Department-specific patterns of bacterial communities and antibiotic resistance in hospital indoor environments

Antibiotic resistance genes and associated bacterial communities in agricultural soils amended with different sources of animal manures

Presence of antibiotic resistance genes in different salinity gradients of freshwater to saltwater marshes in southeast Louisiana, USA

Reducing antibiotic resistance genes in soil: The role of organic materials in reductive soil disinfestation.

Dynamics of bacterial community and antibiotic resistance genes in the aquaculture ponds of channel catfish (Ietalurus Punetaus): An association with the mobile genetic elements and environmental factors

The use of antibiotics in livestock production enhances animal growth and health but risks regarding the development of antibiotic resistant bacteria have led to consumer and regulatory pressures to reduce antibiotic use in animal agriculture. The increase and spread of antibiotic resistance genes (ARGs) in the agroecosystem could complicate the treatment of human and animal infections in the future. Across multiple swine and poultry studies, we have found that antibiotic use significantly increased the abundance of ARGs, and the abundance of genes that could facilitate in the horizontal transmission of ARGs. In an individual controlled swine study, we found that ARGs were enriched up to 28,000-fold compared to antibiotic-free control animals. In commercial swine farms, ARG levels were, on average, 200 times higher than background ARGs levels in soils, and individual ARGs were (co-)selected 10- to 100-fold. ARGs frequently clustered in multidrug resistance (MDR) regions, where the abundance of genes conferring resistance to multiple antibiotic classes were tightly correlated. Importantly, therapeutic zinc supplementation also increased the abundance of ARGs, highlighting the role of metals in the co-selection of ARGs. Beyond ARG enrichment, antibiotics also increased the abundance of mobile genetic elements (MGEs), genes that are involved in transferring a gene within or between bacterial cells, abundance, 10 times more than ARGs. ARG and MGE abundances were highly correlated (r² = 0.96), supporting their role in horizontal gene transfer (HGT). Carbadox, a widely used swine antibiotic, promoted lytic bacteriophage activity, increasing the potential for phage-mediated ARG transduction. Bacitracin methylene disalicylate (BMD) in turkeys significantly enriched conjugation-related genes and transduction-associated elements, further demonstrating that antibiotic alternatives may inadvertently promote HGT. The presence of resistance clusters occurred independently of microbiome shifts, suggesting that ARG dissemination is not limited by microbial composition. In addition to increasing ARG and MGE abundance, antibiotic use was also associated with changes in bacterial community composition, including an increase in Proteobacteria, particularly Escherichia coli. Functional metagenomic analyses revealed that antibiotic-fed animals exhibited elevated expression of genes related to energy metabolism, bacterial growth, and stress response, suggesting that antibiotic selection pressures reshape microbial function beyond resistance traits. These findings highlight the need for a comprehensive reassessment of antimicrobial use in livestock production with a One-Health perspective. The widespread selection and mobility of ARGs and MGEs in agricultural systems pose a risk for AMR dissemination into animal, human and environmental reservoirs. Future research should focus on microbiome-based interventions, antibiotic-free growth promoters, and improved surveillance and diagnostic testing strategies to mitigate the spread of resistance while maintaining animal health and productivity.

Transmission mechanisms of antibiotic resistance genes in arsenic-contaminated soil under sulfamethoxazole stress

Microplastics exacerbate antibiotic resistance by regulating microbial and functional gene dynamics in sludge and food waste composting.

Earthworms are capable of redistributing bacteria and antibiotic resistance genes (ARGs) through soil profiles. However, our understanding of the earthworm gut microbiome and its interaction with the antibiotic resistome is still lacking. Here, we characterized the earthworm gut and soil microbiome and antibiotic resistome in natural and agricultural ecosystems at a national scale, and microcosm studies and field experiments were also employed to test the potential role of earthworms in dynamics of soil ARGs. The diversity and structure of bacterial communities were different between the earthworm gut and soil. A significant correlation between bacterial community dissimilarity and spatial distance between sites was identified in the earthworm gut. The earthworm gut consistently had lower ARGs than the surrounding soil. A significant reduction in the relative abundance of mobile genetic elements and dominant bacterial phylotypes that are the likely hosts of ARGs was observed in the earthworm gut compared to the surrounding soil, which might contribute to the decrease of ARGs in the earthworm gut. The microcosm studies and field experiments further confirmed that the presence of earthworms significantly reduced the number and abundance of ARGs in soils. Our study implies that earthworm-based bioremediation may be a method to reduce risks associated with the presence of ARGs in soils.

Spatiotemporal distribution of the planktonic microbiome and antibiotic resistance genes in a typical urban river contaminated by macrolide antibiotics

Phenotypic antibiotic resistance prediction using antibiotic resistance genes and machine learning models in Mannheimia haemolytica.

