Prevalence Of Antibiotic Resistance Genes Research Articles

A global perspective on the abundance, diversity and mobility of antibiotic resistance genes in Escherichia coli

IntroductionEscherichia coli (E. coli), a ubiquitous opportunistic pathogen, poses a growing threat to human health due to the increasing prevalence of antibiotic resistance. However, a comprehensive understanding of the global distribution, diversity, and transmission of antibiotic resistance genes (ARGs) in E. coli remains lacking, hindering effective strategies to combat resistance.MethodsIn this study, we analyzed 94,762 E. coli genome sequences obtained from the NCBI database using advanced bioinformatics tools. ARGs were identified by comparing sequences against a custom ARG database using BLAST. Mobile genetic element (MGE)-associated ARGs were identified by matching with ISfinder databases. Global distribution of ARGs was analyzed by clustering mobile ARG sequences with 99% genetic similarity.ResultsOur analysis revealed that 50.51% of the E. coli genome sequences contained ARGs, totaling 301,317 identified ARG sequences. These ARGs were categorized into 12 major classes and 229 subtypes. Notably, ARGs associated with multi-drug resistance (MDR), β-lactams, macrolide-lincosamide-streptogramins (MLS), tetracyclines, and aminoglycosides were particularly abundant, with the subtypes mdtK, macB, and ampC being especially prevalent. Additionally, significant differences in ARG abundance and diversity were observed across countries, with higher diversity found in high-income nations. Furthermore, 9.28% of the ARG sequences were linked to MGEs, accounting for 98.25% of all ARG subtypes. Notably, 4.20% of mobile ARGs were identified in over 20 countries, with β-lactam and aminoglycoside ARGs being the most widespread.DiscussionThis study provides a comprehensive overview of the global distribution and transmission of ARGs in E. coli. The high abundance of MDR and β-lactam-related ARGs, along with their widespread transmission across countries, highlights the urgent need for global surveillance and control measures. Furthermore, the strong association between ARGs and MGEs underscores the role of horizontal gene transfer in the spread of resistance. The observed variations in ARG diversity between countries suggest that socioeconomic factors, such as healthcare infrastructure and antibiotic usage patterns, significantly influence ARG prevalence. These findings are crucial for informing global strategies to mitigate the spread of antibiotic resistance and improve public health outcomes.

Metagenomics and selective culture reveal the major transfer and prevalence of antibiotic resistance genes in Tibetan Plateau animals

The Tibetan Plateau, despite being the highest and least populated plateau on the Earth, harbors antibiotic-resistant bacteria (ARBs) as well as antibiotic resistance genes (ARGs) in its pristine environment and animals. There is, however, limited knowledge regarding antibiotic resistance in Tibetan Plateau animals. Here, fecal samples of grazing yaks and intestinal content samples of wild rats were collected at altitudes of 2920m and 4360m and subjected to selective culture, PCR, and metagenomic sequencing. The results revealed a higher antibiotic resistance rate in low-altitude regions than in high-altitude regions. The simultaneous presence of bacteria exhibiting different antibiotic resistance phenotypes across multiple samples suggests the potential emergence of multidrug-resistant strains within the animal gut microbiota. Pseudomonas spp. and Escherichia coli were the predominant ARBs. In contrast to low-altitude regions with frequent human activities, ARG dissemination in the Tibetan Plateau did not show a significant correlation with mobile genetic elements. ARGs in high-altitude regions relied more on vertical gene transmission. This study expands our knowledge of antibiotic resistance in grazing and wild animals inhabiting the Tibetan Plateau, thereby highlighting the potential threat posed by antibiotic resistance in this region.

