Co-selection of antibiotic and metal resistance

Mitigating the risk of antibiotic resistance and pathogenic bacteria in swine waste: The role of ectopic fermentation beds

The ectopic fermentation bed (EFB) is used to recycle animal waste, but the fate and dynamic change of antibiotic resistance genes (ARGs) with biocide or heavy metal resistance genes (B/MRGs) and pathogens remain unclear. We performed metagenomic sequencing on 129 samples to study the resistome and bacteriome in pig feces from 24 farms, comparing these profiles with EFBs from five farms, and one farm's EFB was monitored for 154 days. Results showed pig feces from different cities (Chengdu, Meishan, and Chongqing) shared 284 of 311 ARG subtypes, with over 70 % being high-risk ARGs, and 106 of 114 pathogenic bacteria. Swine farms were heavily contaminated with co-occurrences of risky ARGs, B/MRGs, and pathogenic hosts, particularly Escherichia coli and Streptococcus suis being hosts of multidrug ARGs. The application of EFBs markedly mitigated these risks in feces, showing a 3.09-fold decrease in high-risk ARGs, a 72.22 % reduction in B/MRGs, a 3.95-fold drop in prioritized pathogens, an 89.09 % decline in the relative abundance of pig pathogens, and a simplification of their correlation networks and co-occurrence patterns. A mantel analysis revealed that metal contents (Fe, Mn, and Cu) and time influenced pathogen and ARG profiles. Pathogens, ARGs, and risk ARGs exhibited periodic variations, peaking at days 14, 84, and 154, with 70-day intervals. This study provides a comprehensive assessment of the risks associated with pig feces and EFBs and demonstrates that EFBs reduce ARG risks by inhibiting their associations with B/MRGs and pathogens. These findings can help guide and improve the management of antimicrobial resistance and pathogenic contaminants in EFB applications to reduce environmental pollution.

Response of the partial denitrification coupled with anaerobic ammonia oxidation system to disinfectant residues stress

The extensive use of disinfectants, especially NaClO, has resulted in chlorine disinfectant residues entering and impairing the biological treatment system. This study combined with long-term stress and transient shock of chlorine residues to comprehensively evaluate the variations of nitrogen removal performance, microbial community and antibiotic resistance genes composition in the PD/A system. The results showed that low concentration NaClO had no obvious harm to the system, but high concentration (>1 mg/L) NaClO would destroy the nitrogen removal performance of PD/A system. Interestingly, microorganisms in biofilm were more resistant to chlorine residues than that in sludge. Anaerobic ammonia oxidizing bacteria suffered more harm than denitrifying microorganisms, and chlorine residues mainly inhibited the process of converting N2H4 to N2 in anammox reaction. In addition, this study found that sludge showed a more significant increase in ARGs abundance and risk than biofilm. Moreover, risk assessments indicated that chlorine residues increased the risk of ARGs in PD/A systems.

Impact of fluoroquinolone and heavy metal pollution on antibiotic resistance maintenance in aquatic ecosystems

BACKGROUND

Freshwater pollution with compounds used during anthropogenic activities could be a major driver of antibiotic resistance emergence and dissemination in environmental settings. Fluoroquinolones and heavy metals are two widely used aquatic pollutants that show a high stability in the environment and have well-known effects on antibiotic resistance selection. However, the impact of these compounds on antibiotic resistance maintenance in aquatic ecosystems remains unknown. In this study, we used a microcosm approach to determine the persistence of two fluoroquinolones (ciprofloxacin, ofloxacin) and two heavy metals (copper and zinc) in the Rhône river over 27 days. In addition, we established links between antibiotic and metal pollution, alone and in combination, and the composition of freshwater bacterial communities, the selection of specific members and the selection and maintenance of antibiotic and metal resistance genes (ARGs and MRGs) using a metagenomics approach.

RESULTS

Whereas ofloxacin was detected at higher levels in freshwater after 27 days, copper had the strongest influence on bacterial communities and antibiotic and metal resistance gene selection. In addition, heavy metal exposure selected for some ARG-harboring bacteria that contained MRGs. Our research shows a heavy metal-driven transient co-selection for fluoroquinolone resistance in an aquatic ecosystem that could be largely explained by the short-term selection of Pseudomonas subpopulations harboring both fluoroquinolone efflux pumps and copper resistance genes.

CONCLUSION

This research highlights the complexity and compound-specificity of dose-response relationships in freshwater ecosystems and provides new insights into the medium-term community structure modifications induced by overall sub-inhibitory levels of antibiotic and heavy metal pollution that may lead to the selection and maintenance of antibiotic resistance in low-impacted ecosystems exposed to multiple pollutants.

Unveiling pathogenicity and resistance profiles of non-cholera Vibrio from an urban estuary

Vibrio spp. are endowed with high metabolic diversity, being known for their pathogenicity and ability to acquire and disseminate resistance genes. Here, non-cholera Vibrio spp. were isolated from water samples in Guanabara Bay (GB, Brazil), a recreational estuary. Thirty-five strains non-susceptible to antimicrobials were investigated regarding their pathogenic and resistance profiles. Genes encoding for hemolysins and secretion systems were among the detected virulence traits. Beta-lactam, aminoglycoside, and quinolone resistance genes were investigated in strains phenotypically resistant to these classes, revealing the carriage of the blaSHV and aac(6')-Ie-aph(2')-Ia genes in 50% and 11.1% of the tested strains, respectively. Integrons (classes 1 and 3) and heavy metal resistance genes were detected, likely reflecting local pollution levels. Genome sequencing of five strains revealed further insights regarding their associated resistome and virulome, confirming phenotypic-derived results. Our findings imply that pathogenic and antimicrobial-resistant Vibrio spp. are found in the GB, thus posing a risk to public health.

Using a harmonised study design and quantitative tool-box reveals major inconsistencies when investigating the main drivers of water and biofilm antibiotic resistomes in different rivers

The spread of antibiotic resistance (ABR) via surface waters is of increasing concern. Large-scale studies investigating ABR drivers in different water bodies and habitats with uniform quantitative methods are largely missing. Here, we present a comprehensive investigation on ABR occurrence and drivers in water and biofilms of four Austrian rivers over a one-year-cycle using a harmonised quantitative tool-box and study-design. At the bacterial community level, human faecal pollution was a main factor driving the aquatic riverine resistome. Despite relatively low concentrations, also antibiotics and metals showed significant correlations, however to a different extent in the different rivers. At the organismic level, a decoupling of the Escherichia coli resistome from the bacterial community resistomes was observed. In biofilms, the relationships with anthropogenic pollution factors were heterogeneous and markedly dampened. Our results clearly show that general conclusions about the role of biofilms, the influence of pollution or the prevalence of resistance genes or phenotypic resistances must be drawn with caution. Results are dependent on the river and local situation of the sampling sites due to the large environmental heterogeneity. International harmonisation of the methodology and general awareness of this problem shall contribute to better understand environmental ABR to develop effective mitigation strategies.

Antimicrobial effects, and selection for AMR by non-antibiotic drugs in a wastewater bacterial community

Antimicrobial resistance (AMR) is a major threat to human, animal, and crop health. AMR can be directly selected for by antibiotics, and indirectly co-selected for by biocides and metals, at environmentally relevant concentrations. Some evidence suggests that non-antibiotic drugs (NADs) can co-select for AMR, but previous work focused on exposing single model bacterial species to predominately high concentrations of NADs. There is a significant knowledge gap in understanding a range of NAD concentrations, (including lower µg/L concentrations found in the environment) on mixed bacterial communities containing a diverse mobile resistome. Here, we determined the antimicrobial effect and selective potential of diclofenac, metformin, and 17-β-estradiol, NADs that are commonly found environmental pollutants, in a complex bacterial community using a combination of culture based, metagenome, and metratranscriptome approaches. We found that diclofenac, metformin, and 17-β-estradiol at 50 µg/L, 26 µg/L, and 24 µg/L respectively, significantly reduced growth of a bacterial community although only 17-β-estradiol selected for an AMR marker using qPCR (from 7 µg/L to 5400 µg/L). Whole metagenome sequencing indicated that there was no clear selection by NADs for antibiotic resistance genes, or effects on community composition. Additionally, increases in relative abundance of some specific metal resistance genes (such as arsB) were observed after exposure to diclofenac, metformin, and 17-β-estradiol. These results indicate that environmentally relevant concentrations of NADs are likely to affect community growth, function, and potentially selection for specific metal resistance genes.

