibiotics to phosphorus in recovered phosphorus to that of the phosphorus-rich waste. Precipitation-based methods, particularly struvite, demonstrated the lowest RAP, while the RAP in carbon-based adsorbents was 1.8 × 108 times higher than in membrane-based processes. In reviewing literature on the fate of antibiotics in phosphorus recovery processes, several research needs are also highlighted: the fate of non-tetracycline antibiotics, simultaneous investigation of phosphorus and antibiotic fate in membrane- and adsorption-based methods, treatment methods to mitigate the co-occurrence of antibiotics in recovered phosphorus product, and the release of antibiotics from recovered phosphate products.

Biosecurity Practices to Enhance Responsible Antimicrobial Use and Reduce the Burden of Antimicrobial Resistance

The article shows the case for using biosecurity measures to mitigate antimicrobial resistance (AMR) in beef and dairy production through actions of veterinarians and animal caretakers. The impact of biosecurity on the prevention of bacterial infections is discussed, with the goal being to reduce the need for antimicrobial drugs. This is expected to reduce the selection for AMR in pathogens and commensal bacterial organisms in beef and dairy animals. The potential impact of biosecurity on the prevention of dissemination of antimicrobial resistant bacteria and AMR genes in the environment is also described.

Dietary supplementation of S cutellariae radix flavonoid extract improves lactation performance in dairy cows by regulating gastrointestinal microbes, antioxidant capacity and immune function

Scutellariae radix flavonoid extract (SFE) has been acknowledged for its antioxidant, anti-inflammatory and antimicrobial properties in enhancing gastrointestinal microbial communities and improving the host's immunity. Nevertheless, the impacts of dietary supplementation with SFE on the gastrointestinal microbes and host metabolism in dairy cows remain uncertain. Therefore, the aim of this study was to assess the effects of dietary supplementation with SFE on the lactation performance, gastrointestinal microbes, and plasma biochemical parameters of dairy cows. Six ruminally and duodenally cannulated multiparous dairy cows were used in a crossover design over 28-d periods that included a 21-d adaptation and a 7-d sample collection period. Cows were fed a basal diet (CON group) or a basal diet supplemented with SFE at 25 g/d (SFE group). SFE supplementation tended to increase milk yield (P = 0.067) and milk urea N concentration (P = 0.079), and decreased the milk somatic cell counts (SCC, P = 0.036). Cows in the SFE group had lower plasma aspartate aminotransferase (AST), malondialdehyde (MDA), tumor necrosis factor (TNF-α), and interleukin-1β concentrations compared with the CON (P < 0.05). Meanwhile, SFE supplementation increased butyrate concentration in the rumen (P = 0.044). The microbial structure of rumen and duodenum were affected by SFE supplementation (P = 0.009 and P = 0.031; respectively), resulting in enrichment of Butyrivibrio in both parts of the SFE cows (P = 0.034 and P = 0.029; respectively). However, microbial structure and composition of feces were not affected by SFE supplementation. Overall, our study indicated that dietary supplementation with SFE could enhance lactation performance and milk quality in dairy cows by improving the gastrointestinal inner environment and health status.

Comparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China

Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood. In this study, we collected eight samples from a farm in Kaifeng City, China, comprising both fresh and composted pig manure. Using a high-throughput quantitative PCR array, we analyzed differences in ARG expression between these two types of manure. Our findings revealed significant differences in ARG profiles, as demonstrated by principal coordinate analysis (PCoA). Further analysis identified 39 ARGs (log2FC > 1, p < 0.05) in composted pig manure, with 25 genes downregulated and 14 upregulated. Notably, tetB-01, blaOCH, and blaOXY were the most abundant in composted pig manure compared to fresh manure. Additionally, 16S rRNA species profiling revealed that the composting process significantly altered the microbial community structure, with an increased abundance of Firmicutes and a decreased abundance of Bacteroidetes in composted pig manure. In summary, composting substantially transforms both the microbial community structure and the ARG profile in pig manure, underscoring its potential role in modulating the dynamics of ARGs in agricultural environments.

Potential of Pine Biochar to Mitigate Bacterial Hazards Present in Recycled Manure Solids from Dairy Cows

The use of recycled manure solids (RMS) as cow bedding in dairy farms poses concerns due to its potential to harbor pathogenic and antimicrobial-resistant bacteria. This study evaluated the impact of RMS supplementation with biochar at three concentrations (2.5%, 5%, and 10%) on bacterial counts and on the antimicrobial resistance and virulence profiles of Escherichia coli and Enterococcus isolates. The results show that biochar supplementation did not promote a significant reduction in bacterial numbers. Overall, there were no significant changes in the isolates' virulence or resistance profiles, and none of the isolates obtained were classified as high or moderate threats based on their MAR and VIR indexes. The most pathogenic Enterococcus isolates found were present in the control samples. A phylogenetic analysis of E. coli isolates allowed us to identify phylogroup D strains, predominantly in RMS supplemented with 2.5% and 10% biochar, which are associated with higher virulence and resistance. These findings indicate that the biochar concentrations tested were not effective in significantly reducing the bacterial risks associated with RMS. Further research is needed to evaluate different biochar formulations and concentrations, aiming to optimize its potential use for RMS supplementation.

Investigating drug residues in Mongolian milk using a newly developed method with high performance liquid chromatography and a photo diode array

Despite the beneficial impacts of using drugs in animal husbandry, the risks of drug residues in animal products are a concern worldwide. Therefore, most countries have developed systems and methods to detect and monitor drug residues in animal products using high performance liquid chromatography (HPLC) with mass spectrometry (MS). However, MS detectors are not available in all universities; thus, we developed a new method suitable for ultraviolet detection. We first validated a new method targeting tetracycline and albendazole in milk and evaluated these drug residues in 50 samples collected from farms and supermarkets in Mongolia. The practical limit of quantification (PQL) calculated in our newly developed method was suitable to detect the maximum residual limits defined in Codex Alimentarius, and the accuracy and precision of a new method were comparable to previous studies. In particular, inter-day analysis showed great precision, with albendazole showing a 99% recovery rate with ± 3.3 of relative standard deviation (RSD). In addition, we evaluated our drugs contamination, but targeted drugs residues were not detected in the current sample set. However, this may reflect the decreased use of tetracycline in the veterinary field and seasonal use of albendazole in Mongolia. Therefore, these drugs must be continuously monitored. To the best of our knowledge, this is the first report about drug residues in milk published in an international journal by a Mongolian domestic institution. Further investigations of drug residue in Mongolia are urgently needed.

Bio-computational modeling, POM analysis and molecular dynamic simulation for novel synthetic quinolone and benzo[d][1,3]oxazine candidates as antimicrobial inhibitors

The current study offers a metal-free, direct, and successful synthesis technique for a new series of quinolinone and benzo[d][1,3]oxazine, along with an assessment of their biological activities. Heteroannulation of anthranilic acid with carbonyl-containing chemicals (aroyl pyruvate, ethyl acetoacetatete, maleic anhydride, and ethyl cyanoacetate) resulted in the desired quinolones and benzo[d][1,3]oxazines. This technique introduces a number of fundamental breakthroughs in organic synthesis, including metal-free catalysts, smart reaction conditions with column purification, and a wide functional scope. Furthermore, the structure of the newly synthesized chemical series was investigated and validated using spectroscopic techniques. The synthesized series were evaluated for antibacterial (against gram-positive and gram-negative bacterial strains) and antifungal activity. The quinolone and benzo[d][1,3]oxazine candidates had remarkable antibacterial action. Furthermore, molecular docking investigations corroborated the biological studies using the Molecular Operating Environment and Petro Osiris Molinspiration (POM) experiments, which confirmed the activity of compounds 8, 15, and 17. Our studies on the cytotoxic activity of various chemicals have demonstrated that these compounds exhibit minimal toxicity. Specifically, when comparing the cytotoxic effects on human lung fibroblast (WI38) cells to those of Doxorubicin, a well-known chemotherapy agent, compounds 8, 15, and 17 showed weak cytotoxic effects on the normal WI38 cells. This indicates that these compounds may possess some level of selectivity and reduced toxicity towards normal cells, suggesting potential for further exploration as antibacterial agents with a safer profile for normal cells.

