Influence of Soil Characteristics and Proximity to Antarctic Research Stations on Abundance of Antibiotic Resistance Genes in Soils

Microbiome engineering to palliate microbial dysbiosis occurring in agroecosystems

Plant health and productivity are closely tied to the fluctuations of soil microbiomes, which regulate biogeochemical processes and plant-soil interactions. However, environmental and anthropogenic stressors, including climate change, intensive agricultural practices, and industrial activities, disrupt these microbial communities. This microbial imbalance reduces soil fertility, plant health, and biodiversity, threatening agroecosystem sustainability. This review explores the mechanisms driving microbial dysbiosis in soil and plant environments. Plants under stress release chemical signals through root exudates, dynamically recruiting beneficial microbes to counteract microbial imbalances. Moreover, this review evaluates traditional methods to alleviate these stress-induced microbial alterations, such as microbial inoculants and organic soil amendments, alongside innovative strategies like phage therapy, CRISPR, and small RNA-based technologies. Despite these advancements, the practical implementation of microbiome interventions faces significant challenges. These include regulatory hurdles, economic constraints, and the need for long-term field studies to validate efficacy and ensure environmental safety.

Antibiotic resistome in the glacier forelands of polar regions

Antibiotic resistance genes (ARGs) pose a significant threat, exacerbated by climate change impacts on polar regions, particularly melting glaciers and permafrost. While ancient antibiotic resistance exists in the environments, the release and dissemination of ARGs remain poorly understood. This study investigated ARG composition and distribution in 43 metagenomes from Arctic and Antarctic glacier forelands. We identified 154 ARGs, predominantly bacitracin resistance, followed by rifamycin, fosfomycin, vancomycin, tetracycline, and beta-lactam resistance genes. Significant correlations were observed between ARGs and mobile genetic elements (MGEs), with 20 ARGs associated with tnpA MGEs. Actinomycetota and Pseudomonadota were the primary ARG-carrying phyla. Metagenome-assembled genomes revealed Mycobacterium sp., Pseudomonas sp., and Tatlockia sp. as major ARG-harboring pathogens in the glacier forelands. Evolutionarily adapted, distinct ancient ARGs were abundant in the polar environments, varying between different geographic regions. The environmental parameters such as pH and total organic carbon significantly influenced the ARG distribution in the Arctic and Antarctic glacier forelands. This study provides crucial baseline data on antimicrobial resistance, highlighting potential risks associated with rapid environmental change in the regions.

IMPORTANCE

Antibiotic resistance poses a significant global health threat, exacerbated by the release of antibiotic resistance genes from melting glaciers and permafrost due to climate change. This study provides crucial baseline data on the composition and distribution of antibiotic resistance genes in these vulnerable polar environments, which is essential for understanding and mitigating the risks associated with their release. The findings have far-reaching implications for global health security and emphasize the need for further research to address this emerging threat.

Emerging Trends in Antimicrobial Resistance in Polar Aquatic Ecosystems

The global spread of antimicrobial resistance (AMR) threatens to plummet society back to the pre-antibiotic era through a resurgence of common everyday infections' morbidity. Thus, studies investigating antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in urban, agricultural, and clinical settings, as well as in extreme environments, have become increasingly relevant in the One Health perspective. Since the Antarctic and Arctic regions are considered amongst the few remaining pristine environments on Earth, the characterization of their native resistome appears to be of the utmost importance to understand whether and how it is evolving as a result of anthropogenic activities and climate change. In the present review, we report on the phenotypic (e.g., disk diffusion test) and genotypic (e.g., PCR, metagenomics) approaches used to study AMR in the aquatic environment of polar regions, as water represents one of AMR main dissemination routes in nature. Their advantages and limits are described, and the emerging trends resulting from the analysis of ARB and ARGs diffusion in polar waters discussed. The resistome detected in these extreme environments appears to be mostly comparable to those from more anthropized areas, with the predominance of tetracycline, β-lactam, and sulfonamide resistance (and related ARGs). Indeed, AMR is, in all cases, more consistently highlighted in sites impacted by human and wildlife activities with respect to more pristine ones. Surprisingly, aminoglycoside and fluroquinolone determinants seem to have an even higher incidence in the Antarctic and Arctic aquatic environment compared to that from other areas of the world, corroborating the need for a more thorough AMR surveillance in these regions.

Effects of snowmelt runoff on bacterial communities and antimicrobial resistance gene concentrations in an urban river in a cold climate region

Urban rivers are essential for human activities and ecosystems. Urban runoff is a major source of various pollutants in urban rivers. In this study, we investigated the effect of rainfall and snowmelt subsequently causing urban runoff in a cold climate region on bacterial community structures and antimicrobial resistance gene concentrations in an urban river in Sapporo city, Japan, which has an average snowfall of 4.8 m. Bacterial community structures of the river water were analyzed by next generation sequencing of bacterial 16S rRNA genes. The antimicrobial resistance genes, mphA and blaIMP, were determined using quantitative polymerase chain reaction. Rainfall and snowmelt increased the effluent discharge rate of treated wastewater, and river water depth. Rainfall and snowmelt also increased Escherichia coli concentrations by 4-20 folds in the river, probably because of combined sewer overflows, urban runoff, or increased effluent discharge rate of treated wastewater to the river. Urban runoff and the subsequent discharge of treated wastewater decreased the bacterial alpha diversity and increased the species evenness of bacteria. Bacterial beta diversity analysis showed that the discharge of treated wastewater caused by rainfall and snowmelt changed the structure and diversity of the bacterial community in the river. The concentrations of the antimicrobial resistance gene mphA were related to the discharge of treated wastewater. In contrast, the antimicrobial resistance gene blaIMP appeared to be present in the upstream pristine environment. Results of this study should be informative for challenge to reduce the antimicrobial resistance bacteria due to combined sewer overflows by wastewater management authorities.

Assessing the impact of sewage and wastewater on antimicrobial resistance in nearshore Antarctic biofilms and sediments

BACKGROUND

Despite being recognised as a global problem, our understanding of human-mediated antimicrobial resistance (AMR) spread to remote regions of the world is limited. Antarctica, often referred to as "the last great wilderness", is experiencing increasing levels of human visitation through tourism and expansion of national scientific operations. Therefore, it is critical to assess the impact that these itinerant visitors have on the natural environment. This includes monitoring human-mediated AMR, particularly around population concentrations such as visitor sites and Antarctic research stations. This study takes a sequencing discovery-led approach to investigate levels and extent of AMR around the Rothera Research Station (operated by the UK) on the Antarctic Peninsula.

RESULTS

Amplicon sequencing of biofilms and sediments from the vicinity of Rothera Research Station revealed highly variable and diverse microbial communities. Analysis of AMR genes generated from long-reads Nanopore MinION sequencing showed similar site variability in both drug class and resistance mechanism. Thus, no site sampled was more or less diverse than the other, either in the biofilm or sediment samples. Levels of enteric bacteria in biofilm and sediment samples were low at all sites, even in biofilm samples taken from the station sewage treatment plant (STP). It would appear that incorporation of released enteric bacteria in wastewater into more established biofilms or associations with sediment was poor. This was likely due to the inactivation and vulnerability of these bacteria to the extreme environmental conditions in Antarctica.

CONCLUSIONS

Our results suggest minimal effect of a strong feeder source (i.e. sewage effluent) on biofilm and sediment microbial community composition, with each site developing its unique niche community. The factors producing these niche communities need elucidation, alongside studies evaluating Antarctic microbial physiologies. Our data from cultivated bacteria show that they are highly resilient to different environmental conditions and are likely to thrive in a warmer world. Our data show that AMR in the Antarctic marine environment is far more complex than previously thought. Thus, more work is required to understand the true extent of the Antarctic microbiota biodiversity, their associated resistomes and the impact that human activities have on the Antarctic environment.