Antibiotic resistance profile of facultative deep-sea psychro-piezophile bacteria from the Arabian Sea and their relation with physicochemical factors

Antibiotic resistance (ABR) is a significant global challenge, with antibiotics from various sources ending up in the ocean and affecting marine life. Profiling ABR in deep-sea bacteria is crucial for understanding the spread of ABR from environmental microbes to clinical pathogen and vice-versa. We evaluated facultative psychro-piezophile deep-sea bacteria from different depths of the Arabian Sea for their resistance to 20 commercial antibiotics. Bacteria from Zone 5 (2000-3000 m) exhibited the highest multiple antibiotic resistance (MAR) index (0.90), identifying it as a significant reservoir of ABR. Zone 1 (5-100 m) isolates (average 20 %) showed the highest resistance to synthetic antibiotics. Zone 3 (500-1000 m) isolates were highly resistant to diverse classes of antibiotics, separating upper (zone 1 and 2 (100-500 m) and deeper sea zones (zone 4 (1000-2000 m) and 5). The identified isolates belong to Bacillus, Niallia, Escherichia, Cytobacillus, and Pseudomonas genera. Additionally, antibiotic resistance genes (ARGs) such as StrB (2 isolates) and SXT integrase (1 isolate) were detected only in Zone 5 isolates. The SulII gene (19 isolates) was present across all zones. PCA analysis revealed a negative correlation between resistance and physicochemical factors (macronutrients like phosphate (PO43-), nitrate (NO3-), nitrite (NO2-), and ammonia (NH3); micronutrient and heavy metals like (iron (Fe), manganese (Mn), zinc (Zn), copper (Cu), nickel (Ni)), aluminium (Al), cadmium (Cd), and chromium (Cr)), except for Phosphate (0.65). Overall, this study is the first to provide valuable insights into the prevalence of ABR using culture-dependent methods and its correlation with physicochemical factors in the deep-sea environments of the Arabian Sea.

Distribution, removal and potential factors affecting antibiotics occurrence in leachate from municipal solid waste incineration plants in China

Leachate from municipal solid waste (MSW) incineration harbors a plethora of contaminants, including antibiotics and antibiotic resistance genes (ARGs). However, the understanding of such leachate is markedly scant in comparison to that of landfill leachate. In this study, the distribution and removal of 8 sulfonamides (SAs), 4 quinolones (FQs), and 4 macrolides (MLs) antibiotics in leachate from 14 MSW incineration plants in representative cities across different regions of China were investigated. In addition, potential factors affecting the contamination levels of antibiotics and ARGs in fresh leachate were evaluated. The results showed that the total concentration of target antibiotics in fresh leachate ranged from 4406.1 to 14,930.6 ng/L. Notably, the antibiotic distribution in leachate exhibited regional disparities, influenced by economic status, climatic conditions, and waste separation policies. The absolute abundance of total ARGs ranged from 1.3 × 107-4.0 × 108 copies/mL, with the mobile genetic elements intl1 facilitates the dissemination of qnrS, sul1 and sul2. No distinct regional distribution of the ARGs was observed among different cities. Antibiotic and ARGs distributions were significantly correlated with total organic carbon, pH, ammonia nitrogen, heavy metals, and microbial communities. Moreover, SAs were identified as contributors to the proliferation and spread of corresponding ARGs. Fourteen typical "anaerobic-anoxic/aerobic-anoxic/aerobic-ultrafiltration-nanofiltration " treatment processes removed the target antibiotics effectively (76.1 %-97.0 %). Biodegradation was considered to be the dominant antibiotic removal pathway, removing 62.0 %-90.9 % of antibiotics, while sludge adsorption removed only 1.0 %-11.7 %. This research furnishes valuable insights into the fate of antibiotics in MSW incineration leachate.

Co-selection of antibiotic resistance and heavy metal tolerance in bacterial species isolated from automobile scrapyard soils

This study investigates the physicochemical properties, heavy metal concentrations, and bacterial profiles of contaminated scrapyard soils compared to fertile agricultural soil. The results indicate that scrapyard soils exhibit higher bulk density (1.10 1.30 g/cm³), lower organic carbon (0.80 1.10%), and reduced organic matter (1.37 1.90%) levels, suggesting deterioration in soil fertility. Electrical conductivity is significantly elevated (0.70 0.80 dS/m), indicating increased ionic strength. Heavy metal analysis reveals significantly higher concentrations of Pb (14 18 mg/kg), Cd (3 7 mg/kg), Zn (20 40 mg/kg), Cu (23 35 mg/kg), Ni (23 30 mg/kg), and As (3.85 5.5 mg/kg). Bacterial loads in scrapyard soils (3.08 3.76 Log CFU/g) are considerably lower than in control soil (7.88 Log CFU/g), alongside decreased soil enzyme activities, including dehydrogenase (130 170 µg TPF/g/h), urease (110 130 µg NH₄⁺/g/h), phosphatase (70-90 µg pNP/g/h), and catalase (85-95 µg O₂/g/h). The study isolates Sphingomonas paucimobilis, Klebsiella aerogenes, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas reactans, and Bacillus subtilis, which exhibit varying resistance to antibiotics and heavy metals. A strong correlation is observed between heavy metal tolerance and antibiotic resistance (r = 0.78 0.88, P < 0.05), suggesting a synergistic effect where metal exposure enhances bacterial resilience to antibiotics. Notably, the MICs of tetracycline and ampicillin increase substantially in Cd-exposed isolates (up to 35 µg/mL and 25 µg/mL, respectively), while Ni exposure in Pseudomonas reactans results in a two-fold increase in the MIC of chloramphenicol (from 10.5 µg/mL to 20 µg/mL). The correlation between soil enzyme activity and dominant bacterial species further highlights the influence of heavy metal contamination on microbial function. These findings underscore the environmental risks posed by scrapyard contamination and the adaptive mechanisms of multi-resistant bacteria in response to heavy metal stress.

Multidimensional tolerance landscapes reveal antibiotic-environment interactions affecting population dynamics of wastewater bacteria

City sewers harbor diverse bacterial communities that are continuously exposed to a myriad of antibiotic residues resulting from human consumption and excretion. Despite their sub-inhibitory concentrations in sewage, these pharmaceutical residues affect the growth rate and the yield of susceptible wastewater-associated bacteria. Moreover, environmental conditions in sewers are complex, including variations in temperature and, in many coastal city sewers, salinity. These variables can modulate antibiotic tolerance and therefore affect the dynamics of microbial populations. To explore such interactions between antibiotics and abiotic environmental factors, we built continuous multivariate tolerance landscapes for three bacterial species commonly detected in sewage: Escherichia coli, the emerging pathogen Streptococcus suis, and a typical sewer dweller, Arcobacter cryaerophilus. We projected their intrinsic growth rate and carrying capacity onto a complex environment including temperature, salinity, and a range of concentrations of two antibiotics frequently measured in urban wastewater (ciprofloxacin and azithromycin). We revealed that antibiotic tolerance was maximal at salinities close to seawater for both E. coli and S. suis, and that the direction of the interaction between antibiotics and temperature is species dependent. In E. coli, we additionally observed a third-order interaction among salinity, temperature and antibiotics, highlighting the limits of predicting field dynamics of bacterial populations using standard laboratory measures. We projected these tolerance curves onto time series data of temperature and conductivity measured in the sewers of Barcelona. Our model highlights that low concentrations of antibiotics could exclude the most sensitive species, while interactions between antibiotics, temperature, and salinity substantially affected the dynamics of the more tolerant ones.

Unveiling plasmid diversity and functionality in pristine groundwater

BACKGROUND

Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

RESULTS

Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.

CONCLUSIONS

Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.

Resistance and Biodegradation of Triclosan and Propylparaben by Isolated Bacteria from Greywater

We investigated the relationship between antibiotic-resistance genes and the antimicrobial agents, triclosan (TCS) and propylparaben (PPB). The greywater microbiome was repeatedly exposed to triclosan and propylparaben and the effect was analyzed using a combination of PCR, Etest, Biolog, 16S rRNA sequencing, and liquid chromatography. The taxonomic identification points to very similar or even identical isolates, however, the phenotypic analysis suggests that their metabolic potential is different, likely due to genomic variation or differences in the expression of the substrate utilization pathways. For both triclosan and propylparaben, the antibiotic resistance levels among isolates remain consistent regardless of the exposure duration. This suggests that antibiotic-resistance genes are acquired rapidly and that their presence is not directly proportional to the level of micropollutant exposure. In a biodegradation test, TCS was reduced by 50% after 7 h, while PPB decreased only after 75 h. For TCS, the minimal inhibition concentration (MIC) ranged from 64 to above 256 mg/mL. Conversely, for PPB the MIC for the tested strains ranged between 512 and 800 mg/mL. This study highlights the complex interaction between household xenobiotics, greywater microorganisms, and the emergence of antibiotic resistance.

Diverse adaptation strategies of generalists and specialists to metal and salinity stress in the coastal sediments

Understanding the distinct roles and responses of bacterial community to environmental stressors is crucial for effective ecosystem management and conservation. Despite this, there is limited research on how environmental gradients specifically impact generalist and specialist subcommunities. This study investigates these subcommunities in the sediments of Jinzhou Bay, highlighting their distinct responses to environmental gradients. Generalists thrive in disturbed environments due to their broad ecological tolerances, while specialists show higher diversity in the stable, less contaminated upstream areas. At the genus level, Porphyrobacter and Subgroup_23 were identified as the dominant taxa of generalists, while Woeseia and Lutibacter were the dominant species of specialists. Physicochemical parameters, especially metals and salinity, significantly influence subcommunity composition. Generalists are adaptable to a wider range of factors, whereas specialists are affected by specific parameters, reflecting their narrower niches. The generalists exhibit a greater abundance of salinity tolerance genes compared to the specialists; however, this trend does not extend to metal resistance genes. Keystone taxa, primarily specialists, play crucial roles in maintaining community stability. Our results underscore the importance of considering both generalists and specialists in ecological assessments, offering insights for the management and conservation of bacterial microbial diversity in coastal ecosystems.

