Contribution of environmental factors on the distribution of antibiotic resistance genes in agricultural soil

Combined use of digestate and inorganic fertilizer alleviates the burden of class 1 integrons in perennial ryegrass rhizosphere without compromising aerial biomass production

Antimicrobial resistance (AMR) is one of the main global health challenges. Anaerobic digestion (AD) can significantly reduce the burden of antibiotic resistance genes (ARGs) in animal manures. However, the reduction is often incomplete. The agronomic use of digestates requires assessments of their effects on soil ARGs. The objective of this study was to assess the effect of digestate on the abundance of ARGs and mobile genetic elements (MGEs) in the rhizosphere of ryegrass (Lolium perenne L.) and to determine whether half-dose replacement of digestate with urea (combined fertilizer) can be implemented as a safer approach while maintaining a similar biomass production. A greenhouse assay was conducted during 190 days under a completely randomized design with two experimental factors: fertilizer type (unfertilized control and fertilized treatments with equal N dose: digestate, urea and combined fertilizer) and sampling date (16 and 148 days after the last application). The results indicated that the digestate significantly increased the abundance of clinical class 1 integrons (intI1 gene) relative to the unfertilized control at both sampling dates (P < 0.05), while the combined fertilizer only increased them at the first sampling. Sixteen days after completing the fertilization scheme only the combined fertilizer and urea significantly increased the biomass production relative to the control (P < 0.05). Additionally, by the end of the assay, the combined fertilizer showed significantly lower levels of the macrolide-resistance gene ermB than digestate and a cumulative biomass similar to urea or digestate. Overall, the combined fertilizer can alleviate the burden of integrons and ermB while simultaneously improving biomass production.

Bioelectrochemical remediation of soil antibiotic and antibiotic resistance gene pollution: Key factors and solution strategies

In recent years, owing to the overuse and improper handling of antibiotics, soil antibiotic pollution has become increasingly serious and an environmental issue of global concern. It affects the quality and ecological balance of the soil and allows the spread of antibiotic resistance genes (ARGs), which threatens the health of all people. As a promising soil remediation technology, bioelectrochemical systems (BES) are superior to traditional technologies because of their simple operation, self-sustaining operation, easy control characteristics, and use of the metabolic processes of microorganisms and electrochemical redox reactions. Moreover, they effectively remediate antibiotic contaminants in soil. This review explores the application of BES remediation mechanisms in the treatment of antibiotic contamination in soil in detail. The advantages of BES restoration are highlighted, including the effective removal of antibiotics from the soil and the prevention of the spread of ARGs. Additionally, the critical roles played by microbial communities in the remediation process and the primary parameters influencing the remediation effect of BES were clarified. This study explores several strategies to improve the BES repair efficiency, such as adjusting the reactor structure, improving the electrode materials, applying additives, and using coupling systems. Finally, this review discusses the current limitations and future development prospects, and how to improve its performance and promote its practical applications. In summary, this study aimed to provide a reference for better strategies for BES to effectively remediate soil antibiotic contamination.

Unravelling the mechanisms of antibiotic and heavy metal resistance co-selection in environmental bacteria

The co-selective pressure of heavy metals is a contributor to the dissemination and persistence of antibiotic resistance genes in environmental reservoirs. The overlapping range of antibiotic and metal contamination and similarities in their resistance mechanisms point to an intertwined evolutionary history. Metal resistance genes are known to be genetically linked to antibiotic resistance genes, with plasmids, transposons, and integrons involved in the assembly and horizontal transfer of the resistance elements. Models of co-selection between metals and antibiotics have been proposed, however, the molecular aspects of these phenomena are in many cases not defined or quantified and the importance of specific metals, environments, bacterial taxa, mobile genetic elements, and other abiotic or biotic conditions are not clear. Co-resistance is often suggested as a dominant mechanism, but interpretations are beset with correlational bias. Proof of principle examples of cross-resistance and co-regulation has been described but more in-depth characterizations are needed, using methodologies that confirm the functional expression of resistance genes and that connect genes with specific bacterial hosts. Here, we comprehensively evaluate the recent evidence for different models of co-selection from pure culture and metagenomic studies in environmental contexts and we highlight outstanding questions.

