Untreated swine wastes changed antibiotic resistance and microbial community in the soils and impacted abundances of antibiotic resistance genes in the vegetables

Tetracycline antibiotics in agricultural soil: Dissipation kinetics, transformation pathways, and structure-related toxicity

Tetracyclines (TCs) are the most common antibiotics in agricultural soil, due to their widespread usage and strong persistence. Biotic and abiotic degradation of TCs may generate toxic transformation products (TPs), further threatening soil ecological safety. Despite the increasing attention on the environmental behavior of TCs, a systematic review on the dissipation of TCs, evolution of TPs, and structure-toxicity relationship of TCs in agricultural soil remains lacking. This review aimed to provide a comprehensive overview of the environmental fate of TCs in agricultural soil. We first introduced the development history and structural features of different generations of TCs. Then, we comparatively evaluated the dissipation kinetics, transportation pathways, and ecological impacts of three representative TCs, namely tetracycline (TC), oxytetracycline (OTC), and chlortetracycline (CTC), in agricultural soil. The results showed that the dissipation kinetics of TCs generally followed the first-order kinetic model, with the median dissipation half-lives ranging from 20.0 to 38.8 days. Among the three TCs, OTC displayed the lowest dissipation rates due to its structural stability. The typical degradation pathways of TCs in soil included epimerization/isomerization, demethylation, and dehydration. Isomerization and dehydration reactions may lead to the formation of more toxic TPs, while demethylation was accompanied by the alteration of the minimal pharmacophore of TCs thus potentially reducing the toxicity. Toxicological experiments are urgently needed in future to comprehensively evaluate the ecological risks of TCs in agricultural soil.

Exploring bacterial diversity and antimicrobial resistance gene on a southern Brazilian swine farm

The bacterial composition of and the circulation of antimicrobial resistance genes (ARGs) in waste from Brazilian swine farms are still poorly understood. Considering that antimicrobial resistance (AMR) is one of the main threats to human, animal, and environmental health, the need to accurately assess the load of ARGs released into the environment is urgent. Therefore, this study aimed to characterize the microbiota in a swine farm in southern Brazil and the resistome in swine farm wastewater treated in a series of waste stabilization ponds (WSPs). Samples were collected from farm facilities and the surrounding environment, representing all levels of swine manure within the treatment system. Total metagenomic sequencing was performed on samples from WSPs, and 16S-rDNA sequencing was performed on all the collected samples. The results showed increased bacterial diversity in WSPs, characterized by the presence of Caldatribacteriota, Cloacimonadota, Desulfobacterota, Spirochaetota, Synergistota, and Verrucomicrobiota. Furthermore, resistance genes to tetracyclines, lincosamides, macrolides, rifamycin, phenicol, and genes conferring multidrug resistance were detected in WSPs samples. Interestingly, the most abundant ARG was linG, which confers resistance to the lincosamides. Notably, genes conferring macrolide (mphG and mefC) and rifamycin (rpoB_RIF) resistance appeared in greater numbers in the late WSPs. These drugs are among the high-priority antibiotic classes for human health. Moreover, certain mobile genetic elements (MGEs) were identified in the samples, notably tnpA, which was found in high abundance. These elements are of particular concern due to their potential to facilitate the dissemination of ARGs among bacteria. In summary, the results indicate that, in the studied farm, the swine manure treatment system could not eliminate ARGs and MGEs. Our results validate concerns about Brazil's swine production system. The misuse and overuse of antimicrobials during animal production must be avoided to mitigate AMR.

Characteristics and driving factors of antibiotic resistance genes in aquaculture products from freshwater ponds in China Yangtze River Delta

Antibiotic resistance genes (ARGs) are widespread in aquaculture and pose a huge threat to aquaculture organisms and human health. In this study, occurrences and relative abundances of ARGs were analysed in the guts of products cultured in freshwater ponds in the Yangtze River Delta region in China. A total of 29 ARGs were found in the gut samples, with detection frequencies ranging from 4.8% to 81%, and the relative abundances (ARGs/16S rRNA) ranging from 10-7 to 1. In addition, the human dietary intake of ARGs via aquaculture products was assessed, where the daily intake of most ARGs via aquaculture products was higher than those via PM2.5 and drinking water, but lower than that via vegetables. The relative abundances of MGE (IS613, Tp614, tnpA and int1) were significantly correlated with those of multiple ARGs, indicating the horizontal gene transfer (HGT) of ARGs among gut microorganisms. Proteobacteria, Firmicutes and Actinobacteria were the dominated microbial communities found in the guts of aquaculture products. In addition, significant correlations were found between Cyanobacteria and int1, between Nitrospira and tetE, and between sul2 and aadA2, indicating potential same hosts of these genes. In addition, results from co-correlation indicated both HGT (dominated by MGEs) of ARGs and the enrichment of ARGs in bacteria. MGEs, mostly int1, were more effective than bacteria in increasing the ARG abundance. This study could provide a better understanding of the transmission of ARGs in the aquaculture environment and improve the quality of aquaculture products and the ecology.

Food waste compost and digestate as novel fertilizers: Impacts on antibiotic resistome and potential risks in a soil-vegetable system

As a novel agricultural practice, the reuse of food waste compost and digestate as fertilizers leads to a circular economy, but inevitably introduces bio-contaminants such as antibiotic resistance genes (ARGs) into the agroecosystem. Moreover, heavy metal and antibiotic contamination in farmland soil may exert selective pressures on the evolution of ARGs, posing threats to human health. This study investigated the fate, influencing mechanisms and potential risks of ARGs in a soil-vegetable system under different food waste fertilization and remediation treatments and soil contamination conditions. Application of food waste fertilizers significantly promoted the pakchoi growth, but resulted in the spread of ARGs from fertilizers to pakchoi. A total of 56, 80, 84, 41, and 73 ARGs, mobile genetic elements (MGEs) and metal resistance genes (MRGs) were detected in the rhizosphere soil (RS), bulk soil (BS), control soil (CS), root endophytes (RE), and leaf endophytes (LE), respectively. Notably, 7 genes were shared in the above five subgroups, indicating a specific soil-root-endophytes transmission pathway. 36 genes were uniquely detected in the LE, which may originate from airborne ARGs. The combined application of biochar and fertilizers reduced the occurrence of ARGs and MGEs to some extent, showing the remediation effect of biochar. The average abundance of ARGs in the RS, BS and CS was 3.15 × 10-2, 1.31 × 10-2 and 2.35 × 10-1, respectively. Rhizosphere effects may reduce the abundance of ARGs in soil. The distribution pattern of ARGs was influenced by the types of soil, endophyte and contaminant. MGEs is the key driver shaping ARGs dynamics. Soil properties and pakchoi growth status may affect the bacterial composition, and consequently regulate ARGs fate, while endophytic ARGs were more impacted by biotic factors. Moreover, the average daily doses of ARGs from pakchoi consumption is 107-109 copies/d/kg, and its potential health risks should be emphasized.

Effect of wheat crops on the persistence and attenuation of antibiotic resistance genes in soil after swine wastewater application

Swine wastewater (SW) application introduces antibiotic resistance genes (ARGs) into farmland soils. However, ARG attenuation in SW-fertigated soils, especially those influenced by staple crops and soil type, remains unclear. This study investigated twelve soil ARGs and one mobile genetic element (MGE) in sandy loam, loam, and silt loam soils before and after SW application in wheat-planted and unplanted soils. The results revealed an immediate increase in the abundance of ARGs in soil by two orders of magnitude above background levels following SW application. After SW application, the soil total ARG abundance was attenuated, reaching background levels at 54 days; However, more individual ARGs were detected above the detection limit than pre-application. Among the 13 genes, acc(6')-lb, tetM, and tetO tended to persist in the soil during wheat harvest. ARG half-lives were up to four times longer in wheat-planted soils than in bare soils. Wheat planting decreased the persistence of acc(6')-lb, ermB, ermF, and intI2 but increased the persistence of others such as sul1 and sul2. Soil type had no significant impact on ARG and MGE fates. Our findings emphasize the need for strategic SW application and the consideration of crop cultivation effects to mitigate ARG accumulation in farmland soils.

Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota

Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower® PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.

Comprehensive Assessment of Environmental Emissions, Fate, and Risks of Veterinary Antibiotics in China: An Environmental Fate Modeling Approach

China is one of the major global consumers of veterinary antibiotics. Insufficient recognition of emissions and environmental contamination hamper global efforts to prevent antibiotic resistance development. This pioneering study combined empirical data and modeling approaches to predict total 2010-2020 emissions of 80 veterinary antibiotics ranging from 23,110 to 40,850 tonnes/year, after 36-50% antibiotic removal by manure treatment. Following an initial increase of 10% from 2010 to 2015, emissions declined thereafter by 43%. While 85% of emissions discharged into soils, approximately 56%, 23%, and 18% of environmental residue were ultimately distributed in soils, freshwaters, and seawaters under steady-state conditions. In 2020, 657 (319-1470) tonnes entered the ocean from inland freshwaters. Median ∑antibiotics concentrations were estimated at 4.7 × 103 ng/L in freshwaters and 2.9 ng/g in soils, with tetracyclines and sulfonamides as the predominant components. We identified 44 veterinary antibiotics potentially posing high risks of resistance development in freshwaters, with seven exhibiting high risks in >10% of Chinese freshwater areas. Tetracyclines were the category with the most antibiotics exhibiting elevated risks; however, sulfamethylthiazole demonstrated the highest individual compound risk. The Haihe River Basin displayed the highest susceptibility overall. The findings offer valuable support for control of veterinary antibiotic contamination in China.

Swine farming shifted the gut antibiotic resistome of local people

Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.

Efficacy of new generation biosorbents for the sustainable treatment of antibiotic residues and antibiotic resistance genes from polluted waste effluent

Antimicrobials are frequently used in both humans and animals for the treatment of bacterially-generated illnesses. Antibiotic usage has increased for more than 40% from last 15 years globally per day in both human populations and farm animals leading to the large-scale discharge of antibiotic residues into wastewater. Most antibiotics end up in sewer systems, either directly from industry or healthcare systems, or indirectly from humans and animals after being partially metabolized or broken down following consumption. To prevent additional antibiotic compound pollution, which eventually impacts on the spread of antibiotic resistance, it is crucial to remove antibiotic residues from wastewater. Antibiotic accumulation and antibiotic resistance genes cannot be effectively and efficiently eliminated by conventional sewage treatment plants. Because of their high energy requirements and operating costs, many of the available technologies are not feasible. However, the biosorption method, which uses low-cost biomass as the biosorbent, is an alternative technique to potentially address these problems. An extensive literature survey focusing on developments in the field was conducted using English language electronic databases, such as PubMed, Google Scholar, Pubag, Google books, and ResearchGate, to understand the relative value of the available antibiotic removal methods. The predominant techniques for eliminating antibiotic residues from wastewater were categorized and defined by example. The approaches were contrasted, and the benefits and drawbacks were highlighted. Additionally, we included a few antibiotics whose removal from aquatic environments has been the subject of extensive research. Lastly, a few representative publications were identified that provide specific information on the removal rates attained by each technique. This review provides evidence that biosorption of antibiotic residues from biological waste using natural biosorbent materials is an affordable and effective technique for eliminating antibiotic residues from wastewater.

Studies on the airborne bacterial communities and antimicrobial resistance genes in duck houses based on metagenome and PCR analysis

The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics. Livestock and poultry farms, as key sites for prevalence of antibiotic-resistant bacteria (ARB), can spread antimicrobial resistance genes (ARGs) through microbial aerosols and affect public health. In this study, total suspended particulate matter (TSP) and airborne culturable microorganisms were collected from duck houses in Tai'an, Shandong Province, and the bacterial communities and airborne ARGs were analyzed using metagenomics and PCR methods. The results showed that the bacterial communities in the air of duck houses were mainly Actinobacteria, Firmicutes, Proteobactria, Chlamydia, and Bcateroidetes at the phylum level. At the genus level, the air was dominated by Corynebacterium, Jeotgalicoccus, Staphylococcus, Brevibacterium, and Megacoccus, and contained some pathogenic bacteria such as Staphylococcus aureus, Corynebacterium diphtheriae, Klebsiella oxytoca, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were also potential hosts for ARGs. The airborne ARGs were mainly macrolides (10.97%), penicillins (10.73%), cephalosporins (8.91%), streptozotocin (8.91%), and aminoglycosides (8.02%). PCR detected 27 ARGs in airborne culturable microorganisms, and comparative analysis between PCR and the metagenomic data revealed that a total of 9 ARGs were found to the same, including macrolides ErmA, ErmF, tetracyclines tetG, tetX, methicarbamazepines dfrA12, dfrA15, aminoglycosides APH3-VI, ANT2-Ⅰ, and sulfonamides sul2. Moreover, inhalation exposure modeling showed that the workers in duck houses inhaled higher concentrations of ARB, human pathogenic bacteria (HPB) and human pathogenic antibiotic-resistant bacteria (HPARB) than hospital workers. These results provide new insights into airborne microorganisms and ARGs in animal farms and lay the foundation for further study.

The soil-microbe-plant resistome: A focus on the source-pathway-receptor continuum

The One World, One Health concept implies that antibiotic resistance (AR) in the soil-microbe-plant resistome is intricately linked to the human resistome. However, the literature is mainly confined to sources and types of AR in soils or microbes, but comprehensive reviews tracking AR in the soil-microbe-plant resistome are limited. The present review applies the source-pathway-receptor concept to understand the sources, behaviour, and health hazards of the soil-microbe-plant resistome. The results showed that the soil-microbe-plant system harbours various antibiotic-resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and mobile genetic elements (MGEs). Anthropogenic sources and drivers include soil application of solid waste, wastewater, biosolids, and industrial waste. Water-, wind-, and human-driven processes and horizontal gene transfer circulate AR in the soil-microbe-plant resistome. The AR in bulk soil, soil components that include soil microorganisms, soil meso- and macro-organisms, and possible mechanisms of AR transfer to soil components and ultimately to plants are discussed. The health risks of the soil-microbe-plant resistome are less studied, but potential impacts include (1) the transfer of AR to previously susceptible organisms and other resistomes, including the human resistome. Overall, the study tracks the behaviour and health risks of AR in the soil-plant system. Future research should focus on (1) ecological risks of AR at different levels of biological organization, (2) partitioning of AR among various phases of the soil-plant system, (3) physico-chemical parameters controlling the fate of AR, and (4) increasing research from low-income regions particularly Africa as most of the available literature is from developed countries.

Effects of microbes in pig farms on occupational exposed persons and the environment

In terms of pig farming, pig gut microbes have a significant effect on farmers and the farm environment. However, it is still unclear which microbial composition is more likely to contribute to this effect. This study collected a total of 136 samples, including pigs' faeces samples, farmers' faeces samples, samples from individuals who had no contact with any type of farm animal (referred to as 'non-exposed' persons), and environmental dust samples (collected from inside and outside pig houses and the farm) from two pig farms, pig farm A and pig farm B. Whereafter, 16S rRNA sequencing and taxonomic composition analysis were performed. According to the study, compared to non-exposed persons, pig farmers had a significantly higher abundance of 7 genera. In addition, the farmers were grouped according to the duration of their occupational exposure, and it was shown that 4 genera, including Turicibacter, Terrisporobacter, and Clostridium_sensu_stricto_1, exhibited a rise in more frequent contact with pigs. As compared to outside the pig house, the environmental dust has a greater concentration of the 3 bacteria mentioned before. Therefore, these 3 microbes can be considered as co-occurring microbes that may exist both in humans and the environment. Also, the 3 co-occurring microbes are involved in the fermentation and production of short-chain fatty acids and their effectiveness decreased as distance from the farm increased. This study shows that the 3 microbes where pig farmers co-occur with the environment come from pig farms, which provides fresh ideas for preventing the spread of microbial aerosols in pig farms and reducing pollution.