AmpClass: an Antimicrobial Peptide Predictor Based on Supervised Machine Learning

In the last decades, antibiotic resistance has been considered a severe problem worldwide. Antimicrobial peptides (AMPs) are molecules that have shown potential for the development of new drugs against antibiotic-resistant bacteria. Nowadays, medicinal drug researchers use supervised learning methods to screen new peptides with antimicrobial potency to save time and resources. In this work, we consolidate a database with 15945 AMPs and 12535 non-AMPs taken as the base to train a pool of supervised learning models to recognize peptides with antimicrobial activity. Results show that the proposed tool (AmpClass) outperforms classical state-of-the-art prediction models and achieves similar results compared with deep learning models.

The Contribution of Dairy Bedding and Silage to the Dissemination of Genes Coding for Antimicrobial Resistance: A Narrative Review

Antimicrobial resistance (AMR) is a concern in the dairy industry. Recent studies have indicated that bedding serves as a reservoir for antimicrobial-resistant bacteria and antimicrobial-resistance genes (ARGs), while silage has been proposed as another possible source. The impact of AMR in dairy farming can be significant, resulting in decreased productivity and economic losses for farmers. Several studies have highlighted the safety implications of AMR bacteria and genes in bedding and silage, emphasizing the need for further research on how housing, bedding, and silage management affect AMR in farm environments. Exposure to sub-lethal concentrations of antibiotics, such as those from contaminated bedding and silage, can prompt bacteria to develop resistance mechanisms. Thus, even if antimicrobial usage is diminished, ARGs may be maintained in the dairy farm environment. By implementing proactive measures to tackle AMR in dairy farming, we can take steps to preserve the health and productivity of dairy cattle while also protecting public health. This involves addressing the prudent use of antibiotics during production and promoting animal welfare, hygiene, and management practices in bedding and farm environments to minimize the risk of AMR development and spread. This narrative review compiles the growing research, positioning the contribution of bedding and silage to the prevalence and dissemination of AMR, which can elicit insights for researchers and policymakers.

How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review

Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.

Effect of anaerobic digestion on pathogens and antimicrobial resistance in the sewage sludge

Antimicrobial resistance (AMR) is recognized as a global threat. AMR bacteria accumulate in sewage sludge however, knowledge on the persistence of human pathogens and AMR in the sludge line of the wastewater treatment is limited. Sludge can be used, with or without additional treatment, as fertilizer in agricultural fields. The aim of this study is to obtain knowledge about presence of human pathogens and AMR in the sewage sludge, before and after the anaerobic digestion (AD) applying innovative combinations of methods. Fifty sludge samples were collected. Cultivation methods combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and Antibiotic Susceptibility Test (AST) were used obtaining knowledge about the microbial community, pathogens, and antibiotic resistant bacteria while the droplet digital Polymerase Chain Reaction (ddPCR) was performed to detect most common AMR genes. In total, 231 different bacterial species were identified in the samples. The most abundant species were spore-forming facultative anaerobic bacteria belonging to Bacillus and Clostridium genera. The AD causes a shift in the microbial composition of the sludge (p = 0.04). Seven pathogenic bacterial species constituting 188 colonies were isolated and tested for susceptibility to Clindamycin, Meropenem, Norfloxacin, Penicillin G, and Tigecycline. Of the Clostridium perfringens and Bacillus cereus isolates 67 and 50 %, respectively, were resistant to Clindamycin. Two B. cereus and two C. perfringens isolates were also resistant to other antibiotics showing multidrug resistance. ARGs (blaOXA, blaTEM, ermB, qnrB, tet(A)-(W), sulI-II) were present at 7-8 Log gene copies/kg of sludge. AD is the main driver of a reduction of some ARGs (1 Log) but resistant bacteria were still present. The results showed the usefulness of the integration of the proposed analytical methods and suggest a decrease in the risk of presence of cultivable pathogens including resistant isolates after AD but a persistent risk of ARGs' horizontal transmission.

Aloe arborescens supplementation in drying-off dairy cows: influence on rumen, rectum and milk microbiomes

BACKGROUND

In the context of the RABOLA project, which aimed to identify operational practices that lead to the reduction of antibiotic use in dairy cattle farming, lyophilised Aloe arborescens was administered orally to cows during the dry-off and peripartum periods. In this specific paper we wanted to examine whether oral administration of Aloe arborescens, in combination with the topical application of a teat sealant could exert an effect on the microbial populations of three cow microbiomes (rumen, milk, rectum), between dry-off and peripartum. Dry-off and peripartum are critical physiological phases of the cow's life, where both the mammary gland and the gastrointestinal tract undergo dramatic modifications, hence the relevance of evaluating the effects of dietary treatments.

METHODS

Thirty multiparous dairy cows were randomly allocated to three groups: Control (antibiotic treatment and internal teat sealant), Sealant (only internal teat sealant) and Aloe (internal teat sealant and Aloe arborescens homogenate administered orally). For 16S rRNA gene sequencing, rumen, rectum and milk samples were collected, not synchronously, at the most critical timepoints around dry-off and calving, considering the physiological activity of each biological site.

RESULTS

The rumen microbiome was predominantly characterized by Bacteroidetes and Firmicutes followed by Proteobacteria, while the rectum exhibited a prevalence of Firmicutes and Bacteroidetes. The milk microbiome mainly comprised Firmicutes, Proteobacteria, Actinobacteria and Bacteroidetes. Alistipes spp., Ruminococcaceae UCG-10 group, Prevotellaceae UCG-001 group, and Bacteroides spp., involved in cellulose and hemicellulose degradation, enhancement of energy metabolism, and peptide breakdown, showed increment in the rectum microbiome with Aloe supplementation. The rectum microbiome in the Aloe group exhibited a significant increase in the Firmicutes to Bacteroidetes ratio and alpha-diversity at seven days after dry-off period. Beta-diversity showed a significant separation between treatments for the rectum and milk microbiomes. Aloe supplementation seemed to enrich milk microbial composition, whereas the Sealant group showed greater diversity compared to the Control group, albeit this included an increase in microorganisms frequently associated with mastitis.

CONCLUSIONS

Aloe arborescens administration during the dry-off period did not demonstrate any observable impact on the microbial composition of the rumen, a finding further supported by volatilome analysis. Instead, the oral Aloe supplementation at dry-off appears to significantly influence the composition of the dairy cow rectum and milk microbiomes in the following lactation.

When the solution becomes the problem: a review on antimicrobial resistance in dairy cattle

Antibiotics' action, once a 'magic bullet', is now hindered by widespread microbial resistance, creating a global antimicrobial resistance (AMR) crisis. A primary driver of AMR is the selective pressure from antimicrobial use. Between 2000 and 2015, antibiotic consumption increased by 65%, reaching 34.8 billion tons, 73% of which was used in animals. In the dairy cattle sector, antibiotics are crucial for treating diseases like mastitis, posing risks to humans, animals and potentially leading to environmental contamination. To address AMR, strategies like selective dry cow therapy, alternative treatments (nanoparticles, phages) and waste management innovations are emerging. However, most solutions are in development, emphasizing the urgent need for further research to tackle AMR in dairy farms.

Nitrogen and Chlorine Co-doped Carbon Dots as a Highly Selective and Sensitive Fluorescent Probe for Sensing of PH, Tetracycline Detection and Cell Imaging

Carbon dots have been widely focused on the field of sensing and detection due to their excellent optical property. Herein, novel orange fluorescent nitrogen and chlorine co-doped carbon dots (N,Cl-CDs) are obtained by one-pot hydrothermal method using o-phenylenediamine and neutral red. Based on the inner filter effect, the prepared N,Cl-CDs can be innovatively developed as an effective "signal-off" multifunctional sensing platform for sensitive determination of tetracycline. The proposed sensor was utilized to realize the determination of tetracycline in Rirver water samples/milk samples (λex = 390 nm, λem = 606 nm) with satisfactory recoveries and relative standard deviations. The linear range of are 0.05 to 45 μM and 45 to135 μM, and detection limit is 3.9 nM (3σ/m). Meanwhile, the luminescent intensity of N,Cl-CDs was reduced gradually when pH changed continuously from 12 to 2, showing a pH-responsive fluorescence property with two linear ranges of pH 3-7 and pH 7-10. In addition, due to the characteristics of low toxicity and excellent biocompatibility, the N, Cl-CDs were also used in the imaging of oocystis cells, which is hopeful to realize the detection of tetracycline in living cells.