Effects of earthworms on antibiotic resistance genes in different soil-plant systems

Earthworms play an important role in the soil environment. To explore the difference in earthworms influence on various media in different soil-plant systems, the abundance of tetracycline, sulfonamide and quinolone resistance genes and the structure of the bacterial community were analysed from five different media including non-rhizosphere soil, rhizosphere soil, phyllosphere, root endophytes and earthworm intestine by real-time quantitative PCR and high-throughput 16S rRNA sequencing. Studies have shown that earthworms can reduce the absolute abundance of antibiotic resistance genes (ARGs) in non-rhizosphere soil. Root endophytes in the soil-cabbage system and rhizosphere soil in the soil-setaria system had the same findings. Earthworms can change the bacterial community structure, especially that of Proteobacteria and Cyanobacteria in the phyllosphere and root endophytes. Redundancy analysis (RDA) results that bacterial community change was the main factor affecting ARGs. In addition, earthworms increased the proportion of Cyanobacteria in root endophytes, and Cyanobacteria was significantly positively correlated with sul3. This study provides a scientific basis for controlling the migration and diffusion of ARGs and reducing environmental risks in soil-plant systems in the future.

Is the application of organic fertilizers becoming an undeniable source of microplastics and resistance genes in agricultural systems?

The application of organic fertilizers is becoming an undeniable source of microplastics and antibiotic resistance genes (ARGs) in agricultural soils. The complex microbial activity further transfers resistance genes and their host bacteria to agricultural products and throughout the entire food chain. Therefore, the current main focus is on reducing the abundance of microplastics and ARGs in organic fertilizers at the source, as well as managing microplastics and ARGs in soil. The control of microplastic abundance in organic fertilizers is currently only achieved through pre-composting selection and other methods. However, there are still many shortcomings in the research on the distribution characteristics, propagation and diffusion mechanisms, and control technologies of ARGs, and some key scientific issues still need to be urgently addressed. The high-temperature composting of organic waste can effectively reduce the abundance of ARGs in organic fertilizers to a certain extent. However, it is also important to consider the spread of ARGs in residual antibiotic-resistant bacteria (ARB). This article systematically explores the pathways and interactions of microplastics and resistance genes entering agricultural soils through the application of organic fertilizers. The removal of microplastics and ARGs from organic fertilizers was discussed in detail. Based on the limitations of existing research, further investigation in this area is expected to provide valuable insights for the development and practical implementation of technologies aimed at reducing soil microplastics and resistance genes.

High prevalence of antibiotic-resistant and metal-tolerant cultivable bacteria in remote glacier environment

Studies of antibiotic-resistant bacteria (ARB) have mainly originated from anthropic-influenced environments, with limited information from pristine environments. Remote cold environments are major reservoirs of ARB and have been determined in polar regions; however, their abundance in non-polar cold habitats is underexplored. This study evaluated antibiotics and metals resistance profiles, prevalence of antibiotic resistance genes (ARGs) and metals tolerance genes (MTGs) in 38 ARB isolated from the glacier debris and meltwater from Baishui Glacier No 1, China. Molecular identification displayed Proteobacteria (39.3%) predominant in debris, while meltwater was dominated by Actinobacteria (30%) and Proteobacteria (30%). Bacterial isolates exhibited multiple antibiotic resistance index values > 0.2. Gram-negative bacteria displayed higher resistance to antibiotics and metals than Gram-positive. PCR amplification exhibited distinct ARGs in bacteria dominated by β-lactam genes blaCTX-M (21.1-71.1%), blaACC (21.1-60.5%), tetracycline-resistant gene tetA (21.1-60.5%), and sulfonamide-resistant gene sulI (18.4-52.6%). Moreover, different MTGs were reported in bacterial isolates, including mercury-resistant merA (21.1-63.2%), copper-resistant copB (18.4-57.9%), chromium-resistant chrA (15.8-44.7%) and arsenic-resistant arsB (10.5-44.7%). This highlights the co-selection and co-occurrence of MTGs and ARGs in remote glacier environments. Different bacteria shared same ARGs, signifying horizontal gene transfer between species. Strong positive correlation among ARGs and MTGs was reported. Metals tolerance range exhibited that Gram-negative and Gram-positive bacteria clustered distinctly. Gram-negative bacteria were significantly tolerant to metals. Amino acid sequences of blaACC,blaCTX-M,blaSHV,blaampC,qnrA, sulI, tetA and blaTEM revealed variations. This study presents promising ARB, harboring ARGs with variations in amino acid sequences, highlighting the need to assess the transcriptome study of glacier bacteria conferring ARGs and MTGs.

