Antibiotics and antibiotic resistance genes in anaerobic digesters and predicted concentrations in agroecosystems

Anaerobic digestion at hyper-mesophilic temperatures: Microbiome and antibiotic resistome in full-scale agricultural biogas plants

Temperatures between 40°C and 50°C are increasingly implemented in full-scale agricultural anaerobic digestion (AD), yet the microbial diversity and antibiotic resistome dynamics within this temperature range remain poorly understood. Here, we defined this range as "hyper-mesophilic" and surveyed five full-scale sites. Significant differences were found in the bacterial community structure, potentially stemming from feedstock combination (high vs low/non-manure) and operating temperature. Sites operating at 44°C exhibited superior attenuation efficiency (81-92 %) for antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) than sites operating at 41°C (41-83 %). High-risk clinically important ARGs such as sul1, lnuA, tet(O), and tet(L) persisted in sites blending livestock manure. Potential hosts of ARGs were identified and included opportunistic human pathogens like Enterococcus faecalis, Staphylococcus aureus, and Clostridioides difficile. The tnpA transposon accounted for > 50 % of the total MGEs and frequently co-localised with ARGs, while the class 1 integrase, intI1, was only detected in manure-blended AD. Based on prevalence in plasmids, ARGs showed higher mobility potential in sites blending chicken manure. The results obtained here provided initial insights into hyper-mesophilic AD and reinforced the importance of conducting surveillance for crop AD, with or without manure, as part of wider efforts to mitigate antimicrobial resistance in agroecosystems.

Effects of sulfamethoxazole and copper on the natural microbial community from a fertilized soil

Cattle manure or its digestate, which often contains antibiotic residues, can be used as an organic fertilizer and copper (Cu) as a fungicide in agriculture. Consequently, both antibiotics and Cu are considered soil contaminants. In this work, microcosms were performed with soil amended with either manure or digestate with Cu and an antibiotic (sulfamethoxazole, SMX) co-presence and the planting of Lactuca sativa. After the addition of the organic amendments, a prompt increase in the microbial activity and at the same time of the sul1 and intI1 genes was observed, although ARGs generally decreased over time. In the amended and spiked microcosms, the microbial community was able to remove more than 99% of SMX in 36 days and the antibiotic did not bioaccumulate in the lettuce. Interestingly, where Cu and SMX were co-present, ARGs (particularly sul2) increased, showing how copper had a strong effect on resistance persistence in the soil. Copper also had a detrimental effect on the plant-microbiome system, affecting plant biomass and microbial activity in all conditions except in a digestate presence. When adding digestate microbial activity, biodiversity and lettuce biomass increased, with or without copper present. Not only did the microbial community favour plant growth, but lettuce also positively influenced its composition by increasing bacterial diversity and classes (e.g., Alphaproteobacteria) and genera (e.g., Bacillus), thus indicating a good-quality soil. KEY POINTS: • Cattle digestate promoted the highest microbial activity, diversity, and plant growth • Cattle digestate counteracted detrimental contaminant effects • Cu presence promoted antibiotic cross-resistance in soil.

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.

Multiresidue determination and predicted risk assessment of emerging contaminants in sediments from Kongsfjorden, Svalbard