Sustainable strategies: Nature-based solutions to tackle antibiotic resistance gene proliferation and improve agricultural productivity and soil quality

The issue of antibiotic resistance is now recognized by the World Health Organisation (WHO) as one of the major problems in human health. Although its effects are evident in the healthcare settings, the root cause should be traced back to the One Health link, extending from animals to the environment. In fact, the use of organic fertilizers in agroecosystems represents one, if not the primary, cause of the introduction of antibiotics and antibiotic-resistant bacteria into the soil. Since the concentrations of antibiotics introduced into the soil are residual, the agroecosystem has become a perfect environment for the selection and proliferation of antibiotic resistance genes (ARGs). The continuous influx of these emerging contaminants (i.e., antibiotics) into the agroecosystem results in the selection and accumulation of ARGs in soil bacteria, occasionally giving rise to multi-resistant bacteria. These bacteria may harbour ARGs related to various antibiotics on their plasmids. In this context, these bacteria can potentially enter the human sphere when individuals consume food from contaminated agroecosystems, leading to the acquisition of multi-resistant bacteria. Once introduced into the nosocomial environment, these bacteria pose a significant threat to human health. In this review, we analyse how the use of digestate as an organic fertilizer can mitigate the spread of ARGs in agroecosystems. Furthermore, we highlight how, according to European guidelines, digestate can be considered a Nature-Based Solution (NBS). This NBS not only has the ability to mitigate the spread of ARGs in agroecosystems but also offers the opportunity to further improve Microbial-Based Solutions (MBS), with the aim of enhancing soil quality and productivity.

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.

Generic role of zeolite in enhancing anaerobic digestion and mitigating diverse inhibitions: Insights from degradation performance and microbial characteristics

Zeolite was shown to mitigate anaerobic digestion (AD) inhibition caused by several inhibitors such as long-chain fatty acids, ammonia, and phenolic compounds. In this paper, we verified the genericity of zeolite's mitigating effect against other types of inhibitors found in AD such as salts, antibiotics, and pesticides. The impacts of inhibitors and zeolite were assessed on AD performance and microbial dynamics. While sodium chloride and erythromycin reduced methane production rates by 34% and 32%, zeolite mitigated the inhibition and increased methane production rates by 72% and 75%, respectively, compared to conditions without zeolite in the presence of these two inhibitors. Noticeably, zeolite also enhanced methane production rate by 51% in the uninhibited control condition. Microbial community structure was analyzed at two representative dates corresponding to the hydrolysis/fermentation and methanogenesis stages through 16S rRNA gene sequencing. The microbial characteristics were further evidenced with common components analysis. Results revealed that sodium chloride and erythromycin inhibited AD by targeting distinct microbial populations, with more pronounced inhibitory effects during hydrolysis and VFAs degradation phases, respectively. Zeolite exhibited a generic effect on microbial populations in different degradation stages across all experimental conditions, ultimately contributing to the enhanced AD performance and mitigation of different inhibitions. Typically, hydrolytic and fermentative bacteria such as Cellulosilyticum, Sedimentibacter, and Clostridium sensu stricto 17, VFAs degraders such as Mesotoga, Syntrophomonas, and Syntrophobacter, and methanogens including Methanobacterium, Methanoculleus, and Methanosarcina were strongly favored by the presence of zeolite. These findings highlighted the promising use of zeolite in AD processes for inhibition mitigation in general.

Quantitative microbial risk assessment for ingestion of antibiotic resistance genes from private wells contaminated by human and livestock fecal sources

We used quantitative microbial risk assessment to estimate ingestion risk for intI1, erm(B), sul1, tet(A), tet(W), and tet(X) in private wells contaminated by human and/or livestock feces. Genes were quantified with five human-specific and six bovine-specific microbial source-tracking (MST) markers in 138 well-water samples from a rural Wisconsin county. Daily ingestion risk (probability of swallowing ≥1 gene) was based on daily water consumption and a Poisson exposure model. Calculations were stratified by MST source and soil depth over the aquifer where wells were drilled. Relative ingestion risk was estimated using wells with no MST detections and >6.1 m soil depth as a referent category. Daily ingestion risk varied from 0 to 8.8 × 10-1 by gene and fecal source (i.e., human or bovine). The estimated number of residents ingesting target genes from private wells varied from 910 (tet(A)) to 1,500 (intI1 and tet(X)) per day out of 12,000 total. Relative risk of tet(A) ingestion was significantly higher in wells with MST markers detected, including wells with ≤6.1 m soil depth contaminated by bovine markers (2.2 [90% CI: 1.1-4.7]), wells with >6.1 m soil depth contaminated by bovine markers (1.8 [1.002-3.9]), and wells with ≤6.1 m soil depth contaminated by bovine and human markers simultaneously (3.1 [1.7-6.5]). Antibiotic resistance genes (ARGs) were not necessarily present in viable microorganisms, and ingestion is not directly associated with infection. However, results illustrate relative contributions of human and livestock fecal sources to ARG exposure and highlight rural groundwater as a significant point of exposure.IMPORTANCEAntibiotic resistance is a global public health challenge with well-known environmental dimensions, but quantitative analyses of the roles played by various natural environments in transmission of antibiotic resistance are lacking, particularly for drinking water. This study assesses risk of ingestion for several antibiotic resistance genes (ARGs) and the class 1 integron gene (intI1) in drinking water from private wells in a rural area of northeast Wisconsin, United States. Results allow comparison of drinking water as an exposure route for antibiotic resistance relative to other routes like food and recreational water. They also enable a comparison of the importance of human versus livestock fecal sources in the study area. Our study demonstrates the previously unrecognized importance of untreated rural drinking water as an exposure route for antibiotic resistance and identifies bovine fecal material as an important exposure factor in the study setting.

Ecotoxicity of five veterinary antibiotics on indicator organisms and water and soil communities

This study explores the environmental effects of five common veterinary antibiotics widely detected in the environment, (chlortetracycline,CTC; oxytetracycline,OTC; florfenicol,FF; neomycin, NMC; and sulfadiazine, SDZ) on four bioindicators: Daphnia magna, Vibrio fischeri, Eisenia fetida, and Allium cepa, representing aquatic and soil environments. Additionally, microbial communities characterized through 16 S rRNA gene sequencing from a river and natural soil were exposed to the antibiotics to assess changes in population growth and metabolic profiles using Biolog EcoPlates™. Tetracyclines are harmful to Vibrio fisheri (LC50 ranges of 15-25 µg/mL), and the other three antibiotics seem to only affect D. magna, especially, SDZ. None of the antibiotics produced mortality in E. fetida at concentrations below 1000 mg/kg. NMC and CTC had the highest phytotoxicities in A. cepa (LC50 = 97-174 µg/mL, respectively). Antibiotics significantly reduced bacterial metabolism at 0.1-10 µg/mL. From the highest to the lowest toxicity on aquatic communities: OTC > FF > SDZ ≈ CTC > NMC and on edaphic communities: CTC ≈ OTC > FF > SDZ > NMC. In river communities, OTC and FF caused substantial decreases in bacterial metabolism at low concentrations (0.1 µg/mL), impacting carbohydrates, amino acids (OTC), and polymers (FF). At 10 µg/mL and above, OTC, CTC, and FF significantly decreased metabolizing all tested metabolites. In soil communities, a more pronounced decrease in metabolizing ability, detectable at 0.1 µg/mL, particularly affected amines/amides and carboxylic and ketonic acids (p < 0.05). These new ecotoxicity findings underscore that the concentrations of these antibiotics in the environment can significantly impact both aquatic and terrestrial ecosystems.