Evaluation of resistance risk in soil due to antibiotics during application of penicillin V fermentation residue

The soil application of hydrothermally treated penicillin V fermentation residue (PFR) is attractive but challenged, due to the concern of the resistance risk in soil related to residual antibiotics. In this study, a lab-scale incubation experiment was conducted to investigate the influence of penicillin V on antibiotic resistance genes (ARGs) in PFR-amended soil via qPCR. The introduced penicillin V in soil could not be persistent, and its degradation occurred mainly within 2 days. The higher number of soil ARGs was detected under 108 mg/kg of penicillin V than lower contents (≤54 mg/kg). Additionally, the relative abundance of ARGs was higher in soil spiked with penicillin V than that in blank soil, and the great increase in the relative abundance of soil ARGs occurred earlier under 108 mg/kg of penicillin V than lower contents. The horizontal gene transfer might contribute to the shift of ARGs in PFR-amended soil. The results indicated that the residual penicillin V could cause the proliferation of soil ARGs and should be completely removed by hydrothermal treatment before soil application. The results of this study provide a comprehensive understanding of the resistance risk posed by penicillin V during the application of hydrothermally pretreated PFR.

Effects of cadmium and copper mixtures on antibiotic resistance genes in rhizosphere soil

The evolvement and development of antibiotic resistance in microorganisms may be influenced by metals; however, it is still unclear how cadmium (Cd) and copper (Cu) combined affect the distribution and presence of antibiotic-resistance genes (ARGs) in rhizosphere soil. The aims of this research were to (1) compare the distribution patterns of bacterial communities and ARGs in response to the effects of Cd and Cu both separately and combined; (2) explore the possible mechanisms underlying the variation in soil bacterial communities and ARGs in addition to the combined effects of Cd, Cu, and various environmental variables (nutrients, pH, etc.); and (3) provide a reference for assessing the risks of metals (Cd and Cu) and ARGs. The findings showed that the multidrug resistance genes acrA and acrB and the transposon gene intI-1 were present in high relative abundance in bacterial communities. Cadmium and Cu had a substantial interaction effect on the abundance of acrA, whereas Cu had a notable main effect on the abundance of intI-1. According to the network analysis, the strong links between bacterial taxa and specific ARGs revealed that most ARGs were hosted by Proteobacteria, Actinobacteria, and Bacteroidetes. According to structural equation modeling, Cd had a larger effect on ARGs than Cu. Compared to previous analyses of ARGs, bacterial community diversity had little effect on ARGs in this study. Overall, the results may have important consequences for determining the possible hazard of soil metals and extend the understanding of how Cd and Cu co-select ARGs in rhizosphere soils.

Prevalence of multidrug-resistant and extended-spectrum β-lactamase-producing Escherichia coli from chicken farms in Egypt

Background and Aim

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli strains exhibit antibiotic resistance and are known to infect humans worldwide. This study assessed the phenotypic and genotypic prevalence of ESBL-resistant E. coli isolates recovered from the respiratory tracts of chickens in El-Sharkia Governorate, Egypt.