The present work provides the first data on the occurrence of different classes of pharmaceuticals and personal care products (PPCPs) in surface marine sediments from an Arctic fjord (Kongsfjorden, Svalbard Islands, Norway). The target compounds included: ciprofloxacin; enrofloxacin; amoxicillin; erythromycin; sulfamethoxazole; carbamazepine; diclofenac; ibuprofen; acetylsalicylic acid; paracetamol; caffeine; triclosan; N,N-diethyl-meta-toluamide; 17β-estradiol; 17α-ethinyl estradiol and estrone. Sampling was performed in the late summer, when high sedimentation rates occur, and over 5 years (2018-2022). Based on the environmental concentrations (MECs) found of emerging contaminants and the relative predicted no-effect concentrations (PNECs), an environmental risk assessment (ERA) for sediments was performed, including the estimation of the Risk Quotients (RQs) of selection and propagation of antimicrobial resistance (AMR) in this Arctic marine ecosystem. Sediments were extracted by Pressurized Liquid Extraction (PLE) and the extracts were purified by Solid Phase Extraction (SPE). Analytical determination was conducted with liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS). PPCPs were detected in the sediments along the fjord in all the years investigated, with overall concentrations similar in most cases to those reported in urbanized areas of the planet and ranging from a minimum of 6.85 ng/g for triclosan to a maximum of 684.5 ng/g for ciprofloxacin. This latter was the only antibiotic detected but was the most abundant compound (32 %) followed by antipyretics (16 %), hormones (14 %), anti-inflammatories (13 %), insect repellents (11 %), stimulants (9 %), and disinfectants (5 %). Highest concentrations of all PPCPs detected were found close to the Ny-Ålesund research village, where human activities and the lack of appropriate wastewater treatment technologies were recognized as primary causes of local contamination. Finally, due to the presence in the sediments of the PPCPs investigated, the ERA highlights a medium (0.1 < RQ < 1) to high risk (RQ > 1) for organisms living in this Arctic marine ecosystem, including high risk of the spread of AMR.

Regulation of ARGs abundance by biofilm colonization on microplastics under selective pressure of antibiotics in river water environment

Interactions of microplastics (MPs) biofilm with antibiotic resistance genes (ARGs) and antibiotics in aquatic environments have made microplastic biofilm an issue of keen scholarly interest. The process of biofilm formation and the degree of ARGs enrichment in the presence of antibiotic-selective pressure and the impact on the microbial community need to be further investigated. In this paper, the selective pressure of ciprofloxacin (CIP) and illumination conditions were investigated to affect the physicochemical properties, biomass, and extracellular polymer secretion of polyvinyl chloride (PVC) microplastic biofilm. In addition, relative copy numbers of nine ARGs were analyzed by real-time quantitative polymerase chain reaction (qPCR). In the presence of CIP, microorganisms in the water and microplastic biofilm were more inclined to carry associated ARGs (2-3 times higher), which had a contributing effect on ARGs enrichment. The process of pre-microplastic biofilm formation might have an inhibitory effect on ARGs (total relative abundance up to 0.151) transfer and proliferation compared to the surrounding water (total relative abundance up to 0.488). However, in the presence of CIP stress, microplastic biofilm maintained the abundance of ARGs (from 0.151 to 0.149) better compared to the surrounding water (from 0.488 to 0.386). Therefore, microplastic biofilm act as abundance buffer island of ARGs stabilizing the concentration of ARGs. In addition, high-throughput analyses showed the presence of antibiotic-resistant (Pseudomonas) and pathogenic (Vibrio) microorganisms in biofilm under different conditions. The above research deepens our understanding of ARGs enrichment in biofilm and provides important insights into the ecological risks of interactions between ARGs, antibiotics, and microplastic biofilm.

The Potential of Wood Vinegar to Replace Antimicrobials Used in Animal Husbandry-A Review

The indiscriminate use of antimicrobials in animal husbandry can result in various types of environmental contamination. Part of the dose of these products is excreted, still active, in the animals' feces and urine. These excreta are widely used as organic fertilizers, which results in contamination with antimicrobial molecules. The impacts can occur in several compartments, such as soil, groundwater, and surface watercourses. Also, contamination by antimicrobials fed or administrated to pigs, chickens, and cattle can reach the meat, milk, and other animal products, which calls into question the sustainability of using these products as part of eco-friendly practices. Therefore, a search for alternative natural products is required to replace the conventional antimicrobials currently used in animal husbandry, aiming to mitigate environmental contamination. We thus carried out a review addressing this issue, highlighting wood vinegar (WV), also known as pyroligneous acid, as an alternative antimicrobial with good potential to replace conventional products. In this regard, many studies have demonstrated that WV is a promising product. WV is a nontoxic additive widely employed in the food industry to impart a smoked flavor to foods. Studies have shown that, depending on the WV concentration, good results can be achieved using it as an antimicrobial against pathogenic bacteria and fungi and a valuable growth promoter for poultry and pigs.