Research on Bacterial Diversity and Antibiotic Resistance in the Dairy Farm Environment in a Part of Shandong Province

Antimicrobials are extensively utilized in dairy farms to prevent and control diseases in cattle. However, their use contributes to the emergence of antimicrobial-resistant bacteria (ARB) and antimicrobial-resistant genes (ARG), and these can be transmitted to the environment. Regular monitoring of antimicrobial resistance (AMR) is crucial for implementing effective mitigation strategies. This research aimed to assess the environmental microbial species present on dairy farms in Shandong Province and characterize the antimicrobial resistance profiles of the isolates. Five dairy farms located in Shandong Province were selected, representing the prevalent large-scale farming patterns in the area. Sampling took place from April to June 2022, with a total of 223 isolates collected from various environmental locations within each farm (bedding, sports field, and milking parlor). Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was employed to identify the species of the clinical isolates. The main pathogens isolated were Aerococcus viridans (5.38%, n = 12), Corynebacterium xerosis (4.93%, n = 11), and Acinetobacter lwoffii (4.03%, n = 9). Among the bacterial isolates, resistance to lincomycin was highest at 91%, and 88% were resistant to sulfadiazine. Antimicrobial resistance genes were detected in only a small proportion of the isolates, the most common of which was sul1. These findings highlight the necessity for careful evaluation of antimicrobial usage in maintaining their effectiveness in human medicine. Understanding the microbial species present and their antimicrobial resistance profiles aids in focusing efforts toward sustainable antimicrobial use and safeguarding human health.

Potential Causes of Spread of Antimicrobial Resistance and Preventive Measures in One Health Perspective-A Review

Antimicrobial resistance, referring to microorganisms' capability to subsist and proliferate even when there are antimicrobials is a foremost threat to public health globally. The appearance of antimicrobial resistance can be ascribed to anthropological, animal, and environmental factors. Human-related causes include antimicrobial overuse and misuse in medicine, antibiotic-containing cosmetics and biocides utilization, and inadequate sanitation and hygiene in public settings. Prophylactic and therapeutic antimicrobial misuse and overuse, using antimicrobials as feed additives, microbes resistant to antibiotics and resistance genes in animal excreta, and antimicrobial residue found in animal-origin food and excreta are animals related contributive factors for the antibiotic resistance emergence and spread. Environmental factors including naturally existing resistance genes, improper disposal of unused antimicrobials, contamination from waste in public settings, animal farms, and pharmaceutical industries, and the use of agricultural and sanitation chemicals facilitatet its emergence and spread. Wildlife has a plausible role in the antimicrobial resistance spread. Adopting a one-health approach involving using antimicrobials properly in animals and humans, improving sanitation in public spaces and farms, and implementing coordinated governmental regulations is crucial for combating antimicrobial resistance. Collaborative and cooperative involvement of stakeholders in public, veterinary and ecological health sectors is foremost to circumvent the problem effectively.

TET-Yeasate: An engineered yeast whole-cell lysate-based approach for high performance tetracycline degradation

The widespread of tetracycline (TC) residues in anthropogenic and natural environments pose an immediate threat to public health. Herein, we established the TET-Yeasate, an approach based on whole-cell lysate of engineered yeast, to mitigate the TC contamination in environment. The TET-Yeasate is defined as the biological matrix of whole cell lysate from engineered yeast that containing TC-degradative components (Tet(X), NADPH, Mg2+) and protective macromolecules. The TET-Yeasate was able to efficiently eliminate TC residues in tap water (98.8%), lake water (77.6%), livestock sewage (87.3%) and pharmaceutical wastewater (35.3%) without necessity for exogenous addition of expensive cofactors. The TET-Yeasate was further developed into lyophilized form for ease of storage and delivery. The TET-Yeasate in lyophilized form efficiently removed up to 74.6% TC residue within 0.25 h. In addition, the lyophilization confers promising resilience to TET-Yeasate against adverse temperatures and pH by maintaining degradation efficacy of 85.69%-97.83%. The stability test demonstrated that the biomacromolecules in lysate served as natural protectants that exerted extensive protection on TET-Yeasate during the 14-day storage at various conditions. In addition, 5 potential degradation pathways were elaborated based on the intermediate products. Finally, the analysis indicated that TET-Yeasate enjoyed desirable bio- and eco-safety without introduction of hazardous intermediates and spread of resistance genes. To summary, the TET-Yeasate based on whole cell lysate of engineered yeast provides a cost-effective and safe alternative to efficiently remove TC residues in environment, highlighting the great potential of such whole-cell based methods in environmental decontamination.

Transmission of livestock-associated methicillin-resistant Staphylococcus aureus between animals, environment, and humans in the farm

Staphylococcus aureus (S. aureus) is a fearsome bacterial pathogen that can colonize and infect humans and animals. Depending on the different sources, MRSA is classified as hospital-associated methicillin-resistant S. aureus (HA-MRSA), community-associated MRSA (CA-MRSA), and livestock-associated MRSA (LA-MRSA). LA-MRSA is initially associated with livestock, and clonal complexes (CCs) were almost always 398. However, the continued development of animal husbandry, globalization, and the widespread use of antibiotics have increased the spread of LA-MRSA among humans, livestock, and the environment, and other clonal complexes such as CC9, CC5, and CC8 have gradually emerged in various countries. This may be due to frequent host switching between humans and animals, as well as between animals. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements (MGEs) such as phages, pathogenicity islands, and plasmids as well as further host-specific mutations allowing it to expand into new host populations. This review aimed to provide an overview of the transmission characteristics of S. aureus in humans, animals, and farm environments, and also to describe the main prevalent clones of LA-MRSA and the changes in MGEs during host switching.

Contribution of Manure-Spreading Operations to Bioaerosols and Antibiotic Resistance Genes' Emission

Manure spreading from farm animals can release antibiotic-resistant bacteria (ARB) carrying antimicrobial resistance genes (ARGs) into the air, posing a potential threat to human and animal health due to the intensive use of antibiotics in the livestock industry. This study analyzed the effect of different manure types and spreading methods on airborne bacterial emissions and antibiotic resistance genes in a controlled setting. Cow, poultry manure, and pig slurry were spread in a confined environment using two types of spreaders (splash plate and dribble bar), and the resulting emissions were collected before, during, and after spreading using high-volume air samplers coupled to a particle counter. Total bacteria, fecal indicators, and a total of 38 different subtypes of ARGs were further quantified by qPCR. Spreading poultry manure resulted in the highest emission rates of total bacteria (1011 16S gene copies/kg manure spread), Archaea (106 16S gene copies/kg manure), Enterococcus (105 16S gene copies/kg manure), and E. coli (104 16S gene copies/kg manure), followed by cow manure and pig slurry with splash plates and the dribble bar. Manure spreading was associated with the highest rates of airborne aminoglycoside genes for cow and poultry (106 gene copies/kg manure), followed by pig slurry (104 gene copies/kg manure). This study shows that the type of manure and spreading equipment can affect the emission rates of airborne bacteria, and ARGs.

Combined effects of amoxicillin and copper on nitrogen transformation and the microbial mechanisms during aerobic composting of cow manure

Pollutants in livestock manure have a compound effect during aerobic composting, but research to date has focused more on single factors. This study investigated the effects of adding amoxicillin (AMX), copper (Cu) and both (ACu) on nitrogen transformation and the microbial mechanisms in cow manure aerobic composting with wheat straw. In this study, compared with CK, AMX, Cu, and ACu increased NH₃ cumulative emissions by 32.32%, 41.78% and 8.32%, respectively, due to their inhibition of ammonia oxidation. Coexisting AMX and Cu decreased the absolute abundances of amoA/ nxrA genes and increased the absolute abundances of nirS /nosZ genes, but they had an antagonistic effect on the changes in functional gene abundances. Pseudomonas and Luteimonas were enriched during the thermophilic and cooling periods due to the addition of AMX and ACu, which enhanced denitrification in these two groups. Moreover, adding AMX and/or Cu led to more complex bacterial networks, but the effect of the two pollutants was lower than those of the individual pollutants. These findings provide theoretical and experimental support for controlling typical combined pollution with antibiotics and heavy metals in livestock manure.