Materials and Methods

We obtained 250 lung samples (one lung/bird) from 50 chicken farms (5 chickens/farm) to isolate, identify, and serotype E. coli. Antimicrobial resistance susceptibility was determined using the disk diffusion method, while the ESBL phenotype was identified using double disk synergy. We detected the β-lactamase genes, blaTEM, and blaSHV, using a polymerase chain reaction.

Results

The results showed that 140/250 (56%) were infected with E. coli. All the serogroups of isolated E. coli exhibited high multi-antimicrobial resistance index values (>0.2), and 65.7% were confirmed to have ESBL. Among the isolates with the ESBL phenotypes, 55 (60%) and 32 (35%) contained the blaTEM and blaSHV genes, respectively.

Conclusion

The widespread distribution of multidrug-resistant and ESBL-producing E. coli among poultry farms is a significant human health hazard. These results will help the Egyptian authorities to implement a national one-health approach to combat the antimicrobial resistance problem.

Spatial and temporal distribution characteristics of antibiotics and heavy metals in the Yitong River basin and ecological risk assessment

Due to rapid socioeconomic development, antibiotic pollution and heavy metal pollution are receiving increasing amounts of attention. Both antibiotics and heavy metals in the environment are persistent and toxic, and the interactions between the pollutants create potential long-term hazards for the ecological environment and human health as mixed pollutants. In this study, the surface water of the Yitong River in Changchun was used as the research object, and the hazards associated with antibiotics and heavy metals in the surface water were assessed by analyzing the spatial and temporal distribution characteristics of antibiotics and heavy metals and by using ecological risk assessment and human health risk assessment models. The results showed that ofloxacin (OFL) and norfloxacin (NOR) varied seasonally according to the seasonal climate, with total concentrations ranging from 17.65 to 902.47 ng/L and ND to 260.49 ng/L for OFL and NOR, respectively, and from 8.30 to 120.40 μg/L, 1.52 to 113.41 μg/L and 0.03 to 0.04 μg/L for copper (Cu), zinc (Zn) and cadmium (Cd), respectively. In terms of spatial distribution, the concentration of antibiotics in the urban sections, which had intensive human activities, was higher than that in the suburban sections, while the concentration of heavy metals in the suburban sections, which had intensive agricultural operations, was greater than that in the urban section. Ecological risk evaluation showed that NOR and OFL were present in the water bodies at a high-risk level, Cd was at a low pollution level, and the heavy metal Cd was the primary pollutant associated with health risks toward for adults and children, and it was mainly at a medium risk level. Additionally, both antibiotics and heavy metals posed higher health risks for children than for adults.

Growth-Promoting Effects of Zhenqi Granules on Finishing Pigs

Developing nonantibiotic livestock growth promoters attracts intensive interest in the post-antibiotic era. In this study, we investigated the growth-promoting efficacy of Zhenqi granules (ZQ) in pigs and further explored the possible mechanisms by transcriptomics analysis. Weaned piglets (52 days old with an average body weight of 17.92 kg) were fed with diets supplemented with different doses of ZQ (0 g/kg, 1 g/kg, and 2 g/kg) for 30 days and continued observations for an additional 32 days after removing ZQ from the diets. Compared with the control group, the average daily gain, carcass weight, average back fat thickness, and fat meat percentage of the group supplemented with 1 g/kg of ZQ showed a significant increase, and the feed/gain ratio was lower. The group supplemented with 2 g/kg of ZQ also showed a significant increase in average daily gain and average backfat thickness. A transcriptomics analysis revealed that the supplementation of ZQ at 1 g/kg upregulated the expression of genes related to collagen biosynthesis and lipid biosynthesis in skeletal muscle and liver. This effect was primarily through upregulating the mRNA levels of structural proteins and lipid-related enzymes. This study demonstrates the growth-promoting efficacy of ZQ and provides some insights of the mechanism of growth promotion.