Environmental fate of antibiotic resistance genes in livestock farming

As emerging environmental pollutants, antibiotic resistance genes (ARGs) are prevalent in livestock farms and their surrounding environments. Although existing studies have focused on ARGs in specific environmental media, comprehensive research on ARGs within farming environments and their adjacent areas remains scarce. This review explores the sources, pollution status, and transmission pathways of ARGs from farms to the surrounding environment. Drawing on the "One Health" concept, it also discusses the potential risks of ARGs transmission from animals to human pathogens and the resulting impact on human health. Our findings suggest that the emergence of ARGs in livestock farming environments primarily results from intrinsic resistance and genetic mutations, while their spread is largely driven by horizontal gene transfer. The distribution of ARGs varies according to the type of resistance genes, seasonal changes, and the medium in which they are present. ARGs are disseminated into the surrounding environment via pathways such as manure application, wastewater discharge, and aerosol diffusion. They may be absorbed by humans, accumulating in the intestinal microbiota and subsequently affecting human health. The spread of ARGs is influenced by the interplay of microbial communities, antibiotics, heavy metals, emerging pollutants, and environmental factors. Additionally, we have outlined three control strategies: reducing the emergence of ARGs at the source, controlling their spread, and minimizing human exposure. This article provides a theoretical framework and scientific guidance for understanding the cross-media migration of microbial resistance in livestock farming environments.

Is use of antimicrobial growth promoters linked to antimicrobial resistance in food-producing animals? A systematic review

Antimicrobial resistance (AMR) poses a global threat to the health of humans, animals and plants, as well as the environment. In recent years, attention has increasingly focused on the role of antimicrobials as growth promoter (AGPs) in livestock. While the mechanism of action of AGPs is still poorly understood, mounting evidence suggests a link between AGP use and AMR. Consequently, several countries and regions have restricted/banned AGP use in livestock. However, such efforts encounter political, financial, social, and cultural challenges. This systematic review aims to investigate the impact of AGP use on AMR in food-producing animals and focused on the emergence of phenotypic resistance in Escherichia coli isolated from livestock exposed to AGPs. Overall, 7000 studies were screened at title, abstract and full text; from these, 10 were deemed eligible for inclusion in this review. Among the 10 selected studies, seven noted significant increase of AMR associated with AGP use. Significantly increased resistance levels to Highest Priority Critically Important Antimicrobials for human health such as ceftiofur, cefotaxime, ciprofloxacin, and nalidixic acid were observed among other antimicrobials. However, the studies revealed high risk of bias underscoring the need for further research. This review provides a deeper understanding of the consequences of AGP use and occurrence of AMR. It highlights the need for implementing efficient surveillance systems and fostering research into suitable alternatives to AGPs. A shift to sustainable husbandry practices including responsible AMU while safeguarding animal health, productivity and farmers' livelihoods are essential for successful policy implementation.

Distribution and relationship of heavy metals, microbial communities and antibiotic resistance genes in the riparian soils of Daye Lake, China

Heavy metals pose ecological and resistome risks to aquatic systems. To comprehensively assess the health status of aquatic ecosystems, it is necessary to quantify the ecological risks of heavy metals in riparian soils and their associations with microbial communities and antibiotic resistance genes (ARGs), yet related evidence was scarce. This study evaluated the potential ecological risk of heavy metal-contaminated riparian soils of Daye Lake, revealed the distribution of bacterial communities and ARGs by high-throughput sequencing techniques, and explored the association between heavy metals and bacterial communities and ARGs. The results showed that As, Cd, Cu, Pb, and Se were the primary polluting metals in the riparian soils of Daye Lake. Microbial community analysis presented that Proteobacteria (31.5%), Actinobacteria (30.3%), and Acidobacteria (14.1%) appeared to be the top three prevalent phylums, and seven pathogenic genera were identified based on VFDB. Correlation analysis showed that 17 bacterial communities among the top 50 bacterial genera had significant negative associations with heavy metals (r < -0.5; P < 0.05), and 10 bacterial communities had significant positive associations with heavy metals (r > 0.5; P < 0.05), indicating that heavy metals could exert co-selection forces on the microbial community. ARGs analysis presented that vancomycin, multidrug, and aminoglycoside resistance genes were the dominant ARGs. The co-occurrence of ARGs, virulence factor genes (VFGs), and mobile genetic elements (MGEs) (r > 0.8; P < 0.05) suggested high transmission risk of ARGs in environments. The significant correlations of heavy metals and ARGs (P < 0.05), co-occurrence of the resistance genes (MRGs) and ARGs (r > 0.8; P < 0.05), and significant associations between the geochemical enrichment of heavy metals and ARGs (P < 0.05) consistently indicated important impacts of heavy metals on environmental resistome risks. This research firstly revealed the associations between heavy metals and microbial communities and ARGs in riparian soils, which offers valuable insights into risk prevention and pollution control of heavy metals in the environment.

Does the land-use impact the risk of inducing antibiotic tolerance by heavy metal pollution?

The rise of antibiotic-resistant soil microbial communities is a critical global issue. Evidence suggests that heavy metals can select or co-select for tolerance to metals and antibiotics in soil bacteria, but it is unclear if this tolerance varies with land use. We tested the potential of bacterial communities to develop resistance to copper (Cu) or tetracycline (Tet) after amending soils from pristine forests, contaminated forests, and agricultural lands with 3000 mg kg-1 Cu and 6000 mg kg-1 tetracycline, separately. Results showed that bacterial communities of unamended contaminated forest soils had the highest initial tolerance to Cu, while unamended agricultural soils exhibited the highest initial tolerance to tetracycline. The inducibility of bacterial resistance to antibiotics after Cu amendment varied by land use. In pristine forests, Cu amendment significantly increased microbial tetracycline resistance, as indicated by bacterial community tolerance, likely due to higher biodiversity. In contaminated forests, Cu amendment did not induce tetracycline-resistance, as indicated by unchanged bacterial community tolerance, possibly because of existing metal pollution and compromised bacterial communities by metal pollution. In agricultural soils, microbial tetracycline resistance as indicated by bacterial community tolerance developed slowly, becoming evident only after 42 days. These findings reveal significant differences in environmental risks related to soil metal pollution across different land uses, highlighting the need for systematic studies on the mechanisms of bacterial resistance to antibiotics in metal-contaminated soils due to their human health implications.

Co-occurrence of arsenic and sewage pollutants in surface and groundwater and its implications for water treatment using membrane technology

Arsenic (As) enrichment in groundwater stems from natural and hydrogeochemical factors, leading to geological contamination. Groundwater and surface water are interconnected, allowing As migration and surface water contamination. The As contamination poses health risks through contaminated water consumption. Sewage discharge in rich-As water bodies alters environmental conditions, increasing the concentration of organic matter, carbonate and bicarbonate, nitrite, sulfate, and phosphate in water. These changes could enhance As solubilization and release to water. This review investigates the interactions between these contaminants, and their implications for membrane-based water treatment processes. Organic pollutants in surface water promote microbial growth, depleting oxygen and altering redox conditions, which enhances As solubilization and concentration in the water. The interaction between organic pollutants and As primarily occurs through adsorption and complexation, influenced by the pollutants' functional groups and the water's pH. Bicarbonates and pH play critical roles in determining As speciation (As(V) or As(III)), while oxidants like nitrate increase As mobility by promoting its oxidation. When arsenic is primarily present as As(V), membrane-based removal processes tend to be more efficient. Sulfur also affects As dynamics through microbial processes and adsorption onto sulfide minerals. When nitrate and sulfate are present, Donnan exclusion becomes a critical mechanism that affects arsenic removal by NF and RO membranes. Although membrane technologies maintain high As rejection rates (97-99 %), even in the presence of sewage pollutants, this advantage is offset by the challenges of fouling and the generation of highly concentrated waste streams. So, it is urgent to avoid raw or not adequately treated sewage in As-rich environments.

Copper induced augmentation of antibiotic resistance in Acinetobacter baumannii MCC 3114

Increasing antibiotic resistance among the common nosocomial pathogen i.e. Acinetobacter baumannii poses life threat to the health care workers as well as to the society. The dissemination of antibiotic resistance in this pathogen at an alarming rate could be not only due to the overuse of antibiotics but also due to the stress caused by exposure of bacterium to several environmental contaminants in their niches. In the present study, effect of copper stress on augmentation in the antibiotic resistance of A. baumannii MCC 3114 against three clinically used antibiotics was investigated along with the phenotypic and genotypic alterations in the cell. It induced 8, 44 and 22-fold increase in resistance against colistin, ciprofloxacin and levofloxacin, respectively. Moreover, the biofilm formation of adapted culture was significantly enhanced due to a dense EPS around the cell (as revealed by SEM images). The structural changes in EPS were demonstrated by FTIR spectroscopy. The adequate growth of adapted MCC 3114 despite increased level of ROS indicates its persistence in copper and ROS stress. The physiological alterations in cell viz., increased efflux pump activity and decreased membrane permeability was observed. Molecular analysis revealed increased expression of efflux pump related genes, oxidative stress genes, integron and antibiotic resistance genes. In sum, our study revealed that the exposure of the critical pathogen, A. baunmannii to copper in hospital settings and environmental reservoirs can impose adaptive pressure which may lead to genotypic as well phenotypic changes in cell resulting into the augmentation of antibiotic resistance.