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.

One Health challenges for pig reproduction

The current state of the world challenges pig reproduction as an important part of One Health, which involves interrelationships between animal, human and environmental health. The One Health concept underlines a comparative aspect in reproductive physiology and disease occurrence, bridging knowledge from one species to another. Seasonal changes in the environment affect pig reproduction and climate change may further strengthen those effects. Endocrine-disrupting chemicals (EDCs), and specifically phthalates and heavy metals, interfere with endocrine function, and thereby sexual behavior, fertilization capacity and steroidogenesis. Reproductive infections and extended semen storage are important indications for antimicrobial use. Innovative solutions are needed to explore alternatives to antimicrobials. Efforts to ensure reproductive efficiency have prolonged farrowing as litter size has doubled over the past three decades, compromising immune transfer and welfare. Physiological, metabolic and programming related events around parturition are key areas for future One Health research in pig reproduction. In conclusion, climate change challenges reproductive management and breeding. More resilient pigs that can tolerate harsh environment but maintain high reproductive performance are needed. EDCs continue to grow as an environmental challenge for reproductive management and alternatives to antibiotics will be required.

Antibiotic resistome associated with influencing factors in industrial-scale organic waste aerobic composting plants

This study investigated the fate of antibiotic resistance genes (ARGs) and bacterial evolution in six industrial-scale organic wastes aerobic composting plants and identified key factors driving ARGs dynamics. A total of 226 ARGs and 46 mobile genetic elements (MGEs), mainly resistant to aminoglycoside and MLSB, were detected by high-throughput qPCR. Briefly, aerobic composting showed good performance in reducing the diversity and abundance of ARGs, where the total absolute abundance was reduced by 88.34%-97.08% except for cattle manures. Rapid composting may lead to a rebound of ARGs due to long-term storage compared to traditional composting. Hub ARGs and bacterial genera were screened out by co-occurrence patterns. As the dominant phyla in composting, the main potential hosts of ARGs were Firmicutes, Bacteroidota and Proteobacteria. Structural equation model indicated that MGEs and heavy metals were key factors affecting ARGs dynamics. In addition, nutrients and bacterial α-diversity can indirectly influence ARGs by affecting MGEs.

Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant

Poultry farming is a major livelihood in South and Southeast Asian economies where it is undergoing rapid intensification to meet the growing human demand for dietary protein. Intensification of poultry production systems is commonly supported by increased antimicrobial drug use, risking greater selection and dissemination of antimicrobial resistance genes (ARGs). Transmission of ARGs through food chains is an emerging threat. Here, we investigated transmission of ARGs from chicken (broiler and layer) litter to soil and Sorghum bicolor (L.) Moench plants based on field and pot experiments. The results demonstrate ARGs transmission from poultry litter to plant systems under field as well as experimental pot conditions. The most common ARGs could be tracked for transmission from litter to soil to plants were identified as detected were cmx, ErmX, ErmF, lnuB, TEM-98 and TEM-99, while common microorganisms included Escherichia coli, Staphylococcus aureus, Enterococcus faecium, Pseudomonas aeruginosa, and Vibrio cholerae. Using next generation sequencing and digital PCR assays we detected ARGs transmitted from poultry litter in both the roots and stems of S. bicolor (L.) Moench plants. Poultry litter is frequently used as a fertiliser because of its high nitrogen content; our studies show that ARGs can transmit from litter to plants and illustrates the risks posed to the environment by antimicrobial treatment of poultry. This knowledge is useful for formulating intervention strategies that can reduce or prevent ARGs transmission from one value chain to another, improving understanding of impacts on human and environmental health. The research outcome will help in further understanding the transmission and risks posed by ARGs from poultry to environmental and human/animal health.

Mariculture affects antibiotic resistome and microbiome in the coastal environment

Antibiotics are increasingly used and released into the marine environment due to the rapid development of mariculture, resulting in spread of antibiotic resistance. The pollution, distribution, and characteristics of antibiotics, antibiotic resistance genes (ARGs) and microbiomes have been investigated in this study. Results showed that 20 antibiotics were detected in Chinese coastal environment, with predominance of erythromycin-H₂O, enrofloxacin and oxytetracycline. In coastal mariculture sites, antibiotic concentrations were significantly higher than in control sites, and more types of antibiotics were detected in the South than in the North of China. Residues of enrofloxacin, ciprofloxacin and sulfadiazine posed high resistance selection risks. β-Lactam, multi-drug and tetracycline resistance genes were frequently detected with significantly higher abundance in the mariculture sites. Of the 262 detected ARGs, 10, 26, and 19 were ranked as high-risk, current-risk, future-risk, respectively. The main bacterial phyla were Proteobacteria and Bacteroidetes, of which 25 genera were zoonotic pathogens, with Arcobacter and Vibrio in particular ranking in the top10. Opportunistic pathogens were more widely distributed in the northern mariculture sites. Phyla of Proteobacteria and Bacteroidetes were the potential hosts of high-risk ARGs, while the conditional pathogens were associated with future-risk ARGs, indicating a potential threat to human health.

Occurrence profiling and environmental risk assessment of veterinary antibiotics in vegetable soils at Chongqing region, China

Veterinary antibiotics (VAs) are emerging contaminants in soils as they may pose high risks to the ecosystem and human health. Identifying VAs accumulation in soils is essential for assessing their potential risks. Therefore, we investigated the distribution of VAs in soils from vegetable fields and evaluated their potential ecological and antimicrobial resistance risks in the Chongqing region of the Three Gorges Reservoir area, China. Results indicated that twenty-six species of VAs, including nine sulfonamides (SAs), seven quinolones (QNs), four tetracyclines (TCs), four macrolides (MLs), and two other species of VAs were detected in soils, with their accumulative levels ranging from 1.4 to 3145.7 μg kg^-1. TCs and QNs were the dominant VAs species in soils with high detection frequencies (100% TCs and 80.6% for QNs) and accumulative concentration (up to 1195 μg kg^-1 for TCs and up to 485 μg kg^-1 for QNs). Risk assessment indices showed that VAs (specifically SAs, TCs, and QNs) in most vegetable soils would pose a medium to high risk to the ecosystem and antimicrobial resistance. Mixture of VAs posed a higher risk to soil organisms, antimicrobial resistance, and plants than to aquatic organisms. Modeling analysis indicated that socioeconomic conditions, farmers' education levels, agricultural practices, and soil properties were the main factors governing VAs accumulation and environmental risks. Farmers with a high educational level owned large-scale farms and were more willing to use organic fertilizers for vegetable production, which eventually led to high VAs accumulation in vegetable soil. These findings would provide a reference for sustainable agricultural and environmental production under the current scenario of chemical fertilizer substitution by organic products and green agricultural development.