Application of the Aliivibrio fischeri bacterium bioassay for assessing single and mixture effects of antibiotics and copper

The Aliivibrio fischeri bioassay was successfully applied in order to evaluate the acute effect of sulfamethoxazole (SMX), ciprofloxacin (CIP), chlortetracycline (CTC) and copper (Cu), alone or in binary, ternary, and overall mixture. The toxicity results are reported in terms of both effective concentrations, which inhibited 50% of the bacterium bioluminescence (EC50%), and in Toxic Units (TUs). The TUs were compared with predicted values obtained using the Concentration Addition model (CA). Finally, the toxicity of water extracts from a soil contaminated by the three antibiotics (7 mg Kg-1 each) in the presence/absence of copper (30 mg Kg-1) was also evaluated. Copper was the most toxic chemical (EC50: 0.78 mg L-1), followed by CTC (EC50: 3.64 mg L-1), CIP (96 mg L-1) and SMX (196 mg L-1). Comparing the TU and CA values of the mixtures, additive effects were generally found. However, a synergic action was recorded in the case of the CIP+Cu co-presence and antagonistic effects in the case of CTC+Cu and the ternary mixture (containing each antibiotic at 0.7 mg L-1), were identified. Soil water extracts did not show any toxicity, demonstrating the buffering ability of the soil to immobilize these chemicals.

Impact of COVID-19 pandemic on profiles of antibiotic-resistant genes and bacteria in hospital wastewater

The COVID-19 pandemic has severely affected healthcare worldwide and has led to the excessive use of disinfectants and antimicrobial agents. However, the impact of excessive disinfection measures and specific medication prescriptions on the development and dissemination of bacterial drug resistance during the pandemic remains unclear. This study investigated the influence of the pandemic on the composition of antibiotics, antibiotic resistance genes (ARGs), and pathogenic communities in hospital wastewater using ultra-performance liquid chromatography-tandem mass spectrometry and metagenome sequencing. The overall level of antibiotics decreased after the COVID-19 outbreak, whereas the abundance of various ARGs increased in hospital wastewater. After COVID-19 outbreak, blaOXA, sul2, tetX, and qnrS had higher concentrations in winter than in summer. Seasonal factors and the COVID-19 pandemic have affected the microbial structure in wastewater, especially of Klebsiella, Escherichia, Aeromonas, and Acinetobacter. Further analysis revealed the co-existence of qnrS, blaNDM, and blaKPC during the pandemic. Various ARGs significantly correlated with mobile genetic elements, implying their potential mobility. A network analysis revealed that many pathogenic bacteria (Klebsiella, Escherichia, and Vibrio) were correlated with ARGs, indicating the existence of multi-drug resistant pathogens. Although the calculated resistome risk score did not change significantly, our results suggest that the COVID-19 pandemic shifted the composition of residual antibiotics and ARGs in hospital wastewater and contributed to the dissemination of bacterial drug resistance.

Insight into the spatiotemporal distribution of antibiotic resistance genes in estuarine sediments during long-term ecological restoration

