Role of Horizontal Gene Transfer in the Dissemination of Antimicrobial Resistance in Food Animal Production

Salmonella spp. in Domestic Ruminants, Evaluation of Antimicrobial Resistance Based on the One Health Approach-A Systematic Review and Meta-Analysis

Salmonella spp. pose a global threat as a leading cause of foodborne illnesses, particularly prevalent in the European Union (EU), where it remains the second cause of foodborne outbreaks. The emergence of antimicrobial resistance (AMR) in Salmonella spp. has become a critical concern, complicating treatment strategies and escalating the risk of severe infections. The study focuses on large and small ruminants, identifying a prevalence of Salmonella spp. in slaughterhouses and revealing varied AMR rates across antimicrobial families throughout a meta-analysis. Also, comparison with AMR in human medicine was carried out by a systematic review. The results of the present meta-analysis displayed a prevalence of Salmonella spp. in large and small ruminants at slaughterhouses of 8.01% (8.31%, cattle; 7.04%, goats; 6.12%, sheep). According to the AMR of Salmonella spp., 20, 14, and 13 out of 62 antimicrobials studied were classified as low (<5%), high (>5% but <10%), and very high (>10%), respectively. Salmonella spp. did not display AMR against aztreonam, mezlocillin, ertapenem, meropenem, cefoxitin, ceftazidime, levofloxacin, tilmicosin, linezolid, fosfomycin, furazolidone, quinupristin, trimethoprim and spectinomycin. In contrast, a prevalence of 100% of AMR has been described against ofloxacin, lincomycin, and cloxacillin. In the context of the main antibiotics used in the treatment of human salmonellosis, azithromycin was shown to have the highest resistance among Salmonella spp. isolates from humans. Regarding cephalosporins, which are also used for the treatment of salmonellosis in humans, the prevalence of Salmonella spp. resistance to this class of antibiotics was similar in both human and animal samples. Concerning quinolones, despite a heightened resistance profile in Salmonella spp. isolates from ruminant samples, there appears to be no discernible compromise to the efficacy of salmonellosis treatment in humans since lower prevalences of AMR in Salmonella spp. isolated from human specimens were observed. Although the resistance of Salmonella spp. indicates some degree of concern, most antibiotics are not used in veterinary medicine. Thus, the contribution of cattle, sheep and goats to the rise of antibiotic resistance of Salmonella spp. and its potential impact on public health appears to be relatively insignificant, due to their low prevalence in carcasses and organs. Nevertheless, the observed low prevalence of Salmonella spp. in ruminants at slaughterhouse and the correspondingly low AMR rates of Salmonella spp. to key antibiotics employed in human medicine do not indicate that ruminant livestock poses a substantial public health risk concerning the transmission of AMR. Thus, the results observed in both the meta-analysis and systematic review suggests that AMR is not solely attributed to veterinary antibiotic use but is also influenced by factors such as animal health management (i.e., biosecurity measures, prophylactic schemes) and human medicine.

Effect of chemotherapeutic agents on natural transformation frequency in Acinetobacter baylyi

Natural transformation is the ability of a bacterial cell to take up extracellular DNA which is subsequently available for recombination into the chromosome (or maintenance as an extrachromosomal element). Like other mechanisms of horizontal gene transfer, natural transformation is a significant driver for the dissemination of antimicrobial resistance. Recent studies have shown that many pharmaceutical compounds such as antidepressants and anti-inflammatory drugs can upregulate transformation frequency in the model species Acinetobacter baylyi. Chemotherapeutic compounds have been shown to increase the abundance of antimicrobial resistance genes and increase colonization rates of potentially pathogenic bacteria in patient gastrointestinal tracts, indicating an increased risk of infection and providing a pool of pathogenicity or resistance genes for transformable commensal bacteria. We here test for the effect of six cancer chemotherapeutic compounds on A. baylyi natural transformation frequency, finding two compounds, docetaxel and daunorubicin, to significantly decrease transformation frequency, and daunorubicin to also decrease growth rate significantly. Enhancing our understanding of the effect of chemotherapeutic compounds on the frequency of natural transformation could aid in preventing the horizontal spread of antimicrobial resistance genes.