Swine farm groundwater is a hidden hotspot for antibiotic-resistant pathogenic Acinetobacter

Acinetobacter is present in the livestock environment, but little is known about their antibiotic resistance and pathogenic species in the farm groundwater. Here we investigated antibiotic resistance of Acinetobacter in the swine farm groundwater (JZPG) and residential groundwater (JZG) of a swine farming village, in comparison to a nearby (3.5 km) non-farming village (WTG) using metagenomic and culture-based approaches. Results showed that the abundance of antibiotic resistome in some JZG and all JZPG (~3.4 copies/16S rRNA gene) was higher than that in WTG (~0.7 copies/16S rRNA gene), indicating the influence of farming activities on both groundwater types. Acinetobacter accounted for ~95.7% of the bacteria in JZG and JZPG, but only ~8.0% in WTG. They were potential hosts of ~95.6% of the resistome in farm affected groundwater, which includes 99 ARG subtypes against 23 antibiotic classes. These ARGs were associated with diverse intrinsic and acquired resistance mechanisms, and the predominant ARGs were tetracyclines and fluoroquinolones resistance genes. Metagenomic binning analysis elucidated that non-baumannii Acinetobacter including A. oleivorans, A. beijerinckii, A. seifertii, A. bereziniae and A. modestus might pose environmental risks because of multidrug resistance, pathogenicity and massive existence in the groundwater. Antibiotic susceptibility tests showed that the isolated strains were resistant to multiple antibiotics including sulfamethoxazole (resistance ratio: 96.2%), levofloxacin (42.5%), gatifloxacin (39.0%), ciprofloxacin (32.6%), tetracycline (32.0%), doxycycline (29.0%) and ampicillin (12.0%) as well as last-resort polymyxin B (31.7%), colistin (24.1%) and tigecycline (4.1%). The findings highlight potential prevalence of groundwater-borne antibiotic-resistant pathogenic Acinetobacter in the livestock environment.

Insights into the panorama of antibiotic resistome in cropland soils amended with vermicompost in China

The accumulation and propagation of animal-derived antibiotic resistance genes (ARGs) pose great challenges to agricultural ecosystems. Vermicompost has drawn global attention as a new type of eco-friendly organic fertilizer. However, the effects of vermicompost application on ARGs in soil are still unclear. Here, we conducted a nationwide large-scale survey to explore the impact of vermicompost application on ARGs and the host in cropland fields as well as their regional differences. Vermicompost application was found to alter the pattern of ARGs, reduce the transfer of mobile genetic elements (MGEs), and mitigate the proliferation of high-risk bla-ARGs in soil. Regional differences in vermicompost-derived ARGs were observed in croplands, with less ARG-spreading risk in brown and yellow-brown soils. Total ARG abundance was present at the lowest level (1.24 × 10⁵-3.57 × 10⁷ copies/g) in vermicomposted soil compared with the croplands using animal manure (e.g., swine, chicken, and cow manure). Furthermore, vermicompost application increased the abundance of beneficial bacteria like Ilumatobacter and Gaiella, while reducing the abundance of Acidobacteria and Pseudarthrobacter. Network analysis showed that vermicompost altered ARG host bacteria and reduced the numbers of potential ARG hosts in soil. Microbes played a key role in ARG changes in vermicompost-treated soil. Our study provides valuable insight into the response of soil ARGs and the host to vermicompost in cropland ecosystem, and also provides a novel pathway for controlling the propagation of animal-derived ARGs.

Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms

In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.

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.

Adaptation of Rhizosphere Microbial Communities to Continuous Exposure to Multiple Residual Antibiotics in Vegetable Farms

The constant application of manure-based fertilizers in vegetable farms leads to antibiotic residue accumulation in soils, which has become a major stressor affecting agroecosystem stability. The present study investigated the adaptation profiles of rhizosphere microbial communities in different vegetable farms to multiple residual antibiotics. Multiple antibiotics, including trimethoprim, sulfonamides, quinolones, tetracyclines, macrolides, lincomycins, and chloramphenicols, were detected in the vegetable farms; the dominant antibiotic (trimethoprim) had a maximum concentration of 36.7 ng/g. Quinolones and tetracyclines were the most prevalent antibiotics in the vegetable farms. The five most abundant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi and Firmicutes, while the five most abundant phyla in root samples were Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Myxococcota. Macrolides were significantly correlated with microbial community composition changes in soil samples, while sulfonamides were significantly correlated with microbial community composition changes in root samples. Soil properties (total carbon and nitrogen contents and pH) influenced the shifts in microbial communities in rhizosphere soils and roots. This study provides evidence that low residual antibiotic levels in vegetable farms can shift microbial community structures, potentially affecting agroecosystem stability. However, the degree to which the shift occurs could be regulated by environmental factors, such as soil nutrient conditions.

Airborne bacterial community and antibiotic resistome in the swine farming environment: Metagenomic insights into livestock relevance, pathogen hosts and public risks

Globally extensive use of antibiotics has accelerated antimicrobial resistance (AMR) in the environment. As one of the biggest antibiotic consumers, livestock farms are hotspots in AMR prevalence, especially those in the atmosphere can transmit over long distances and pose inhalation risks to the public. Here, we collected total suspended particulates in swine farms and ambient air of an intensive swine farming area. Bacterial communities and antibiotic resistomes were analyzed using amplicon and metagenomic sequencing approaches. AMR risks and inhalation exposure to potential human-pathogenic antibiotic-resistant bacteria (HPARB) were subsequently estimated with comparison to the reported hospital samples. The results show that swine farms shaped the airborne bacterial community by increasing abundances, reducing diversities and shifting compositions. Swine feces contributed 77% of bacteria to swine farm air, and about 35% to ambient air. Airborne antibiotic resistomes in swine farms mainly conferred resistance to tetracyclines, aminoglycosides and lincosamides, and over 48% were originated from swine feces. Distinct to the hospital air, Firmicutes were dominant bacteria in swine farming environments with conditional pathogens including Clostridium, Streptococcus and Aerococcus being major hosts of antibiotic resistance genes (ARGs). Therein, genomes of S. alactolyticus carrying (transposase/recombinase-associated) ARGs and virulence factor genes were retrieved from the metagenomes of all swine feces and swine farm air samples, but they were not detected in any hospital air samples. This suggests the indication of S. alactolyticus in swine farming environments with potential hazards to human health. Swine farm air faced higher AMR risks than hospital air and swine feces. The inhalation intake of HPARB by a swine farm worker was about three orders of magnitude higher than a person who works in the hospital. Consequently, this study depicted atmospheric transmission of bacteria and antibiotic resistomes from swine feces to the environment.

Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.

Chronic exposure to ampicillin alters lung microbial composition in laboratory rat

PURPOSE

High-throughput sequencing technologies have revealed that the lungs contain a variety of low biomass microbiota associated with various lung diseases. Rat model is an important tool to understand the possible causal relationship between pulmonary microbiota and diseases. Antibiotic exposure can alter the microbiota, however, a direct influence of long-term ampicillin exposure on commensal bacteria of healthy lungs has not been investigated, which could be useful in the study of the relation between microbiome and long-term lung diseases, especially in animal model-making of lung diseases.

METHODS

The rats were aerosolized ampicillin of different concentrations for five months, and then the effect on the lung microbiota was investigated using 16S rRNA gene sequencing.

RESULTS

The ampicillin treatment by a certain concentration (LA5, 0.2 ml of 5 mg/ml ampicillin) administration leads to profound changes in the rat lung microbiota but not in the low critical ampicillin concentration (LA01 and LA1, 0.1 and 1 mg/ml ampicillin), when compared to the untreated group (LC). The genus Acidobacteria_Gp16 dominated the ampicillin treated lung microbiota while the genera Brucella, Acinetobacter, Acidobacteria_Gp14, Sphingomonas, and Tumebacillus dominated the untreated lung microbiota. The predicted KEGG pathway analysis profile revealed some difference in the ampicillin treated group.