Multidrug-Resistant Uropathogens in Companion Animals: A Comprehensive Study from Clinical Cases and a Genomic Analysis of a CTX-M-14-Producing Escherichia coli ST354, a Leading Cause of Urinary Tract Infections

Urinary tract infections (UTIs) are common in small animals, posing significant clinical challenges due to their recurrence and discomfort. This study investigated the bacterial causes and antimicrobial resistance patterns of UTIs in dogs and cats presented to an important Veterinary Teaching Hospital in São Paulo, Brazil, the largest city in Latin America. Samples were collected from 31 dogs and 9 cats via ultrasound-guided cystocentesis. Bacterial cultures were performed, species identification was accomplished with matrix-assisted laser desorption ionization-time of flight mass spectrometry, and antimicrobial susceptibility testing was done using the Kirby-Bauer method. Escherichia coli was the most frequently isolated pathogen, accounting for 27.9% of cases, followed by Staphylococcus pseudintermedius, Proteus mirabilis, and Klebsiella pneumoniae. Ampicillin resistance was observed in 70.4% of enterobacteria, with many E. coli strains exhibiting multidrug resistance. Whole-genome sequencing of an extended-spectrum beta-lactamase-producing uropathogenic Escherichia coli strain from a feline patient was performed; it was identified as ST354, a leading cause of UTIs worldwide in humans and animals, carrying the blaCTX-M-14 gene and other resistance determinants. Phylogenetic analysis indicated genetic proximity between this strain and others from Brazilian poultry and environmental sources. These findings emphasize the need for antimicrobial resistance surveillance in veterinary UTIs and advocate for stricter antibiotic stewardship to inform diagnostic and therapeutic approaches within a One Health perspective.

Expanding the focus of the One Health concept: links between the Earth-system processes of the planetary boundaries framework and antibiotic resistance

The scientific community warns that our impact on planet Earth is so acute that we are crossing several of the planetary boundaries that demarcate the safe operating space for humankind. Besides, there is mounting evidence of serious effects on people's health derived from the ongoing environmental degradation. Regarding human health, the spread of antibiotic resistant bacteria is one of the most critical public health issues worldwide. Relevantly, antibiotic resistance has been claimed to be the quintessential One Health issue. The One Health concept links human, animal, and environmental health, but it is frequently only focused on the risk of zoonotic pathogens to public health or, to a lesser extent, the impact of contaminants on human health, i.e., adverse effects on human health coming from the other two One Health "compartments". It is recurrently claimed that antibiotic resistance must be approached from a One Health perspective, but such statement often only refers to the connection between the use of antibiotics in veterinary practice and the antibiotic resistance crisis, or the impact of contaminants (antibiotics, heavy metals, disinfectants, etc.) on antibiotic resistance. Nonetheless, the nine Earth-system processes considered in the planetary boundaries framework can be directly or indirectly linked to antibiotic resistance. Here, some of the main links between those processes and the dissemination of antibiotic resistance are described. The ultimate goal is to expand the focus of the One Health concept by pointing out the links between critical Earth-system processes and the One Health quintessential issue, i.e., antibiotic resistance.

Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems

Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M2 = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.

Mass lysis of predatory bacteria drives the enrichment of antibiotic resistance in soil microbial communities

Numerous studies have investigated the effects of antibiotics on the evolution and maintenance of antimicrobial resistance (AMR). However, the impact of microbial interactions in antibiotic-free environments on resistance within complex communities remains unclear. We investigated whether the predatory bacterium M. xanthus, which can produce antimicrobials and employ various contact-dependent and -independent prey-killing mechanisms, influences the abundance of antibiotic-resistant bacteria in its local environment simply through its presence, regardless of active predation. We observed an association between the presence of M. xanthus in soil and the frequency of antibiotic-resistant bacteria. Additionally, culture-based and metagenomic analysis showed that coculturing M. xanthus with soil-derived communities in liquid cultures enriched AMR among non-myxobacterial isolates. This is because the lysis of M. xanthus, triggered during the starvation phase of the coculture experiments, releases diffusible growth-inhibitory compounds that enrich pre-existing resistant bacteria. Furthermore, our results show that death during multicellular fruiting body formation-a starvation-induced stress response in M. xanthus that results in over 90% cell death-also releases growth-inhibitory molecules that enrich resistant bacteria. Hence, the higher abundance of resistant bacteria in soil communities, where M. xanthus can be detected, was because of the diffusible growth-inhibitory substances that were released due to the death of M. xanthus cells during fruiting body formation. Together, our findings demonstrate how the death of M. xanthus, an important aspect of its life cycle, can impact antibiotic resistomes in natural soil communities without the anthropogenic influx of antibiotics.

Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems

BACKGROUND

Plasmids act as vehicles for the rapid spread of antibiotic resistance genes (ARGs). However, few studies of the resistome at the community level distinguish between ARGs carried by mobile genetic elements and those carried by chromosomes, and these studies have been limited to a few ecosystems. This is the first study to focus on ARGs carried by the metaplasmidome on a global scale.

RESULTS

This study shows that only a small fraction of the plasmids reconstructed from 27 ecosystems representing 9 biomes are catalogued in public databases. The abundance of ARGs harboured by the metaplasmidome was significantly explained by bacterial richness. Few plasmids with or without ARGs were shared between ecosystems or biomes, suggesting that plasmid distribution on a global scale is mainly driven by ecology rather than geography. The network linking plasmids to their hosts shows that these mobile elements have thus been shared between bacteria across geographically distant environmental niches. However, certain plasmids carrying ARGs involved in human health were identified as being shared between multiple ecosystems and hosted by a wide variety of hosts. Some of these mobile elements, identified as keystone plasmids, were characterised by an enrichment in antibiotic resistance genes (ARGs) and CAS-CRISPR components which may explain their ecological success. The ARGs accounted for 9.2% of the recent horizontal transfers between bacteria and plasmids.

CONCLUSIONS

By comprehensively analysing the plasmidome content of ecosystems, some key habitats have emerged as particularly important for monitoring the spread of ARGs in relation to human health. Of particular note is the potential for air to act as a vector for long-distance transport of ARGs and accessory genes across ecosystems and continents. Video Abstract.

Adaptations of the Genus Bradyrhizobium to Selected Elements, Heavy Metals and Pesticides Present in the Soil Environment

Rhizobial bacteria perform a number of extremely important functions in the soil environment. In addition to fixing molecular nitrogen and transforming it into a form available to plants, they participate in the circulation of elements and the decomposition of complex compounds present in the soil, sometimes toxic to other organisms. This review article describes the molecular mechanisms occurring in the most diverse group of rhizobia, the genus Bradyrhizobium, allowing these bacteria to adapt to selected substances found in the soil. Firstly, the adaptation of bradyrhizobia to low and high concentrations of elements such as iron, phosphorus, sulfur, calcium and manganese was shown. Secondly, the processes activated in their cells in the presence of heavy metals such as lead, mercury and arsenic, as well as radionuclides, were described. Additionally, due to the potential use of Bradyrhziobium as biofertilizers, their response to pesticides commonly used in agriculture, such as glyphosate, sulfentrazone, chlorophenoxy herbicides, flumioxazine, imidazolinone, atrazine, and insecticides and fungicides, was also discussed. The paper shows the great genetic diversity of bradyrhizobia in terms of adapting to variable environmental conditions present in the soil.

Co-resistance is the dominant mechanism of co-selection and dissemination of antibiotic resistome in nano zinc oxide polluted soil

The broader soil bacterial community responses at ecotoxicologically relevant levels of nano ZnO (nZnO) focussing on co-selection of antibiotic resistance (AR) were investigated. nZnO imposed a stronger influence than the bulk counterpart (bZnO) on antibiotic resistance genes (ARGs) with multidrug resistance (MDR) systems being predominant (63 % of total ARGs). Proliferation of biomarker ARGs especially for last resort antibiotic like vancomycin was observed and Streptomyces hosted multiple ARGs. nZnO was the major driver of the resistome with efflux systems dominating the AR mechanism. Environmental risk associated with nZnO was mediated through metal driven co-selection of ARGs and their probable transfer to eukaryotic hosts through horizontal gene transfer (HGT) via mobile genetic elements (MGEs). Novel resistance genes tetA, mdtA, int and tnpA validated in our study can be used as biomarkers for rapid detection of nZnO toxicity in soils. qRT-PCR validation of resistome in the rhizosphere soil microbiome of turmeric indicated that Zn levels decreased by 16 % compared to bulk soil with 80 % bioaccumulation in rhizomes at 1000 mg Zn kg-1 and subsequent down regulation of ARGs. Expression of key biosynthetic genes for curcumin in turmeric rhizomes showed an increase up to 500 mg Zn kg-1 as nZnO. Validation of co-selection phenomenon in microcosm with 10 mg kg-1 tetracycline without added Zn indicated 20 % upregulation of Zn resistance genes (ZRGs) like czcA, yiip and zntA.