Antibiotic Resistance Genes in Plague Ecosystems: Threatening the Emergence of Resistant Plague

The study aimed to investigate the prevalence of antibiotic resistance genes (ARGs) within the ecosystem of natural plague foci, assessing their potential impact on the efficacy of plague treatments. Employing 16S rRNA gene sequencing and high-throughput quantitative PCR, microbial communities and ARGs were detected, with subsequent analysis of interactions among ARGs, mobile genetic elements (MGEs), environmental factors, and microbial species. Tetracycline resistance genes were found to be dominant, with multidrug and tetracycline resistance ARGs primarily associated with marmots and ecological soil, while pikas predominantly harbored β-lactam resistance ARGs. High detection rates were observed for resistance genes rpsl and sul1, which are relevant to streptomycin and sulfonamides, antibiotics commonly used in plague treatment. The total dissolved solids (TDS) in soil significantly promoted the presence of tetR-02, and Ni was found to inhibit vanHB. The tnpA-03 MGE was identified as a significant contributor to the dissemination of the aadE gene. The high prevalence of ARGs, particularly rpsl and sul1, poses a potential risk to the efficacy of main antibiotic treatments for plague. The study suggests that environmental microbiomes may be the greatest risk factor for the emergence of drug-resistant Yersinia pestis, given the low misuse of antibiotics in animals within natural plague foci. Monitoring the risk of drug-resistant strain emergence and preparing alternative antibiotic or combination therapy strategies based on ARG pollution levels in plague-affected areas is deemed necessary.

Investigation of Various Toxigenic Genes and Antibiotic and Disinfectant Resistance Profiles of Staphylococcus aureus Originating from Raw Milk.

This study investigated the toxigenic genes and antimicrobial resistance profiles of Staphylococcus aureus strains isolated from 260 raw milk samples collected from dairy farms in Türkiye. The results indicated that 60.7% of staphylococcal enterotoxin genes (sea, seb, sed, seg, sei, sej, sek, seq, sem, seo, and seu) and 21.4% of the tst and eta genes were positive, with most enterotoxin-positive samples carrying more than one gene. The sec, see, seh, sel, sen, sep, and etb genes were not identified in any samples. The prevalence of antibiotic resistance genes (mecA, blaR, blaI, blaZ, vanA, ermT, tetK, aac/aph, ant, dfrA, tcaR, IS256, and IS257) was high at 89.2%, with bla being the most frequently detected gene (75%). The mecA gene was present in 14.2% of samples, while tcaR was detected in 78.5%. Nevertheless, the mecC was not identified. Disinfectant resistance genes (qacA/B, qacC, qacJ, smr) were detected in 21.4% of the samples. The results of the disk diffusion test showed that 64.2% of strains were resistant to penicillin G and ampicillin, with additional resistance found for cefoxitin, teicoplanin, levofloxacin, norfloxacin, and other antibiotics. These findings highlight a significant public health and food safety risk associated with raw milk due to the presence of S. aureus strains with toxigenic genes and high antimicrobial resistance.

Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents

The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.

Antibiotic Resistance Genes in Global Food Transformation System: Edible Insects vs. Livestock.

Antibiotic-resistant genes (ARGs) pose a significant threat to the global food transformation system. The increasing prevalence of ARGs in food has elicited apprehension about public health safety. The widespread dissemination of ARGs in food products, driven by the inappropriate use of antibiotics, presents significant adversity for the safety of emerging future food sources such as edible insects. As the world faces increasing challenges related to food security, climate change, and antibiotic resistance, edible insects offer a sustainable and resilient food source. The intriguing possibility of edible insects serving as a less conducive environment for ARGs compared to livestock warrants further exploration and investigation. In this recent work, we listed ARGs from edible insects detected so far by in vitro approaches and aimed to construct a fair comparison with ARGs from livestock based on relevant genes. We also presented our argument by analyzing the factors that might be responsible for ARG abundance in livestock vs. edible insects. Livestock and edible insects have diverse gut microbiota, and their diets differ with antibiotics. Consequently, their ARG abundance may vary as well. In addition, processed edible insects have lower levels of ARGs than raw ones. We hypothesize that edible insects could potentially contain a lower abundance of ARGs and exhibit a diminished ability to disseminate ARGs relative to livestock. A regulatory framework could help intercept the increasing prevalence of ARGs. Due diligence should also be taken when marketing edible insects for consumption.

Metagenomic insights into plasmid-mediated antimicrobial resistance in poultry slaughterhouse wastewater: antibiotics occurrence and genetic markers.