Profiles and natural drivers of antibiotic resistome in multiple environmental media in penguin-colonized area in Antarctica

Profiles and driving mechanisms of antibiotic resistome in the polar region are important for exploring the natural evolution of antibiotic resistance genes (ARGs). Here, we evaluated the profiles of antibiotic resistome in multiple media on Inexpressible Island, Terra Nova Bay, Antarctica. Average concentrations of ARGs in intracellular DNA (iARGs) among water (3.98 × 106 copies/L), soil (3.41 × 107 copies/kg), and penguin guano (7.04 × 107 copies/kg) were higher than those of ARGs in extracellular DNA (eARGs) among water (1.99 × 104 copies/L), soil (1.75 × 106 copies/kg), and penguin guano (8.02 × 106 copies/kg). It was indicated that the transmission of ARGs across different media occurs with around 77.8% of iARGs from soil and 86.7% of iARGs from penguins observed in water, and 80.7% of iARGs and 56.7% of eARGs from penguins found in soil. Annual inputs of ARGs from Adélie penguins on Inexpressible Island have increased since 1983. Bacitracin, multidrug, and aminoglycoside resistance genes were the main ARGs among water, soil, and penguin guano. Primary medium-risk ARGs associated with human pathogenic bacteria were multidrug resistance genes, and main low-risk ARGs associated with mobile genetic elements (MGEs) were aminoglycoside resistance genes. Antibiotic-resistant bacteria (ARB) from soil and penguins were more phylogenetically related to aquatic antibiotic-resistant mesophiles than aquatic antibiotic-resistant psychrophiles. MGEs, ARB, bacterial diversities, antibiotics, and metals could explain total ARGs between water and soil. Intracellular MGEs were the most significant in-situ driver of iARGs in water, reflecting that horizontal gene transfer could facilitate the spread of ARGs in water. Penguins were important ex-situ drivers of environmental antibiotic resistome, which was linked with risky ARGs between water and soil. These findings highlight the major roles of natural drivers (e.g., MGEs and penguins) in shaping environmental antibiotic resistome in polar areas, improving our understanding of the evolution of environmental microbiome.

Distribution of tetracyclines and sulfonamides resistance genes around a smallholder pig farm: Modeling and attribution

Livestock farm is a major source of antibiotics and antibiotic resistance genes (ARGs) pollution. ARGs can directly enter the environment through runoff and air deposition. The impact extent and the driving factors require further investigation to inform effective policies and actions to mitigate their spread. This study investigated a smallholder pig farm and its surrounding areas to understand the spread of ARGs. Topsoil samples were collected from 56 different sites within one kilometer of the farm, and a comprehensive analysis was conducted to reveal effects of soil properties, antibiotic residues, microbiome, mobilome on the variation of typical ARGs. The results confirmed that the ARGs reduced exponentially with increasing distance from the farm, with a goodness of fit (R2) of 0.7 for total ARGs. For tetracyclines (TC) and sulfonamides (SA) resistance genes, the fitting R2 exceeded 0.9. Model estimates allowed for quantitative comparisons of in-farm increments, out-farm background levels, and spread abilities of ARGs with distinct resistance mechanisms. SA-specific resistance genes (SRGs, 0.097 copies/16S rRNA gene) and TC-specific resistance genes (TRGs, 0.036 copies/16S rRNA gene) showed higher within-farm increases compared to multidrug resistance genes (MDRGs, 0.020 copies/16S rRNA gene). MDRGs, however, had a higher background level and a greater impact distance (0.18 km, 4.4 times the farm radius). Additionally spread abilities of TRGs varied by resistance mechanism, with ribosome protection proteins showing greater spread than TC inactivating enzymes and TC efflux pumps, likely due to different fitness costs. Correlation analysis and structural equation modeling indicated that changes in bacterial community composition and mobilome are primary factors influencing ARGs variation during their spread. Abiotic factors like soil nutrients and antibiotics also selectively enriched ARGs within the farm. These findings provide insights into the ARGs dissemination and could inform strategies to prevent their spread from smallholder livestock farms.

Biofilm enhanced the mitigations of antibiotics and resistome in sulfadiazine and trimethoprim co-contaminated soils

Reducing antibiotic levels in soil ecosystems is vital to curb the dissemination of antimicrobial resistance genes (ARGs) and mitigate global health threats. However, gaps persist in understanding how antibiotic resistome can be suppressed during antibiotic degradation. Herein, we investigate the efficacy of a biochar biofilm incorporating antibiotics-degrading bacterial strain (Arthrobacter sp. D2) to mitigate antibiotic resistome in non-manured and manure-amended soils with sulfadiazine (SDZ) and trimethoprim (TMP) contamination. Results show that biofilm enhanced SDZ degradation by 83.0% within three days and increased TMP attenuation by 55.4% over 60 days in non-manured soils. In the non-manured black soil, the relative abundance of ARGs increased initially after biofilm inoculation. However, by day 30, it decreased by 20.5% compared to the controls. Moreover, after 7 days, biofilm reduced TMP by 38.5% in manured soils and decreased the total ARG abundance by 19.0%. Thus, while SDZ degradation did not increase sulfonamide resistance genes, TMP dissipation led to a proliferation of insertion sequences and related TMP resistance genes. This study underscores the importance of antibiotic degradation in reducing related ARGs while cautioning against the potential proliferation and various ARGs transfer by resistant microorganisms.

Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish

Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.

Anthropogenic activities significantly interfered distribution and co-occurrence patterns of antibiotic resistance genes in a small rural watershed in Southwest China

The prevalence and spread of antibiotic resistance genes (ARGs) have been a significant concern for global public health in recent years. Small rural watersheds are the smallest units of factor mobility for agricultural production in China, and their ARG profiles are the best scale of the contamination status, but the mapping and the distribution and diffusion of ARGs in the water and soil of small rural watersheds are inadequate. In this study, based on microbial metagenomics, we invested prevalence maps of 209 ARGs corresponding to typical commonly used antibiotics (including multidrug, aminoglycoside, macrolide-lincosamide-streptogramin B (MLSB), and β-Lactamase) in water and soil in different agricultural types, as well as within water-soil interfaces in small rural watersheds in Southwest China. The results revealed that the most abundant ARGs in water and soil were consistent, but different in subtypes, and anthropogenic activities affect the transport of ARGs between water and soils. Livestock wastewater discharges influenced the diversity and abundance of ARGs in water, while in soil it is planting type and fertilizer management, and thus interfered with the co-occurrence patterns between bacteria and ARGs. Co-occurrence analysis revealed that Proteobacteria, Actinobacteria, and Bacteroidetes were the predominant ARG hosts in water and soil, but soil exhibited a more intricate ARG-bacterial association. Overall, this study provides integrated profiles of ARGs in water and soil influenced by anthropogenic activities at the small watershed scale in a typical rural area and provides a baseline for comparisons of ARGs.

Unravelling the evolutionary dynamics of antibiotic resistance genes in the infant gut microbiota during the first four months of life

BACKGROUND

Alongside microbiota development, the evolution of the resistome is crucial in understanding the early-life acquisition and persistence of Antibiotic Resistance Genes (ARGs). Therefore, the aim of this study is to provide a comprehensive view of the evolution and dynamics of the neonatal resistome from 7 days to 4 months of age using a high-throughput qPCR platform.

METHODS

In the initial phase, a massive screening of 384 ARGs using a high-throughput qPCR in pooled healthy mother-infant pairs feces from the MAMI cohort was carried out to identify the most abundant and prevalent ARGs in infants and in mothers. This pre-analysis allowed for later targeted profiling in a large number of infants in a longitudinal manner during the first 4 months of life. 16S rRNA V3-V4 amplicon sequencing was performed to asses microbial composition longitudinally. Potential factors influencing the microbiota and ARGs in this period were also considered, such as mode of birth and breastfeeding type.

RESULTS

Following the massive screening, the top 45 abundant ARGs and mobile genetic elements were identified and studied in 72 infants during their first months of life (7 days, 1, 2, and 4 months). These genes were associated with resistance to aminoglycosides, beta-lactams and tetracyclines, among others, as well as integrons, and other mobile genetic elements. Changes in both ARG composition and quantity were observed during the first 4 months of life: most ARGs abundance increased over time, but mobile genetic elements decreased significantly. Further exploration of modulating factors highlighted the effect on ARG composition of specific microbial genus, and the impact of mode of birth at 7 days and 4 months. The influence of infant formula feeding was observed at 4-month-old infants, who exhibited a distinctive resistome composition.