Ratiometric Sensing for Ultratrace Tetracycline Using Electrochemically Active Metal-Organic Frameworks as Response Signals

A novel ratiometric sensor using an electrochemically active metal-organic framework of Mo@MOF-808 and NH₂-UiO-66 as response signals was developed to detect tetracycline (TET) in ultratrace quantities. To achieve the dual-response strategy, Mo@MOF-808, with a reduction peak at -1.06 V, and NH₂-UiO-66, with an oxidation peak at 0.724 V, were used as signal probes directly. Concretely, Mo@MOF-808, single-stranded DNA (ssDNA), and complex system (Apt@NH₂-UiO-66) of aptamer (Apt) and NH₂-UiO-66 were sequentially immobilized on the electrode. With the addition of TET, Apt was hybridized with TET and Apt@NH₂-UiO-66 was detached from the electrode, resulting in an increase in the current at -1.06 V and a decrease in the current at 0.724 V. Through this strategy, the sensor achieved a wide linear range (0.1-10000 nM) and a low limit of detection (0.009792 nM) for TET. Moreover, the ratiometric sensor exhibited better sensitivity, reproducibility, and stability than a single-signal sensor. Furthermore, the constructed sensor was successfully applied to detect TET in milk samples, suggesting excellent application prospects.

Assessing the bioavailability of antibiotics in soil with the diffusive gradients in thin films (DGT)

The diffusive gradients in thin films (DGT) technique is an excellent method for investigating the dynamic processes of antibiotics in soils. However, whether it is applicable in antibiotic bioavailability assessment is yet to be disclosed. This study employed DGT to determine the antibiotic bioavailability in soil, and compared the results with plant uptake, soil solutions, and solvent extraction methods. DGT exhibited predictive capability for plant taking in antibiotics proved by the significant linear relationship between the DGT based concentration (C_DGT) and antibiotic concentration in roots and shoots. Although the performance of soil solution was acceptable based on linear relationship analysis, its stability was weaker than DGT. The results based on plant uptake and DGT indicated the bioavailable antibiotic contents in different soils were inconsistent because of the distinct mobility and resupply of sulphonamides and trimethoprim in different soils, as represented by K_d and R_ds, which were affected by soil properties. Plant species played an important role in antibiotic uptake and translocation. Antibiotic uptake by plants depends on antibiotic, plant and soil. These results confirmed the capability of DGT in determining antibiotic bioavailability for the first time. This work provided a simple and powerful tool for environmental risk evaluation of antibiotics in soils.

Knowledge and Practices of Cypriot Bovine Farmers towards Effective and Safe Manure Management

Manure from bovine farms is commonly used as an organic fertiliser. However, if not properly managed, it can spread significant biological and chemical hazards, threatening both human and animal health. The effectiveness of risk control hugely relies on farmers' knowledge regarding safe manure management and on the application of suitable management practices. This study aims to evaluate the knowledge and practices of Cypriot bovine farmers towards safer manure management, from its generation to its final use, in line with the One Health approach. Factors affecting farmers' knowledge and applied practices are also investigated through a questionnaire survey. The questionnaire was developed and sent to all eligible bovine farmers in Cyprus (n = 353), and 30% (n = 105) of them returned the completed questionnaire. Results revealed there are some gaps in farmers' knowledge. The use of manure for fertilising crops dominated. Only half of the farmers stored manure in appropriate facilities, with 28.5% of them using a dedicated area with cement floors and 21.5% utilising leakproof tanks. The majority (65.7%) stored manure for more than three months before its use as a fertiliser in a dried form. In multiple regression analysis, education level and farming purpose were significant determinants of farmer knowledge. In conclusion, Cypriot farmers' knowledge must be reinforced to ensure proper manure management. The results highlight the importance of providing relevant training to farmers. Although the current practices partially decrease manure pathogens, interventions to promote the use of more effective treatment methods, such as biogas transformation and composting, would be beneficial.

Developing a biogas centralised circular bioeconomy using agricultural residues - Challenges and opportunities

Anaerobic digestion (AD) can be used as a stand-alone process or integrated as part of a larger biorefining process to produce biofuels, biochemicals and fertiliser, and has the potential to play a central role in the emerging circular bioeconomy (CBE). Agricultural residues, such as animal slurry, straw, and grass silage, represent an important resource and have a huge potential to boost biogas and methane yields. Under the CBE concept, there is a need to assess the long-term impact and investigate the potential accumulation of specific unwanted substances. Thus, a comprehensive literature review to summarise the benefits and environmental impacts of using agricultural residues for AD is needed. This review analyses the benefits and potential adverse effects related to developing biogas-centred CBE. The identified potential risks/challenges for developing biogas CBE include GHG emission, nutrient management, pollutants, etc. In general, the environmental risks are highly dependent on the input feedstocks and resulting digestate. Integrated treatment processes should be developed as these could both minimise risks and improve the economic perspective.

Sustainable on-farm strategy for the disposal of antibiotic fermentation residue: Co-benefits for resource recovery and resistance mitigation

Antibiotic fermentation residue is a key issue for the sustainable operation of pharmaceutical companies, and its improper disposal may cause antibiotic resistance transfer in the environment. However, little is known about the resource recycling strategy of this pharmaceutical waste. Herein, we used hydrothermal spray-dried (HT+SD) and multi-plate dryer (MD) methods to produce bio-organic fertilizers and applied them to an internal recycling model of a field trial. The concentrations of antibiotics (penicillin, cephalosporin, and erythromycin) in the bio-fertilizer, wastewater, and exhaust gas were in the range of 0.002-0.68 mg/kg, ≤ 0.35 ng/mL, and 0.03-0.89 ng/mL, respectively. The organic matter and total nitrogen, phosphorus, and potassium contents were approximately 80% and 10%, respectively. The soil bacterial community was similar among the fertilizer treatments in the same crop cultivation. A total of 233 antibiotic resistance genes (ARGs) and 43 mobile genetic elements (MGEs) were detected, including seven Rank I ARGs and five Rank II ARGs. Random forest analysis showed that gene acc(3)-Via and plasmid trb-C were biomarkers, for which the resistance and the transfer mechanisms were antibiotic inactivation and conjugation, respectively. The results imply that AFR recycling disposal mode is a promising prospect for pharmaceutical waste management.

Comprehensive analysis of the fates and risks of veterinary antibiotics in a small ecosystem comprising a pig farm and its surroundings in Northeast China

This study investigated the behavior of veterinary antibiotics (VAs) in a small farm ecosystem. Manure and environmental samples were collected around a large pig farm in northeast China. Thirty-four VAs in six categories were analyzed. Then, a multimedia fugacity model was used to estimate the fates of VAs in the environment. The results showed that VAs were prevalent in manure, soil, water, and sediment, but not in crops. Compared with fresh manure, VA levels were significantly lower in surface manure piles left in the open air for 3-6 months. The main VAs, tetracyclines and quinolones, decreased by 427.12 and 158.45 µg/kg, respectively. VAs from manure piles were transported to the surroundings and migrated vertically into deep soil. The concentrations of ∑VAs detected in agricultural soils were 0.03-4.60 µg/kg; > 94% of the mass inventory of the VAs was retained in soil organic matter (SOM), suggesting that SOM is the main reservoir for antibiotics in soil. Risk assessment and model analysis indicated that the negative impact of mixed antibiotics at low concentrations in farmland on crops may be mediated by indirect effects, rather than direct effects. Our findings highlight the environmental fates and risks of antibiotics from livestock farms.

Combined effects of spent mushroom substrate and dicyandiamide on carbendazim dissipation in soils: Double-edged sword effects and potential risk controls

Repeated and high-dose carbendazim applications have caused serious soil carbendazim contamination, and eco-friendly and economical approaches have been suggested to promote carbendazim removal in agricultural soil. Spent mushroom substrate (SMS) is a special recycled resource after harvesting mushrooms and can be utilized in contaminated soil amendment. The SMS application into agricultural soil might increase antibiotic resistance gene abundances, and the health risks of SMS application might be reduced with reasonable management to adjust the related electron transport of soil nitrification or denitrification. In this study, the SMS and nitrification inhibitor dicyandiamide were used to remediate agricultural soil contaminated with the carbendazim, and the carbendazim contents, soil microbial biomass, activities and community and human disease genes were determined. Compared to the control treatment, the combined applications of SMS and dicyandiamide significantly decreased soil carbendazim content by 38.14% but significantly enhanced soil β-glucosidase, chitinase, arylsulfatase, urease and electron transfer system activities. The relative abundances of Proteobacteria and Actinobacteria were increased by 11.0% and 8.2% with the SMS application, respectively. The carbendazim residues were negatively correlated with the soil pH, electron transfer system activities and relative abundances of Proteobacteria and Actinobacteria. The relative abundances of human disease genes were also dramatically increased with the SMS application, but compared to the SMS alone, extra dicyandiamide application significantly reduced the relative abundances of human disease genes in soils. The SMS applications into fungicide-contaminated soils could generate double-edged sword effects of facilitating fungicide dissipation but leading to potential health risk increase, while applying the dicyandiamide with SMS might be an effective strategy to decrease the negative effect of health risk.