Slaughterhouse wastewater represents important convergence and concentration points for antimicrobial residues, bacteria, and antibiotic resistance genes (ARG), which can promote antimicrobial resistance propagation in different environmental compartments. This study reports the assessment of the metaplasmidome-associated resistome in poultry slaughterhouse wastewater treated by biological processes, employing metagenomic sequencing. Antimicrobial residues from a wastewater treatment plant (WWTP) that treats poultry slaughterhouse influents and effluents were investigated through high-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS). Residues from the macrolide, sulfonamide, and fluoroquinolone classes were detected, the latter two persisting after the wastewater treatment. The genetic markers 16S rRNA rrs (bacterial community) and uidA (Escherichia coli) were investigated by RT-qPCR and the sul1 and int1 genes by qPCR. After treatment, the 16S rRNA rrs, uidA, sul1, and int1 markers exhibited reductions of 0.67, 1.07, 1.28, and 0.79 genes copies, respectively, with no statistical significance (p > 0.05). The plasmidome-focused metagenomics sequences (MiSeq platform (Illumina®)) revealed more than 100 ARG in the WWTP influent, which can potentially confer resistance to 14 pharmacological classes relevant in the human and veterinary clinical contexts, in which the qnr gene (resistance to fluoroquinolones) was the most prevalent. Only 7.8% of ARG were reduced after wastewater treatment, and the remaining 92.2% were associated with an increase in the prevalence of ARG linked to multidrug efflux pumps, substrate-specific for certain classes of antibiotics, or broad resistance to multiple medications. These data demonstrate that wastewater from poultry slaughterhouses plays a crucial role as an ARG reservoir and in the spread of AMR into the environment.

Localized heating coupling with radical oxidation eliminating antibiotic resistance genes (ARGs) in interfacial photothermal Fenton-like disinfection process

Conventional oxidative disinfection processes are inefficient in eliminating intracellular antibiotic resistance genes (iARGs) due to the barrier of the cell membrane and the competitive reaction of cellular constituents within antibiotic-resistant bacteria (ARB), resulting in the widespread prevalence of ARGs in recycled water. This study presented the first application of localized heating coupling with advanced oxidation to destroy the resistant Escherichia coli cells and improved subsequent iARGs (blaTEM-1) degradation in a novel photothermal Fenton-like disinfection process. The Fe-Mn@CNT microfiltration membrane, comprising carbon nanotubes wrapped with Fe and Mn nanoparticles (Fe-Mn@CNT), was employed as a nanomaterial for photothermal conversion and H2O2 activation. The highly efficient absorption of full-spectrum photons by CNTs enabled the Fe-Mn@CNT membrane to concentrate light to generate localized intense heat, resulting in the destruction of ARB nearby, and the subsequent release of iARGs. Interfacial heat favored Fe-Mn-induced H2O2 activation, leading to the production of more ·OH, which in turn promoted the oxidation for ARG degradation and ARB cell damage. The results of the acetylcysteine quenching experiments indicated that interfacial heating and radical oxidation-induced accumulation of intracellular reactive oxygen species contributed to the elimination of about 1-log iARGs through direct attack. The integrity of the cell membrane, the morphology of ARB and the variation of i/e ARG copy numbers were observed to reveal that the introduction of interfacial heating aggravated the cell lysis and accelerated the iARGs release, resulting in the inactivation of 7.27-log ARB and the elimination of 4.64-log iARGs and 2.23-log eARGs. Localized heating coupling with ·OH oxidation achieved a 143 % increase in iARGs removal compared to the conventional Fenton-like oxidation. The interfacial photothermal Fenton-like disinfection process exhibited remarkable material stability, robust disinfection performance, and effective suppression of horizontal gene transfer, underscoring its immense potential to mitigate the risk of ARG dissemination in reclaimed water systems.

Prevalence of antibiotic resistance genes in bacteria from Gomti and Ganga rivers: implications for water quality and public health.