Antimicrobial and Metal Resistance Genes in Bacteria Isolated from Mine Water in Austria

Background/Objectives: Microbiomes surrounding mining sites have been found to harbor both antibiotic resistance genes and metal resistance genes. Within the "One Health" framework, which spans human, veterinary and environmental health, it is crucial to determine whether bacterial metal resistance (MR) genes can independently trigger antimicrobial resistance (AMR) or if they are linked to AMR genes and co-transferred horizontally. Methods and Results: Bacteria were isolated from an active and an inactive mining site in the alpine region of Austria. Most of the isolated bacteria harbored antimicrobial and metal resistance genes (88%). MALDI-TOF and whole genome sequencing (WGS) revealed that species from the Pseudomonadaceae family were the most identified, accounting for 32.5%. All Pseudomonas spp. carried AMR genes from the mex family, which encode multidrug efflux pumps. β-lactamase production encoded by bla genes were detected as the second most common (26%). The same AMR genes have often been detected within a particular bacterial genus. No tetracycline resistance gene has been identified. Among metal resistance genes, rufB (tellurium resistance) was the most prevalent (33%), followed by recGM (selenium resistance, 30%), copA (copper resistance, 26%), and mgtA (magnesium and cobalt resistance, 26%). Notably, the mer gene family (mercury resistance) was found exclusively in isolates from the inactive mining site (n = 6). In addition, genes associated with both antimicrobial and metal resistance, including arsBM, acrD, and the mer operon, were identified in 19 out of the 43 isolates. Conclusions: Bacteria isolated from mine water harbored both MR and AMR genes. Given the exceptional diversity of bacterial species in these settings, 16S rRNA gene sequence analysis is the recommended method for accurate species identification. Moreover, the presence of multi-drug transporters and transferable resistance genes against critically important antimicrobials such as fluoroquinolones and colistin identified in these environmental bacteria emphasizes the importance of retrieving environmental data within the "One Health" framework.

Antibiotic resistance genes in anaerobic digestion: Unresolved challenges and potential solutions

Antimicrobial resistance (AMR) threatens public health, necessitating urgent efforts to mitigate the global impact of antibiotic resistance genes (ARGs). Anaerobic digestion (AD), known for volatile solid reduction and energy generation, also presents a feasible approach for the removal of ARGs. This review encapsulates the existing understanding of ARGs and antibiotic-resistant bacteria (ARB) during the AD process, highlighting unresolved challenges pertaining to their detection and quantification. The questions raised and discussed include: Do current ARGs detection methods meet qualitative and quantitative requirements? How can we conduct risk assessments of ARGs? What happens to ARGs when they come into co-exposure with other emerging pollutants? How can the application of internal standards bolster the reliability of the AD resistome study? What are the potential future research directions that could enhance ARG elimination? Investigating these subjects will assist in shaping more efficient management strategies that employ AD for effective ARG control.

Antibiotic and Heavy Metal Resistance in Bacteria from Contaminated Agricultural Soil: Insights from a New Zealand Airstrip

BACKGROUND/OBJECTIVES

Agricultural soils accumulate inorganic contaminants from the application of phosphate fertilisers. An airstrip located at Belmont Regional Park (BRP), near Wellington, New Zealand, has been found to have a gradient of cadmium contamination due to spillage of superphosphate fertiliser.

METHODS

Soil samples from the BRP airstrip with a gradient of cadmium contamination, were used as a novel source to explore bacterial communities' resistance to heavy metals (HMs) and any co-selected antibiotic (Ab) resistance.

RESULTS

Differences between BRP soil samples with higher levels of HMs compared to those with lower HM concentrations showed significantly more bacterial isolates resistant to both HMs (40.6% versus 63.1% resistant to 0.01 mM CdCl2, p < 0.05) and Abs (23.4% versus 37.8% resistant to 20 μg/mL tetracycline, p < 0.05) in soils with higher initial levels of HMs (1.14 versus 7.20 mg kg-1 Cd). Terminal restriction fragment length polymorphism (TRFLP) and 16S rDNA next-generation sequencing profiling investigated changes in HM-induced bacterial communities. Significant differences were observed among the bacterial community structures in the selected BRP soil samples. Conjugative transfer of cadmium resistance from 23-38% of cadmium-resistant isolates to a characterised recipient bacterial strain in vitro suggested many of these genes were carried by mobile genetic elements. Transconjugants were also resistant to zinc, mercury, and Abs. Higher levels of HMs in soil correlated with increased resistance to HMs, Abs, and elevated levels of HMs thus disturbed the bacterial community structure in BRP soil significantly.

CONCLUSIONS

These findings suggest that HM contamination of agricultural soil can select for Ab resistance in soil bacteria with potential risks to human and animal health.

Understanding Bacterial Resistance to Heavy Metals and Nanoparticles: Mechanisms, Implications, and Challenges

Antimicrobial resistance is a global health problem as it contributes to high mortality rates in several infectious diseases. To address this issue, engineered nanoparticles/nano-formulations of antibiotics have emerged as a promising strategy. Nanoparticles are typically defined as materials with dimensions up to 100 nm and are made of different materials such as inorganic particles, lipids, polymers, etc. They are widely dispersed in the environment through various consumer products, and their clinical applications are diverse, ranging from contrast agents in imaging to carriers for gene and drug delivery. Nanoparticles can also act as antimicrobial agents either on their own or in combination with traditional antibiotics to produce synergistic effects, earning them the label of "next-generation therapeutics." They have also shown great effectiveness against multidrug-resistant pathogens responsible for nosocomial infections. However, overexposure or prolonged exposure to sublethal doses of nanoparticles can promote the development of resistance in human pathogens. The resistance can arise from various factors such as genetic mutation, horizontal gene transfer, production of reactive oxygen species, changes in the outer membrane of bacteria, efflux-induced resistance, cross-resistance from intrinsic antibiotic resistance determinants, plasmid-mediated resistance, and many more. Continuous exposure to nanoparticles can also transform an antibiotic-susceptible bacterial pathogen into multidrug resistance. Considering all these, the current review focuses on the mode of action of different heavy metals and nanoparticles and possible mechanisms through which bacteria attain resistance towards these heavy metals and nanoparticles.

Global dissemination of the beta-lactam resistance gene blaTEM-1 among pathogenic bacteria

Antibiotic resistance presents a burgeoning global health crisis, with over 70 % of pathogenic bacteria now exhibiting resistance to at least one antibiotic. This study leverages a vast dataset of 618,853 pathogenic bacterial genomes from the NCBI pathogen detection database, offering comprehensive insights into antibiotic resistance patterns, species-specific profiles, and transmission dynamics of resistant pathogens. We centered our investigation on the beta-lactam resistance gene blaTEM-1, found in 43,339 genomes, revealing its extensive distribution across diverse species and isolation sources. The study unveiled the prevalence of 15 prominent antibiotic resistance genes (ARGs), including those conferring resistance to beta-lactam, aminoglycoside, and tetracycline antibiotics. Distinct resistance patterns were observed between Gram-positive and Gram-negative bacteria, indicating the influence of phylogeny on resistance dissemination. Notably, the blaTEM-1 gene demonstrated substantial prevalence across a wide array of bacterial species (8) and a high number of isolation sources (11). Genetic context analysis revealed associations between blaTEM-1 and mobile genetic elements (MGEs) like transposons and insertion sequences. Additionally, we observed recent horizontal transfer events involving clusters of blaTEM-1 genes and MGEs underscore the potential of MGEs in facilitating the mobilization of ARGs. Our findings underscore the importance of adopting a One Health approach to global genomic pathogen surveillance, aiming to uncover the transmission routes of ARGs and formulate strategies to address the escalating antibiotic resistance crisis.

Antibiotic resistance in plastisphere

Microbial life on plastic debris, called plastisphere, has invoked special attention on aquatic ecosystems as emerging habitats for antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). There is scarce information concerning how properties of plastics influence ARGs and ARB, the effect of biofilms on enrichment of ARGs and ARB, and, especially, the influence of plastic transformation on ARGs and ARB. Limited research has shown that microplastic (MP) surfaces influence proliferation of antibiotic resistance (AR), aged MPs exhibit increased toxicity due to more adsorption-desorption of AR, and MP transformation is correlated with disseminating AR. Prevention measures of AR include minimizing MP releasing into aquatic environments and sewage treatment plants. The future research should aim to identify the interface mechanisms of transformed MNPs and antibiotics alone, or mixed with other contaminants, property changes of MNPs, and associated toxicity evaluation.

