A multi-dimensional framework for selecting antibiotic resistance gene indicators in wastewater surveillance of antimicrobial resistance

Introduction: the secret lives of microbial mobile genetic elements.

Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.

Hospital sewage have been associated with incorporation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into microbes, which is considered as a key indicator for the spread of antimicrobial resistance (AMR). The compositions of dental waste water (DWW) contain heavy metals, the evolution of AMR and its effects on the water environment in the context of heavy metal environment have not been seriously investigated. Thus, our major aims were to elucidate the evolution of AMR in DWW. DWW samples were collected from a major dental department. The presence of microbial communities, ARGs, and MGEs in untreated and treated (by filter membrane and ozone) samples were analyzed using metagenomics and bioinformatic methods. DWW-associated resistomes included 1,208 types of ARGs, belonging to 29 antibiotic types/subtypes. The most abundant types/subtypes were ARGs of multidrug resistance and of antibiotics that were frequently used in the clinical practice. Pseudomonas putida, Pseudomonas aeruginosa, Chryseobacterium indologenes, Sphingomonas laterariae were the main bacteria which hosted these ARGs. Mobilomes in DWW consisted of 93 MGE subtypes which belonged to 8 MGE types. Transposases were the most frequently detected MGEs which formed networks of communications. For example, ISCrsp1 and tnpA.5/4/11 were the main transposases located in the central hubs of a network. These significant associations between ARGs and MGEs revealed the strong potential of ARGs transmission towards development of antimicrobial-resistant (AMR) bacteria. On the other hand, treatment of DWW using membranes and ozone was only effective in removing minor species of bacteria and types of ARGs and MGEs. DWW contained abundant ARGs, and MGEs, which contributed to the occurrence and spread of AMR bacteria. Consequently, DWW would seriously increase environmental health concerns which may be different but have been well-documented from hospital waste waters.

Ecological functions coupled with plasmid and phage-mediated dissemination drive the global prevalence of high-risk antimicrobial resistance genes in influent.

BackgroundAntibiotics and antibiotic resistance genes (ARGs) threaten ecological sustainability and human health, especially the drinking water sources of the Douhe Reservoir, which have critical significance amid their direct use by people and the ecological hub of flora and fauna. Although antibiotics and ARGs pollution in reservoirs have been reported, it is of no practical significance to only study the changes (increase or decrease) of the abundance and diversity of ARGs, and it is more important to explore the mechanisms of the changes affecting ARGs. Thus, the occurrence and prevalence characterizations of the spatial and seasonal of the ARGs, mobile genetic elements (MGEs) and bacterial communities were comprehensively studied in present study.Results263 ARG (nine types of ARGs) and 51 MGE subtypes were detected in 56 samples, and the characteristics of the temporal and spatial distribution of ARGs, MGEs and the composition of bacterial communities were significantly different. Moreover, the correlation among the ARGs, bacterial communities, MGEs and environmental factors were defined, and the co-occurrence patterns associated with ARG subtypes, bacterial genera, and MGE subtypes between water and sediment of the Douhe Reservoir were different.ConclusionsIn summary, ARGs were ubiquitous presence in water and sediment of the Douhe Reservoir, and the multidrug, aminoglycoside and macrolide–lincosamide–streptogramin B (MLSB) were main types of ARGs. Bacterial genera and the environmental factors [such as temperature (T), nitrate–nitrogen (NO– 3–N), total dissolved nitrogen (TDN), and total phosphorus (TP)] significantly affected the distribution pattern of ARGs. Overall, this research revealed the spatiotemporal change and transmission mechanisms of ARGs in the typical drinking water sources of reservoirs, which will supply clues to ensure the safety of water sources.

Antibiotic and heavy metal resistance genes in sewage sludge survive during aerobic composting