CONCLUSIONS

The study demonstrated the effects of different concentrations of ampicillin treatment on lung microbiota of rats in a relatively long term. It could serve as a basis for the clinical use of antibiotic and the use of ampicillin to control certain bacteria in the animal model-making of respiratory diseases such as chronic obstructive pulmonary disease.

Accumulation and risk assessment of antibiotics in edible plants grown in contaminated farmlands: A review

The extensive occurrence of antibiotics in farmland soil might threaten food safety. The bioaccumulation potential of antibiotics in edible vegetables and crops grown under realistic farming scenarios was reviewed and the human health risk was assessed. A total of 51 antibiotics were documented in 37 species of daily consumed crops. Among different classes of antibiotics, tetracyclines (TCs) exhibited higher residue levels in plants than quinolones (QNs), sulfonamides (SAs), and macrolides (MLs), with median values ranging from 5.10 to 15.4 μg/kg dry weight. The favored accumulation of TCs in plants was probably linked to their relatively higher residual concentrations in soils and greater bioconcentration factors. Compared with the plants grown in open field, accumulation of antibiotics was higher in plant grown under greenhouse condition, probably due to the higher residue levels of antibiotics in the greenhouse soil with intensive application of manure. Cocktails of antibiotics were investigated in potato, corn, carrot, tomato, lettuce, and wheat. Among them, corn exhibited relatively high median concentrations of antibiotics (0.400-203 μg/kg dry weight). Antibiotics tended to accumulate in plant root and their concentrations in fruit were generally low. Risk assessment revealed that human health risk was under the alert line through the daily consumption of antibiotic contaminated vegetables and food crops.

Domestic refrigerators: An overlooked breeding ground of antibiotic resistance genes and pathogens

Domestic refrigerator is a widely used appliance to keep food fresh and retard food spoilage in household. However, our understanding of microbial health risk associated with food under such circumstance still remains very poor. Here, typical types of food (vegetable, fish, and pork) were kept in a domestic refrigerator at 4 °C for 3-30 days. Temporal dynamics of antibiotic resistome, pathogens, bacterial and fungal communities during this period were investigated via high-throughput quantification and Illumina sequencing technologies. Results showed that a large number (21-134) of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were detected across the three food types, including 10.06 % of high-risk ARGs classified by their risk ranks. Moreover, four bacterial pathogens (i.e., Bacillus cereus, Cronobacter spp., Klebsiella pneumoniae and Staphylococcus aureus) targeted by marker genes including the pathogen-specific genes or virulence factor genes, and some potential fungal pathogens (e.g., Fusarium, Candida, and Aspergillus) were detected, indicating the occurrence of microbial risk even at the normally regarded safe storage temperature. Among all food types, the total bacterial density and ARG abundances in fish rapidly increased after only 3 days, much faster than vegetable and pork after 10 days. In addition, fish samples contained the highest ARG and pathogen abundances, indicating its potentially higher health risk than other food types. Finally, the shifts of ARG pattern were mainly contributed by bacterial communities and MGEs. This study highlights that food preserved in refrigerator at 4 °C could still be an unneglected microbial risk, and raises awareness of improving food safety in domestic environment.

Antibiotic resistant bacteria: A bibliometric review of literature

Antibiotic-resistant bacteria (ARB) are a serious threat to the health of people and the ecological environment. With this problem becoming more and more serious, more countries made research on the ARB, and the research number has been sharply increased particularly over the past decade. Therefore, it is quite necessary to globally retrace relevant researches on the ARB published from 2010 to 2020. This will help researchers to understand the current research situation, research trends and research hotspots in this field. This paper uses bibliometrics to examine publications in the field of ARB from 2010 to 2020 that were retrieved from the Web of Science (WOS). Our study performed a statistical analysis of the countries, institutions, journals, authors, research areas, author keywords, Essential Science Indicators (ESI) highly cited papers, and ESI hotspots papers to provide an overview of the ARB field as well as research trends, research hotspots, and future research directions in the field. The results showed that the number of related studies is increasing year by year; the USA is most published in the field of ARB; China is the most active in this field in the recent years; the Chinese Acad Sci published the most articles; Sci. Total Environ. published the greatest number of articles; CM Manaia has the most contributions; Environmental Sciences and Ecology is the most popular research area; and "antibiotic resistance," "antibiotics," and "antibiotic resistance genes" were the most frequently occurring author keywords. A citation analysis showed that aquatic environment-related antibiotic resistance is a key research area in this field, while antimicrobial nanomaterial-related research is a recent popular topic.

The variations of antibiotics and antibiotic resistance genes in two subtropical large river basins of south China: Anthropogenic impacts and environmental risks

Emission of antibiotics into riverine environments affects aquatic ecosystem functions and leads to the development of antibiotic resistance. Here, the profiles of forty-four antibiotics and eighteen antibiotic resistance genes (ARGs) were analyzed in two large rivers of the Pearl River System. In addition, the risks of ecotoxicity and resistance selection posed by the antibiotics were estimated. As compared to the reservoirs, the river sections close to the urban and livestock areas contained more antibiotics and ARGs. Seasonal variations of antibiotics (higher in the dry season) and relative ARGs (normalized by 16S rRNA gene, higher in the wet season) were found in the water, but not in the sediment. Sulfonamide resistance genes were the most prevalent ARGs in both river water and sediment. Antibiotic concentration was correlated with ARG abundance in the water, indicating that antibiotics play a critical role in ARG spread. In addition, oxytetracycline was the most abundant antibiotic with concentrations up to 2030 ng/L in the water and 2100 ng/g in the sediment respectively, and posed the highest risks for resistance selection. Oxytetracycline, tetracycline and sulfamethoxazole were expected to be more ecotoxicologically harmful to aquatic organisms, while ofloxacin, enrofloxacin, norfloxacin, chlortetracycline, oxytetracycline and tetracycline posed ecotoxicological risks in the sediment. The Nanliujiang river with intensive livestock activities was contaminated by antibiotics and ARGs and faced high ecotoxicological and resistance selection risks. Collectively, these findings reflect the impacts of anthropogenic activities on the spread of antibiotic resistance in large river basins.

High concentration of ammonia sensitizes the response of microbial electrolysis cells to tetracycline

Microbial electrolysis cell (MEC) is a promising technology for effective energy conversion of wastewater organics to biogas. Yet, in swine wastewater treatment, the complex contaminants including antibiotics may affect MEC performance, while the high ammonia concentration might increase this risk by increasing cell membrane permeability. In this work, the responses of MECs on tetracycline (TC) with low and high ammonia loadings (80 and 1000 mg L^-1) were fully investigated. The TC of 0 to 1 mg L^-1 slightly improved MEC performance in current production and electrochemical characteristics with low ammonia loading, while TC ≥ 4 mg L^-1 started to show negative effects. Generally, the high ammonia loading sensitized MECs to TC concentration, inducing the current and COD removal of MECs to sharply decline with TC ≥ 0.5 mg L^-1. The positive effect of high ammonia loading on MEC due to conductivity increase was counteracted with TC ≥ 1 mg L^-1. The co-contamination of TC and ammonia significantly decreased the bioactivity and biomass of anode biofilm. Although the high concentration of co-existing TC and ammonia inhibited MEC performance, the reactors still obtained positive energy feedback. The network analyses indicated that the effluent suspension contributed much to antibiotic resistance gene (ARG) transmission, while the microplastics (MPs) in wastewater greatly raised the risks of ARGs spreading. This work systematically examined the synergetic effects of TC and ammonia and the transmission of ARGs in MEC operation, which is conducive to expediting the application of MECs in swine wastewater treatment.