Understanding the role of insects in the acquisition and transmission of antibiotic resistance

Antibiotic resistance (AR) is a global healthcare threat that requires a comprehensive assessment. Poorly regulated antibiotic stewardship in clinical and non-clinical settings has led to a horizontal dissemination of AR. A variety of often neglected elements facilitate the circulation of AR from antibiotic sinks like concentrated animal feeding operations and healthcare settings to other environments that include healthy human communities. Insects are one of those elements that have received underwhelming attention as vectors of AR, despite their well-known role in transmitting clinically relevant pathogens. We here make an exhaustive attempt to highlight the role of insects as zoonotic reservoirs of AR by discussing the available literature and deriving realistic inferences. We review the AR associated with insects housing various human-relevant environments, namely, animal farm industry, edible-insects enterprise, healthcare institutes, human settlements, agriculture settings and the wild. We also provide evidence-based accounts of the events of the transmission of AR from insects to humans. We evaluate the clinical threats associated with insect-derived AR and propose the adoption of more sophisticated strategies to understand and mitigate future AR concerns facilitated by insects. Future works include a pan-region assessment of insects for AR in the form of AR bacteria (ARB) and AR determinants (ARDs) and the introduction of modern techniques like whole-genome sequencing, metagenomics, and in-silico modelling.

Effect of graphene and graphene oxide on antibiotic resistance genes during copper-contained swine manure anaerobic digestion

Copper is an important selectors for antibiotic resistance genes (ARGs) transfer because of metal-antibiotic cross-resistance and/or coresistance. Due to carbon-based materials' good adsorption capacity for heavy metals, graphene and graphene oxide have great potential to reduce ARGs abundance in the environment with copper pollution. To figure out the mechanics, this study investigated the effects of graphene and graphene oxide on the succession of ARGs, mobile genetic elements (MGEs), heavy metal resistance genes (HMRGs), and bacterial communities during copper-contained swine manure anaerobic digestion. Results showed that graphene and graphene oxide could reduce ARGs abundance in varying degrees with the anaerobic reactors that contained a higher concentration of copper. Nevertheless, graphene decreased the abundance of ARGs more effectively than graphene oxide. Phylum-level bacteria such as Firmicutes, Bacteroidetes, Spirochaetes, and Verrucomicrobiaat were significantly positively correlated with most ARGs. Network and redundancy analyses demonstrated that alterations in the bacterial community are one of the main factors leading to the changes in ARGs. Firmicutes, Bacteroidetes, and Spirochaetes were enriched lower in graphene reactor than graphene oxide in anaerobic digestion products, which may be the main reason that graphene is superior to graphene oxide in reduced ARGs abundance. Additionally, ARGs were close to HMRGs than MGEs in the treatments with graphene, the opposite in graphene oxide reactors. Therefore, we speculate that the reduction of HMRGs in graphene may contribute to the result that graphene is superior to graphene oxide in reduced ARGs abundance in anaerobic digestion.

Organic amendment treatments for antimicrobial resistance and mobile element genes risk reduction in soil-crop systems

Agricultural fertilization with organic amendments of animal origin often leads to antibiotic resistance dissemination. In this study, we evaluated the effect of different treatments (anaerobic digestion, biochar application, ozonation, zerovalent iron nanoparticle application, and spent mushroom substrate addition) on the resistome in dairy cow manure-derived amendments (slurry, manure, and compost). Anaerobic digestion and biochar application resulted in the highest reduction in antibiotic resistance gene (ARG) and mobile genetic element (MGE) gene abundance. These two treatments were applied to cow manure compost, which was then used to fertilize the soil for lettuce growth. After crop harvest, ARG and MGE gene absolute and relative abundances in the soil and lettuce samples were determined by droplet digital PCR and high-throughput qPCR, respectively. Prokaryotic diversity in cow manure-amended soils was determined using 16S rRNA metabarcoding. Compared to untreated compost, anaerobic digestion led to a 38% and 83% reduction in sul2 and intl1 absolute abundances in the soil, respectively, while biochar led to a 60% reduction in intl1 absolute abundance. No differences in lettuce gene abundances were observed among treatments. We conclude that amendment treatments can minimize the risk of antibiotic resistance in agroecosystems.

Degradation of antibiotics by electrochemical advanced oxidation processes (EAOPs): Performance, mechanisms, and perspectives

Global consumption and discharge of antibiotics have led to the rapid development and spread of bacterial antibiotic resistance. Among treatment strategies, electrochemical advanced oxidation processes (EAOPs) are gaining popularity for treating water/wastewater containing antibiotics due to their high efficiency and easiness of operation. In this review, we summarize various forms of EAOPs that contribute to antibiotic degradation, including common electrochemical oxidation (EO), electrolyte enhanced EO, electro-Fenton (EF) processes, EF-like process, and EAOPs coupling with other processes. Then we assess the performance of various EAOPs in antibiotic degradation and discuss the influence of key factors, including electrode, initial concentration and type of antibiotic, operation conditions, electrolyte, and water quality. We also review mechanisms and degradation pathways of various antibiotics degradation by EAOPs, and address the species and toxicity of intermediates produced during antibiotics treatment. Finally, we highlight challenges and critical research needs to facilitate the application of EAOPs in antibiotic treatment.

Residual enrofloxacin in cattle manure increased persistence and dissemination risk of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion is a common approach to dispose and recycle livestock manures, and the agricultural application of anaerobic digestives represents an important pathway of spreading antibiotic resistance genes (ARGs) from livestock manures to soils. Enrofloxacin is a clinically important fluoroquinolone antibiotic with high residual concentrations in livestock manure, and propagation of fluoroquinolone resistance genes poses a huge risk to public health. Compared with other antibiotics, enrofloxacin is relatively durable in anaerobic digestion system. However, its effect on the persistence of ARGs during anaerobic digestion and its mechanism are not clear. In this study, we investigated effects of 0, 4, and 8 mg/L enrofloxacin on the abundance, persistence, and transferring risk of five plasmid-mediated fluroquinolone ARGs and five typic clinically important non-fluoroquinolone ARGs during cattle manure digestion. The responses of integrons and microbial communities to enrofloxacin were assessed to uncover the underlying mechanisms. All the ten detected ARGs were highly persistent in anaerobic digestion, among them seven ARGs increased over 8.2 times after digestion. Network analysis revealed that the potential hosts of ARGs were critical functional taxa during anaerobic digestion, which can explain the high persistence of ARGs. Residual enrofloxacin significantly increased the abundance of aac(6')-ib-cr, sul1, intI1, and intI2 throughout the digestion, but had no impact on the other ARGs, demonstrating its role in facilitating horizontal gene transfer of the plasmid-mediated aac(6')-ib-cr. The influence of enrofloxacin on microbial communities disappeared at the end of digestion, but the ARG profiles remained distinctive between the enrofloxacin treatments and the control, suggesting the high persistence of enrofloxacin induced ARGs. Our results suggested the high persistence of ARGs in anaerobic digestion system, and highlighted the role of residual enrofloxacin in livestock manure in increasing dissemination risk of fluroquinolone resistance genes.