BackgroundApplication of swine manure to soils exacerbates environmental antimicrobial resistance (AMR). However, a comprehensive evaluation of anaerobic digestion’s (AD) mitigation potential against AMR and its influencing factors in swine manure-to-soil systems remains lacking.MethodsWe employed mass spectrometry, metagenomics, and whole-genome sequencing (WGS) to investigate the fate of antibiotics, metals, and antibiotic resistance genes (ARGs) across manures, slurries, and soils from eight pig farms.ResultsAnaerobic digestion reduced antibiotic and metal (except ciprofloxacin) content and risks in manure, but had limited effects on total ARG abundance, while increasing ARG network modularity. High-risk ARG abundance significantly increased from 404.7 in manure to 843.2 in slurries, with health-risk scores rising 1.88-fold during anaerobic digestion. Metagenomic analysis showed metal resistance gene (MRG) diversity and abundance decreased during anaerobic digestion, along with reduced ARG-MRG co-occurrence frequency, whereas mobile genetic element (MGE) diversity and ARG-MGE co-occurrence frequency increased. Escherichia coli was identified as the dominant ARG host. WGS of E. coli strains confirmed horizontal gene transfer (HGT) of nine ARGs (e.g., sul3 and blaTEM-1), and metagenomics suggested HGT of four ARGs (e.g., tet(M)) across different pathogens. Chromium concentrations, bacterial communities and MGEs were significantly associated with ARG profiles. Long-term slurry application resulted in elevated antibiotic, metal, and ARG concentrations in soils, with concomitant increases in high-risk ARGs and health risks.ConclusionThis study demonstrates AD’s limited effect on mitigating overall ARG abundance and highlights MGEs as critical drivers of ARG maintenance and dissemination from manure to soil process, guiding manure treatment optimization to reduce agricultural AMR risks.

Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

Characteristics of phytoplankton-zooplankton communities and the roles in the transmission of antibiotic resistance genes under the pressure of river contamination

Bioelectrochemistry increases the risk of resistance genes proliferation and transfer with sulfamethoxazole pressure decreasing in constructed wetlands: An overlooked double-edged effect.

Escherichia 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. In 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. Our 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. This 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.

Antibiotic resistance in the Ganga River: Investigation of antibiotic resistant bacteria and antibiotic resistance genes, and public health risk assessment

Antimicrobial resistance (AMR) is a critical global health concern. While AMR research has primarily focused on medical and veterinary settings, the spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) through natural environments, including soil, remains poorly understood. This study investigates the relationship between soil physico-chemical properties and ARG abundance in environments with varying levels of anthropogenic impact. Soil samples were collected from agricultural fields after harvest (both manured and non-manured, but fertilized with mineral fertilizers) and forests, analyzed for 24 physico-chemical parameters, and subjected to DNA extraction. High-throughput qPCR was used to quantify 27 clinically relevant ARGs and 5 mobile genetic elements (MGEs) in the samples. Results revealed significant differences in soil properties between arable and forest soils, particularly in water content, humus levels, sand and silt proportions, and mercury concentration (p ≤ 0.05). Arable soils exhibited a significantly higher abundance of ARGs and MGEs (p = 0.0247), with certain resistance genes found exclusively in agricultural environments. Correlation analysis identified strong positive associations between MGEs and ARGs, highlighting the role of genetic elements in AMR dissemination. Additionally, soil properties such as aluminum, nitrogen, and magnesium showed positive correlations with ARG and MGE abundance, while sand content and the carbon-to-nitrogen ratio displayed inverse correlations. The results indicate that heavy metal contamination may play a substantial role in AMR spread through co-selection mechanisms. These findings emphasize the influence of environmental factors on AMR dynamics and highlight the need to integrate soil ecology into AMR mitigation strategies within the One Health framework.

Antimicrobial resistance (AMR) is a serious issue that is continuously growing and spreading, leading to a dwindling number of effective treatments for infections that were easily treatable with antibiotics in the past. Animal farms are a major hotspot for AMR, where antimicrobials are often overused, misused, and abused, in addition to overcrowding of animals.In this study, we investigated the risk of AMR transmission from a farm to nearby residential areas by examining the overall occurrence of endotoxins, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) in the air of a cattle farm. We assessed various factors, including the season and year, day and nighttime, and different locations within the farm building and its vicinity.The most abundant ARGs detected were tetW, aadA1, and sul2, genes that encode for resistances towards antibiotics commonly used in veterinary medicine. While there was a clear concentration gradient for endotoxin from the middle of the farm building to the outside areas, the abundance of ARGs and MGEs was relatively uniform among all locations within the farm and its vicinity. This suggests that endotoxins preferentially accumulated in the coarse particle fraction, which deposited quickly, as opposed to the ARGs and MGEs, which might concentrate in the fine particle fraction and remain longer in the aerosol phase. The occurrence of the same genes found in the air samples and in the manure indicated that ARGs and MGEs in the air mostly originated from the cows, continuously being released from the manure to the air.Although our atmospheric dispersion model indicated a relatively low risk for nearby residential areas, farm workers might be at greater risk of getting infected with resistant bacteria and experiencing overall respiratory tract issues due to continuous exposure to elevated concentrations of endotoxins, ARGs and MGEs in the air of the farm.

Unveiling dynamics of size-dependent antibiotic resistome associated with microbial communities in full-scale wastewater treatment plants