Rivers serve as a significant habitat and water sources for diverse organisms, including humans. An important environmental and public health concern is the increase in antibiotic-resistant bacteria (ARBs) and genes (ARGs) in aquatic ecosystems brought about by excessive pollutant flow. The research highlighted that river water, which is receiving discharge from wastewater treatment plants, is harbouring multidrug-resistant bacteria. River water samples were collected in January, April, July and October 2022 from three separate locations of each Gomti and Ganga river. A total of 114 bacteria were isolated from Gomti as well as the Ganga River. All the isolates were tested for their resistance to various antibiotics by disc diffusion method. The isolated bacteria were tested for the antibiotic resistance genes using PCR and were identified by 16s rRNA sequencing. The ARBs percentages for each antibiotic were as follows: ampicillin (100%); cefotaxime (96.4, 63.1%); erythromycin (52.6, 57.8%); amikacin (68.4, 50.8%); tetracycline (47.3, 54.3%); nalidixic acid (47.3, 45.6%); streptomycin (68.4, 49.1%); gentamycin (43.8, 35%); chloramphenicol (26.3, 33.3%); neomycin (49.1, 29.8%) and ciprofloxacin (24.5, 7.01%). Further, antibiotic resistance genes in Gomti and Ganga water samples disclose distinctive patterns, including resistance to ermB (25, 40%); tetM (25, 33.3%); ampC (44.4, 40%) and cmlA1 (16.6%). Notably cmlA1 resistant genes were absent in all bacterial strains of the Gomti River. Additionally, gyrA gene was not found in both the river water samples. The presence of ARGs in the bacteria from river water shows threat of transferring these genes to native environmental bacteria. To protect the environment and public health, constant research is necessary to fully understand the extent and consequences of antibiotic resistance in these aquatic habitats.

Marine microbial community taxonomic and functional indicators to volcanic and anthropogenic stressors in Deception Island, Antarctica

In recent years, the growth in Antarctic tourism has stimulated research on the anthropogenic impacts on the region, boosted by advances in OMIC technologies applied to polar microbial communities. This study aimed to assess the human impacts on marine prokaryotic and viral communities of Deception Island by identifying potential taxonomic, functional, and resistome indicators of both anthropogenic and natural/volcanic pressures. Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla, with notable variations attributed to volcanic activity and anthropogenic pressure. The abundance of Euryarchaeota in regions with increased volcanic activity underlines their adaptability to extreme conditions. Their mercury resistance coupled with their ability to cope with toxic heavy metals is a critical component in managing volcanic mercury concentrations. Actinobacteria, Cyanobacteria, Planctomycetes, and Synergistetes showed distinctive abundance patterns with potential ecological implications related to volcanic environments. Functional analyses revealed the enrichment of functions associated with metal-based, hydrocarbon degradation, and nitrogen metabolism. Submarine volcanic vents contributed significantly to the shape of functional diversity. Identification of specific functions related to nosocomial infections and gastroenteritis highlights the impact of anthropogenic activities on functional traits. Antibiotic resistance genes (ARGs) showed nuanced patterns influenced by both anthropogenic pressure and volcanic activity. Actinobacteria were correlated with increased ARG abundance, which was enhanced by wastewater disposal. Remarkably, Fumarole Bay showed an increased prevalence of certain ARGs, despite a lower anthropogenic impact, suggesting a unique selective pressure induced by volcanic activity. The responsiveness of these indicators to varying levels of pressure characterizes them as valuable tools for assessing and mitigating anthropogenic impacts on the marine waters of Deception Island.

Prevalence of antibiotic resistance genes in different drinking water treatment processes in a northwest Chinese city.

Antibiotic resistance genes (ARGs) are an emerging issue which are receiving increasing concerns in drinking water safety. However, the factors (e.g. treatment processes and water quality) affecting the removal efficiency of ARGs in the drinking water treatment plants (DWTPs) is still unclear. This work investigated the ARG profiles in each treatment process of two DWTPs located in a northwest Chinese city. The results showed that tetracycline and sulfonamide resistance genes were predominant among the 14 targeted ARGs. After the treatment, the Z water treatment plant which demonstrated a higher removal rate of ARGs (ranging from 50 to 80%), compared to the S plant (50-75%). And the average removal rate of tetracycline resistance genes (tetA, tetG, tetQ, tetX) was about 49.18% (S plant) and 67.50% (Z plant), as well as the removal rate of 64.2% and 72.9% for sulfonamide resistance (sul1 and sul2) at S and Z water plants, respectively. It was found that the relative abundance of main microbial communities (such as Bacteroidota, Actinobacteria, Verrucomicrobiota, Roseomonas), α-diversity index, as well as the abundance of pathogenic bacteria were all significantly reduced after different treatment processes. Network co-occurrence analysis revealed that Methylocystis possibly was the potential host for most ARGs, and sul1 was found across a broad spectrum of microorganisms in the drinking water environment. Adonis analysis showed that heavy metals and microbial communities explain solely 44.1% and 35.7% of variances of ARGs within DWTPs. This study provides insights into the contamination status and removal efficiencies of ARGs in DWTPs, offering valuable references for future studies on ARG removal, propagation, and diffusion patterns in drinking water treatment.