With the widespread use of antibiotics in medicine and agriculture, the spread of antibiotic resistance genes （ARGs） in the environment has become a serious threat to ecological balance and human health, particularly for its role in facilitating the emergence of multidrug-resistant pathogens. The study of riverine environments as a major transmission route for ARGs and closely related mobile genetic elements （MGEs） is of great importance. MGEs exacerbate the spread of resistance genes by facilitating the horizontal transfer of ARGs in bacterial populations. Although studies have been conducted to explore the interactions between MGEs and ARGs, there is still a relative lack of research on the spatial and temporal differences in the distribution of MGEs in rivers and their drivers. This study selected two rural rivers （with a total of six sampling points） and three urban rivers （with a total of nine sampling points） within Shijiazhuang as research subjects, and sediment samples were collected in December 2020 and April 2021. By employing metagenomic sequencing technology, this study comprehensively compared and analyzed the spatiotemporal distribution characteristics and influencing factors of MGEs in the sediment of urban and rural rivers. The results showed that： ① In December, 1 738 types of MGEs （60572 RPKM） and 1 604 types of MGEs （26916 RPKM） were detected in urban and rural rivers, respectively. In April, 1 790 types of MGEs （74354 RPKM） and 1 631 types of MGEs （32062 RPKM） were detected in urban and rural rivers, respectively. ② The types and abundance of MGEs in urban rivers were greater than those in rural rivers, and the types and abundance of MGEs in April were greater than those in December. ③ ISPa38, IS26, and tnpA were the most significantly different typical MGEs among the rivers in urban and suburban Shijiazhuang. ④ PCoA and NMDS analyses showed significant spatiotemporal differences in MGEs between urban and rural rivers. ⑤ Correlation analysis and co-occurrence results indicated that the abundance of MGEs in urban rivers was significantly positively correlated with antibiotic concentration, industrial enterprises, sewage treatment plants, total population, livestock farming, and aquaculture. In suburban rivers, the abundance of MGEs was mainly significantly positively correlated with antibiotic concentration, livestock farming, aquaculture, and total population. Overall, by comparing the spatiotemporal heterogeneity of MGEs in urban and rural rivers and identifying the main driving factors of MGEs in urban and suburban rivers, this study provides data support for subsequent risk management and control of antibiotic resistance in different rivers.

Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks

Background: Streptococcus dysgalactiae subsp. equisimilis (SDSE) is an important human pathogen. Recently, several studies have described the incidence of antibiotic resistance for SDSE worldwide, however, the data on the presence of corresponding genes and their possible association with mobile genetic elements are still limited. Objective: The objective of this research was to analyze the macrolide resistance in SDSE and to identify genetic determinants, mechanisms of resistance, and association with mobile genetic elements. Methods: A total of 9 SDSE strains from the collection of Joint Russian-Vietnamese Tropical Research and Technological Center (Hanoi, Vietnam) were used. These strains were previously isolated from throat swabs of children with pharyngotonsillitis in 6 provinces in Vietnam from 2012 to 2015. Antimicrobial resistance was tested by disk diffusion method. The presence of antibiotic resistance genes (ARG) was analyzed by PCR. The strains were characterized by emm typing and multilocus sequence typing (MLST). Illumina sequencing was employed for genome analysis of 4 representative SDSE isolates. Analysis of genetic elements with antibiotic resistance determinants was done using PubMed database and BLAST-searches. Artemis was used for comparative analysis of genetic elements. Results: In our study, we identified emm types that were similar to those reported in other studies. All SDSE isolates remained susceptible to penicillin, but presented alarming level of resistance to macrolides, tetracyclines, and fluoroquinolones. Most of the erythromycin-resistant strains were also characterized by clindamycin-resistance (MLSB phenotype). Both erm and different alleles of mef genes widely distributed among streptococcus pyogenes and Streptococcus pneumoniae were detected, except erm (TR) gene. The genetic elements carrying resistance determinants showed significant interspecies similarities, indicating conjugative transfer of antibiotic resistance genes between streptococcal species. Conclusion: Identification of the novel antibiotic resistance genes in SDSE indicates the necessity of monitoring of antibiotic resistance spreading and gene transfer in this bacterium.

The organic material amendment has been proven to change the soil antibiotic resistance genes (ARGs) profile, which may threaten human health through the food chain, but the effects and mechanisms of different organic materials on ARGs in paddy soils are less explored. In this study, a field experiment was set up with the treatments of conventional chemical fertilization (NPK) and common organic material amendment [rice straw (RS), swine manure (SM), and biochar (BC)] to explore the effects and mechanisms. In total, 84 unique ARGs were found across the soil samples with different organic material amendments, and they conferred resistance to the major antibiotic classes. Compared with NPK, SM significantly increased the detected number and relative abundance of ARGs. A higher detected number of ARGs than NPK was observed in BC, whereas BC had a lower relative abundance of ARGs than NPK. Compared with NPK, a detected number decrease was observed in RS, although abundance showed no significant differences. Compared with other treatments, a higher detected number and relative abundance of mobile genetic elements (MGEs) were observed in BC, indicating a higher potential for horizontal gene transfer. There were significantly positive relationships between the relative abundances of total ARGs and MGEs and the bacterial abundance. The network analysis suggested the important role of MGEs and bacterial communities in shaping the ARGs profile. Mantel test and redundancy analysis (RDA) suggested that soil carbon, nitrogen, and C/N were the major chemical drivers of the ARGs profile. The risk of ARGs spreading to the food chain should be considered when applying SM and biochar, which shifted the ARGs and MGEs profiles, respectively. Pre-treatment measures need to be studied to reduce the dissemination of ARGs in paddy fields.

Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors