Biofilm-producing ability of methicillin-resistant Staphylococcus aureus clinically isolated in China.

BACKGROUND: Staphylococcus aureus, a commensal bacterium, colonizes the skin and mucous membranes of approximately 30% of the human population. Apart from conventional resistance mechanisms, one of the pathogenic features of S. aureus is its ability to survive in a biofilm state on both biotic and abiotic surfaces. Due to this characteristic, S. aureus is a major cause of human infections, with Methicillin-Resistant Staphylococcus aureus (MRSA) being a significant contributor to both community-acquired and hospital-acquired infections. RESULTS: Analyzing non-repetitive clinical isolates of MRSA collected from seven provinces and cities in China between 2014 and 2020, it was observed that 53.2% of the MRSA isolates exhibited varying degrees of ability to produce biofilm. The biofilm positivity rate was notably high in MRSA isolates from Guangdong, Jiangxi, and Hubei. The predominant MRSA strains collected in this study were of sequence types ST59, ST5, and ST239, with the biofilm-producing capability mainly distributed among moderate and weak biofilm producers within these ST types. Notably, certain sequence types, such as ST88, exhibited a high prevalence of strong biofilm-producing strains. The study found that SCCmec IV was the predominant type among biofilm-positive MRSA, followed by SCCmec II. Comparing strains with weak and strong biofilm production capabilities, the positive rates of the sdrD and sdrE were higher in strong biofilm producers. The genetic determinants ebp, icaA, icaB, icaC, icaD, icaR, and sdrE were associated with strong biofilm production in MRSA. Additionally, biofilm-negative MRSA isolates showed higher sensitivity rates to cefalotin (94.8%), daptomycin (94.5%), mupirocin (86.5%), teicoplanin (94.5%), fusidic acid (81.0%), and dalbavancin (94.5%) compared to biofilm-positive MRSA isolates. The biofilm positivity rate was consistently above 50% in all collected specimen types. CONCLUSIONS: MRSA strains with biofilm production capability warrant increased vigilance.

Siderophore-harboring gut bacteria and fecal siderophore genes for predicting the responsiveness of fecal microbiota transplantation for active ulcerative colitis.

BACKGROUND: Predictive markers for fecal microbiota transplantation (FMT) outcomes in patients with active ulcerative colitis (UC) are poorly defined. We aimed to investigate changes in gut microbiota pre- and post-FMT and to assess the potential value in determining the total copy number of fecal bacterial siderophore genes in predicting FMT responsiveness. METHODS: Patients with active UC (Mayo score ≥ 3) who had undergone two FMT procedures were enrolled. Fecal samples were collected before and 8 weeks after each FMT session. Patients were classified into clinical response and non-response groups, based on their Mayo scores. The fecal microbiota profile was accessed using metagenomic sequencing, and the total siderophore genes copy number via quantitative real-time polymerase chain reaction. Additionally, we examined the association between the total siderophore genes copy number and FMT efficacy. RESULTS: Seventy patients with UC had undergone FMT. The clinical response and remission rates were 50% and 10% after the first FMT procedure, increasing to 72.41% and 27.59% after the second FMT. The cumulative clinical response and clinical remission rates were 72.86% and 25.71%. Compared with baseline, the response group showed a significant increase in Faecalibacterium, and decrease in Enterobacteriaceae, consisted with the changes of the total bacterial siderophore genes copy number after the second FMT (1889.14 vs. 98.73 copies/ng, P < 0.01). Virulence factor analysis showed an enriched iron uptake system, especially bacterial siderophores, in the pre-FMT response group, with a greater contribution from Escherichia coli. The total baseline copy number was significantly higher in the response group than non-response group (1889.14 vs. 94.86 copies/ng, P < 0.01). A total baseline copy number cutoff value of 755.88 copies/ng showed 94.7% specificity and 72.5% sensitivity in predicting FMT responsiveness. CONCLUSIONS: A significant increase in Faecalibacterium, and decrease in Enterobacteriaceae and the total fecal siderophore genes copy number were observed in responders after FMT. The siderophore genes and its encoding bacteria may be of predictive value for the clinical responsiveness of FMT to active ulcerative colitis.

Effect of environmental factors on conjugative transfer of antibiotic resistance genes in aquatic settings.