Environmentally Relevant Concentrations of Tetracycline Promote Horizontal Transfer of Antimicrobial Resistance Genes via Plasmid-Mediated Conjugation

The ubiquitous presence of antimicrobial-resistant organisms and antimicrobial resistance genes (ARGs) constitutes a major threat to global public safety. Tetracycline (TET) is a common antimicrobial agent that inhibits bacterial growth and is frequently detected in aquatic environments. Although TET may display coselection for resistance, limited knowledge is available on whether and how it might influence plasmid-mediated conjugation. Subinhibitory concentrations (3.9-250 ng/mL) of TET promoted horizontal gene transfer (HGT) via the mobilizable plasmid pVP52-1 from the donor Vibrio parahaemolyticus NJIFDCVp52 to the recipient Escherichia coli EC600 by 1.47- to 3.19-fold. The transcription levels of tetracycline resistance genes [tetA, tetR(A)], conjugation-related genes (traA, traD), outer membrane protein genes (ompA, ompK, ompV), reactive oxygen species (ROS)-related genes (oxyR, rpoS), autoinducer-2 (AI-2) synthesis gene (luxS), and SOS-related genes (lexA, recA) in the donor and recipient were significantly increased. Furthermore, the overproduced intracellular ROS generation and increased cell membrane permeability under TET exposure stimulated the conjugative transfer of ARGs. Overall, this study provides important insights into the contributions of TET to the spread of antimicrobial resistance.

Protecting the Last Line of Defense: Analytical Approaches for Sample Preparation and Determination of the Reserve Group of Antibiotics in the Environment

Drug resistance in microorganisms is a serious threat to life and health due to the limited number of antibiotics that show efficacy in treating infections and the difficulty in discovering new compounds with antibacterial activity. To address this issue, the World Health Organization created the AWaRe classification, a tool to support global and national antimicrobial stewardship programs. The AWaRe list categorizes antimicrobials into three groups - Access, Watch, and Reserve - according to their intended use. The Reserve group comprises "last resort" medicines used solely for treating infections caused by bacterial strains that are resistant to other treatments. It is therefore necessary to protect them, not only by using them as prudently as possible in humans and animals, but also by monitoring their subsequent fate. Unmetabolized antibiotics enter the environment through hospital and municipal wastewater or from manure, subsequently contaminating bodies of water and soils, thus contributing to the emergence and spread of antibiotic resistance. This article presents a review of determination methods for the Reserve group of antimicrobials in water, wastewater, and manure. Procedures for extracting and determining these substances in environmental samples are described, showing the limited research available, which is typically on a local level.

Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle

A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals' gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG, P < 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.IMPORTANCEThe increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals' performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.

Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids

BACKGROUND

The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.

RESULTS

In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.

CONCLUSIONS

Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.

The antibiotic resistance reservoir of the lung microbiome expands with age in a population of critically ill patients

Antimicrobial resistant lower respiratory tract infections are an increasing public health threat and an important cause of global mortality. The lung microbiome can influence susceptibility of respiratory tract infections and represents an important reservoir for exchange of antimicrobial resistance genes. Studies of the gut microbiome have found an association between age and increasing antimicrobial resistance gene burden, however, corollary studies in the lung microbiome remain absent. We performed an observational study of children and adults with acute respiratory failure admitted to the intensive care unit. From tracheal aspirate RNA sequencing data, we evaluated age-related differences in detectable antimicrobial resistance gene expression in the lung microbiome. Using a multivariable logistic regression model, we find that detection of antimicrobial resistance gene expression was significantly higher in adults compared with children after adjusting for demographic and clinical characteristics. This association remained significant after additionally adjusting for lung bacterial microbiome characteristics, and when modeling age as a continuous variable. The proportion of adults expressing beta-lactam, aminoglycoside, and tetracycline antimicrobial resistance genes was higher compared to children. Together, these findings shape our understanding of the lung resistome in critically ill patients across the lifespan, which may have implications for clinical management and global public health.

Ningalins, Pyrrole-Bearing Metabolites Isolated from Didemnum spp. Synthesis and MDR-Reversion Activity in Cancer Therapy

Multi-Drug Resistance (MDR) is one of the most frequent problems observed in the course of cancer chemotherapy. Cells under treatment, tend to develop survival mechanisms to drug-action thus generating drug-resistance. One of the most important mechanism to get it is the over expression of P-gp glycoprotein, which acts as an efflux-pump releasing the drug outside of the cancer cell. A strategy for a succesfull treatment consists in the co-administration of one compound that acts against P-gp and another which acts against the cell during chemotherapy. Ningalins are pyrrole-containing naturally occurring compounds isolated mainly from the marine tunicate Didemnum spp and also they are some of the top reversing agents in MDR treatment acting on P-gp. Considering the relevance displayed for some of these isolated alkaloids or their core as a drug for co-administration in cancer therapy, all the total synthesis described to date for the members of ningalins family are reviewed herein.

Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes

Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.