CONCLUSIONS

This study illustrates the ARG evolution and dynamics in the infant gut by use of a targeted, high-throughput, quantitative PCR-based method. An increase in antibiotic resistance over the first months of life were observed with a fundamental role of delivery mode in shaping resistance profiles. Further, we highlighted the influence of feeding methods on the resistome development. These findings offer pivotal insights into dynamics of and factors influencing early-life resistome, with potential avenues for intervention strategies.

The significance of environmentally bioavailable antimicrobials in driving antimicrobial resistance in soils

Antimicrobial resistance (AMR) stands as an escalating public health crisis fueled by antimicrobial residues in the environment, particularly in soil, which acts as a reservoir for antimicrobial resistance genes (ARGs). Merely quantifying the total extractable concentration of antimicrobials, instead of bioavailable fractions, may substantially underestimate their minimal selection concentration for propagating ARGs. To shed light on the role of bioavailability in ARG abundance within soil, a systematic bioavailability assessment method was established for accurately quantifying the partitioning of multi-class antimicrobials in representative Chinese soils. Microcosm studies unveiled that antimicrobials persisting in the bioavailable fraction could potentially prolong their selection pressure duration to trigger AMR. Notably, the co-occurrence of pesticide or steroid hormone influenced the development trends of ARG subtypes, with fluoroquinolone resistance genes (RGs) being particularly susceptible. Partial least squares path model (PLS-PM) analysis uncovered potentially distinct induction mechanisms of antimicrobials: observable results suggested that extractable residual concentration may exert a direct selection pressure on the development of ARGs, while bioavailable concentration could potentially play a stepwise role in affecting the abundance of mobile genetic elements and initiating ARG dissemination. Such unprecedented scrutinization of the interplay between bioavailable antimicrobials in soils and ARG abundance provides valuable insights into strategizing regulatory policy or guidelines for soil remediation.

Characterization of the soil resistome and mobilome in Namib Desert soils

The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.

Penguin-Driven Dissemination and High Enrichment of Antibiotic Resistance Genes in Lake Sediments across Antarctica

Numerous penguins can propagate pathogens with antibiotic resistance genes (ARGs) into Antarctica. However, the effects of penguin dissemination on the lake ARGs still have received little attention via guano deposition. Here, we have profiled ARGs in ornithogenic sediments subject to penguin guano (OLS) and nonornithogenic sediments (NOLS) from 16 lakes across Antarctica. A total of 191 ARGs were detected in all sediment samples, with a much higher abundance and diversity in OLS than in NOLS. Surprisingly, highly diverse and abundant ARGs were found in the OLS with a detection frequency of >40% and an absolute abundance of (2.34 × 109)-(4.98 × 109) copies g-1, comparable to those in coastal estuarine sediments and pig farms. The strong correlations of identified resistance genes with penguin guano input amount, environmental factors, mobile genetic elements, and bacterial community, in conjunction with network and redundancy analyses, all indicated that penguins were responsible for the dissemination and high enrichment of ARGs in lake sediments via the guano deposition, which might greatly outweigh local human-activity effects. Our results revealed that ARGs could be carried into lakes across the Antarctica through penguin migration, food chains, and guano deposition, which were closely connected with the widespread pollution of ARGs at the global scale.

Co-occurrence patterns of gut microbiome, antibiotic resistome and the perturbation of dietary uptake in captive giant pandas

The microbiome is a key source of antibiotic resistance genes (ARGs), significantly influenced by diet, which highlights the interconnectedness between diet, gut microbiome, and ARGs. Currently, our understanding is limited on the co-occurrence among gut microbiome, antibiotic resistome in the captive giant panda and the perturbation of dietary uptake, especially for the composition and forms in dietary nutrition. Here, a qPCR array with 384 primer sets and 16 S rRNA gene amplicon sequencing were used to characterize the antibiotic resistome and microbiomes in panda feces, dietary bamboo, and soil around the habitat. Diet nutrients containing organic and mineral substances in soluble and insoluble forms were also quantified. Organic and mineral components in water-unextractable fractions were 7.5 to 139 and 637 to 8695 times higher than those in water-extractable portions in bamboo and feces, respectively, while the latter contributed more to the variation (67.5 %) of gut microbiota. Streptococcus, Prevotellaceae, and Bacteroides were the dominant genera in giant pandas. The ARG patterns in panda guts showed higher diversity in old individuals but higher abundance in young ones, driven directly by the bacterial community change and mobile genetic element mediation and indirectly by dietary intervention. Our results suggest that dietary nutrition mainly accounts for the shift of gut microbiota, while bacterial community and mobile genetic elements influenced the variation of gut antibiotic resistome.

Spread of antibiotic resistance genes to Antarctica by migratory birds

Recent studies have highlighted the presence of antibiotic resistance genes (ARGs) in Antarctica, which are typically indicative of human activity. However, these studies have concentrated in the Antarctic Peninsula region, and relatively less is known about ARG prevalence in East Antarctica, where human activity levels are lower compared to the Antarctic Peninsula. In addition, the mechanisms of ARG transmission to Antarctica through natural or anthropogenic pathways remain unclear. In this study, we analyzed the fecal samples of Adélie penguins and South polar skuas by using high-throughput sequencing and microfluidic quantitative PCR to detect potential pathogens and ARGs at their breeding colonies near Syowa Station in East Antarctica. These results revealed the presence of several potential pathogens in the fecal matter of both bird species. However, the HF183 marker, which indicates human fecal contamination, was absent in all samples, as well as seawater sampled near the breeding colonies. This suggests that the human fecal contamination was negligible in our study area. In addition to pathogens, we found a significant number of ARGs and metal resistance genes in the feces of both Adélie penguins and South polar skuas, with higher detection rates in skuas than in penguins. To better understand how these birds acquire and transmit these genes, we analyzed the migratory patterns of Adélie penguins and South polar skuas by geolocator tracking. We found that the skuas migrate to the tropical and subtropical regions of the Indian Ocean during the austral winter. On the other hand, Adélie penguins exhibited a more localized migration pattern, mainly staying within Antarctic waters. Because the Indian Ocean is considered one of the major reservoirs of ARGs, South polar skuas might be exposed to ARGs during their winter migration and transfer these genes to Antarctica.

Antibiotic resistance in wildlife from Antarctic Peninsula

Although considered one of the most pristine ecosystems, Antarctica has been largely influenced by human activities during the last 50 years, affecting its unique biodiversity. One of the major global threats to health is the emergence of antibiotic-resistant bacteria that may be actively transferred to wildlife. We cultured and tested for antibiotic resistance in 137 cloacal and fresh fecal samples of several avian and marine mammal species from the Antarctic Peninsula, the most impacted area in Antarctica. Alarmingly, 80 % of the isolates showed antibiotic resistance, either phenotypically or genotypically. Most of the resistant bacteria, such as Enterobacteriaceae and Enterococcus species, are part of local gastrointestinal microbiota. Penguins and pinnipeds harbored a great diversity of antibiotic resistance and must be eligible as sentinels for future studies. These results show that antibiotic resistance has rapidly transferred to bacteria in Antarctic wildlife, which is a global matter of concern.

A database on the abundance of environmental antibiotic resistance genes

Antimicrobial resistance (AMR) poses a severe threat to global health. The wide distribution of environmental antibiotic resistance genes (ARGs), which can be transferred between microbiota, especially clinical pathogens and human commensals, contributed significantly to AMR. However, few databases on the spatiotemporal distribution, abundance, and health risk of ARGs from multiple environments have been developed, especially on the absolute level. In this study, we compiled the ARG occurrence data generated by a high-throughput quantitative PCR platform from 1,403 samples in 653 sampling sites across 18 provinces in China. The database possessed 291,870 records from five types of habitats on the abundance of 290 ARGs, as well as 8,057 records on the abundance of 30 mobile genetic elements (MGEs) from 2013 to 2020. These ARGs conferred resistance to major common types of antibiotics (a total of 15 types) and represented five major resistance mechanisms, as well as four risk ranks. The database can provide information for studies on the dynamics of ARGs and is useful for the health risk assessment of AMR.