Antimicrobial-resistance genes (ARGs) are spread among bacteria by horizontal gene transfer, however, the effect of environmental factors on the dynamics of the ARG in water environments has not been very well understood. In this systematic review, we employed the regression tree algorithm to identify the environmental factors that facilitate/inhibit the transfer of ARGs via conjugation in planktonic/biofilm-formed bacterial cells based on the results of past relevant research. Escherichia coli strains were the most studied genus for conjugation experiments as donor/recipient in the intra-genera category. Conversely, Pseudomonas spp., Acinetobacter spp., and Salmonella spp. were studied primarily as recipients across inter-genera bacteria. The conjugation efficiency (ce) was found to be highly dependent on the incubation period. Some antibiotics, such as nitrofurantoin (at ≥0.2 µg ml-1) and kanamycin (at ≥9.5 mg l-1) as well as metallic compounds like mercury (II) chloride (HgCl2, ≥3 µmol l-1), and vanadium (III) chloride (VCl3, ≥50 µmol l-1) had enhancing effect on conjugation. The highest ce value (-0.90 log10) was achieved at 15°C-19°C, with linoleic acid concentrations <8 mg l-1, a recognized conjugation inhibitor. Identifying critical environmental factors affecting ARG dissemination in aquatic environments will accelerate strategies to control their proliferation and combat antibiotic resistance.

Removal of intracellular and extracellular antibiotic resistance genes and virulence factor genes using electricity-intensified constructed wetlands.

Constructed wetland (CW) is considered a promising technology for the removal of emerging contaminants. However, its removal performance for antibiotic resistance genes (ARGs) is not efficient and influence of virulence factor genes (VFGs) have not been elucidated. Here, removal of intracellular and extracellular ARGs as well as VFGs by electricity-intensified CWs was comprehensively evaluated. The two electrolysis-intensified CWs can improve the removal of intracellular ARGs and MGEs to 0.96- and 0.85-logs, respectively. But cell-free extracellular ARGs (CF-eARGs) were significantly enriched with 1.8-logs in the electrolysis-intensified CW. Interestingly, adding Fe-C microelectrolysis to the electrolysis-intensified CW is conducive to the reduction of CF-eARGs. However, the detected number and relative abundances of intracellular and extracellular VFGs were increased in all of the three CWs. The biofilms attached onto the substrates and rhizosphere are also hotspots of both intracellular and particle-associated extracellular ARGs and VFGs. Structural equation models and correlation analysis indicated that ARGs and VFGs were significantly cooccurred, suggesting that VFGs may affect the dynamics of ARGs. The phenotypes of VFGs, such as biofilm, may act as protective matrix for ARGs, hindering the removal of resistance genes. Our results provide novel insights into the ecological remediation technologies to enhance the removal of ARGs.

Anthropogenic pollution may enhance natural transformation in water, favouring the spread of antibiotic resistance genes.

Aquatic ecosystems are crucial in the antimicrobial resistance cycle. While intracellular DNA has been extensively studied to understand human activity's impact on antimicrobial resistance gene (ARG) dissemination, extracellular DNA is frequently overlooked. This study examines the effect of anthropogenic water pollution on microbial community diversity, the resistome, and ARG dissemination. We analyzed intracellular and extracellular DNA from wastewater treatment plant effluents and lake surface water by shotgun sequencing. We also conducted experiments to evaluate anthropogenic pollution's effect on transforming extracellular DNA (using Gfp-plasmids carrying ARGs) within a natural microbial community. Chemical analysis showed treated wastewater had higher anthropogenic pollution-related parameters than lake water. The richness of microbial community, antimicrobial resistome, and high-risk ARGs was greater in treated wastewaters than in lake waters both for intracellular and extracellular DNA. Except for the high-risk ARGs, richness was significantly higher in intracellular than in extracellular DNA. Several ARGs were associated with mobile genetic elements and located on plasmids. Furthermore, Gfp-plasmid transformation within a natural microbial community was enhanced by anthropogenic pollution levels. Our findings underscore anthropogenic pollution's pivotal role in shaping microbial communities and their antimicrobial resistome. Additionally, it may facilitate ARG dissemination through extracellular DNA plasmid uptake.

Neglected risks of enhanced antimicrobial resistance and pathogenicity in anaerobic digestion during transition from thermophilic to mesophilic.