Comparative analysis of antibiotic resistance genes between fresh pig manure and composted pig manure in winter, China

Antibiotic resistance is a critical global public health issue. The gut microbiome acts as a reservoir for numerous antibiotic resistance genes (ARGs), which influence both existing and future microbial populations within a community or ecosystem. However, the differences in ARG expression between fresh and composted feces remain poorly understood. In this study, we collected eight samples from a farm in Kaifeng City, China, comprising both fresh and composted pig manure. Using a high-throughput quantitative PCR array, we analyzed differences in ARG expression between these two types of manure. Our findings revealed significant differences in ARG profiles, as demonstrated by principal coordinate analysis (PCoA). Further analysis identified 39 ARGs (log2FC > 1, p < 0.05) in composted pig manure, with 25 genes downregulated and 14 upregulated. Notably, tetB-01, blaOCH, and blaOXY were the most abundant in composted pig manure compared to fresh manure. Additionally, 16S rRNA species profiling revealed that the composting process significantly altered the microbial community structure, with an increased abundance of Firmicutes and a decreased abundance of Bacteroidetes in composted pig manure. In summary, composting substantially transforms both the microbial community structure and the ARG profile in pig manure, underscoring its potential role in modulating the dynamics of ARGs in agricultural environments.

Significant effects of bioavailable heavy metals on antibiotic resistome in paddy soils as revealed by metagenomic analysis

Heavy metals (HMs) act as a long-term selective pressure for the emergence and maintenance of antibiotic resistance genes (ARGs) in agricultural soils. However, the effects of HMs on ARG distributions in paddy soils and the underlying mechanisms remain unclear. In this study, 74 soil samples were collected from the paddy fields to explore the impact of HMs on ARG profiles. A total of 468 ARGs were detected in HM-contaminated soils. Variation partitioning analysis (VPA) and redundancy analysis (RDA) demonstrated that the bioavailable HMs contributed more significantly to ARG composition compared to the total HM content (8.59 % vs. 3.97 %). Structural equation models (SEMs) showed that bioavailable HMs affected ARGs mainly by negatively altering the microbial diversity. Furthermore, the co-occurrence analysis of ARGs and metal resistant genes (MRGs) was further performed at the metagenome-assembled genomes (MAGs) level. Consequently, 1145 MAGs that assigned to 29 bacterial phyla were found to concurrently harbor ARGs and MRGs, with the bacterial phyla Pseudomonadota being predominant ARG-MRG-carrying microbes for most coexistence types of ARGs and MRGs, i.e., multidrug-As, polymyxin-Cd, Quinolone-Cd, Beta-lactam-Pb, and multidrug-Zn. Our findings highlight that the extensive coexistence of ARG-MRG in microbial genomes is an important reason for the ARG pollution in HM-contaminated paddy soils.

Detection of mobile genetic elements conferring resistance to heavy metals in Salmonella 4,[5],12:i:- and Salmonella Typhimurium serovars and their association with antibiotic resistance

Salmonella enterica subsp. enterica serovar Typhimurium variant 4,[5],12:i:- (referred to as S. 4,[5],12:i:-) has emerged rapidly as the predominant Salmonella serovar in pigs, often associated with the acquisition of antibiotic resistance (ABR) and heavy metal resistance (HMR) genes. Our study analysed 78 strains of S. 4,[5],12:i:- (n = 57) and S. Typhimurium (n = 21), collected from 1999 to 2021, to investigate the evolution of mobile genetic elements (MGEs) containing HMR and ABR genes. Five MGEs harbouring HMR genes were identified: pUO-STVR2, pSTM45, pUO-STmRV1, SGI-4 and MREL. Among the strains, 91.23 % (52/57) of S. 4,[5],12:i:- carried at least one of these elements, compared to only 14.29 % (3/21) of S. Typhimurium. Since 2008, S. 4,[5],12:i:- have shifted from predominantly carrying pUO-STmRV1 to the emergence of SGI-4 and MREL, reducing ABR genes, reflecting the European Union ban on the use of antibiotics as feed additives. Increased resistance to copper and silver in S. 4,[5],12:i:-, conferred by SGI-4 and MREL, reflected that their acquisition was linked to the ongoing use of heavy metals in food-animal production. However, strains carrying SGI-4 and MREL still exhibit multidrug resistance, emphasising the need for targeted interventions to mitigate multidrug-resistant Salmonella spread in veterinary and public health settings.

Genomic analysis and antibiotic resistance of a multidrug-resistant bacterium isolated from pharmaceutical wastewater treatment plant sludge

Pharmaceutical wastewater treatment plants (PWWTPs) serve as reservoirs for antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs). In this study, a multiantibiotic-resistant strain of Acinetobacter lwoffii (named N4) was isolated from the dewatered sludge of a PWWTP. N4 exhibited high resistance to both antibiotics and metals, with minimum inhibitory concentrations (MICs) of chloramphenicol and cefazolin reaching 1024 mg·L-1 and MICs of Cu2+ and Zn2+ reaching 512 mg·L-1. Co-sensitization experiments revealed that when antibiotics are co-existing with heavy metal ions (such as TET and Cd2+, AMP and Cu2+) could enhance the resistance of N4 to them. Whole-genome sequencing of N4 revealed a genome size of 0.37 Mb encoding 3359 genes. Among these, 23 ARGs were identified, including dfrA26, bl2beCTXM, catB3, qnrB, rosB, tlrC, smeD, smeE, mexE, ceoB, oprN, acrB, adeF, ykkC, ksgA and sul2, which confer resistance through mechanisms such as efflux pumps, enzyme modification and target bypass. Additionally, the N4 genome contained 187 genes associated with human disease and 249 virulence factors, underscoring its potential pathogenicity. Overall, this study provides valuable insights into ARBs in PWWTPs and highlights the potential risks posed by multidrug-resistant strains such as N4.

Contaminant-degrading bacteria are super carriers of antibiotic resistance genes in municipal landfills: A metagenomics-based study

Municipal landfills are hotspot sources of antimicrobial resistance (AMR) and are also important habitats of contaminant-degrading bacteria. However, high diversity of antibiotic resistance genes (ARGs) in landfills hinders assessing AMR risks in the affected environment. More concerned, whether there is co-selection or enrichment of antibiotic-resistant bacteria and contaminant-degrading bacteria in these extremely polluted environments is far less understood. Here, we collected metagenomic datasets of 32 raw leachate and 45 solid waste samples in 22 municipal landfills of China. The antibiotic resistome, antibiotic-resistant bacteria and contaminant-degrading bacteria were explored, and were then compared with other environmental types. Results showed that the antibiotic resistome in landfills contained 1,403 ARG subtypes, with the total abundance over the levels in natural environments and reaching the levels in human feces and sewage. Therein, 49 subtypes were listed as top priority ARGs for future surveillance based on the criteria of enrichment in landfills, mobilizable and present in pathogens. By comparing to those in less contaminated river environments, we elucidated an enrichment of antibiotic-resistant bacteria with contaminant-degrading potentials in landfills. Bacteria in Pseudomonadaceae, Moraxellaceae, Xanthomonadaceae and Enterobacteriaceae deserved the most concerns since 72.2 % of ARG hosts were classified to them. Klebsiella pneumoniae, Acinetobacter nosocomialis and Escherichia coli were abundant multidrug-resistant pathogenic species in raw leachate (∼10.2 % of total microbiomes), but they rarely carried contaminant-degradation genes. Notably, several bacterial genera belonging to Pseudomonadaceae had the most antibiotic-resistant, pathogenic, and contaminant-degrading potentials than other bacteria. Overall, the findings highlight environmental selection for contaminant-degrading antibiotic-resistant pathogens, and provide significant insights into AMR risks in municipal landfills.

Escherichia coli: An arduous voyage from commensal to Antibiotic-resistance

Escherichia coli (E. coli), a normal intestinal microbiota is one of the most common pathogen known for infecting urinary tract, wound, lungs, bone marrow, blood system and brain. Irrational and overuse of commercially available antibiotics is the most imperative reason behind the emergence of the life threatening infections caused due to antibiotic resistant pathogens. The World Health Organization (WHO) identified antimicrobial resistance (AMR) as one of the 10 biggest public health threats of our time. This harmless commensal can acquire a range of mobile genetic elements harbouring genes coding for virulence factors becoming highly versatile human pathogens causing severe intestinal and extra intestinal diseases. Although, E. coli has been the most widely studied micro-organism, it never ceases to astound us with its ability to open up new research avenues and reveal cutting-edge survival mechanisms in diverse environments that impact human and surrounding environment. This review aims to summarize and highlight persistent research gaps in the field, including: (i) the transfer of resistant genes among bacterial species in diverse environments, such as those associated with humans and animals; (ii) the development of resistance mechanisms against various classes of antibiotics, including quinolones, tetracyclines, etc., in addition to β-lactams; and (iii) the relationship between resistance and virulence factors for understanding how virulence factors and resistance interact to gain a better grasp of how resistance mechanisms impact an organism's capacity to spread illness and interact with the host's defences. Moreover, this review aims to offer a thorough overview, exploring the history and factors contributing to antimicrobial resistance (AMR), the different reported pathotypes, and their links to virulence in both humans and animals. It will also examine their prevalence in various contexts, including food, environmental, and clinical settings. The objective is to deliver a more informative and current analysis, highlighting the evolution from microbiota (historical context) to sophisticated diseases caused by highly successful pathogens. Developing more potent tactics to counteract antibiotic resistance in E. coli requires filling in these gaps. By bridging these gaps, we can strengthen our capacity to manage and prevent resistance, which will eventually enhance public health and patient outcomes.