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

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

Deciphering the Role of WWTPs in Cold Environments as Hotspots for the Dissemination of Antibiotic Resistance Genes

Cold environments are the most widespread extreme habitats in the world. However, the role of wastewater treatment plants (WWTPs) in the cryosphere as hotspots in antibiotic resistance dissemination has not been well established. Hence, a snapshot of the resistomes of WWTPs in cold environments, below 5 °C, was provided to elucidate their role in disseminating antibiotic resistance genes (ARGs) to the receiving waterbodies. The resistomes of two natural environments from the cold biosphere were also determined. Quantitative PCR analysis of the aadA, aadB, ampC, blaSHV, blaTEM, dfrA1, ermB, fosA, mecA, qnrS, and tetA(A) genes indicated strong prevalences of these genetic determinants in the selected environments, except for the mecA gene, which was not found in any of the samples. Notably, high abundances of the aadA, ermB, and tetA(A) genes were found in the influents and activated sludge, highlighting that WWTPs of the cryosphere are critical hotspots for disseminating ARGs, potentially worsening the resistance of bacteria to some of the most commonly prescribed antibiotics. Besides, the samples from non-disturbed cold environments had large quantities of ARGs, although their ARG profiles were highly dissimilar. Hence, the high prevalences of ARGs lend support to the fact that antibiotic resistance is a common issue worldwide, including environmentally fragile cold ecosystems.

Phenotypic and resistome analysis of antibiotic and heavy metal resistance in the Antarctic bacterium Pseudomonas sp. AU10

Resistance to antibiotics and heavy metals in Antarctic bacteria has been investigated due to anthropogenic impact on the continent. However, there is still much to learn about the genetic determinants of resistance in native bacteria. In this study, we investigated antibiotic, heavy metal, and metalloid resistance in Pseudomonas sp. AU10, isolated from King George Island (Antarctica), and analyzed its genome to look for all the associated genetic determinants (resistome). We found that AU10 displayed resistance to Cr(VI), Cu(II), Mn(II), Fe(II), and As(V), and produced an exopolysaccharide with high Cr(VI)-biosorption capacity. Additionaly, the strain showed resistance to aminopenicillins, cefotaxime, aztreonam, azithromycin, and intermediate resistance to chloramphenicol. Regarding the resistome, we did not find resistance genes in AU10's natural plasmid or in a prophage context. Only a copper resistance cluster indicated possible horizontal acquisition. The mechanisms of resistance found were mostly efflux systems, several sequestering proteins, and a few enzymes, such as an AmpC β-lactamase or a chromate reductase, which would account for the observed phenotypic profile. In contrast, the presence of a few gene clusters, including the terZABCDE operon for tellurite resistance, did not correlate with the expected phenotype. Despite the observed resistance to multiple antibiotics and heavy metals, the lack of resistance genes within evident mobile genetic elements is suggestive of the preserved nature of AU10's Antarctic habitat. As Pseudomonas species are good bioindicators of human impact in Antarctic environments, we consider that our results could help refine surveillance studies based on monitoring resistances and associated resistomes in these populations.

Occurrence and fate of antibiotic-resistance genes and their potential hosts in high-moisture alfalfa silage treated with or without formic acid bactericide

Silage as the main forage for ruminants could be a reservoir for antibiotic resistance genes (ARGs) through which these genes got access into the animals' system causing a latent health risk. This study employed metagenomics and investigated the ARGs' fate and transmission mechanism in high-moisture alfalfa silage treated with formic acid bactericide. The results showed that there were 22 ARGs types, in which multidrug, macrolide-lincosamide-streptogramine, bacitracin, beta-lactam, fosmidomycin, kasugamycin, and polymycin resistance genes were the most prevalent ARGs types in the ensiled alfalfa. The natural ensiling process increased ARGs enrichment. Intriguingly, after 5 days of ensiling, formic acid-treated silage reduced ARGs abundances by inhibiting host bacterial and plasmids. Although formic acid bactericide enhanced the fermentation characteristics of the high-moisture alfalfa by lowering silage pH, butyric acid concentration, dry matter losses and proteolysis, it increased ARGs abundances in alfalfa silage owing to increases in abundances of ARGs carriers and transposase after 90 days of ensiling. Notably, several pathogens like Staphylococcus, Clostridium, and Pseudomonas were inferred as potential ARGs hosts in high-moisture alfalfa silage, and high-moisture alfalfa silage may harbor a portion of the clinical ARGs. Fundamentally, microbes were distinguished as the foremost driving factor of ARGs propagation in ensiling microecosystem. In conclusion, although formic acid bactericide improved the fermentation characteristics of high-moisture alfalfa during ensiling and reduced ARGs enrichment at the initial ensiling stage, it increased ARGs enrichment at the end of ensiling.

Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves

Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.

Identifying sources of antibiotic resistance genes in the environment using the microbial Find, Inform, and Test framework

Introduction

Antimicrobial resistance (AMR) is an increasing public health concern for humans, animals, and the environment. However, the contributions of spatially distributed sources of AMR in the environment are not well defined.

Methods

To identify the sources of environmental AMR, the novel microbial Find, Inform, and Test (FIT) model was applied to a panel of five antibiotic resistance-associated genes (ARGs), namely, erm(B), tet(W), qnrA, sul1, and intI1, quantified from riverbed sediment and surface water from a mixed-use region.

Results

A one standard deviation increase in the modeled contributions of elevated AMR from bovine sources or land-applied waste sources [land application of biosolids, sludge, and industrial wastewater (i.e., food processing) and domestic (i.e., municipal and septage)] was associated with 34-80% and 33-77% increases in the relative abundances of the ARGs in riverbed sediment and surface water, respectively. Sources influenced environmental AMR at overland distances of up to 13 km.

Discussion

Our study corroborates previous evidence of offsite migration of microbial pollution from bovine sources and newly suggests offsite migration from land-applied waste. With FIT, we estimated the distance-based influence range overland and downstream around sources to model the impact these sources may have on AMR at unsampled sites. This modeling supports targeted monitoring of AMR from sources for future exposure and risk mitigation efforts.

A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments

The environment is an important component in the emergence and transmission of antimicrobial resistance (AMR). Despite that, little effort has been made to monitor AMR outside of clinical and veterinary settings. Partially, this is caused by a lack of comprehensive reference data for the vast majority of environments. To enable monitoring to detect deviations from the normal background resistance levels in the environment, it is necessary to establish a baseline of AMR in a variety of settings. In an attempt to establish this baseline level, we here performed a comprehensive literature survey, identifying 150 scientific papers containing relevant qPCR data on antimicrobial resistance genes (ARGs) in environments associated with potential routes for AMR dissemination. The collected data included 1594 samples distributed across 30 different countries and 12 sample types, in a time span from 2001 to 2020. We found that for most ARGs, the typically reported abundances in human impacted environments fell in an interval from 10-5 to 10-3 copies per 16S rRNA, roughly corresponding to one ARG copy in a thousand bacteria. Altogether these data represent a comprehensive overview of the occurrence and levels of ARGs in different environments, providing background data for risk assessment models within current and future AMR monitoring frameworks.

Metagenomics reveals the abundance and accumulation trend of antibiotic resistance gene profile under long-term no tillage in a rainfed agroecosystem

Widespread soil resistance can seriously endanger sustainable food production and soil health. Conservation tillage is a promising practice for improving soil structure and health. However, the impact of long-term no-tillage on the presence of antibiotic resistance genes in agricultural soils remains unexplored. Based on the long-term (>11 yr) tillage experimental fields that include both conservation tillage practices [no tillage (ZT)] and conventional tillage practices [plough tillage (PT)], we investigated the accumulation trend of antibiotic resistance genes (ARGs) in farmland soils under long-term no-tillage conditions. We aimed to provide a scientific basis for formulating agricultural production strategies to promote ecological environment safety and human health. In comparison to PT, ZT led to a considerable reduction in the relative abundance of both antibiotic resistance genes and antibiotic target gene families in the soil. Furthermore, the abundance of all ARGs were considerably lower in the ZT soil. The classification of drug resistance showed that ZT substantially decreased the relative abundance of Ethambutol (59.97%), β-lactams (44.87%), Fosfomycin (35.82%), Sulfonamides (34.64%), Polymyxins (33.67%), MLSB (32.78%), Chloramphenicol (28.57%), Multi-drug resistance (26.22%), Efflux pump (23.46%), Aminoglycosides (16.79%), Trimethoprim (13.21%), Isoniazid (11.34%), Fluoroquinolone (6.21%) resistance genes, compared to PT soil. In addition, the abundance of the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes decreased considerably. The Mantel test indicated that long-term ZT practices substantially increased the abundance of beneficial microbial flora and inhibited the enrichment of ARGs in soil by improving soil microbial diversity, metabolic activity, increasing SOC, TN, and available Zn, and decreasing pH. Overall, long-term no-tillage practices inhibit the accumulation of antibiotic resistance genes in farmland soil, which is a promising agricultural management measure to reduce the accumulation risk of soil ARGs.