Minimization of antibiotic resistance genes (ARGs) and potential pathogenic antibiotic-resistant bacteria (PARB) during anaerobic digestion (AD) is significantly impacted by temperature. However, knowledge on how ARGs and PARB respond to temperature transition from thermophilic to mesophilic is limited. Here, we combined metagenomic-based with culture-based approaches and revealed the risks of antimicrobial resistance and pathogenicity during transition from 55 °C to 35 °C for AD, with strategies of sharp (ST, one-step by 20 °C/d) and mild (MT, step-wise by 1 °C/d). Results indicated a lower decrease in methane production with MT (by 38.9%) than ST (by 88.8%). Phenotypic assays characterized a significant propagation of multi-resistant lactose-fermenting Enterobacteriaceae and indicator pathogens after both transitions, especially via ST. Further genomic evidence indicated a significant increase of ARGs (29.4-fold), virulence factor genes (1.8-fold) and PARB (65.3-fold) after ST, while slight enrichment via MT. Bacterial succession and enhanced horizontal transfer mediated by mobile genetic elements promoted ARG propagation in AD during transition, which was synchronously exacerbated through horizontal transfer mechanisms mediated by cellular physiological responses (oxidative stress, membrane permeability, bacterial conjugation and transformation) and co-selection mechanisms of biomethanation metabolic functions (acidogenesis and acetogenesis). This study reveals temperature-dependent resistome and pathogenicity development in AD, facilitating microbial risk control.

Polyvinyl chloride microplastics in the aquatic environment enrich potential pathogenic bacteria and spread antibiotic resistance genes in the fish gut.

Microplastics and antibiotics coexist in aquatic environments, especially in freshwater aquaculture areas. However, as the second largest production of polyvinyl chloride (PVC) in the world, the effects of co-exposure to microplastics particles and antibiotics on changes in antibiotic resistance gene (ARG) profiles and the microbial community structure of aquatic organism gut microorganisms are poorly understood. Therefore, in this study, carp (Cyprinus carpio) were exposed to single or combined PVC microplastic contamination and oxytetracycline (OTC) or sulfamethazine (SMZ) for 8 weeks. PVC microplastics can enrich potential pathogenic bacteria, such as Enterobacter and Acinetobacter, among intestinal microorganisms. The presence of PVC microplastics enhanced the selective enrichment and dissemination risk of ARGs. PVC microplastics combined with OTC (OPVC) treatment significantly increased the abundance of tetracycline resistance genes (1.40-fold) compared with that in the OTC exposure treatment, revealing an obvious co-selection effect. However, compared with those in the control group, the total abundance of ARGs and MGEs in the OPVC treatment groups were significantly lower, which was correlated with the reduced abundances of the potential host Enterobacter. Overall, our results emphasized the diffusion and spread of ARGs are more influenced by PVC microplastics than by antibiotics, which may lead to antibiotic resistance in aquaculture.

[Knockdown of motility-related genes of Komagataeibacter xylinus and its effect on bacterial cellulose synthesis].

Bacterial cellulose (BC) is a biopolymer synthesized by bacteria, which possess excellent characteristics such as high water holding capacity, high crystallinity, and high purity. It is widely used in food, medical, cosmetics, and functional films. Komagataeibacter xylinus is a model strain used in BC synthesis research. In bacteria, motility-related genes are associated with BC synthesis, whereas in Komagataeibacter xylinus CGMCC 2955, the functions of motility-related genes and their effects on BC synthesis are not known. To address this gap, we used the λ Red recombinant system to individually knock out motA, motB, and mot2A respectively, and constructed the knockout strains K. x-ΔmotA, K. x-ΔmotB, and K. x-Δmot2A. Additionally, both motA and motB were disrupted to construct the K. x-ΔmotAB mutant. The results demonstrated that knockout strain K. x-ΔmotAB exhibited the highest BC yield, reaching (5.05±0.26) g/L, which represented an increase of approximately 24% compared to wild-type strains. Furthermore, the BC synthesized by this strain exhibited the lowest porosity, 54.35%, and displayed superior mechanical properties with a Young's modulus of up to 5.21 GPa. As knocking out motA and motB genes in K. xylinus CGMCC 2955 did not reduce BC yield; instead, it promoted BC synthesis. Consequently, this research further deepened our understanding of the relationship between motility and BC synthesis in acetic acid bacteria. The knockouts of motA and motB genes resulted in reduced BC porosity and improved mechanical properties, provides a reference for BC synthesis and membrane structure regulation modification.