Prevalence of antibiotic resistance genes in mining-impacted farmland environments

Mining activities produce large quantities of tailings and acid mine drainage, which contain varieties of heavy metals, thereby affecting the downstream farmland soils and crops. Heavy metals could induce antibiotic resistance through co-selection pressure. However, the profiles of antibiotic resistance genes (ARGs) in the mining-affected farmland soils and crops are still unclear. Here we investigated contents of heavy metals, ARG abundances, mobile genetic elements (MGEs), and microbial community in mining-affected farmland soils and vegetables from Shangba village (SB), in comparison to a nearby reference village Taiping (TP). Results showed that in SB group, except for Cr, other metals were all above the Chinese Standards. When compared with the reference group, higher ARG abundances were detected in mining-affected farmland soils and vegetables, with great proportions of genes resistant to sulfonamides, chloramphenicols and tetracyclines. In addition, positive correlations were found between the above three ARG classes and heavy metals concentrations (especially Cu, Pb and Zn). Spearman's correlations revealed that there were positive correlations between sul1 and total nitrogen, as well as tetB/P and pH. Additionally, the Shannon index values were different for the samples from two villages (p < 0.05). Proteobacteria and Actinobacteria were dominant phyla in soil samples. Network analysis suggested that multiple genera (belonging to Proteobacteria and Actinobacteria) were positively associated with many ARGs (p < 0.05), implying they might be potential hosts for ARGs. To sum up, this study provided clear evidence that mining activities caused severe heavy metals pollution to the farmland, thus posing co-selection pressure on the persistence of ARGs in the affected farmland environments.

Metagenomic insights on promoting the removal of resistome in aerobic composting pig manure by lightly burned modified magnesite

The antibiotic resistance genes (ARGs) have become a serious issue facing public health. In this study, light-burned magnesite with a high specific surface area at 650 °C (MS650) was used for aerobic composting, evaluating its effect on the resistome during pig manure composting. Different concentrations of MS650 reduced the abundance of the resistome, including seven high-risk ARGs, class two metal and biocide resistance genes (MBRGs), and human pathogenic bacteria (HPBs). The addition of 2.5 % MS650 (L1) in the composting had the best reduction effect on ARGs, MBRGs and HPBs. ARG and microbial community assembly are deterministic processes. Proteobacteria and Actinobacteria was the main factor associated with the decrease in ARGs, followed by virulence factor genes (VFGs, 44.2 %). The reduction in MBRGs by MS650 mainly suppressed HGT by reducing the Isfinder abundance. To summarize, MS650 is an effective method to improve emission reduction of ARGs and MBRGs. This study provided a theoretical basis for improving the engineering application potential of MS650.

Metagenomic analysis of the dichotomous role of uranium in regulating intracellular and extracellular antibiotic resistance genes in activated sludge

Antibiotic resistance genes (ARGs) in activated sludge include intracellular ARGs (iARGs) and extracellular ARGs (eARGs), both of which are recognized as emerging pollutants. While the activated sludge process has been commonly considered for treating wastewater contaminated with radionuclide, the effects and mechanisms of radioactive heavy metals on the fate of iARGs and eARGs (i/e-ARGs) in activated sludge are largely elusive. Here, the distribution, mobility, and hosts of i/e-ARGs in activated sludge during environmental concentrations (50 μg/L and 5000 μg/L) of radioactive uranium (U) stress were explored via metagenomics. The results revealed that the total relative abundance of iARGs and eARGs decreased by 11.62% and 10.41%, respectively, after 90 days of 50 μg/L of U treatment. In contrast, both i/e-multi- and tetracycline ARGs remarkably increased after being exposed to 5000 μg/L of U. Additionally, exposure to 5000 μg/L of U triggered notable decrease in i/e-insertion sequences and plasmids abundance, but significantly enriched i/e-integrons (p < 0.05). Partial least squares pathway modelling indicated that the prevalence of iARGs and eARGs in activated sludge was primarily driven by bacterial hosts and functional genes, respectively. Our findings revealed the dichotomous variation landscape and mechanisms of i/e-ARGs dynamics in activated sludge during U exposure, offering valuable insights for controlling ARGs risk during radioactive wastewater treatment.

Tire wear particles enhance horizontal gene transfer of antibiotic resistance genes in aquatic ecosystems

Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10-3 at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of MP pollution in various aquatic ecosystems.

A widespread family of ribosomal peptide metallophores involved in bacterial adaptation to metal stress

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a structurally diverse group of natural products that bacteria employ in their survival strategies. Herein, we characterized the structure, the biosynthetic pathway, and the mode of action of a RiPP family called bufferins. With thousands of homologous biosynthetic gene clusters throughout the bacterial phylogenetic tree, bufferins form by far the largest family of RiPPs modified by multinuclear nonheme iron-dependent oxidases (MNIO, DUF692 family). Using Caulobacter vibrioides bufferins as a model, we showed that the conserved Cys residues of their precursors are transformed into 5-thiooxazoles, further expanding the reaction range of MNIO enzymes. This rare modification is installed in conjunction with a partner protein of the DUF2063 family. Bufferin precursors are rare examples of bacterial RiPPs found to feature an N-terminal Sec signal peptide allowing them to be exported by the ubiquitous Sec pathway. We reveal that bufferins are involved in copper homeostasis, and their metal-binding propensity requires the thiooxazole heterocycles. Bufferins enhance bacterial growth under copper stress by complexing excess metal ions. Our study thus describes a large family of RiPP metallophores and unveils a widespread but overlooked metal homeostasis mechanism in bacteria.

Biofilm formation on microplastics and interactions with antibiotics, antibiotic resistance genes and pathogens in aquatic environment

Microplastics (MPs) in aquatic environments easily support biofilm development, which can interact with other environmental pollutants and act as harbors for microorganisms. Recently, numerous studies have investigated the fate and behavior of MP biofilms in aquatic environments, highlighting their roles in the spread of pathogens and antibiotic resistance genes (ARGs) to aquatic organisms and new habitats. The prevalence and effects of MP biofilms in aquatic environments have been extensively investigated in recent decades, and their behaviors in aquatic environments need to be synthesized systematically with updated information. This review aims to reveal the development of MP biofilm and its interactions with antibiotics, ARGs, and pathogens in aquatic environments. Recent research has shown that the adsorption capabilities of MPs to antibiotics are enhanced after the biofilm formation, and the adsorption of biofilms to antibiotics is biased towards chemisorption. ARGs and microorganisms, especially pathogens, are selectively enriched in biofilms and significantly different from those in surrounding waters. MP biofilm promotes the propagation of ARGs through horizontal gene transfer (HGT) and vertical gene transfer (VGT) and induces the emergence of antibiotic-resistant pathogens, resulting in increased threats to aquatic ecosystems and human health. Some future research needs and strategies in this review are also proposed to better understand the antibiotic resistance induced by MP biofilms in aquatic environments.

Recovery of clinically relevant multidrug-resistant Klebsiella pneumoniae lineages from wastewater in Kumasi Metropolis, Ghana

Antimicrobial resistance (AMR) is under-monitored in Africa, with few reports characterizing resistant bacteria from the environment. This study examined physicochemical parameters, chemical contaminants and antibiotic-resistant bacteria in waste stabilization pond effluents, hospital wastewater and domestic wastewater from four sewerage sites in Kumasi. The bacteria isolates were sequenced. Three sites exceeded national guidelines for total suspended solids, biochemical oxygen demand, chemical oxygen demand and electrical conductivity. Although sulfamethoxazole levels were low, the antibiotic was detected at all sites. Multi-drug-resistant Klebsiella pneumoniae and Pseudomonas aeruginosa were isolated with multi-locus sequence typing identifying K. pneumoniae strains as ST18 and ST147, and P. aeruginosa as ST235, all of clinical relevance. A comparison of ST147 genomes with isolates from human infections in Africa showed remarkable similarity and shared AMR profiles. Thirteen of the twenty-one plasmids from ST147 harbored at least one AMR gene, including blaCTX-M-15 linked to copper-resistance genes. Our study demonstrated high bacterial counts and organic matter in the analysed wastewater. The recovery of clinically significant isolates with multiple antibiotic and heavy metal resistance genes from the wastewater samples raises public health concerns.