Effects of g-C3N4 on bacterial community and tetracycline resistance genes in two typical sediments in tetracycline pollution remediation

Photocatalysis, as a novel technique, has been widely used for antibiotic pollution remediation in wastewater. In the processes of degradation and removal of antibiotics, the impact of photocatalysts on microenvironment is very important but remains poorly understood. In the present study, the effect of typical photocatalyst g-C3N4 (Graphitic carbon nitride) on microbial community was investigated in two sediment types (riverbed sediment and pig-farm sediment) polluted by tetracycline (TC) in central southern China. The riverbed sediment and pig farm sediment samples were respectively exposed to g-C3N4 (25, 75, 125 mg⋅kg-1) and TC (60, 120, 180 mg⋅L-1) treatments alone or combination for 30 days, respectively. The bacterial community and antibiotic resistance genes (ARGs) of the treated sediments were analyzed by Illumina sequencing and metagenomic sequencing. Studies had shown that: TC, g-C3N4, and TC/g-C3N4 have significant effects on the changes of microbial communities and components in riverbed sediment, but they do not exist in pig farm sediment. The most alterations of microbial taxa were Acidobacteriota, Actinobacteriota, and Desulfobacterota in riverbed sediment, and Elusimicrobiota in the pig farm sediment under various treatments. Through network analysis, it was found that the distribution of microorganisms in the pig farm sediment is more complex and more stable. The addition of g-C3N4 reduced the absolute abundance of ARGs in the two examined sediments, but not significantly changed their relative abundance of ARGs. The g-C3N4 application was beneficial to the removal of TC residues and to the prevention of the generation and transmission of ARGs in sediments. Our results suggested that g-C3N4 was a suitable photocatalyst with excellent application prospect for the removal of TC residues and the control of ARGs in environment.

Fate and exposure risk of florfenicol, thiamphenicol and antibiotic resistance genes during composting of swine manure

Livestock manure is an important source of antibiotic resistance genes (ARGs) spreading to the environment, posing a potential threat to human health. Here, we investigated the dissipation of florfenicol (FF) and thiamphenicol (TAP), and their effects on the bacterial community, mobile genetic elements (MGEs), and ARGs during composting. The results indicated that FF and TAP dissipated rapidly in compost, with half-life values of 5.1 and 1.6 d, respectively. However, FF could not be completely removed during composting. The FF and TAP residues in manure could reduce the elimination of ARGs and MGEs during composting, and had a negative effect on the physicochemical factors of the compost. Significant correlations were found between floR and intI1, indicating that floR in manure may more easily diffuse to the soil environment. Meanwhile, the presence of FF in manure could increase the abundance of floR. Network analysis showed that Proteobacteria and Firmicutes were the dominant bacterial communities and important potential pathogen hosts carrying ARGs. The predicted environmental concentration of FF in the soil was over 100 μg kg^-1, which indicates that FF poses a potential risk to the natural environment, and we verified this result through field experiments. The results showed that FF dissipated in the soil after it migrated from manure to soil. In contrast, TAP in manure posed lower environmental risk. This study highlights that changed in composting conditions may control the rate of removal of ARGs. Further studies are needed to investigate the best environmental conditions to achieve a faster degradation of FF and a more comprehensive elimination of ARGs during composting.

Joint effects of bacterium and biochar in remediation of antibiotic-heavy metal contaminated soil and responses of resistance gene and microbial community

Soils containing both veterinary antibiotics (VAs) and heavy metals necessitate effective remediation approaches, and microbial and molecular levels of the results should be further examined. Here, a novel material combining waste fungus chaff-based biochar (WFCB) and Herbaspirillum huttiense (HHS1) was established to immobilize copper (Cu) and zinc (Zn) and degrade oxytetracycline (OTC) and enrofloxacin (ENR). Results showed that the combined material exhibited high immobilization of Cu (85.5%) and Zn (64.4%) and great removals of OTC (41.9%) and ENR (40.7%). Resistance genes including tet(PB), tetH, tetR, tetS, tetT, tetM, aacA/aphD, aacC, aadA9, and czcA were reduced. Abundances of potential hosts of antibiotic resistance genes (ARGs) including phylum Proteobacteria and genera Brevundimonas and Rhodanobacter were altered. Total phosphorus and pH were the factors driving the VA degrading microorganisms and potential hosts of ARGs. The combination of WFCB and HHS1 can serve as an important bioresource for immobilizing heavy metals and removing VAs in the contaminated soil.

Manure application: A trigger for vertical accumulation of antibiotic resistance genes in cropland soils

The application of livestock manure increases the dissemination risk of antibiotic resistance genes (ARGs) in farmland soil environment. However, the vertical migration behavior and driving factor of ARGs in manured soil under swine manure application remains undefined. Here, the dynamics of ARGs, mobile genetic elements (MGEs) and bacterial communities in different soil depths (0 - 80 cm) with long-term swine manure application were tracked and conducted using real-time qPCR. Results showed that long-term application of swine manure remarkably facilitated the vertical accumulation of ARGs and MGEs, in particular that the relative abundance of bla_ampC showed significant enrichment with increasing depth. ARGs abundance was similar in the three fields with long-term application of swine manure. (p＞0.05). Procrustes analysis indicated that microbial communities were the dominant drivers of ARGs variation in topsoil, and the changes of environmental factors played a vital role in vertical migration ARGs in cropland soils. Additionally, the variation patterns of high-risk ARGs (i.e., bla_ampC, bla_TEM-1) were influenced by the dominant bacteria (Actinomycetes) and pH. This study illustrated that the swine manure application promoted the vertical migration of ARGs, including multidrug resistance determinants, highlighting the ecological risk caused by long-term manure application.

Effect of g-C3N4 on biodiversity and structure of bacterial community in sediment of Xiangjiang River under tetracycline pressure

Photocatalysts have been widely prepared and used in wastewater treatment. Although the influence of photocatalyst application on survival and activity of organisms has been examined, its impact on composition and diversity of microbial community is not fully understood. In this study, the impact of photocatalyst g-C₃N₄ (Graphitic carbon nitride) on microbial communities in riverbed sediments polluted by antibiotic tetracycline (TC) was investigated. The sediment samples collected from the Xiangjiang River of China were exposed to different concentrations of TC, g-C₃N₄ and TC/g-C₃N₄ and the bacterial community were analyzed by Illumina sequencing. The results showed that the dominant bacterial phyla were Acidobacteriota, Proteobacteria, Actinobacteriota, and Chloroflexi in the study site. When compared to the control treatments, the application of TC, g-C₃N₄ and TC/g-C₃N₄ exhibited distinguishable effects on bacterial community structure in sediments. The presence of TC had greater influence on bacterial composition, while g-C₃N₄ and TC/g-C₃N₄ had less influence on bacteria. The diversity and richness of microorganisms in sediment increased under g-C₃N₄ application and reached the highest values when g-C₃N₄ was 75 mg/kg. The photocatalyst g-C₃N₄ restored bacterial community diversity affected by TC, reduced the TC residues in aquatic environment, and eliminated the side effects of TC application in sediments. Our study indicated that g-C₃N₄ was an environmentally friendly photocatalyst with lightly negative effects on microbial community in riverbed sediments, and could be used for effective remediation of TC-contaminated environments.

Implications of the use of organic fertilizers for antibiotic resistance gene distribution in agricultural soils and fresh food products. A plot-scale study

The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In order to help designing agricultural practices that minimize the spread of ARG, we fertilized, sown, and harvested lettuces and radish plants in experimental land plots for two consecutive agricultural cycles using four types of fertilizers: mineral fertilization, sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) identified a small, but significant overlap (<10%) between soil's and fertilizer microbiomes. Clinically relevant ARG were found in higher loads (up to 100 fold) in fertilized soils than in the initial soil, particularly in those treated with organic fertilizers, and their loads grossly correlated to the amount of antibiotic residues found in the corresponding fertilizer. Similarly, low, but measurable ARG loads were found in lettuce (tetM, sul1) and radish (sul1), corresponding the lowest values to samples collected from minerally fertilized fields. Comparison of soil samples collected along the total period of the experiment indicated a relatively year-round stability of soil microbiomes in amended soils, whereas ARG loads appeared as unstable and transient. The results indicate that ARG loads in soils and foodstuffs were likely linked to the contribution of bacteria from organic fertilizer to the soil microbiomes, suggesting that an adequate waste management and good pharmacological and veterinarian practices may significantly reduce the presence of these ARGs in agricultural soils and plant products.