Utilizing co-abundances of antimicrobial resistance genes to identify potential co-selection in the resistome.

The rapid spread of antimicrobial resistance (AMR) is a threat to global health, and the nature of co-occurring antimicrobial resistance genes (ARGs) may cause collateral AMR effects once antimicrobial agents are used. Therefore, it is essential to identify which pairs of ARGs co-occur. Given the wealth of next-generation sequencing data available in public repositories, we have investigated the correlation between ARG abundances in a collection of 214,095 metagenomic data sets. Using more than 6.76∙108 read fragments aligned to acquired ARGs to infer pairwise correlation coefficients, we found that more ARGs correlated with each other in human and animal sampling origins than in soil and water environments. Furthermore, we argued that the correlations could serve as risk profiles of resistance co-occurring to critically important antimicrobials (CIAs). Using these profiles, we found evidence of several ARGs conferring resistance for CIAs being co-abundant, such as tetracycline ARGs correlating with most other forms of resistance. In conclusion, this study highlights the important ARG players indirectly involved in shaping the resistomes of various environments that can serve as monitoring targets in AMR surveillance programs. IMPORTANCE: Understanding the collateral effects happening in a resistome can reveal previously unknown links between antimicrobial resistance genes (ARGs). Through the analysis of pairwise ARG abundances in 214K metagenomic samples, we observed that the co-abundance is highly dependent on the environmental context and argue that these correlations can be used to show the risk of co-selection occurring in different settings.

Detection and Quantification of Conjugative Transfer of Mobile Genetic Elements Carrying Antibiotic Resistance Genes.

Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IMEs frequently form tandems or nested composite elements, which make their identification difficult. To evaluate their mobility, it is necessary to (i) select the suitable donor-recipient pairs for mating assays, (ii) do PCR excision tests to confirm that the genetic element is able to excise from the chromosome as a circular intermediate, and (iii) evaluate the transfer of the genetic element by conjugation by doing mating assays. In addition to a dissemination of resistance genes between S. suis strains, MGEs can lead to a spreading of resistance genes in the environment and toward pathogenic bacteria. This propagation had to be considered in a One Health perspective.

Costs of antibiotic resistance genes depend on host strain and environment and can influence community composition.

Antibiotic resistance genes (ARGs) benefit host bacteria in environments containing corresponding antibiotics, but it is less clear how they are maintained in environments where antibiotic selection is weak or sporadic. In particular, few studies have measured if the direct effect of ARGs on host fitness is fixed or if it depends on the host strain, perhaps marking some ARG-host combinations as selective refuges that can maintain ARGs in the absence of antibiotic selection. We quantified the fitness effects of six ARGs in 11 diverse Escherichia spp. strains. Three ARGs (blaTEM-116, cat and dfrA5, encoding resistance to ß-lactams, chloramphenicol, and trimethoprim, respectively) imposed an overall cost, but all ARGs had an effect in at least one host strain, reflecting a significant strain interaction effect. A simulation predicts these interactions can cause the success of ARGs to depend on available host strains, and, to a lesser extent, can cause host strain success to depend on the ARGs present in a community. These results indicate the importance of considering ARG effects across different host strains, and especially the potential of refuge strains to allow resistance to persist in the absence of direct selection, in efforts to understand resistance dynamics.

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human.