In this study, we aimed to investigate the long-term spatiotemporal changes in hydrodynamics, antibiotics, nine typical subtypes of antibiotic resistance genes (ARGs), class 1 integron gene (intI1), and microbial communities in the sediments of a semi-enclosed estuary during ecological restoration with four treatment stages (influent (#1), effluent of the biological treatment area (#2), oxic area (#3), and plant treatment area (#4)). Ecological restoration of the estuary reduced common pollutants (nitrogen and phosphorus) in the water, whereas variations in ARGs showed noticeable seasonal and spatial features. The absolute abundance of ARGs at sampling site #2 considerably increased in autumn and winter, while it significantly increased at sampling site #3 in spring and summer. The strong intervention of biological treatment (from #1 to #2) and aerators (from #2 to #3) in the estuary substantially affected the distribution of ARGs and dominant antibiotic-resistant bacteria (ARB). The dominant ARB (Thiobacillus) in estuarine sediments may have low abundance but important dissemination roles. Meanwhile, redundancy and network analysis revealed that the microbial communities and intl1 were key factors related to ARG dissemination, which was affected by spatial and seasonal ecological restoration. A positive correlation between low flow velocity and certain ARGs (tetM, tetW, tetA, sul2, and ermC) was observed, implying that flow optimization should also be considered in future ecological restoration to remediate ARGs. Furthermore, the absolute abundance of ARGs can be utilized as an index to evaluate the removal capacity of ARGs by estuarine restoration.

Digestate from Agricultural Biogas Plants as a Reservoir of Antimicrobials and Antibiotic Resistance Genes-Implications for the Environment

Antimicrobials and antibiotic resistance genes (ARGs) in substrates processed during anaerobic digestion in agricultural biogas plants (BPs) can reach the digestate (D), which is used as fertilizer. Antimicrobials and ARGs can be transferred to agricultural land, which increases their concentrations in the environment. The concentrations of 13 antibiotics in digestate samples from biogas plants (BPs) were investigated in this study. The abundance of ARGs encoding resistance to beta-lactams, tetracyclines, sulfonamides, fluoroquinolones, macrolide-lincosamide-streptogramin antibiotics, and the integrase genes were determined in the analyzed samples. The presence of cadmium, lead, nickel, chromium, zinc, and mercury was also examined. Antimicrobials were not eliminated during anaerobic digestion. Their concentrations differed in digestates obtained from different substrates and in liquid and solid fractions (ranging from 62.8 ng/g clarithromycin in the solid fraction of sewage sludge digestate to 1555.9 ng/L doxycycline in the liquid fraction of cattle manure digestate). Digestates obtained from plant-based substrates were characterized by high concentrations of ARGs (ranging from 5.73 × 102 copies/gDcfxA to 2.98 × 109 copies/gDsul1). The samples also contained mercury (0.5 mg/kg dry mass (dm)) and zinc (830 mg/kg dm). The results confirmed that digestate is a reservoir of ARGs (5.73 × 102 to 8.89 × 1010 copies/gD) and heavy metals (HMs). In addition, high concentrations of integrase genes (105 to 107 copies/gD) in the samples indicate that mobile genetic elements may be involved in the spread of antibiotic resistance. The study suggested that the risk of soil contamination with antibiotics, HMs, and ARGs is high in farms where digestate is used as fertilizer.

Bioaccumulation of antibiotics and resistance genes in lettuce following cattle manure and digestate fertilization and their effects on soil and phyllosphere microbial communities

The degradation and bioaccumulation of selected antibiotics such as the sulfonamide sulfamethoxazole (SMX) and the fluoroquinolones enrofloxacin (ENR) and ciprofloxacin (CIP) were investigated in soil microcosm experiments where Lactuca sativa was grown with manure or digestate (1%) and spiked with a mixture of the three antibiotics (7.5 mg/kg each). The soil, rhizosphere and leaf phyllosphere were sampled (at 0 and 46 days) from each microcosm to analyze the antibiotic concentrations, main resistance genes (sul1, sul2, qnrS, aac-(6')-Ib-crand qepA), the intI1and tnpA mobile genetic elements and the microbial community structure.Overall results showed that SMX and CIP decreased (70-85% and 55-79%, respectively), and ENR was quite persistent during the 46-day experiment. In plant presence, CIP and ENR were partially up-taken from soil to plant. In fact the bioaccumulation factors were > 1, with higher values in manure than digestate amended soils. The most abundant gene in soil was sul2 in digestate- and aac-(6')-Ib-cr in the manure-amended microcosms. In soil, neither sulfamethoxazole-resistance (sul1 and sul2), nor fluoroquinolone-resistance (aac-(6')-Ib-cr, qepA and qnrS) gene abundances were correlated with any antibiotic concentration. On the contrary, in lettuce leaves, the aac-(6')-Ib-cr gene was the most abundant, in accordance with the fluoroquinolone bioaccumulation. Finally, digestate stimulated a higher soil microbial biodiversity, introducing and promoting more bacterial genera associated with antibiotic degradation and involved in soil fertility and decreased fluoroquinolone bioaccumulation.

Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment-A Review

Over the past few decades, due to the excessive consumption of drugs in human and veterinary medicine, the antimicrobial resistance (AR) of microorganisms has risen considerably across the world, and this trend is predicted to intensify. Many worrying research results indicate the occurrence of pools of AR, both directly related to human activity and environmental factors. The increase of AR in the natural environment is mainly associated with the anthropogenic activity. The dissemination of AR is significantly stimulated by the operation of municipal facilities, such as wastewater treatment plants (WWTPs) or landfills, as well as biogas plants, agriculture and farming practices, including animal production and land application of manure. These activities entail a risk to public health by spreading bacteria resistant to antimicrobial products (ARB) and antibiotic resistance genes (ARGs). Furthermore, subinhibitory concentrations of antimicrobial substances additionally predispose microbial consortia and resistomes to changes in particular environments that are permeated by these micropollutants. The current state of knowledge on the fate of ARGs, their dissemination and the complexity of the AR phenomenon in relation to anthropogenic activity is inadequate. This review summarizes the state-of-the-art knowledge on AR in the environment, in particular focusing on AR spread in an anthropogenically altered environment and related environmental consequences.

Semi-solid anaerobic co-digestion of source-separated fecal slag and food waste: focusing on methane production, ecological risk assessment, and quality evaluation as fertilizer

Toilet revolution is driven by the urgent need for solutions to improve sanitation and access to high-quality organic fertilizer for rural areas, which is tagged "resource recovery from human waste." This study provides a possible solution via semi-solid anaerobic co-digestion (Aco-D) of source-separated fecal slag (SFS) and food waste (FW) (3:1). A comprehensive investigation of Aco-D at different inoculum/substrate ratios (ISR) was conducted. Results revealed that the reactor with ISR of 1:4 reached the highest methane yield (255.05 mL/gVS), which enhanced Methanosaetaceae, Methanomicrobiales, and Syntrophomonas. Additionally, the reactor with low feedstock (ISR of 1:2) showed higher removal efficiency of antibiotics (74.75%). The ecological risk of digestate decreased to an insignificant hazard quotient level, and the contents of nutrients and heavy metals were in line with the standard requirement for fertilizer. This study could serve as an alternative technology to support further research in SFS management and digestate utilization as fertilizer.

Fertilization and Soil Microbial Community: A Review

The present paper reviews the most recent advances regarding the effects of chemical and organic fertilizers on soil microbial communities. Based on the results from the articles considered, some details are presented on how the use of various types of fertilizers affects the composition and activity of soil microbial communities. Soil microbes have different responses to fertilization based on differences in the total carbon (C), nitrogen (N) and phosphorus (P) contents in the soil, along with soil moisture and the presence of plant species. These articles show that the use of chemical fertilizers changes the abundance of microbial populations and stimulates their growth thanks to the nutrient supply added. Overall, however, the data revealed that chemical fertilizers have no significant influence on the richness and diversity of the bacteria and fungi. Instead, the abundance of individual bacterial or fungal species was sensitive to fertilization and was mainly attributed to the changes in the soil chemical properties induced by chemical or organic fertilization. Among the negative effects of chemical fertilization, the decrease in enzymatic activity has been highlighted by several papers, especially in soils that have received the largest amounts of fertilizers together with losses in organic matter.