Antibiotic Residue in Milk and Meat Products: A Scientific Overview

The need for food is rising globally as the human population continues to rise. People in better socioeconomic countries have a tendency to substitute meat and high quality items for grains in their diets. Over the past thirty years, there has been a seventy percent increase in their choice of chicken as a protein source. Antibiotics accumulate in animal tissues as a result of overuse and misuse in treating illnesses and fostering animal growth. From there, they enter human bodies through the food chain. This study provides a detailed assessment of comparative studies on the dangers to human health posed by antibiotic residue (AR) in foods, including milk and meat from animal sources. The usage of several veterinary antibiotics in animal farms, which can result in ARs, is the main topic of this review's early section. Later on, there has been a thorough discussion of ARs in dietary items, such as milk and meat. People from underdeveloped and impoverished nations are particularly susceptible to infectious diseases brought on by bacteria that are resistant to antibiotics, according to review research on the problems with antibiotic use and human health. Towards the conclusion of the review, a few alternative strategies are outlined, taking into account their potential exposure to substitute antibiotics as growth promoters and reducing the prevalence of antibiotic resistant genes. These strategies include the use of probiotics, prebiotics, organic acids, phytogenic feed additives, and other substances.

Prevalence of antibiotic resistance genes, heavy metal, and bacterial community composition in sea sediments influenced by Eriocheir sinensis breeding aquaculture.

Eriocheir sinensis is the main aquaculture species in China. With the continuous expansion of the aquaculture scale, the demand for E. sinensis seedlings was also increased. The water used in breeding has well-nourished and its discharge into the sea posed significant risks. This study sampled the wastewater discharge points of the E. sinensis seedlings in Sheyang County, Jiangsu Province, and the areas far from the discharge points that were not affected in March and May 2023, respectively. A large number of antibiotic resistance genes (ARGs) were found in the sediment of the wastewater discharge area, and the highest ARG was sulfonamide ARG-sul1 using qPCR analysis, while ARGs were almost undetectable in the areas not affected by wastewater discharge. The 16S rRNA sequence analysis results showed that the main bacterial phyla at the wastewater discharge point were Bacteroidetes, Proteobacteria, and Thermodesulfobacteria. In the control point, the main bacterial phyla were Proteobacteria, Chlorobacterium, and Thermodesulfobacteria. There were significant differences in the composition of microbial communities between the two points, and the samples at the wastewater discharge point were more clustered and had higher similarity. The correlation network and redundancy analysis indicated that the phyla Bacteroidetes, Firmicutes, and Proteobacteria at the wastewater discharge points were positively correlated with most ARGs. The wastewater discharge had no effect on heavy metals from the two points. This study sets a foundation for future research by identifying key microbial taxa as potential ARG carriers and examining the interactions between microbial communities, ARGs, and heavy metals.

Whole-Genome Sequencing Reveals Temporal Trends in Antibiotic Resistance Genes in Escherichia coli Causing Pediatric Urinary Tract Infections in Central Vietnam.

(1) Background: Pediatric urinary tract infections (UTIs) pose significant challenges due to drug-resistant Escherichia coli (E. coli) strains. This study utilizes whole-genome sequencing to analyze temporal trends in antibiotic resistance genes (ARGs) in clinical E. coli isolates from pediatric UTI cases in central Vietnam. (2) Methods: We conducted whole-genome sequencing on 71 E. coli isolates collected from pediatric UTI patients between 2018 and 2020. ARGs were identified, and their prevalence over time was analyzed. Statistical tests were used to correlate ARG presence with antibiotic resistance. (3) Results: Of the 47 E. coli isolates with complete data, 40 distinct ARGs were identified, with a median of 10 resistance genes per isolate. A significant increase in the total number of ARGs per isolate was observed over time, from an average of 8.88 before June 2019 to 11.63 after. Notably, the prevalence of the aadA2 gene (aminoglycoside resistance) rose from 0% to 26.7%, and that of the blaNDM-5 gene (beta-lactam and carbapenem resistance) increased from 0% to 23.3%. Key correlations include blaEC with cephalosporin resistance, blaNDM-5 with carbapenem resistance, and sul2 with sulfamethoxazole/trimethoprim resistance. (4) Conclusions: Whole-genome sequencing reveals complex and evolving antibiotic resistance patterns in pediatric E. coli UTIs in central Vietnam, with a marked increase in ARG prevalence over time. Continuous surveillance and targeted treatments are essential to address these trends. Understanding genetic foundations is crucial for effective intervention strategies.