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

Numerous studies have revealed the spread mechanism of antibiotic resistance genes (ARGs) in single antibiotic-contaminated soils. However, the comprehensive impacts of heavy metals and antibiotics on ARGs and the underlying mechanisms are still unknown. Here, high-throughput quantitative PCR and high-throughput sequencing were used to investigate changes in ARGs and bacterial communities under various sulfamethoxazole (SMX) regimes (0, 1, 10, 50 mg kg^-1) in arsenic (As) contaminated soils. The study found that the abundances of ARGs, mobile genetic elements (MGEs), and heavy metal resistance genes (HMRGs) significantly increased in the soil fortified at 10 and 50 mg kg^-1 SMX concentrations. The ARGs abundance increased with the increase in the MGEs abundance. Many significant positive correlations between various ARGs subtypes and HMRGs subtypes were found. These results indicate that the HMRGs and MGEs positively contributed to the enrichment of ARGs in As-contaminated soils under SMX stress. Meanwhile, the abundance of copiotrophic (Actinobacteriota) reduced and oligotrophic (Gemmatimonadota) increased, indicating that the life history strategy of the community changed. In addition, Gemmatimonadota was positively correlated to ARGs, HMRGs, and MGEs, suggesting that Gemmatimonadota, which can cope with As and SMX stress, was the host for resistance genes in the soil. Finally, the study found that MGEs play a determinant role in ARGs proliferation due to the direct utilization of HGT, and the indirect effect for ARGs spread under a co-selection mechanism of ARGs and HMRGs, while the bacterial community showed indirect influences by altering environmental factors to act on MGEs. Collectively, this study revealed new insights into the mechanisms of resistance gene transmission under combined SMX and As contamination in soil ecosystems.

Dry-to-wet fluctuation of moisture contents enhanced the mineralization of chloramphenicol antibiotic

Due to livestock wastewater irrigation, soil is becoming one of the major sinks of antibiotics in the environment. Recently, it is getting recognized that a variety of minerals under low moisture conditions can induce strong catalytic hydrolysis to antibiotics. However, the relative importance and implication of soil water content (WC) for natural attenuation of soil residual antibiotics has not been well recognized. In order to explore the optimal moisture levels and the key soil properties dominating for the high catalytic hydrolysis activities of soils, this study collected 16 representative soil samples across China, and assessed their performances to degrade chloramphenicol (CAP) under different moisture levels. The results showed that the soils with low organic matter contents (< 20 g/kg) and high amounts of crystalline Fe/Al were particularly effective in catalyzing CAP hydrolysis when exposed to low WC (< 6%, wt/wt), leading to CAP hydrolysis half-lives of <40 d Higher WC greatly suppressed the catalytic activity of the soil. By utilizing this process, it is possible to integrate abiotic and biotic degradation to enhance the mineralization of CAP, attributing to that the hydrolytic products are more available for soil microorganisms. As expected, the soils experienced periodic dry-to-wet moisture conditions (i.e., the WC shifting from 1 to 5% to 20-35%, wt/wt) exhibited higher degradation and mineralization of ¹⁴C-CAP, in comparison with the constant wet treatment. Meanwhile, the bacterial community composition and the specific genera showed that the dry-to-wet fluctuation of soil WC relieved the antimicrobial stress to bacterial community. Our study verifies the critical role of soil WC in mediating the natural attenuation of antibiotics, and guides to remove antibiotics from both wastewater and soil.

Exploring antibiotic resistance load in paddy-upland rotation fields amended with commercial organic and chemical/slow release fertilizer

Agricultural fertilization caused the dissemination of antibiotic resistance genes (ARGs) in agro-ecological environment, which poses a global threat to crop-food safety and human health. However, few studies are known about the influence of different agricultural fertilization modes on antibiotic resistome in the paddy-upland rotation soils. Therefore, we conducted a field experiment to compare the effect of different fertilization (chemical fertilizer, slow release fertilizer and commercial organic fertilizer replacement at various rates) on soil antibiotic resistome in paddy-upland rotation fields. Results revealed that a total of 100 ARG subtypes and 9 mobile genetic elements (MGEs) occurred in paddy-upland rotation soil, among which MDR-ARGs, MLSB-ARGs and tet-ARGs were the dominant resistance determinants. Long-term agricultural fertilization remarkably facilitated the vertical accumulation of ARGs, in particular that bla ampC and tetO in relative abundance showed significant enrichment with increasing depth. It's worth noting that slow release fertilizer significantly increased soil ARGs, when comparable to manure with 20% replacing amount, but chemical fertilizer had only slight impact on soil ARGs. Fertilization modes affected soil microbial communities, mainly concentrated in the surface layer, while the proportion of Proteobacteria with the highest abundance decreased gradually with increasing depth. Furthermore, microbial community and MGEs were further proved to be essential factors in regulating the variability of ARGs of different fertilization modes by structural equation model, and had strong direct influence (λ = 0.61, p < 0.05; λ = 0. 55, p < 0.01). The results provided scientific guidance for reducing the spreading risk of ARGs and control ARG dissemination in agricultural fertilization.

Occurrence and prevalence of antibiotic resistance genes in apple orchard after continual application of anaerobic fermentation residues of pig manure

Fermented organic fertilizers made from pig manure contaminated with antibiotics are widely used in fruit tree production. However, their effects on the residual antibiotics and the spread of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in apple orchards are still largely unknown. In the present study, we detected 100 ARGs and 10 MGEs that were transferred from pig manure to an apple orchard. Compared with the original pig manure, significantly greater concentrations of tetracycline, chlortetracycline, oxytetracycline, sulfadiazine, and salfamethyldiazine were observed in anaerobic fermentation residues of the pig manure. The total relative abundance levels of ARGs on the apple pericarp surface, in the orchard soil treated with biogas slurry, and in the orchard soil treated with biogas residue were 122.5, 5.2, 1.4 times higher than those in pristine soil, respectively, which were primarily attributed to the increase in the relative abundance of some ARG subtypes, including blaCTX-M, blaTEM, ermC, sul2, tetO, vgaB, and vgb. Long-term biogas slurry and biogas residue applications to orchard soil enriched bioaccumulation of 10 ARGs and 1 MGEs on the apple pericarp surface with 67.98 the highest factor. This research indicates that the application of anaerobic fermentation residues of pig manure promoted the spread of ARGs in the soil and fruits and increased the level of ARG pollution in the orchard. Results of this study highlight the importance of assessing the ecological safety of organic fertilizers from the perspective of ARGs and indicate that efforts should be devoted to further reducing ARG levels in pig manure before its application to farmland.

Spread and driving factors of antibiotic resistance genes in soil-plant system in long-term manured greenhouse under lead (Pb) stress

Livestock manure is often used as fertilizer in greenhouses, resulting in simultaneous enrichment of heavy metals and antibiotic resistance genes (ARGs) in soils. The soil-plant system is a non-negligible way to spread ARGs; however, the effects of lead (Pb) on the spread of ARGs and their driving factors in the greenhouse soil-plant system remain unclear. In this present study, the occurrence of ARGs in greenhouse soils and their spread into plants under Pb stress were studied. Overall, Pb promoted the accumulation of ARGs in root endophytes at 10, 50, and 100 mg/kg as well as in soils at 10 and 200 mg/kg, but reduced the total relative abundance of ARGs in leaf endophytes. Particularly, Pb increased the mobile genetic elements (MGEs) relative abundance and endophytic bacterial community diversity in roots, consistent with the change in the total relative abundance of ARGs. Network analysis revealed that bacterial community and MGEs may jointly affect the migration of ARGs in the soil-plant system of greenhouses. Overall, this study extended our knowledge of how Pb can promote the transmission of ARGs to plant roots from greenhouse soils receiving long-term manure applications, which must be considered when assessing the risk of ARGs to public health.