BACKGROUND: Aquaculture is an important food source worldwide. The extensive use of antibiotics in intensive large-scale farms has resulted in resistance development. Non-intensive aquaculture is another aquatic feeding model that is conducive to ecological protection and closely related to the natural environment. However, the transmission of resistomes in non-intensive aquaculture has not been well characterized. Moreover, the influence of aquaculture resistomes on human health needs to be further understood. Here, metagenomic approach was employed to identify the mobility of aquaculture resistomes and estimate the potential risks to human health. RESULTS: The results demonstrated that antibiotic resistance genes (ARGs) were widely present in non-intensive aquaculture systems and the multidrug type was most abundant accounting for 34%. ARGs of non-intensive aquaculture environments were mainly shaped by microbial communities accounting for 51%. Seventy-seven genera and 36 mobile genetic elements (MGEs) were significantly associated with 23 ARG types (p < 0.05) according to network analysis. Six ARGs were defined as core ARGs (top 3% most abundant with occurrence frequency > 80%) which occupied 40% of ARG abundance in fish gut samples. Seventy-one ARG-carrying contigs were identified and 75% of them carried MGEs simultaneously. The qacEdelta1 and sul1 formed a stable combination and were detected simultaneously in aquaculture environments and humans. Additionally, 475 high-quality metagenomic-assembled genomes (MAGs) were recovered and 81 MAGs carried ARGs. The multidrug and bacitracin resistance genes were the most abundant ARG types carried by MAGs. Strikingly, Fusobacterium_A (opportunistic human pathogen) carrying ARGs and MGEs were identified in both the aquaculture system and human guts, which indicated the potential risks of ARG transfer. CONCLUSIONS: The mobility and pathogenicity of aquaculture resistomes were explored by a metagenomic approach. Given the observed co-occurrence of resistomes between the aquaculture environment and human, more stringent regulation of resistomes in non-intensive aquaculture systems may be required. Video Abstract.

Detection of the antibiotic resistance genes content of intestinal Bacteroides, Parabacteroides and Phocaeicola isolates from healthy and carbapenem-treated patients from European countries.

BACKGROUND: Bacteroides fragilis group (BFG) species are the most significant anaerobic pathogens and are also the most antibiotic-resistant anaerobic species. Therefore, surveying their antimicrobial resistance levels and investigating their antibiotic resistance mechanisms is recommended. Since their infections are endogenous and they are important constituents of the intestinal microbiota, the properties of the intestinal strains are also important to follow. The aim of this study was to investigate the main antibiotic gene content of microbiota isolates from healthy people and compare them with the gene carriage of strains isolated from infections. RESULTS: We detected 13, mainly antibiotic resistance determinants of 184 intestinal BFG strains that were isolated in 5 European countries (Belgium, Germany, Hungary, Slovenia and Turkey) and compared these with values obtained earlier for European clinical strains. Differences were found between the values of this study and an earlier one for antibiotic resistance genes that are considered to be mobile, with higher degrees for cfxA, erm(F) and tet(Q) and with lower degrees for msrSA, erm(B) and erm(G). In addition, a different gene prevalence was found depending on the taxonomical groups, e.g., B. fragilis and NBFB. Some strains with both the cepA and cfiA ß-lactamase genes were also detected, which is thought to be exceptional since until now, the B. fragilis genetic divisions were defined by the mutual exclusion of these two genes. CONCLUSIONS: Our study detected the prevalences of a series of antibiotic resistance genes in intestinal Bacteroides strains which is a novelty. In addition, based on the current and some previous data we hypothesized that prevalence of some antibiotic resistance genes detected in the clinical and intestinal BFG strains were different, which could be accounted with the differential composition of the Bacteroides microbiota and/or the MGE mobilities at the luminal vs. mucosal sites of the intestine.

Environmental microbiome diversity and stability is a barrier to antimicrobial resistance gene accumulation.

When antimicrobial resistant bacteria (ARB) and genes (ARGs) reach novel habitats, they can become part of the habitat's microbiome in the long term if they are able to overcome the habitat's biotic resilience towards immigration. This process should become more difficult with increasing biodiversity, as exploitable niches in a given habitat are reduced for immigrants when more diverse competitors are present. Consequently, microbial diversity could provide a natural barrier towards antimicrobial resistance by reducing the persistence time of immigrating ARB and ARG. To test this hypothesis, a pan-European sampling campaign was performed for structured forest soil and dynamic riverbed environments of low anthropogenic impact. In soils, higher diversity, evenness and richness were significantly negatively correlated with relative abundance of >85% of ARGs. Furthermore, the number of detected ARGs per sample were inversely correlated with diversity. However, no such effects were present in the more dynamic riverbeds. Hence, microbiome diversity can serve as a barrier towards antimicrobial resistance dissemination in stationary, structured environments, where long-term, diversity-based resilience against immigration can evolve.

Streambed immobilization controls the transport of antibiotic resistance genes in flowing water.