Global trends in antimicrobial resistance on organic and conventional farms

The important hypothesis that organic livestock management reduces the prevalence of antimicrobial resistance is either fiercely supported or bitterly contested. Yet, empirical evidence supporting this view remains fragmentary, in part because relationships between antimicrobial use and drug resistance vary dramatically across contexts, hosts, pathogens, and country-specific regulations. Here, we synthesize global policies and definitions of 'organic' and ask if organic farming results in notable reductions in the prevalence of antimicrobial resistance when directly examined alongside conventional analogs. We synthesized the results of 72 studies, spanning 22 countries and five pathogens. Our results highlight substantial variations in country-specific policies on drug use and definitions of 'organic' that hinder broad-scale and generalizable patterns. Overall, conventional farms had slightly higher levels of antimicrobial resistance (28%) relative to organic counterparts (18%), although we found significant context-dependent variation in this pattern. Notably, environmental samples from organic and conventional farms often exhibited high levels of resistance to medically important drugs, underscoring the need for more stringent and consistent policies to control antimicrobial contaminants in the soil (particularly on organic farms, where the application of conventional manure could faciliate the spread antimicrobial resistance). Taken together, these results emphasize the challenges inherent in understanding links between drug use and drug resistance, the critical need for global standards governing organic policies, and greater investment in viable alternatives for managing disease in livestock.

Methicillin Resistant Staphylococcus aureus: Molecular Mechanisms Underlying Drug Resistance Development and Novel Strategies to Combat

Antimicrobial resistance (AMR) represents a major threat to global health. Infection caused by Methicillin-resistant Staphylococcus aureus (MRSA) is one of the well-recognized global public health problem globally. In some regions, as many as 90% of S. aureus infections are reported to be MRSA, which cannot be treated with standard antibiotics. WHO reports indicated that MRSA is circulating in every province worldwide, significantly increasing the risk of death by 64% compared to drug-sensitive forms of the infection which is attributed to its antibiotic resistance. The emergence and spread of antibiotic-resistant MRSA strains have contributed to its increased prevalence in both healthcare and community settings. The resistance of S. aureus to methicillin is due to expression of penicillin-binding protein 2a (PBP2a), which renders it impervious to the action of β-lactam antibiotics including methicillin. The other is through the production of beta-lactamases. Although the treatment options for MRSA are limited, there are promising alternatives to antibiotics to combat the infections. Innovative therapeutic strategies with wide range of activity and modes of action are yet to be explored. The review highlights the global challenges posed by MRSA, elucidates the mechanisms underlying its resistance development, and explores mitigation strategies. Furthermore, it focuses on alternative therapies such as bacteriophages, immunotherapy, nanobiotics, and antimicrobial peptides, emphasizing their synergistic effects and efficacy against MRSA. By examining these alternative approaches, this review provides insights into the potential strategies for tackling MRSA infections and combatting the escalating threat of AMR. Ultimately, a multifaceted approach encompassing both conventional and novel interventions is imperative to mitigate the impact of MRSA and ensure a sustainable future for global healthcare.

Unveiling Rare Pathogens and Antibiotic Resistance in Tanzanian Cholera Outbreak Waters

The emergence of antibiotic resistance is a global health concern. Therefore, understanding the mechanisms of its spread is crucial for implementing evidence-based strategies to tackle resistance in the context of the One Health approach. In developing countries where sanitation systems and access to clean and safe water are still major challenges, contamination may introduce bacteria and bacteriophages harboring antibiotic resistance genes (ARGs) into the environment. This contamination can increase the risk of exposure and community transmission of ARGs and infectious pathogens. However, there is a paucity of information on the mechanisms of bacteriophage-mediated spread of ARGs and patterns through the environment. Here, we deploy Droplet Digital PCR (ddPCR) and metagenomics approaches to analyze the abundance of ARGs and bacterial pathogens disseminated through clean and wastewater systems. We detected a relatively less-studied and rare human zoonotic pathogen, Vibrio metschnikovii, known to spread through fecal--oral contamination, similarly to V. cholerae. Several antibiotic resistance genes were identified in both bacterial and bacteriophage fractions from water sources. Using metagenomics, we detected several resistance genes related to tetracyclines and beta-lactams in all the samples. Environmental samples from outlet wastewater had a high diversity of ARGs and contained high levels of blaOXA-48. Other identified resistance profiles included tetA, tetM, and blaCTX-M9. Specifically, we demonstrated that blaCTX-M1 is enriched in the bacteriophage fraction from wastewater. In general, however, the bacterial community has a significantly higher abundance of resistance genes compared to the bacteriophage population. In conclusion, the study highlights the need to implement environmental monitoring of clean and wastewater to inform the risk of infectious disease outbreaks and the spread of antibiotic resistance in the context of One Health.