Evaluation of antibacterial oxygen/ozone mixture in vitro activity on bacteria isolated from cervico-vaginal mucus of cows with acute metritis

Ozone is an oxidating gas showing a strong microbicidal activity on bacteria, fungi, viruses and protozoa. The aim of this study was to test the in vitro bacteriocidal action of an Ozone/Oxygen gas mixture on bacteria isolated from the cervico-vaginal mucus of cows affected by acute metritis. A pilot study was initially carried out on reference strains (Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 25923 and Mycoplasma bovigenitalium ATCC 19852) that were tested with three different treatments: a control positive baseline group (B-group) was incubated without gas treatment, a control positive oxygen group (O₂-group) was treated with pure oxygen 100%, and the treated group (T-group) was exposed to a gaseous constant flow of an Ozone/Oxygen mixture, at 50, 35, 20 μg Ozone/ml and for 5, 3 and 1 min for every different Ozone concentration. In both positive control groups, the number of colony forming units (CFU) per ml was higher than 300 CFU/ml (E. coli and S. aureus) and higher than 30 CFU/ml for M. bovigenitalium, after incubation. The T-groups showed a minimal bacterial growth equal to or lower than 1 CFU/ml per plate. Based on the results of the pilot study, a second phase was performed on bacteria isolated from the cervico-vaginal mucus (Klebsiella pneumoniae, Enterobacter agglomerans, E. coli, Proteus mirabilis and M. bovigenitalium) using the lower concentration of 20 μg/ml of Ozone for the minimum exposure time of 1 min. The E. coli and S. aureus reference strains and the clinical isolates (K. pneumoniae, E. agglomerans, E. coli, P. mirabilis) were incubated at 37 °C for 48 h and the colonies were manually counted at 24 h and 48 h following inoculation. The cultures of M. bovigenitalium (both ATCC and clinical isolate) were incubated in a jar with modified atmosphere conditions with 5% CO₂ at 37 °C for 4-7 days and colony counting was performed. The second phase showed a low number of CFUs (equal to or less than 7 CFU/ml) for the clinical isolates K. pneumoniae, E. agglomerans, E. coli and P. mirabilis, and, of note, for M. bovigenitalium, both ATCC and clinical isolate, the growth was completely inhibited. Ozone was demonstrated to have a bacteriocidal activity. This study encourages further research of in vivo application of low doses of gaseous Ozone for the treatment of metritis in cows by using minimal exposure times.

Assessing the fate of antibiotics and agrochemicals during anaerobic digestion of animal manure

Antibiotics and pesticides are used extensively by the livestock industry. Agricultural chemicals can pose potential human and environmental health risks due to their toxicity and through their contributions to antimicrobial resistance, and strategies to reduce their emission into the environment are urgently needed. Anaerobic digestion (AD) is a sustainable technology for manure management that produces biogas while also providing an opportunity to degrade agricultural chemicals that are present in manure. While the effects of selected chemicals on biogas production have been investigated previously, little is known about chemical transformations during AD. Using lab-scale AD batch reactors containing dairy manure, degradation kinetics and transformation products (TPs) were investigated for twenty compounds that are likely to be present in manure management systems and that we hypothesized would transform during AD. Digestate samples were extracted using a modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) method and analyzed using liquid chromatography - high-resolution mass spectrometry. Eleven of the tested chemicals degraded, leading to the formation of 47 TPs. Three compounds degraded abiotically only, two degraded biotically only, and six degraded both abiotically and biotically. These results suggest that in addition to renewable energy generation, AD contributes to the degradation of chemical contaminants present in agricultural waste streams. However, the potential toxic effects of TPs require further investigation.

Quantifying Antibiotic Distribution in Solid and Liquid Fractions of Manure Using a Two-Step, Multi-Residue Antibiotic Extraction

Antibiotic distribution and analysis within liquid and solid fractions of manure are highly variable due to each compound’s respective physiochemical properties. This study developed and evaluated a uniform method extracting 10 antibiotics from 4 antibiotic classes (tetracycline, sulfonamides, macrolides, and β-lactam) from unprocessed manure, solid−liquid separated manure, and composted solids. Through systematic manipulation of previously published liquid chromatography tandem mass spectrometry methods; this study developed an extraction protocol with optimized recovery efficiencies for varied manure substrates. The method includes a two-step, liquid-solid extraction using 10 mL of 0.1 M EDTA-McIlviane buffer followed by 10 mL of methanol. Antibiotics recoveries from unprocessed manure, separated liquids, separated solids, and heat-treated solids using the two-step extraction method had relative standard deviations < 30% for all but ceftiofur. Total antibiotic recoveries were 67−131% for tetracyclines, 56% for sulfonamide, 49−53% for macrolides, and 1.3−66% for β-lactams. This is the first study to use one protocol to assess four classes of antibiotics in liquid and solid manure fractions. This study allowed for more precise risk assessment of antibiotic transport in manure waste stream applied to fields as a liquid or solid compost.

An exhaustive investigation on antibiotics contamination from livestock farms within sensitive reservoir water area: Spatial density, source apportionment and risk assessment

Although the studies on antibiotic contamination are common at present, large-scale sampling studies drawing highly representative conclusions are still scarce. This study conducted a comprehensive investigation on a total of 1183 samples from 70 livestock farms within a sensitive area around reservoir waters. 45 types of antibiotics belonging to 5 different classes were monitored. This is the first analysis to comprehensively investigate the density distribution, source apportionment, ecological and health risk of antibiotics in an entire area of sensitive waters. The results showed that the layer manure samples had highest detection rate of antibiotics (0.0 %-96.1 %, average value = 30.7 %) followed by pig manure samples. Oxytetracycline had the highest concentration of 712.16 mg/kg in a pig manure sample. Different from using antibiotic concentration as a proxy for pollution level, the spatial density was calculated by averaging antibiotic concentration to area and converting different livestock to pig equivalent. The spatial density of pig equivalent can more realistically reflect the pollution caused by different breeds of livestocks. It was shown that the pig farms contributed higher to total antibiotic density than the layer and cattle farms did. After assessed, a few antibiotics (oxytetracycline, chlorotetracycline and tetracycline) have posed high ecological risks to soil around the farms. However, none of them caused hazard quotient (HQ) risk and carcinogenic risk (CR) to human health in the water of reservoir. Children were more likely to be at hazard risk than adults. Antibiotic mass fluctuation rules were analyzed along the chain (feed → livestock waste → soil → surface water). Feed, livestock waste and soil had similar diversity, but the antibiotic concentrations continued to decline, implying the possible sources of antibiotic residues were similar. Thus, it is important to reduce unnecessary antibiotic use to prevent the potential long-term risk of antibiotics.

Composting effect and antibiotic removal under a new temperature control strategy

The main objective of this study was to investigate the feasibility of a new temperature control strategy in the co-composting process to accelerate operation cycle and remove antibiotics from mixed organic wastes. The evaluation of the composting process showed that composting with temperature control (TC) was completed within 14 days. The final compost of TC exhibited a 10% higher degradation of organic matters, more humus formation and 11.25% lower heavy metals concentration than conventional composting (CC), which fully met the Chinese National Agricultural Organic Fertilizer Standard requirements. The degradation extent and kinetic of macrolides, tetracyclines, sulfonamides and fluoroquinolones showed that the removal efficiency of total antibiotics in TC was 23.58% higher than CC, with less half-life, which was significantly correlated with higher temperature. Particularly, the highest removal was observed for sulfonamides (87.45%) in TC, the half-life of which was reduced by 75.95% compared with CC. The higher degradation rate was attributed to enhanced decomposition of unstable antibiotics and degrading activity of microbes at high temperature. The microbiological analysis showed that the external heating led to a distinct composition and succession of bacterial community in TC. Firmicutes, Proteobacteria, Actinobacteriota and Bacteroidota were dominant and the emergence of Patescibacteria and Chloroflexi at cooling period in TC proved that the later composting environment was in an oligotrophic state. Current research provided a promising rapid composting approach for high-quality fertilizer production and antibiotic management in organic waste disposal.

Extended-Spectrum Beta-Lactamases Producing Enterobacteriaceae in the USA Dairy Cattle Farms and Implications for Public Health

Antimicrobial resistance (AMR) is one of the top global health threats of the 21th century. Recent studies are increasingly reporting the rise in extended-spectrum beta-lactamases producing Enterobacteriaceae (ESBLs-Ent) in dairy cattle and humans in the USA. The causes of the increased prevalence of ESBLs-Ent infections in humans and commensal ESBLs-Ent in dairy cattle farms are mostly unknown. However, the extensive use of beta-lactam antibiotics, especially third-generation cephalosporins (3GCs) in dairy farms and human health, can be implicated as a major driver for the rise in ESBLs-Ent. The rise in ESBLs-Ent, particularly ESBLs-Escherichia coli and ESBLs-Klebsiella species in the USA dairy cattle is not only an animal health issue but also a serious public health concern. The ESBLs-E. coli and -Klebsiella spp. can be transmitted to humans through direct contact with carrier animals or indirectly through the food chain or via the environment. The USA Centers for Disease Control and Prevention reports also showed continuous increase in community-associated human infections caused by ESBLs-Ent. Some studies attributed the elevated prevalence of ESBLs-Ent infections in humans to the frequent use of 3GCs in dairy farms. However, the status of ESBLs-Ent in dairy cattle and their contribution to human infections caused by ESBLs-producing enteric bacteria in the USA is the subject of further study. The aims of this review are to give in-depth insights into the status of ESBL-Ent in the USA dairy farms and its implication for public health and to highlight some critical research gaps that need to be addressed.