Antibiotic resistance is a serious global health issue, resulting in at least 1.2 million deaths in 2019. The environment is a potentially important reservoir of antibiotic resistance; however, the fate of Antibiotic Resistance Genes (ARGs) in the environment remains poorly characterized. One important environmental source of ARGs is manure used as a soil amendment. ARGs from manure may then enter nearby flowing waterbodies, where the factors governing their downstream transport remain unknown. To address this, we conducted experiments by spiking cattle manure in an artificial stream to estimate removal rates (k; m-1) for three ARGs (mefA, tetQ, and tetW) and a ruminant fecal marker (bacR). We then used a Stochastic Mobile-Immobile Model (SMIM) to separate the overall removal into two components, rs, and rh, corresponding to immobilizations in the surface (i.e., water column) and subsurface (i.e., streambed), respectively. Finally, we applied the SMIM across four model streams to predict the downstream travel distance of ARGs and bacR. Our results showed measurable removal for all targets in all experimental replicates (n = 3) and no differences were found in the removal rates among replicates for any target (ANCOVA; p > 0.05). We found that the removal of bacR was significantly lower than tetW (p < 0.05) and slightly lower than mefA (p = 0.088), while tetQ removal was slightly different from tetW's (p = 0.072). We also found that rh values were orders of magnitude larger than rs for ARGs and bacR (t-test; p < 0.05). These findings suggest that ARGs and bacR are being removed from the water column through immobilization reactions occurring in the streambed. Additionally, we predicted that the 90 % removal (or D90) of targets occurs within the first 500 m in all model streams except in a slow-flow pastoral stream, which required 1400 m of downstream transport for 90 % removal. Our findings and model stand out as promising tools to predict the fate of ARGs in streams and will contribute to improving and managing agricultural practices that employ animal manure.

Investigation of high-risk antibiotic resistance bacteria and their associated antibiotic resistance genes in different agricultural soils with biogas slurry from China.

High-risk antibiotic-resistant bacteria (ARB) and their accompanying antibiotic resistance genes (ARGs) seriously threaten public health. As a crucial medium for ARB and ARGs spread, soils with biogas slurry have been widely investigated. However, few studies focused on high-risk multi-drug resistant bacteria (MDRB) and their associated ARGs. This study examined ARB distribution in different agricultural soils with biogas slurry across 12 districts in China. It identified high-risk MDRB in various soil backgrounds, elucidating their resistance and spread mechanism. The findings revealed that diverse cultured ARB were enriched in soils with biogas slurry, especially soil ciprofloxacin ARB, which were enriched (>2.5 times) in 68.4 % of sampling sites. Four high-risk MDRB isolated from Hebei, Zhejiang, Shanxi, and Gansu districts were identified as severe or opportunistic pathogens, which carried abundant mobile genetic elements (MGEs) and 14 known high risk ARGs, including aac(3)-IId, aac(6')-Ib3, aph(6)-Id, aac(6')-Ib3, aadA1, blaOXA-10, blaTEM-1B, dfrA12, dfrA14, cmlA1, sul1, floR, tet(M) and tet(L). The antibiotics accumulation, diverse ARGs and MGEs enrichment, and proliferation of pathogenic bacteria could be potential driving factors of their occurrence and spread. Therefore, the coexistence of the high-risk MDRB and ARGs combined with the associated MGEs in soils with biogas slurry should be further investigated to develop technology and policy for reducing their negative influences on the effectiveness of clinical antibiotics.

Unraveling the determinants of antibiotic resistance evolution in farmland under fertilizations.

Organic fertilization is a major driver potentiating soil antibiotic resistance in farmland. However, it remains unclear how bacterial antibiotic resistance evolves in fertilized soils and even spreads to crops. Compared with no fertilizer and commercial fertilizer treatments, organic fertilizers markedly increased the abundance of soil antibiotic resistance genes (ARGs) but the relatively weaker transfer of resistance genes from soil to crops. The introduction of organic fertilizers enriches the soil with nutrients, driving indigenous microorganisms towards a K-strategy. The pH, EC, and nutrients as key drivers influenced the ARGs abundance. The neutral (pH 7.2), low salt (TDS 1.4 %) and mesotrophic (carbon content 3.54 g/L) habitats similar to the soil environment conditioned by organic fertilizers. These environmental conditions clearly prolonged the persistence of resistant plasmids, and facilitated their dissemination to massive conjugators soil microbiome but not to plant endophytes. This suggested that organic fertilizers inhibited the spread of ARGs to crops. Moreover, the composition of conjugators showed differential selection of resistant plasmids by endophytes under these conditions. This study sheds light on the evolution and dissemination of antibiotic resistance in farmlands and can aid in the development of antimicrobial resistance control strategies in agriculture.