Long-term impacts of conservation pasture management in manuresheds on system-level microbiome and antibiotic resistance genes

Animal manure improves soil fertility and organic carbon, but long-term deposition may contribute to antibiotic resistance genes (ARGs) entering the soil-water environment. Additionally, long-term impacts of applying animal manure to soil on the soil-water microbiome, a crucial factor in soil health and fertility, are not well understood. The aim of this study is to assess: (1) impacts of long-term conservation practices on the distribution of ARGs and microbial dynamics in soil, and runoff; and (2) associations between bacterial taxa, heavy metals, soil health indicators, and ARGs in manures, soils, and surface runoff in a study following 15 years of continuous management. This management strategy consists of two conventional and three conservation systems, all receiving annual poultry litter. High throughput sequencing of the 16S ribosomal RNA was carried out on samples of cattle manure, poultry litter, soil, and runoff collected from each manureshed. In addition, four representative ARGs (intl1, sul1, ermB, and blactx-m-32) were quantified from manures, soil, and runoff using quantitative PCR. Results revealed that conventional practice increased soil ARGs, and microbial diversity compared to conservation systems. Further, ARGs were strongly correlated with each other in cattle manure and soil, but not in runoff. After 15-years of conservation practices, relationships existed between heavy metals and ARGs. In the soil, Cu, Fe and Mn were positively linked to intl1, sul1, and ermB, but trends varied in runoff. These findings were further supported by network analyses that indicated complex co-occurrence patterns between bacteria taxa, ARGs, and physicochemical parameters. Overall, this study provides system-level linkages of microbial communities, ARGs, and physicochemical conditions based on long-term conservation practices at the soil-water-animal nexus.

Genomic Characterization of a Tetracycline-Resistant Strain of Brochothrix thermosphacta Highlights Plasmids Partially Shared between Various Strains

The Gram-positive bacterium Brochothrix thermosphacta is a spoilage agent commonly found on meat products. While the tet(L) gene, which confers resistance to tetracycline, has been identified in certain strains of B. thermosphacta, only a limited number of studies have investigated this gene and its potential presence on mobile DNA elements. This study aims to analyze the tetracycline-resistant strain B. thermosphacta BT469 at the genomic level to gain insight into the molecular determinants responsible for this resistance. Three plasmids have been identified in the strain: pBT469-1, which contains a tetR gene; pBT469-2, which harbours the tet(L) gene responsible for tetracycline resistance; and pBT469-3, which carries genes encoding for a thioredoxin and a phospholipase A2. Homology searches among sequences in public databases have revealed that the plasmid pBT469-2 is currently unique to the BT469 strain. However, the pBT469-1 plasmid is also found in three other strains of B. thermosphacta. Notably, sequences similar to pBT469-1 and pBT469-2 were also found in other bacterial genera, suggesting that these plasmids may be part of a diverse family present in several bacterial genera. Interestingly, sequences of various strains of B. thermosphacta show a high level of similarity with pBT469-3, suggesting that variants of this plasmid could be frequently found in this bacterium.

Mobile genetic elements drive the multidrug resistance and spread of Salmonella serotypes along a poultry meat production line

The presence of mobile genetic elements in Salmonella isolated from a chicken farm constitutes a potential risk for the appearance of emerging bacteria present in the food industry. These elements contribute to increased pathogenicity and antimicrobial resistance through genes that are related to the formation of biofilms and resistance genes contained in plasmids, integrons, and transposons. One hundred and thirty-three Salmonella isolates from different stages of the production line, such as feed manufacturing, hatchery, broiler farm, poultry farm, and slaughterhouse, were identified, serotyped and sequenced. The most predominant serotype was Salmonella Infantis. Phylogenetic analyses demonstrated that the diversity and spread of strains in the pipeline are serotype-independent, and that isolates belonging to the same serotype are very closely related genetically. On the other hand, Salmonella Infantis isolates carried the pESI IncFIB plasmid harboring a wide variety of resistance genes, all linked to mobile genetic elements, and among carriers of these plasmids, the antibiograms showed differences in resistance profiles and this linked to a variety in plasmid structure, similarly observed in the diversity of Salmonella Heidelberg isolates carrying the IncI1-Iα plasmid. Mobile genetic elements encoding resistance and virulence genes also contributed to the differences in gene content. Antibiotic resistance genotypes were matched closely by the resistance phenotypes, with high frequency of tetracycline, aminoglycosides, and cephalosporins resistance. In conclusion, the contamination in the poultry industry is described throughout the entire production line, with mobile genetic elements leading to multi-drug resistant bacteria, thus promoting survival when challenged with various antimicrobial compounds.

Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings

The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.

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

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