The Phenomenon of Antibiotic Resistance in the Polar Regions: An Overview of the Global Problem

The increasing prevalence of antibiotic resistance is a global problem in human and animal health. This leads to a reduction in the therapeutic effectiveness of the measures used so far and to the limitation of treatment options, which may pose a threat to human health and life. The problem of phenomenon of antibiotic resistance affects more and more the polar regions. This is due to the increase in tourist traffic and the number of people staying at research stations, unmodernised sewage systems in inhabited areas, as well as the migration of animals or the movement of microplastics, which may contain resistant bacteria. Research shows that the presence of antibiotic resistance genes is more dominant in zones of human and wildlife influence than in remote areas. In a polluted environment, there is evidence of a direct correlation between human activity and the spread and survival of antibiotic-resistant bacteria. Attention should be paid to the presence of resistance to synthetic and semi-synthetic antibiotics in the polar regions, which is likely to be correlated with human presence and activity, and possible steps to be taken. We need to understand many more aspects of this, such as bacterial epigenetics and environmental stress, in order to develop effective strategies for minimizing the spread of antibiotic resistance genes. Studying the diversity and abundance of antibiotic resistance genes in regions with less anthropogenic activity could provide insight into the diversity of primary genes and explain the historical evolution of antibiotic resistance.

Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria

Animal fecal samples collected in the summer and winter from 11 herbivorous animals, including sable antelope (SA), long-tailed goral (LTG), and common eland (CE), at a public zoo were examined for the presence of antibiotic resistance genes (ARGs). Seven antibiotics, including meropenem and azithromycin, were used to isolate culturable multidrug-resistant (MDR) strains. The manures from three animals (SA, LTG, and CE) contained 10⁴-fold higher culturable MDR bacteria, including Chryseobacterium, Sphingobacterium, and Stenotrophomonas species, while fewer MDR bacteria were isolated from manure from water buffalo, rhinoceros, and elephant against all tested antibiotics. Three MDR bacteria-rich samples along with composite samples were further analyzed using nanopore-based technology. ARGs including lnu(C), tet(Q), and mef(A) were common and often associated with transposons in all tested samples, suggesting that transposons carrying ARGs may play an important role for the dissemination of ARGs in our tested animals. Although several copies of ARGs such as aph(3')-IIc, bla_L1, bla_IND-3, and tet(42) were found in the sequenced genomes of the nine MDR bacteria, the numbers and types of ARGs appeared to be less than expected in zoo animal manure, suggesting that MDR bacteria in the gut of the tested animals had intrinsic resistant phenotypes in the absence of ARGs.

Geographic patterns and determinants of antibiotic resistomes in coastal sediments across complex ecological gradients

Coastal areas are highly influenced by terrestrial runoffs and anthropogenic disturbances, commonly leading to ecological gradients from bay, nearshore, to offshore areas. Although the occurrence and distribution of sediment antibiotic resistome are explored in various coastal environments, little information is available regarding geographic patterns and determinants of coastal sediment antibiotic resistomes across ecological gradients at the regional scale. Here, using high-throughput quantitative PCR, we investigated the geographic patterns of 285 antibiotic resistance genes (ARGs) in coastal sediments across a  ~  200  km scale in the East China Sea. Sediment bacterial communities and physicochemical properties were characterized to identify the determinants of sediments antibiotic resistome. Higher richness and abundance of ARGs were detected in the bay samples compared with those in nearshore and offshore samples, and significant negative correlations between the richness and/or abundance of ARGs and the distance to coastline (DTC) were identified, whereas different types of ARGs showed inconsistency in their relationships with DTC. The composition of antibiotic resistome showed significant correlations with nutrition-related variables (including NH4 +-N, NO3 --N, and total phosphorus) and metals/metalloid (including As, Cu, Ni, and Zn), suggesting that terrestrial disturbances largely shape the antibiotic resistome. The Bipartite network showed strong associations between ARGs and mobile genetic elements (MGEs), and Partial Least Squares Path Modeling further revealed that terrestrial disturbance strength (as indicated by DTC) directly affected abiotic environmental conditions and bacterial community composition, and indirectly affected antibiotic resistome via MGEs. These findings provide insights into regional variability of sediment antibiotic resistome and its shaping path across complex ecological gradients, highlighting terrestrial disturbances as determinative forces in shaping coastal sediment antibiotic resistomes.

Antibiotic Resistomes and Microbiomes in the Surface Water along the Code River in Indonesia Reflect Drainage Basin Anthropogenic Activities

Water and sanitation are important factors in the emergence of antimicrobial resistance in low- and middle-income countries. Drug residues, metals, and various wastes foster the spread of antibiotic resistance genes (ARGs) with the help of mobile genetic elements (MGEs), and therefore, rivers receiving contaminants and effluents from multiple sources are of special interest. We followed both the microbiome and resistome of the Code River in Indonesia from its pristine origin at the Merapi volcano through rural and then city areas to the coast of the Indian Ocean. We used a SmartChip quantitative PCR with 382 primer pairs for profiling the resistome and MGEs and 16S rRNA gene amplicon sequencing to analyze the bacterial communities. The community structure explained the resistome composition in rural areas, while the city sampling sites had lower bacterial diversity and more ARGs, which correlated with MGEs, suggesting increased mobility potential in response to pressures from human activities. Importantly, the vast majority of ARGs and MGEs were no longer detectable in marine waters at the ocean entrance. Our work provides information on the impact of different influents on river health as well as sheds light on how land use contributes to the river resistome and microbiome.

Unravelling the Portuguese Coastal and Transitional Waters' Microbial Resistome as a Biomarker of Differential Anthropogenic Impact

Portugal mainland and Atlantic archipelagos (Madeira and Azores) provide a wide array of coastal ecosystems with varying typology and degrees of human pressure, which shape the microbial communities thriving in these habitats, leading to the development of microbial resistance traits. The samples collected on the Portuguese northeast Atlantic coast waters show an unequivocal prevalence of Bacteria over Archaea with a high prevalence of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several taxa, such as the Vibrio genus, showed significant correlations with anthropogenic pollution. These anthropogenic pressures, along with the differences in species diversity among the surveyed sites, lead to observed differences in the presence and resistance-related sequences' abundance (set of all metal and antibiotic resistant genes and their precursors in pathogenic and non-pathogenic bacteria). Gene ontology terms such as antibiotic resistance, redox regulation and oxidative stress response were prevalent. A higher number of significant correlations were found between the abundance of resistance-related sequences and pollution, inorganic pressures and density of nearby population centres when compared to the number of significant correlations between taxa abundance at different phylogenetic levels and the same environmental traits. This points towards predominance of the environmental conditions over the sequence abundance rather than the taxa abundance. Our data suggest that the whole resistome profile can provide more relevant or integrative answers in terms of anthropogenic disturbance of the environment, either as a whole or grouped in gene ontology groups, appearing as a promising tool for impact assessment studies which, due to the ubiquity of the sequences across microbes, can be surveyed independently of the taxa present in the samples.

Effects of Broad-Spectrum Antibiotic (Florfenicol) on Resistance Genes and Bacterial Community Structure of Water and Sediments in an Aquatic Microcosm Model

This study evaluates the effects of a broad-spectrum antibiotic (florfenicol) on antibiotic resistance genes (ARGs) and bacterial community structure in aquatic environments. We constructed an indoor aquatic microcosm model, adding different concentrations of florfenicol (0.1, 1, 10, 100 mg L-1), and water and sediment samples were collected after 0, 7, 30, and 60 days. qPCR and 16S rDNA amplicon sequencing were used to study the changes in the ARGs and bacterial community structure of the collected samples. The results show that the inclusion of florfenicol resulted in an increased abundance of the floR and optrA genes. Adding 100 mg L-1 florfenicol to the water increased the abundance of optrA gene copies with the maximum on the Day 7, and increased the abundance of floR gene copies with the maximum on Day 30. Adding 100 mg L-1 florfenicol to the sediment increased the abundance of floR and optrA genes by one order of magnitude on Day 60. Meanwhile, the average number of operational taxonomic units (OTUs) in the water samples was 257, and the average number of OTUs in sediment samples was 823. The bacterial community diversity and richness in sediments were higher than those in water. The difference between the maximal and minimal values of the Shannon diversity index in the water and sediment samples was 4.36 and 1.95, respectively. The effect of florfenicol on the bacterial community structure in water was much higher than that in sediment. At 30 days, the diversity index and richness index of the florfenicol treatment groups with 1 and 10 mg L-1 concentrations began to increase; at 60 days, the diversity and richness indices of the 100 mg L-1 florfenicol treatment group began to increase. The samples at the same sampling time in the sediments clustered closer together. The results of this study provide a scientific basis for guiding the rational use of florfenicol in aquaculture, maintaining a healthy and stable microecological environment in aquaculture, and provide theoretical data for environmental ecological risk assessment and safety management caused by microbial resistance under the abuse of florfenicol.

Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes

Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.

Effects of iron mineral adhesion on bacterial conjugation: Interfering the transmission of antibiotic resistance genes through an interfacial process

Bacterial conjugation is one of the most prominent ways for antibiotic resistance genes (ARGs) transmission in the environment. Interfacial interactions between natural colloidal minerals and bacteria can alter the effective contact of bacteria, thereby affecting ARGs conjugation. Understanding the impact of iron minerals, a core component of colloidal minerals, on ARGs conjugation can help assess and intervene in the risk of ARGs transmission. With three selected iron minerals perturbation experiments, it was found that the conjugative transfer of plasmid that carried kanamycin resistance gene was 1.35 - 3.91-fold promoted by low concentrations of iron minerals (i.e., 5 - 100 mg L^-1), but inhibited at high concentrations (i.e., 1000 - 2000 mg L^-1) as 0.10 - 0.22-fold. Conjugation occurrence was highly relevant to the number of bacteria adhering per unit mass of mineral, thus switch in the adhesion modes of mineral-bacterial determined whether the conjugate transfer of ARGs was facilitated or inhibited. In addition, a unified model was formularized upon the physicochemical and physiological effects of adhesion on conjugation, and it can be used in estimating the critical inhibitory concentration of different iron minerals on conjugation. Our findings indicate natural colloidal minerals have great potential for applications in preventing the environmental propagation of ARGs through interfacial interactions.

Tracking antibiotic resistance through the environment near a biosolid spreading ground: Resistome changes, distribution, and metal(loid) co-selection

The application of urban wastewater treatment plants (WWTPs) products to agricultural lands has contributed to the rising level of antibiotic resistance and drawn a critical public health concern. It has not been thoroughly investigated at which spatial scales a biosolid applied area as a potentially predominant source affects surrounding soil resistomes. This study investigated distribution and impact of WWTP biosolids treated with anaerobic digestion on an agricultural area. Heterotrophic plate counts (HPCs) and quantitative polymerase chain reaction (qPCR) were performed for detection of selected antibiotic-resistant bacteria (ARB), selected antibiotic resistance genes (ARGs), intI1 genes, and 16S rRNA genes. Biosolid samples contained significantly higher levels of selected ARGs than the raw agricultural soils (p < 0.05). The average relative abundances of intI1, sul1, bla_SHV, and ermB genes were significantly higher in biosolid-amended soils than nearby agricultural soils (p < 0.05). Spatial interpolation analysis of relative gene abundances of intI1, sul1, sul2, and tetW across the studied area further indicated directional trends towards the northwest and southeast directions, highlighting possible airborne spread. Concentrations of Co, Cu, Ni, and Fe were found to be significantly and positively correlated with relative abundances of intI1, sul1, and tetW genes (p < 0.05). The resistance ratios of culturable antibiotic-resistant bacteria in agricultural soils with biosolid amendments were generally identical to those without biosolid amendments. This study will advance the understanding of the antibiotic resistome in agricultural soils impacted by long-term waste reuse and inform the evaluation strategies for future biosolids application and management.

Abundance and diversity of antibiotic resistance genes and bacterial communities in the western Pacific and Southern Oceans

This study investigated the abundance and diversity of antibiotic resistance genes (ARGs) and the composition of bacterial communities along a transect covering the western Pacific Ocean (36°N) to the Southern Ocean (74°S) using the Korean icebreaker R/V Araon (total cruise distance: 14,942 km). The relative abundances of ARGs and bacteria were assessed with quantitative PCR and next generation sequencing, respectively. The absolute abundance of ARGs was 3.0 × 10⁶ ± 1.6 × 10⁶ copies/mL in the western Pacific Ocean, with the highest value (7.8 × 10⁶ copies/mL) recorded at a station in the Tasman Sea (37°S). The absolute abundance of ARGs in the Southern Ocean was 1.8-fold lower than that in the western Pacific Ocean, and slightly increased (0.7-fold) toward Terra Nova Bay in Antarctica, possibly resulting from natural terrestrial sources or human activity. β-Lactam and tetracycline resistance genes were dominant in all samples (88-99%), indicating that they are likely the key ARGs in the ocean. Correlation and network analysis showed that Bdellovibrionota, Bacteroidetes, Cyanobacteria, Margulisbacteria, and Proteobacteria were positively correlated with ARGs, suggesting that these bacteria are the most likely ARG carriers. This study highlights the latitudinal profile of ARG distribution in the open ocean system and provides insights that will help in monitoring emerging pollutants on a global scale.

Biological units of antimicrobial resistance and strategies for their containment in animal production

The increasing prevalence of antimicrobial resistant bacterial infections has ushered in a major global public health crisis. Judicious or restricted antimicrobial use in animal agriculture, aiming to confine the use for the treatment of infections, is the most commonly proposed solution to reduce selection pressure for resistant bacterial strains and resistance genes. However, a multifaceted solution will likely be required to make acceptable progress in reducing antimicrobial resistance, due to other common environmental conditions maintaining antimicrobial resistance and limited executionary potential as human healthcare and agriculture will continue to rely heavily on antimicrobials in the foreseeable future. Drawing parallels from systematic approaches to the management of infectious disease agents and biodiversity loss, we provide examples that a more comprehensive approach is required, targeting antimicrobial resistance in agroecosystems on multiple fronts simultaneously. We present one such framework, based on nested biological units of antimicrobial resistance, and describe established or innovative strategies targeting units. Some of the proposed strategies are already in use or ready to be implemented, while some require further research and discussion among scientists and policymakers. We envision that antimicrobial resistance mitigation strategies for animal agriculture combining multiple tools would constitute powerful ecosystem-level interventions necessary to mitigate antimicrobial resistance.

Antimicrobial resistance in Antarctica: is it still a pristine environment?

Although the rapid spread of antimicrobial resistance (AMR), particularly in relation to clinical settings, is causing concern in many regions of the globe, remote, extreme environments, such as Antarctica, are thought to be relatively free from the negative impact of human activities. In fact, Antarctica is often perceived as the last pristine continent on Earth. Such remote regions, which are assumed to have very low levels of AMR due to limited human activity, represent potential model environments to understand the mechanisms and interactions underpinning the early stages of evolution, de novo development, acquisition and transmission of AMR. Antarctica, with its defined zones of human colonisation (centred around scientific research stations) and large populations of migratory birds and animals, also has great potential with regard to mapping and understanding the spread of early-stage zoonotic interactions. However, to date, studies of AMR in Antarctica are limited. Here, we survey the current literature focussing on the following: i) Dissection of human-introduced AMR versus naturally occurring AMR, based on the premise that multiple drug resistance and resistance to synthetic antibiotics not yet found in nature are the results of human contamination ii) The potential role of endemic wildlife in AMR spread There is clear evidence for greater concentrations of AMR around research stations, and although data show reverse zoonosis of the characteristic human gut bacteria to endemic wildlife, AMR within birds and seals appears to be very low, albeit on limited samplings. Furthermore, areas where there is little, to no, human activity still appear to be free from anthropogenically introduced AMR. However, a comprehensive assessment of AMR levels in Antarctica is virtually impossible on current data due to the wide variation in reporting standards and methodologies used and poor geographical coverage. Thus, future studies should engage directly with policymakers to promote the implementation of continent-wide AMR reporting standards. The development of such standards alongside a centralised reporting system would provide baseline data to feedback directly into wastewater treatment policies for the Antarctic Treaty Area to help preserve this relatively pristine environment. Video Abstract.