Effects of 3-year organic farming management on soil antibiotic resistant genes and virulence factors in a double rice cropping system.

Investigating the antibiotic resistance genes (ARGs) and virulence factors (VFs) within soil microbial communities is crucial for understanding microbial ecology and the evolution of antibiotic resistance. However, the study of ARGs, VFs, and their predominant microbial hosts in soils under varying rice production management practices remains largely underexplored. To this end, a three-year field experiment was conducted under organic management within a double rice cropping system in South China. The study revealed that, in contrast to conventional management (CK), organic farming practices did not significantly alter the total reads of ARGs and VFs. However, there was a notable alteration in the ARGs abundance at the antibiotic class level, such as an increase (P < 0.05) in the abundance of Multidrug ARGs (by 1.7 %) and a decrease (P < 0.05) in Rifamycin (by 17.5 %) and Fosfomycin ARGs (by 15.3 %). Furthermore, a significant shift in VFs was observed under organic farming compared to CK, characterized by an increase (P < 0.05) in offensive VFs and a decrease (P < 0.05) in nonspecific VFs and the regulation of virulence-associated genes. Key microbial taxa identified as influencing ARGs and VFs in the tested soil samples, e.g., Proteobacteria. The findings highlight the need for more detailed attention to soil ecology within organic rice production systems in South China, particularly concerning the significant alterations observed in ARGs and VFs.

Enhanced removal of ciprofloxacin and associated antibiotic-resistant genes from wastewater using a biological aeration filters in combination with Fe3O4-modified zeolite.

Antibiotics release into the water environment through sewage discharge is a significant environmental concern. In the present study, we investigated the removal of ciprofloxacin (CIP) in simulated sewage by biological aeration filter (BAF) equipped with Fe3O4-modified zeolite (Fe3O4@ZF). Fe3O4@ZF were prepared with impregnation method, and the Fe3O4 particles were successfully deposited on the surface of ZF in an amorphous form according to the results of XPS and XRD analysis. The modification also increased the specific surface area (from 16.22 m²/g to 22 m²/g) and pore volume (from 0.0047 cm³/g to 0.0063 cm³/g), improving the adsorption efficiency of antibiotics. Fe3O4 modified ZF improved the treatment performance significantly, and the removal efficiency of CIP in BAF-Fe3O4@ZF was 79%±2.4%. At 10ml/L CIP, the BAF-Fe3O4@ZF reduced the relative abundances of antibiotics resistance genes (ARGs) int, mexA, qnrB and qnrS in the effluent by 57.16%, 39.59%, 60.22%, and 20.25%, respectively, which effectively mitigate the dissemination risk of ARGs. The modification of ZF increased CIP-degrading bacteria abundance, such as Rhizobium and Deinococcus-Thermus, and doubled bacterial ATP activity, promoting CIP degradation. This study offers a viable, efficient method to enhance antibiotic treatment and prevent leakage via sewage discharge.

Metagenomic airborne resistome from urban hot spots through the One Health lens.

Human activities are a significant contributor to the spread of antibiotic resistance genes (ARGs), which pose a serious threat to human health. These ARGs can be transmitted through various pathways, including air, within the context of One Health. This study used metagenomics to monitor the resistomes in urban air from two critical locations: a wastewater treatment plant and a hospital, both indoor and outdoor. The presence of cell-like structures was confirmed through fluorescence microscopy. The metagenomic analysis revealed a wide variety of ARGs and a high diversity of antibiotic-resistant bacteria in the airborne particles collected. The wastewater treatment plant showed higher relative abundances with 32 ARG hits per Gb and m3, followed by the main entrance of the hospital (indoor) with ≈5 ARG hits per Gb and m3. The hospital entrance exhibited the highest ARG richness, with a total of 152 different ARGs classified into nine categories of antibiotic resistance. Common commensal and pathogenic bacteria carrying ARGs, such as Moraxella, Staphylococcus and Micrococcus, were detected in the indoor airborne particles of the hospital. Interestingly, no ARGs were shared among all the samples analysed, indicating a highly variable dynamic of airborne resistomes. Furthermore, the study found no ARGs in the airborne viral fractions analysed, suggesting that airborne viruses play a negligible role in the dissemination of ARGs.