A first study of meat-borne enterococci from butcher shops: prevalence, virulence characteristics, antibiotic resistance and clonal relationship.

IntroductionEnterococcus, which used to be thought of as a harmless commensal living in the digestive tract, has now become a highly resistant and highly contagious pathogen that makes nosocomial infections much more common. This study examined enterococci species and their antibiotic resistance phenotypes and genotypes and virulence gene content in Turkish ground beef samples. Methodology A total of 100 ground beef samples were analyzed between May 2020 and May 2021. The isolated strains were identified via matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and confirmed using polymerase chain reaction (PCR) after which they were divided into several species using PCR and tested for antibiotic resistance against 19 antimicrobial agents using the disc diffusion method. The genetic similarity analysis, pulsed-field gel electrophoresis (PFGE) was performed. Results A total of 93 isolates in ground beef were identified, comprised of E. faecalis 72.04%; E. hirae- 11.82%; E. casseliflavous- 7.52%; E. faecium- 5.3%; E. gallinarium- 3.23%. The virulence genes observed in Enterococcus species were distributed as follows: gelE 88.1%, ace 53.7%, efaA 40.8%, asaI 19.3%, esp 6.4%, and cylA 1.07%. A high antibiotic resistance was recorded for tetracycline (43.01%), followed by ampicilin (17.2%), and chloramphenicol (13.9%). 17.2% of Enterococcus isolates were multidrug-resistant. The study determined the high prevalence of antibiotic resistance genes, specifically for tet(L) 10 (10.7%), aac(6')Ie-aph(2")-la 3 (3.2%), and ermB 3 (3.2%). The presence of efflux pump genes were identified in 74.1% of Enterococcus isolates. Genetic characterization of 67 E. faecalis isolates by PFGE revealed 41 pulsed-field gel electrophoresis (PFGE) patterns that were grouped into 15 clusters, which presented more than one strain with 100% similarity. Conclusion Isolates obtained from several areas and butchers had comparable patterns of PFGE, suggesting that the presence of circulating E. faecalis poses a potential public health concern in diverse districts. To mitigate the health hazards associated with the contamination of enterococci from raw to cooked meats, it is necessary to enhance the disinfection of butcheries, promote excellent hand hygiene among butchers, and implement appropriate meat storage and handling methods to prevent bacterial development.

Antibiotic resistance genes and crAssphage in hospital wastewater and a canal receiving the treatment effluent

Hospital wastewater is a major hotspot for the spread of antimicrobial resistance (AMR) in aquatic ecosystems. This study aimed to investigate the prevalence of antibiotic resistance genes (ARGs) and their correlation with crAssphage in a hospital wastewater treatment plant (HWWTP) and a receiving canal. Water samples were analyzed for 94 ARGs and crAssphage relative to the 16S rRNA using high-throughput quantitative polymerase chain reaction (HT-qPCR). Subsequently, 7 ARGs and crAssphage were selected and quantified using qPCR. The results showed that the detected genes ranged from 79 to 93 out of 95 genes. The raw wastewater (WW) samples had the highest gene diversity compared to the upstream canal, which had less diversity than downstream samples, as determined by HT-qPCR. The blaGES was the most abundant in WW samples, while qacEΔ1, merA, IS6100, tnpA, and IS26 showed high prevalence throughout the treatment processes. The concentrations of intI1, sul1, blaTEM,blaNDM,blaVIM,tetQ, mcr-1, crAssphage, and 16S rRNA, measured using qPCR, were the highest in WW and significantly reduced in treated water samples. Although some water quality parameters, such as total suspended solids and dissolved oxygen, did not significantly differ before and after treatment, removal efficiency ranged from 0.60 to 3.23 log reduction values (LRV). The highest LRV was observed for the tetQ, whereas the mcr-1 had the lowest LRV. Strong positive correlations among the absolute concentrations of ARGs and crAssphage were observed (Spearman's rho = 0.6–1.0), and biochemical oxygen demand correlated with blaTEM and blaVIM (Spearman's rho = 0.6). These results indicate that crAssphage and water quality could reflect the distribution of other ARGs throughout the HWWTP. Further studies are needed to underscore the importance of monitoring ARGs and genetic markers such as crAssphage in HWWTPs and their receiving waters to enhance our understanding of ARG distribution.