Insights into the impact of manure on the environmental antibiotic residues and resistance pool

The intensive use of antibiotics in the veterinary sector, linked to the application of manure-derived amendments in agriculture, translates into increased environmental levels of chemical residues, AR bacteria (ARB) and antibiotic resistance genes (ARG). The aim of this review was to evaluate the current evidence regarding the impact of animal farming and manure application on the antibiotic resistance pool in the environment. Several studies reported correlations between the prevalence of clinically relevant ARB and the amount and classes of antibiotics used in animal farming (high resistance rates being reported for medically important antibiotics such as penicillins, tetracyclines, sulfonamides and fluoroquinolones). However, the results are difficult to compare, due to the diversity of the used antimicrobials quantification techniques and to the different amounts and types of antibiotics, exhibiting various degradation times, given in animal feed in different countries. The soils fertilized with manure-derived products harbor a higher and chronic abundance of ARB, multiple ARG and an enriched associated mobilome, which is also sometimes seen in the crops grown on the amended soils. Different manure processing techniques have various efficiencies in the removal of antibiotic residues, ARB and ARGs, but there is only a small amount of data from commercial farms. The efficiency of sludge anaerobic digestion appears to be dependent on the microbial communities composition, the ARB/ARG and operating temperature (mesophilic vs. thermophilic conditions). Composting seems to reduce or eliminate most of antibiotics residues, enteric bacteria, ARB and different representative ARG in manure more rapidly and effectively than lagoon storage. Our review highlights that despite the body of research accumulated in the last years, there are still important knowledge gaps regarding the contribution of manure to the AMR emergence, accumulation, spread and risk of human exposure in countries with high clinical resistance rates. Land microbiome before and after manure application, efficiency of different manure treatment techniques in decreasing the AMR levels in the natural environments and along the food chain must be investigated in depth, covering different geographical regions and countries and using harmonized methodologies. The support of stakeholders is required for the development of specific best practices for prudent – cautious use of antibiotics on farm animals. The use of human reserve antibiotics in veterinary medicine and of unprescribed animal antimicrobials should be stopped and the use of antibiotics on farms must be limited. This integrated approach is needed to determine the optimal conditions for the removal of antibiotic residues, ARB and ARG, to formulate specific recommendations for livestock manure treatment, storage and handling procedures and to translate them into practical on-farm management decisions, to ultimately prevent exposure of human population.

Medicinal Chemistry of Inhibitors Targeting Resistant Bacteria

The discovery of antibiotics was a revolutionary feat that provided countless health benefits. The identification of penicillin by Alexander Fleming initiated the era of antibiotics, represented by constant discoveries that enabled effective treatments for the different classes of diseases caused by bacteria. However, the indiscriminate use of these drugs allowed the emergence of resistance mechanisms of these microorganisms against the available drugs. In addition, the constant discoveries in the 20th century generated a shortage of new molecules, worrying health agencies and professionals about the appearance of multidrug-resistant strains against available drugs. In this context, the advances of recent years in molecular biology and microbiology have allowed new perspectives in drug design and development, using the findings related to the mechanisms of bacterial resistance to generate new drugs that are not affected by such mechanisms and supply new molecules to be used to treat resistant bacterial infections. Besides, a promising strategy against bacterial resistance is the combination of drugs through adjuvants, providing new expectations in designing new antibiotics and new antimicrobial therapies. Thus, this manuscript will address the main mechanisms of bacterial resistance under the understanding of medicinal chemistry, showing the main active compounds against efflux mechanisms, and also the application of the use of drug delivery systems, and finally, the main potential natural products as adjuvants or with promising activity against resistant strains.

Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Dairy manure is a nutrition source for cropland soils and also simultaneously serves as a contamination source of antibiotic resistance genes (ARGs). In this study, five classes of antibiotics including aminoglycosides, beta-lactams, macrolides, sulfonamides, and tetracyclines, were spiked in dairy manure and incubated with soil for 60 days. The high throughput qPCR and 16S rRNA amplicon sequencing were used to detect temporal shifts of the soil antibiotic resistomes and bacterial community. Results indicated dairy manure application increased the ARG abundance by 0.5-3.7 times and subtype numbers by 2.7-3.7 times and changed the microbial community structure in soils. These effects were limited to the early incubation stage. Selection pressure was observed after the addition of sulfonamides. Bacterial communities played an important role in the shifts of ARG profiles and accounted for 44.9% of the resistome variation. The incubation period, but not the different antibiotic treatments, has a strong impact on the bacteria community. Firmicutes and Bacteroidetes were the dominant bacterial hosts for individual ARGs. This study advanced our understanding of the effect of dairy manure and antibiotics on the antibiotic resistome in soils and provided a reference for controlling ARG dissemination from dairy farms to the environment.

Preliminary Investigation of the Effects of Rosemary Extract Supplementation on Milk Production and Rumen Fermentation in High-Producing Dairy Cows

Rosemary extract (RE) has been used as an antioxidant in cosmetics and food additives, indicating its potential as a feed additive to improve adaptation in high-producing dairy cows. Here, we investigated the effects of RE supplementation on lactation performance and rumen fermentation in high-producing dairy cows. Thirty multiparous cows were blocked into 15 groups based on milk production and were randomly assigned to one of two treatments: 0 or 28 g/d of RE supplementation to the basic diet per cow. The experiment was conducted over a 74-day period, which included an initial two-week adaptation period. We observed significant increases in milk and milk lactose yields following RE supplementation. Somatic cell count tended to decrease by treatment. Additionally, superoxide dismutase concentration significantly increased and malonaldehyde level decreased after RE supplementation. Sequencing of 16S rRNA revealed that RE supplementation significantly affected the microbial composition and decreased the richness of the microbiota. Specifically, the abundance of the genus Prevotella was significantly decreased by RE supplementation and was correlated with volatile fatty acids in the Mantel test, whereas no significant correlation was found for other genera. Our findings provide fundamental information on the potential for RE as a feed additive for dairy cows to improve antioxidant status and enhance propionate generation.

Anti-inflammation of isoliquiritigenin via the inhibition of NF-κB and MAPK in LPS-stimulated MAC-T cells

Background

The application of plant extracts has received great interest for the treatment of bovine mastitis. Isoliquiritigenin (ISL) is a rich dietary flavonoid that has significant antioxidative, anti-inflammatory and anticancer activities. This study was conducted to explore the protective efficacy and related mechanism of ISL against lipopolysaccharide (LPS)-stimulated oxidation and inflammation in bovine mammary epithelial cells (MAC-T) by in vitro experiments.

Results

Real-time PCR and ELISA assays indicated that ISL treatment at 2.5, 5 and 10 μg/mL significantly reduced the mRNA and protein expression of the oxidative indicators cyclooxygenase-2 and inducible nitric oxide synthase (P < 0.01), and of the inflammatory cytokines interleukin-6 (P < 0.05), interleukin-1β (P < 0.01) and tumor necrosis factor-α (P < 0.01) in LPS-stimulated MAC-T cells. Moreover, Western blotting and immunofluorescence tests indicated that the phosphorylation levels of nuclear factor kappa (NF-κB) p65 and the inhibitor of NF-κB were significantly decreased by ISL treatment, thus blocking the nuclear transfer of NF-κB p65. In addition, ISL attenuated the phosphorylation levels of p38, extracellular signal-regulated kinase and c-jun NH2 terminal kinase.

Conclusions

Our data demonstrated that ISL downregulated the LPS-induced inflammatory response in MAC-T cells. The anti-inflammatory and antioxidative activity of ISL involves the NF-κB and MAPK cascades.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-022-03414-1.