Effects of Oxytetracycline/Lead Pollution Alone and in the Combined Form on Antibiotic Resistance Genes, Mobile Genetic Elements, and Microbial Communities in the Soil

The application of livestock manure is the leading cause of antibiotic and heavy metal pollution in agricultural soil. However, the effects of oxytetracycline (OTC) and lead (Pb) pollution in the single or combined form on antibiotic resistance genes (ARGs) in the soil need to be further studied. This study was planned to investigate the effects of OTC and Pb application on ARGs, mobile genetic elements (MGEs), and bacterial abundance in the soil. The relative abundance of ARGs and MGEs increased by 0.31-fold and 0.03-fold after the addition of 80 mg kg^-1 Pb to the soil, and by 0.49-fold and 0.03-fold after the addition of 160 mg kg^-1 Pb. In addition, under the premise of the existence of OTC, the inhibitory effect of a low concentration of Pb on ARG is stronger than that of a high concentration of Pb, resulting in a lower abundance of ARGs. The abundance of ARGs and MGEs increased by 0.11-fold and 0.17-fold after the addition of OTC (30 mg kg^-1) to the soil at a Pb concentration of 80 mg kg^-1 and by 0.18-fold and 0.04-fold at a Pb concentration of 160 mg kg^-1. The addition of OTC and Pb in the soil also decreased the many bacterial communities such as Bacteroidetes, Proteobacteria, Acidobacteria, and Firmicutes. Redundancy analysis (RDA) showed that organic matter content and pH were positively correlated with the abundance of ARGs and MGEs. At the same time, electrical conductivity (EC) had a negative correlation with the abundance of ARGs and MGEs in the soil. Intl1 was significantly associated with tetB, sul1, tetQ, sul2, and sul3. Network analysis illustrated that Actinobacteria, Bacteroidetes, and Proteobacteria were the main host bacteria causing changes in the abundance of ARGs and MGEs, and they were also predominant phylum in the culture environment. This conclusion can provide a reference for the related research of ARGs in soil.

Metagenomic analysis reveals antibiotic resistance genes and virulence factors in the saline-alkali soils from the Yellow River Delta, China

The propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in the saline-alkali soils and associated environmental factors remains unknown. In this study, soil samples from the Yellow River Delta, China with four salinity gradients were characterized by their physiochemical properties, and shotgun metagenomic sequencing was used to identify the ARGs and VFs carried by microorganisms. Soil salinization significantly reduced the relative abundances of Solirubrobacterales, Propionibacteriales, and Micrococcales, and quorum sensing in microorganisms. The number of ARGs and VFs significantly decreased in medium and high saline-alkali soils as compared with that in non-saline-alkali soil, however, the ARGs of Bacitracin, and the VFs of iron uptake system, adherence, and stress protein increased significantly in saline-alkali soils. Spearman analysis showed that the ARGs of fluoroquinolone, tetracycline, aminoglycoside, beta-lactam, and tigecycline were positively correlated with soil pH. Similarly, we observed an increased contribution to the ARGs and VFs by taxa belonging to Solirubrobacterales and Gemmatimonadales, respectively. The control plot was mainly improved from saline-alkali land through application of animal manure, which tended to contain large amounts of ARGs and VFs in this study. Further studies are needed to observe ARGs and VFs in the saline-alkali land for multiple years and speculate the potential risks caused by varied ARGs and VFs to the soil ecosystem and human health.