Environmental risks in swine biogas slurry-irrigated soils: A comprehensive analysis of antibiotic residues, resistome, and bacterial pathogens

Simple anaerobic digestion is insufficient to completely remove residual parent antibiotics and antibiotic resistance genes (ARGs) from animal manure. ARG prevalence in swine biogas slurry-irrigated soils threatens human health. However, comprehensive analysis of antibiotic residues, high-resolution resistance gene profiles, and pathogenic microbiomes in biogas slurry-irrigated soils is very limited. Here, we comprehensively determined the antibiotics, resistome, and potential pathogens distribution in these soils, using high-performance liquid chromatography-tandem mass spectrometry, high-throughput quantitative PCR, and 16S rRNA gene sequencing. The results revealed a significant enrichment of tetracyclines and fluoroquinolones antibiotics and ARGs in soils with prolonged biogas slurry irrigation, with a total of 12 antibiotics, 175 unique ARGs, and 9 mobile genetic elements (MGEs) detected. Quantification of veterinary antibiotic residues (especially chlortetracycline) showed significant correlations with multiple ARGs. The abundance of ARGs and MGEs was highest in the biogas slurry-irrigated soils, denoting a tight link between the application of biogas slurry and the spread of antibiotic resistance. The presence of 50 potential pathogenic bacterial genera, including 13 with multidrug resistance, was identified. Variation partitioning, combined with hierarchical partitioning analysis, indicated that Firmicutes, MGEs, and tetracyclines were the key drivers shaping the ARG profiles in biogas slurry-irrigated soils. The findings offer insights into the mechanisms of antibiotic residue and ARGs spread from the agricultural practice of biogas slurry irrigation, underscoring the necessity of sustainable soil management to mitigate the spread of antibiotic resistance.

Differential drivers on the occurrence of antibiotic resistance genes in agricultural soils and crops: Evidence from the different fertilization regimes

Organic fertilizer application caused bacterial resistance contamination in farming systems has been widely documented, and long-term fertilization will exacerbate the migration of antibiotic resistance genes (ARGs) to crops and humans. However, it remains unclear whether a combined pattern of chemical and organic fertilizer application can arrest the high prevalence of ARGs in soil-crop. Here we investigated the ARGs occurrence under different fertilization regimes, and explored the mechanisms by which micro-ecological shifts and geochemical factors in modulating the ARGs fate in soil and crop. The results showed that the soil ARGs abundance was highest under 100% organic fertilizer, while the highest ARGs abundance in crops was observed at 100% chemical fertilizer. Application of organic fertilizers with more than 50% ration intensified the soil accumulation and migration of tetA, sul1, sul2 and macA genes. And, multidrug_transporter, macA and sul1 were co-shared in soil and crop, where ARGs potential hosts differed complete in the two, suggesting that these ARGs may be transferred across media by horizontal transfer. Procrustes analysis revealed that soil microbial community was significantly correlated with ARG hosts, and soil microbial evolutionary pathway was congruent with antibiotic resistance, suggesting that fertilizers affect soil ARGs abundance mainly by altering soil microbial composition and their ecological evolutionary trajectories. While, no significant correlation was observed between endophytes and crop ARG host. Structural equations demonstrated that soil nutrients and crop growth characteristics contributed largely to the prevalence of crop ARGs. This outcome will provide new insights into the high prevalence of ARGs in soil and crop, and offer fertilizer recommendations for effectively curbing antibiotic-resistance contamination in farming systems.

Unveiling the overlooked threat: antibiotic resistance in groundwater near an abandoned sulfuric acid plant in Xingyang, China.

Groundwater near a sulfuric acid plant in Xingyang, Henan, China was sampled from seven distinct sites to explore the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs). Results showed that genes aadA, blaCTX-M, tetA, qnrA, and sul1 were detected with 100% frequency followed by aac(6')-Ib (85.71%), ermB (85.71%), and tetX (71.42%). Most abundant ARGs were sul1 in LSA2 (1.15 × 1011 copies/mL), tetA in LSA6 (4.95 × 1010 copies/mL), aadA in LSA2 (4.56 × 109 copies/mL), blaCTX-M in LSA4 (1.19 × 109 copies/mL), and ermB in LSA5 (1.07 × 109 copies/mL). Moreover, in LSA2, intl1 as a marker of class 1 integron emerged as the most abundant gene as part of MGE (2.25 × 1011 copies/mL), trailed by ISCR1 (1.57 × 109 copies/mL). Environmental factors explained 81.34% of ARG variations, with a strong positive correlation between the intl2 and blaCTX-M genes, as well as the ISCR1 gene and qnrA, tetA, intl2, and blaCTX-M. Furthermore, the intI1 gene had a strong positive connection with the aadA, tetA, and sul1 genes. Moreover, the aac(6')-Ib gene was associated with As, Pb, Mg, Ca, and HCO3-. The intl2 gene was also shown to be strongly associated with Cd. Notably, network analysis highlighted blaCTX-M as the most frequently appearing gene across networks of at least five genera. Particularly, Lactobacillus, Plesiomonas, and Ligilactobacillus demonstrated correlations with aadA, qnrA, blaCTX-M, intI2, and ISCR1. Based on 16S rRNA sequencing, the dominant phyla were Proteobacteria, Firmicutes, Bacteroidota, Acidobacteriota, and Actinobacteriota, with dominant genera including Pseudomonas, Ligilactobacillus, Azoarcus, Vogesella, Streptococcus, Plesiomonas, and Ferritrophicum. These findings enhance our understanding of ARG distribution in groundwater, signaling substantial contamination by ARGs and potential risks to public health.

Fertilizing drug resistance: Dissemination of antibiotic resistance genes in soil and plant bacteria under bovine and swine slurry fertilization

The increasing global demand for food production emphasizes the use of organic animal fertilizers, such as manure and slurry, to support sustainable agricultural practices. However, recent studies highlight concerns about antibiotic resistance determinants in animal excrements, posing a potential risk of spreading antibiotic resistance genes (ARGs) in agricultural soil and, consequently, in food products.This study examines the dissemination of ARGs within the soil and plant-associated microbiomes in cherry radish following the application of swine and bovine slurry. In a 45-day pot experiment, slurry-amended soil, rhizospheric bacteria, and endophytic bacteria in radish roots and leaves were sampled and analyzed for 21 ARGs belonging to 7 Antibiotic Resistance Phenotypes (ARPs). The study also assessed slurry's impact on soil microbiome functional diversity, enzymatic activity, physicochemical soil parameters, and the concentration of 22 selected antimicrobials in soil and plant tissues.Tetracyclines and β-lactams were the most frequently identified ARGs in bovine and swine slurry, aligning with similar studies worldwide. Swine slurry showed a higher prevalence of ARGs in soil and plant-associated bacteria, particularly TET genes, reflecting pig antibiotic treatments. The persistent dominance of TET genes across slurry, soil, and plant microbiomes highlights significant influence of slurry application on gene occurrence in plant bacteria. The presence of ARGs in edible plant parts underscores health risks associated with raw vegetable consumption. Time-dependent dynamics of ARG occurrence highlighted their persistent presence throughout the experiment duration, influenced by the environmental factors and antibiotic residuals. Notably, ciprofloxacin, which was the only one antimicrobial detected in fertilized soil, significantly impacted bovine-amended variants. Soil salinity modifications induced by slurry application correlated with changes in ARG occurrence. Overall, the research underscores the complex relationships between agricultural practices, microbial activity, and antibiotic resistance dissemination, emphasizing the need for a more sustainable and health-conscious farming approaches.