Swine manure facilitates the spread of antibiotic resistome including tigecycline-resistant tet(X) variants to farm workers and receiving environment

The prevalence of antibiotic resistance genes (ARGs) in livestock and poultry manure is a severe threat to human health. However, the comprehensive characterization of antibiotic resistance in swine, workers, and the receiving environment is still lacking in the actual breeding environment. Hence, the ARG profile and the potential bacterial hosts producing among swine manure (including sows, piglets, finishing pigs, and nursery pigs), worker feces, and the receiving environment (including sediment and vegetable soil) were comprehensively analyzed based on the metagenomic method. The results showed that swine manure exhibited the high levels of richness and diversity of ARGs. Inactivating tetracycline resistance genes such as tet(X), tet(X1), and tet(X10) were prevalent on swine farms. Workers and the environment were the primary recipients of ARGs, and shared ARGs accounted for at least 90% of their ARG abundances. Network analysis revealed that Escherichia, Acinetobacter, and Erysipelothrix were the most dominant genera co-occurring with specific shared ARGs. The abundance of coexisting ARGs in swine at different developmental stages accounted for 76.4% to 90.8% of the shared ARGs in swine, workers, and environmental samples. The Mantel test revealed that Firmicutes and Proteobacteria had a significant correlation with the ARG profiles. In addition, variation partitioning analysis (VPA) showed that the joint effects of mobile genetic elements (MGEs) and bacterial communities accounted for 24.7% of the resistome variation and played a significant role in the ARG profiles. These results improve our understanding of the transmission and persistence of ARGs in the actual breeding environment.

Characteristics and Global Occurrence of Human Pathogens Harboring Antimicrobial Resistance in Food Crops: A Scoping Review

Background

The role of the crop environment as a conduit for antimicrobial resistance (AMR) through soil, water, and plants has received less attention than other sectors. Food crops may provide a link between the agro-environmental reservoir of AMR and acquisition by humans, adding to existing food safety hazards associated with microbial contamination of food crops.

Objectives

The objectives of this review were: (1) to use a systematic methodology to characterize AMR in food crop value chains globally, and (2) to identify knowledge gaps in understanding exposure risks to humans.

Methods

Four bibliographic databases were searched using synonyms of AMR in food crop value chains. Following two-stage screening, phenotypic results were extracted and categorized into primary and secondary combinations of acquired resistance in microbes of concern based on established prioritization. Occurrence of these pathogen-AMR phenotype combinations were summarized by sample group, value chain stage, and world region. Sub-analyses on antimicrobial resistance genes (ARG) focused on extended-spectrum beta-lactamase and tetracycline resistance genes.

Results

Screening of 4,455 citations yielded 196 studies originating from 49 countries, predominantly in Asia (89 studies) and Africa (38). Observations of pathogen-phenotype combinations of interest were reported in a subset of 133 studies (68%). Primary combinations, which include resistance to antimicrobials of critical importance to human medicine varied from 3% (carbapenem resistance) to 13% (fluoroquinolones), whereas secondary combinations, which include resistance to antimicrobials also used in agriculture ranged from 14% (aminoglycoside resistance) to 20% (aminopenicillins). Salad crops, vegetables, and culinary herbs were the most sampled crops with almost twice as many studies testing post-harvest samples. Sub-analysis of ARG found similar patterns corresponding to phenotypic results.

Discussion

These results suggest that acquired AMR in opportunistic and obligate human pathogens is disseminated throughout food crop value chains in multiple world regions. However, few longitudinal studies exist and substantial heterogeneity in sampling methods currently limit quantification of exposure risks to consumers. This review highlights the need to include agriculturally-derived AMR in monitoring food safety risks from plant-based foods, and the challenges facing its surveillance.

The vertical migration of antibiotic-resistant genes and pathogens in soil and vegetables after the application of different fertilizers

The prevalence of bacterial resistance caused by the application of animal manure has become an important environmental issue. Herein, the vertical migration of antibiotic resistance genes (ARGs) and pathogens in soil and vegetables after the application of different fertilizers was explored. The results showed that the application of composted manure considerably enhanced the abundance of most ARGs and pathogens, especially in surface soil and pakchoi roots. Moreover, the soil ARGs increased partially from log 1.93 to log 4.65 after the application of composted manure, and six pathogens were simultaneously detected. It was observed that the increase in soil depth decreased most ARGs and pathogens by log 1.04-2.24 and 53.98 %~85.54 %, respectively. This indicated that ARGs and pathogens still existed in the deep soil (80-100 cm). Moreover, total organic carbon had a significant influence on the pathogen distribution, whereas bacterial communities primarily drove the vertical migration of ARGs rather than environmental factors. Although most of the ARG-host associations observed in the surface soil were disappeared in deep soil as revealed by network analysis, some co-occurrence pattern still occurred in deep soil, suggesting that some ARGs might be carried to deep soil by their host bacteria. These results were novel in describing the vertical migration of ARGs in the environment after the application of different fertilizers, providing ideas for curbing their migration to crops.

Investigation of the microbial community structure and diversity in the environment surrounding a veterinary antibiotic production factory

The ecological toxicity caused by antibiotic residues and resistance genes in the environment affects the community structures and activities of environmental microorganisms; the ecological toxicity effects of a long-term exposure to low doses antibiotic residues on microorganisms have not however been well-studied. In this work, sequence analysis and species annotation of the full-length 16S rRNA gene were carried out on the extracted whole genome by a 3-generation sequencing method to analyze the diversity of the microbial populations and the population differences among different sampling sites in the environment surrounding a veterinary antibiotic production factory. A total of 1720 OTUs (Operational Taxonomic Unit, OTU) were found, of which 1055 OTUs were in the river samples and 993 OTUs were in the soil samples. 643 and 438 bacterial strains were identified in the river water and soil samples respectively. The bacterial populations are classified into 29 phylum, 612 genus, and 849 species. The dominant phylum of bacteria was Proteobacteria, which was also the absolutely dominant phylum. Shannon diversity index of the bacteria showed that the bacterial abundance in downstream river was significantly higher than that in an upstream non-polluted area (P < 0.001), but the difference of bacterial abundance between soil samples was not significant. There were 61 biomarkers in the river water samples from different sampling points, and 14 biomarkers in soil samples. It was found by the difference statistics of the microbial community that there are multiple biomarkers between this veterinary drug production site and the upstream non-polluted area. Significant differences between multiple functional genes were also found in metabolic pathways of the microorganisms. A similar trend was found for the distribution of antibiotic resistance genes (ARGs). It is concluded that the population composition of microorganisms and diversity are likely related to antibiotic residues and to the distributions of ARGs in the environment surrounding the antibiotic production factory.

Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system

The application of manure compost may cause the transmission of antibiotic resistance genes (ARGs) in agroecological environment, which poses a global threat to public health. However, the driving factors for the transmission of ARGs from animal manure to agroecological systems remains poorly understood. Here, we explored the spatiotemporal variation in ARG abundance and bacterial community composition as well as relative driving factors in a soil-lettuce system amended with swine manure compost. The results showed that ARGs abundance had different variation trends in soil, lettuce phylloplane and endophyere after the application of swine manure compost. The temporal variations of total ARGs abundance had no significant different in soil and lettuce phylloplane, while lettuce endosphere enriched half of ARGs to the highest level at harvest. There was a significant linear correlation between ARGs and integrase genes (IGs). In contrast to the ARGs variation trend, the alpha diversity of soil and phylloplane bacteria showed increasing trends over planting time, and endosphere bacteria remained stable. Correlation analysis showed no identical ARG-related genera in the three parts, but the shared Proteobacteria, Pseudomonas, Halomonas and Chelativorans, from manure compost dominated ARG profile in the soil-lettuce system. Moreover, redundancy analysis and structural equation modelling showed the variations of ARGs may have resulted from the combination of multiple driving factors in soil-lettuce system. ARGs in soil were more affected by the IGs, antibiotic and heavy metals, and bacterial community structure and IGs were the major influencing factors of ARG profiles in the lettuce. The study provided insight into the multiple driving factors contribute to the variations of typical ARGs in different parts of soil-lettuce system, which was conducive to the risk assessment of ARGs in agroecosystem and the development of effective prevention and control measures for ARGs spread in the environment.

Antibiotic Resistance: From Pig to Meat

Pork meat is in high demand worldwide and this is expected to increase. Pork is often raised in intensive conditions, which is conducive to the spread of infectious diseases. Vaccines, antibiotics, and other biosafety measures help mitigate the impact of infectious diseases. However, bacterial strains resistant to antibiotics are more and more frequently found in pig farms, animals, and the environment. It is now recognized that a holistic perspective is needed to sustainably fight antibiotic resistance, and that an integrated One Health approach is essential. With this in mind, this review tackles antibiotic resistance throughout the pork raising process, including their microbiome; many factors of their environment (agricultural workers, farms, rivers, etc.); and an overview of the impact of antibiotic resistance on pork meat, which is the end product available to consumers. Antibiotic resistance, while a natural process, is a public health concern. If we react, and act, collectively, it is expected to be, at least partially, reversible with judicious antibiotic usage and the development of innovative strategies and tools to foster animal health.

Transmission Routes of the Microbiome and Resistome from Manure to Soil and Lettuce

The land application of animal manure can introduce manure microbiome and resistome to croplands where food crops are grown. The objective of this study was to characterize the microbiome and resistome on and in the leaves of lettuce grown in manured soil and identify the main transmission routes of microbes and antibiotic resistance genes (ARGs) from soil to the episphere and endosphere of lettuce. Shotgun metagenomic results show that manure application significantly altered the composition of the microbiome and resistome of surface soil. SourceTracker analyses indicate that manure and original soil were the main source of the microbiome and resistome of the surface soil and rhizosphere soil, respectively. Manure application altered the microbiome and resistome in the episphere of lettuce (ADONIS p < 0.05), and surface soil accounted for ∼81% of the microbes and ∼62% of the ARGs in episphere. Manure application had limited impacts on the microbiome and resistome in the endosphere (ADONIS p > 0.05). Our results show that manure-borne microbes and ARGs reached the episphere primarily through surface soil and some epiphytic microbes and ARGs further entered the endosphere. Our findings can inform the development of pre- and postharvest practices to minimize the transmission of manure-borne resistome from food crops to consumers.

An overview on endophytic bacterial diversity habitat in vegetables and fruits

Nowadays, scientific research revolution is going on in many areas, and the human health is one of them. However, in the earlier studies, it was observed that most of the people health in the world affects by consumptions of contaminated food which is dangerous for human health and country economy. Recent studies showed that the fresh vegetables and fruits are the major habitat for endophytic bacterial communities. Salmonella and Escherichia coli both are the very common bacteria founds in fresh vegetables and fruits. Generally, many people eat vegetables and fruits without cooking (in the form of salad). The continued assumption of such food increases the health risk factor for foodborne diseases. So, from the last decades, many researchers working to understand about the relationship of endophytic microbes with plants either isolated bacteria are pathogenic or nonpathogenic. Moreover, most of the endophytes were identified by using 16S rRNA sequencing method. Hence, this review elaborates on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. Furthermore, it is emphasized on the environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathogenesis.

Fate of antibiotic resistance genes in farmland soil applied with three different fertilizers during the growth cycle of pakchoi and after harvesting

The increasing prevalence of antibiotic resistance genes (ARGs) in the soil environment poses a serious threat to crop safety and even public health. In this study, the fate of ARGs in the soil was investigated during the growth period of pakchoi and after harvesting with the application of different kinds of fertilizers. The result showed that increasing rate of soil ARGs during the growth period of pakchoi followed the order of composted manure > commercial fertilizer > mineral fertilizer. After harvesting, soil ARGs abundance treated with mineral fertilizer, commercial fertilizer or composted manure significantly increased by 0.63, 3.19 and 8.65 times (p < 0.05), respectively, compared with the non-fertilized soil. The ARGs abundance in the pakchoi treated with composted manure was significantly higher than that of treatments with mineral fertilizer and commercial organic fertilizer. These findings indicated the application of composted pig manure would significantly increase the pollution load of ARGs in farmland soil and plant, and also promote the proliferation of farmland ARGs. Principal component analysis suggested that bacterial communities might have a significant influence on ARGs changes during the growth period of pakchoi. Network analysis further indicated ARGs changes may be mainly related to their host bacteria (including Gammaproteobacteria, Flavobacteriia and Bacilli). The results provided a proper method and useful information on reducing transmission risk of ARGs and control the propagation of ARGs in agricultural activities.

Effects of two ecological earthworm species on tetracycline degradation performance, pathway and bacterial community structure in laterite soil

This study explored the change of tetracycline degradation efficiency, metabolic pathway, soil physiochemical properties and degraders in vermiremediation by two earthworm species of epigeic Eisenia fetida and endogeic Amynthas robustus. We found a significant acceleration of tetracycline degradation in both earthworm treatments, and 4-epitetracycline dehydration pathway was remarkably enhanced only by vermiremediation. Tetracycline degraders from soils, earthworm intestines and casts were different. Ralstonia and Sphingomonas were potential tetracycline degraders in soils and metabolized tetracycline through direct dehydration pathway. Degraders in earthworm casts (Comamonas, Acinetobacter and Stenotrophomonas) and intestines (Pseudomonas and Arthrobacter) dehydrated 4-epitetracycline into 4-epianhydrotetracycline. More bacterial lineages resisting tetracycline were found in earthworm treatments, indicating the adaptation of soil and intestinal flora under tetracycline pressure. Earthworm amendment primarily enhanced tetracycline degradation by neutralizing soil pH and consuming organic matters, stimulating both direct dehydration and epimerization-dehydration pathways. Our findings proved that vermicomposting with earthworms is effective to alter soil microenvironment and accelerate tetracycline degradation, behaving as a potential approach in soil remediation at tetracycline contaminated sites.

Elimination of antibiotic resistance genes from excess activated sludge added for effective treatment of fruit and vegetable waste in a novel vermireactor

Elimination of antibiotic resistance genes (ARGs) from excess activated sludge (EAS) mixed for effective treatment of different fruit and vegetable waste (FVW) by using a novel vermireactor consisted of substrate and bed compartments was investigated. ARGs (tet G, tet M and sul 1) and mobile genetic element gene (intl 1) were targeted and, through quantitative analysis of their abundances in both the compartments and the fresh cast of earthworms, significant reductions in substrate compartments were confirmed for the treatments for FVW added with EAS and EAS alone even if the reduction extents differed among the types of FVW. Apparent reductions were not found in the bed compartment where the final products accumulated. For the fresh cast, the relative abundances of ARGs and intl 1 against to the total bacterial 16S rDNA decreased markedly. The present study provided an insight for proper controlling of ARGs during vermicomposting of FVW and EAS.