The fate of antibiotic resistance genes, microbial community, and potential pathogens in the maricultural sediment by live seaweeds and oxytetracycline

Three common seaweeds including Ulva fasciata, Codium cylindricum and Ishige okamurai were used for the remediation of maricultural wastewater and sediment in the presence/absence of trace level of oxytetracycline (OTC) in lab-scale experiments. Higher NO₃^--N and PO₄^3--P removal rates were achieved due to the presence of seaweeds, and trace OTC also had a positive effect on NO₃^--N removal. A slight variation of 2.10-2.15% were observed in the total relative abundances of antibiotic resistance genes (ARGs) of different sediment samples after one-month operation. However, the variation of ARGs profiles by the co-existence of different seaweeds and OTC was in the descending order of Ishige okamurai > Codium cylindricum > Ulva fasciata, which was in accordance with the variation of microbial hosts at genus level. The abundance of dominant tetracycline resistance genes promoted by the co-existence of different seaweeds and OTC in compared with the presence of single seaweed or OTC via metagenomic sequencing and qPCR analysis, and the co-existence of Ishige okamurai and OTC exhibited the largest impact. The potential pathogens were more sensitive to the co-existence of seaweed and OTC than single seaweeds. Meanwhile, a variety of ARGs were enriched in the pathogens, and the dominant pathogenic bacteria of Vibrio had 133 Vibrio species with 28 subtypes of ARGs. The variation of ARGs profiles in the sediment were strongly related with the dominant phyla Proteobacteria, Actinobacteria, Firmicutes, Planctomycetes and Cyanobacteria. Besides, Nitrate level exhibited more significant effect on ∑ARGs, ARGs resistant to vancomycin and streptogramin_a, while phosphate level exhibited more positively significant effect on ARGs resistant to fosmidomycin, ATFBT and cephalosporin.

Insights in the Development and Uses of Alternatives to Antibiotic Growth Promoters in Poultry and Swine Production

The overuse and misuse of antibiotics has contributed to the rise and spread of multidrug-resistant bacteria. To address this global public health threat, many countries have restricted the use of antibiotics as growth promoters and promoted the development of alternatives to antibiotics in human and veterinary medicine and animal farming. In food-animal production, acidifiers, bacteriophages, enzymes, phytochemicals, probiotics, prebiotics, and antimicrobial peptides have shown hallmarks as alternatives to antibiotics. This review reports the current state of these alternatives as growth-promoting factors for poultry and swine production and describes their mode of action. Recent findings on their usefulness and the factors that presently hinder their broader use in animal food production are identified by SWOT (strength, weakness, opportunity, and threat) analysis. The potential for resistance development as well as co- and cross-resistance with currently used antibiotics is also discussed. Using predetermined keywords, we searched specialized databases including Scopus, Web of Science, and Google Scholar. Antibiotic resistance cannot be stopped, but its spreading can certainly be hindered or delayed with the development of more alternatives with innovative modes of action and a wise and careful use of antimicrobials in a One Health approach.

An integrated multidisciplinary-based framework for characterizing environmental risks of heavy metals and their effects on antibiotic resistomes in agricultural soils

In this study, a new integrated multidisciplinary-based framework has been proposed to better understand the environmental risks of heavy metals (HMs) in agricultural soils. The source apportionment results revealed by a multilinear engine model were incorporated into the geochemical indexes and the probabilistic health risk assessment models for identifying the source-oriented risks of HMs in the environment. High-throughput sequencing-based metagenomic assembly analysis was used for characterizing the prevalence and dissemination risk of antibiotic resistomes and their associations with the geochemical enrichment of HMs in the soils. Results showed agricultural and industrial activities were the main sources of HMs in the environment. Although the soils were contaminated moderately by HMs and the health risks posed by soil metals were negligible for both adult and children, source-oriented risk evaluation suggested agricultural activities contributed relatively higher contamination and health risks than the other sources. Notably, abundant and diverse antibiotic resistant genes, mobile gene elements, virulence factors, and antibiotic-resistant bacterial pathogens were identified in the agricultural soils, as well as their co-occurrences on the same contigs, implying a non-negligible resistome risk. Further, statistical and network analyses showed the geochemical enrichment of HMs exerted significant effects on the antibiotic resistomes in the environment.