Emerging antibiotic and heavy metal resistance in spore-forming bacteria from pig manure, manure slurry and fertilized soil

Spore-forming bacteria (SFB), like Bacillus, are the gram-positive bacteria with broad-spectrum activity that is one of the commonly used strains of probiotics. However, these bacteria also have significant resistance. In this study, we systematically investigated pig manure, manure slurry and soil by 16S rRNA high-throughput sequencing and traditional culture techniques. We found the SFB was widespread in manure, manure slurry and soil, Firmicutes was one of the main dominant phyla in pig manure, manure slurry and soil, the relative abundance of Bacillus were 0.98%, 0.01%, and 2.57%, respectively, and metals such as copper have complex relationships with bacteria. We isolated 504 SFB from 369 samples, with the highest number identified as Bacillus subtilis. SFB strains showed varying degrees of antibiotic resistance; the greatest against erythromycin, followed by imipenem. The MICs of SFB varied greatly against different heavy metals; with high (est) resistance against Zn2+, followed by Cu2+. Second-generation whole genome sequencing (WGS) revealed that nine Bacillus strains carried different subtypes of vancomycin resistance genes, among which vanRM had the highest frequency. The strain W129 included the vanRA-vanRM-vanSA-vanZF cluster. The nine Bacillus strains also contained antibiotic genes such as aminoglycoside (ant(9)-Ia), β-lactam (bcII), and macrolide (msrE). Twenty-six Bacillus isolates carried copper resistance clusters, including csoR-copZ, copA-copZ-csoR, and copZ-copA. WGS showed that strain W166 carried 11 vancomycin resistance genes and 11 copper resistance genes. There were 4 vancomycin resistance genes and 14 copper resistance genes on the W129 chromosome. Strain W129 also harbors the plasmid pLKYM01 that contains an intact transposon consisting of insertion sequence and vancomycin resistance genes vanYF and vanRA. This study explores the potential risks of using pig manure and fertilized soil to inform safe and effective use of probiotics in agriculture. It highlights scientific evidence for concern over the safe utilization and control of animal waste products.

Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance

Bacterial hosts in vegetable phylloplanes carry mobile genetic elements, such as plasmids and transposons that are associated with integrons. These mobile genetic elements and their cargo genes can enter human microbiomes via consumption of fresh agricultural produce, including uncooked vegetables. This presents a risk of acquiring antimicrobial resistance genes from uncooked vegetables. To better understand horizontal gene transfer of class 1 integrons in these compartments, we applied epicPCR, a single-cell fusion-PCR surveillance technique, to link the class 1 integron integrase (intI1) gene with phylogenetic markers of their bacterial hosts. Ready-to-eat salads carried class 1 integrons from the phyla Bacteroidota and Pseudomonadota, including four novel genera that were previously not known to be associated with intI1. We whole-genome sequenced Pseudomonas and Erwinia hosts of pre-clinical class 1 integrons that are embedded in Tn402-like transposons. The proximal gene cassette in these integrons was identified as a chlorite dismutase gene cassette, which we showed experimentally to confer chlorite resistance. Chlorine-derived compounds such as acidified sodium chlorite and chloride dioxide are used to disinfectant raw vegetables in food processing facilities, suggesting selection for chlorite resistance in phylloplane integrons. The spread of integrons conferring chlorite resistance has the potential to exacerbate integron-mediated antimicrobial resistance (AMR) via co-selection of chlorite resistance and AMR, thus highlighting the importance of monitoring chlorite residues in agricultural produce. These results demonstrate the strength of combining epicPCR and culture-based isolation approaches for identifying hosts and dissecting the molecular ecology of class 1 integrons.

Evolution and maintenance of a large multidrug-resistant plasmid in a Salmonella enterica Typhimurium host under differing antibiotic selection pressures

The dissemination of antibiotic resistance genes (ARGs) through plasmids is a major mechanism for the development of bacterial antimicrobial resistance. The adaptation and evolution mechanisms of multidrug-resistant (MDR) plasmids with their hosts are not fully understood. Herein, we conducted experimental evolution of a 244 kb MDR plasmid (pJXP9) under various conditions including no antibiotics and mono- or combinational drug treatments of colistin (CS), cefotaxime (CTX), and ciprofloxacin (CIP). Our results showed that long-term with or without positive selections for pJXP9, spanning approximately 600 generations, led to modifications of the plasmid-encoded MDR and conjugative transfer regions. These modifications could mitigate the fitness cost of plasmid carriage and enhance plasmid maintenance. The extent of plasmid modifications and the evolution of plasmid-encoded antibiotic resistance depended on treatment type, particularly the drug class and duration of exposure. Interestingly, prolonged exposure to mono- and combinational drugs of CS and CIP resulted in a substantial loss of the plasmid-encoded MDR region and antibiotic resistance, comparable to the selection condition without antibiotic. By contrast, combinational treatment with CTX contributed to the maintenance of the MDR region over a long period of time. Furthermore, drug selection was able to maintain and even amplify the corresponding plasmid-encoded ARGs, with co-selection of ARGs in the adjacent regions. In addition, parallel mutations in chromosomal arcA were also found to be associated with pJXP9 plasmid carriage among endpoint-evolved clones from diverse treatments. Meanwhile, arcA deletion improved the persistence of pJXP9 plasmid without drugs. Overall, our findings indicated that plasmid-borne MDR region deletion and chromosomal arcA inactivation mutation jointly contributed to co-adaptation and co-evolution between MDR IncHI2 plasmid and Salmonella Typhimurium under different drug selection pressure.IMPORTANCEThe plasmid-mediated dissemination of antibiotic resistance genes has become a significant concern for human health, even though the carriage of multidrug-resistant (MDR) plasmids is frequently associated with fitness costs for the bacterial host. However, the mechanisms by which MDR plasmids and bacterial pairs evolve plasmid-mediated antibiotic resistance in the presence of antibiotic selections are not fully understood. Herein, we conducted an experimental evolution of a large multidrug-resistant plasmid in a Salmonella enterica Typhimurium host under single and combinatorial drug selection pressures. Our results show the adaptive evolution of plasmid-encoded antibiotic resistance through alterations of the MDR region in the plasmid, in particular substantial loss of the MDR region, in response to different positive selections, especially mono- and combinational drugs of colistin and ciprofloxacin. In addition, strong parallel mutations in chromosomal arcA were associated with pJXP9 carriage in Salmonella Typhimurium from diverse treatments. Our results thus highlight promoting the loss of the plasmid's MDR region could offer an alternative approach for combating plasmid-encoded antibiotic resistance.

Influence of decades-long irrigation with secondary treated wastewater on soil microbial diversity, resistome dynamics, and antibiotrophy development

In arid and semi-arid regions, the use of treated wastewater (TWW) for irrigation is gaining ground to alleviate pressure on natural water sources. Despite said treatment, the existing methods fail to eliminate potentially dangerous contaminants. As such, this study assessed the impact of long-term TWW irrigation (5 and 25 years) on soil physicochemical properties and bacterial resistance to heavy metals (Pb, Cu, Cd) and antibiotics (tetracycline and amoxicillin). The results revealed heightened salinity and conductivity and reduced pH in irrigated soils. TWW induces harmful effects by reducing microbial density and size, leading to the disappearance of sensitive populations. Conversely, resilient populations, which mainly utilize antibiotics as a carbon source, have adapted. Metagenomic 16S amplicon sequencing analysis demonstrated a shift, notably reducing Actinobacteria, Bacteroidetes, and Firmicutes while increasing Acidobacteriota and Patescibacteria in treated soils. Operational Taxonomic Units affiliated with either Halomonadacea, or Saccharimonadacea and Vicinamibacteracea, were defined as indicators of the absence or presence of TWW contamination, respectively. We conclude that TWW irrigation significantly increases bacterial resistance to heavy metals, whereas the impact of antibiotics is nuanced, with antibiotrophy leveraging lower concentrations in treated soils.

A multi-pronged approach to assessing antimicrobial resistance risks in coastal waters and aquaculture systems

Antimicrobial resistance (AMR) is a global challenge that has impacted aquaculture and surrounding marine environments. In this study, a year-long monitoring program was implemented to evaluate AMR in two different aquaculture settings (i.e., open cage farming, recirculating aquaculture system (RAS)) and surrounding marine environment within a tropical coastal region. The objectives of this study are to (i) investigate the prevalence and co-occurrence of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), antibiotics (AB) and various associated chemical compounds at these study sites; (ii) explore the contributing factors to development and propagation of AMR in the coastal environment; and (iii) assess the AMR risks from different perspectives based on the three AMR determinants (i.e., ARB, ARGs and AB). Key findings revealed a distinct pattern of AMR across the different aquaculture settings, notably a higher prevalence of antibiotic-resistant Vibrio at RAS outfalls, suggesting a potential accumulation of microorganisms within the treatment system. Despite the relative uniform distribution of ARGs across marine sites, specific genes such as qepA, blaCTX-M and bacA, were found to be abundant in fish samples, especially from the RAS. Variations in chemical contaminant prevalence across sites highlighted possible anthropogenic impacts. Moreover, environmental and seasonal variations were found to significantly influence the distribution of ARGs and chemical compounds in the coastal waters. Hierarchical cluster analysis that was based on ARGs, chemical compounds and environmental data, categorized the sites into three distinct clusters which reflected strong association with location, seasonality and aquaculture activities. The observed weak correlations between ARGs and chemical compounds imply that low environmental concentrations may be insufficient for resistance selection. A comprehensive risk assessment using methodologies such as the multiple antibiotic resistance (MAR) index, comparative AMR risk index (CAMRI) and Risk quotient (RQ) underscored the complexity of AMR risks. This research significantly contributes to the understanding of AMR dynamics in natural aquatic systems and provides valuable insights for managing and mitigating AMR risks in coastal environments.