Application of magnetic biochar/quaternary phosphonium salt to combat the antibiotic resistome in livestock wastewater

The overuse and misuse of antibiotics in animal breeding for disease treatment and growth enhancement have been major drivers of the occurrence, diffusion, and accumulation of antibiotic resistance genes (ARGs) in wastewater. Strategies to combat ARG dissemination are pressingly needed for human and ecological safety. To achieve this goal, a biochar-based polymer, magnetic biochar/quaternary phosphonium salt (MBQ), was applied in livestock wastewater and displayed a high performance in bacterial deactivation and ARG decrease. Efficient antibacterial effects were achieved by both MBQ and quaternary phosphonium salt; however, the abundance and fold change of ARGs in the MBQ treatment indicated a more powerful ARG dissemination control than quaternary phosphonium salt. The application of MBQ evidently reduced the microbial diversity and may primarily be responsible for altering the ARG profiles in wastewater. Network, redundancy, and variation partitioning analyses were further employed to reveal that the microbial community and the presence of mobile genetic elements were two critical factors shaping the pattern of the antibiotic resistome in livestock wastewater. Considered together, these findings extend the application field of biochar and have important implications for reducing ARG dissemination risks in livestock wastewater.

Metagenomic analysis reveals microbiome and resistome in the seawater and sediments of Kongsfjorden (Svalbard, High Arctic)

Kongsfjorden in the high Arctic, a typical Arctic fjord, experienced long-time input of nutrients and pollutants from the remote and local resources, providing a platform for characterizing the diversity and distribution of antibiotic resistance genes (ARGs). However, the microbiome and antibiotic resistome in this pristine marine system have not been well documented. The present study aimed to characterize the diversity and distribution of bacterial communities and associated ARGs in seawater (12 samples) and sediments (13 samples) of Kongsfjorden via metagenomic analysis. In terms of both bacterial community compositions and ARG profiles, the seawater was significantly distinct from sediment. Only 29 ARG subtypes were detected in the Arctic seawater and sediments. Furthermore, three geochemical factors (i.e., longitude, depth, and PO₄^3-) greatly influenced the bacterial communities in sediment samples, while longitude, depth, and latitude were crucial geochemical factors influencing the ARG profiles in sediment samples. Procrustes analysis revealed a significant correlation between bacterial community compositions and ARG profiles in seawater and sediment samples. Further analysis revealed the metagenome-assembled genomes (MAGs) with ARG subtypes. Overall, our study provides insights into the microbiome and resistome in a pristine Arctic fjord, thereby providing vital information for environmental management.

Influence of soil characteristics and metal(loid)s on antibiotic resistance genes in green stormwater infrastructure in Southern California

The synergetic effects of metal(loid)s and soil characteristics on bacterial antibiotic resistance genes (ARGs) in green stormwater infrastructure (GSI) has been relatively understudied. Surface soil samples from six GSIs in Southern California over three time periods were assessed for selected ARGs, class 1 integron-integrase genes (intI1), 16S rRNA genes, and bioavailable and total concentrations of nine metal(loid)s, to investigate the relationships among ARGs, soil characteristics, and co-occurring metal(loid)s. Significant correlations existed among relative gene abundances (sul1, sul2, tetW, and intI1), total metal(loid)s (arsenic, copper, lead, vanadium, and zinc), and bioavailable metal(loid) (arsenic) (r = 0.29-0.61, p_adj < 0.05). Additionally, soil texture, organic matter, and nutrients within GSI appeared to be significantly correlated with relative gene abundances of sul1, sul2, and tetW (r = -0.57 to 0.59, p_adj < 0.05). Multiple regression models significantly improved the estimation of ARGs in GSI when considering multiple effects of soil characteristics and metal(loid)s (r = 0.74, p_adj < 0.001) compared to correlation results. Total arsenic was a significant (positive) correlate in all the regression models of relative gene abundances. This work provides new insights into co-dependencies between GSI ARGs and co-occurring metal(loid)s, indicating the need for risk assessment of metal(loid)-influenced ARG proliferation.

Grassland ecology system: A critical reservoir and dissemination medium of antibiotic resistance in Xilingol Pasture, Inner Mongolia

Antibiotic resistance is a major threat to human health. It is necessary to explore all the potential sources and comprehend the pathways that antibiotic resistance genes (ARGs) are transmitted. In this study, by applying high-throughput quantitative PCR and high-throughput sequencing, ARGs and microbial community structure were determined, to understand the reservoirs and spread of ARGs in the Xilingol grassland system. A total of 151,140 and 138 different ARGs were observed in manure, soil, and water samples, respectively. Only 12 ARGs were shared in all environmental and animal manure samples. Multidrug defense system, such as efflux pump, was the most dominant factor in manure and soil samples, followed by antibiotic deactivation processes. These genes coffering resistance to major classes of antibiotics including β_Lactamase (bla_SFO, fox5, bla_CTX-M-04, bla_OXY), vancomycin (vanC-03, vanXD), MLSB (vatE-01, mphA-01), aminoglycoside (aadA2-01), Multidrug (oprJ) and others (oprD, qacEdelta1-02), except sulfonamide and tetracycline. The 12 ARGs were significantly enriched in water samples compared to manure and soil samples (p < 0.01) and demonstrated that the water environment was an important transmission source of ARGs in the grassland. The highest enrichment was up to 324.5-fold. Moreover, the 12 shared ARGs were positively correlated with the mobile genetic elements (p < 0.01). The nonrandom co-occurrence network patterns between ARGs and microbial community suggested that a total of three bacterial phyla were viewed as the potential ARGs hosts. These findings indicate that ARGs were highly enriched in water samples, demonstrating that the water environment was a critical source and sink of ARGs in the grassland system. It may illuminate the mechanism stressing the effects of human activity on the occurrence and transmission of ARGs in the grassland system.

Performance Efficiency of Conventional Treatment Plants and Constructed Wetlands towards Reduction of Antibiotic Resistance

Domestic and industrial wastewater discharges harbor rich bacterial communities, including both pathogenic and commensal organisms that are antibiotic-resistant (AR). AR pathogens pose a potential threat to human and animal health. In wastewater treatment plants (WWTP), bacteria encounter environments suitable for horizontal gene transfer, providing an opportunity for bacterial cells to acquire new antibiotic-resistant genes. With many entry points to environmental components, especially water and soil, WWTPs are considered a critical control point for antibiotic resistance. The primary and secondary units of conventional WWTPs are not designed for the reduction of resistant microbes. Constructed wetlands (CWs) are viable wastewater treatment options with the potential for mitigating AR bacteria, their genes, pathogens, and general pollutants. Encouraging performance for the removal of AR (2-4 logs) has highlighted the applicability of CW on fields. Their low cost of construction, operation and maintenance makes them well suited for applications across the globe, especially in developing and low-income countries. The present review highlights a better understanding of the performance efficiency of conventional treatment plants and CWs for the elimination/reduction of AR from wastewater. They are viable alternatives that can be used for secondary/tertiary treatment or effluent polishing in combination with WWTP or in a decentralized manner.

Seasonal disparities and source tracking of airborne antibiotic resistance genes in Handan, China

The transmission of airborne antibiotic resistance genes (ARGs) loaded on particle is a significant global public health concern. Up to date, the dispersal pattern of airborne ARGs remains unclear despite their critical role in multiregional transmission. In this study, airborne ARGs loaded on fine particulate matter (PM_2.5) and source tracking based on the airflow trajectories were performed by the potential source contribution function (PSCF) and concentration weighted trajectory (CWT) model. The results show that the absolute abundance of ARG subtypes were generally twice times higher in the winter season than that in the summer season, which could be attributable to winter haze events with high particulate matter concentrations in Handan. Exogenous input from serious haze events and local release of ARGs loaded on PM_2.5 of air masses may cause higher levels of ARGs in the winter. Moreover, based on the positive correlation between the abundance of ARGs and PM_2.5 concentration, a source tracing model of airborne ARGs was proposed to the estimate of ARGs release and dissemination. This study highlights airborne ARGs transmission loaded on PM_2.5 of air masses, which facilitating the global spread of antibiotic resistance.