Higher spreading risk of antibacterial biocide and heavy metal resistance genes than antibiotic resistance genes in aerobic granular sludge

Beta-blocker drives the conjugative transfer of multidrug resistance genes in pure and complex biological systems

Drug resistance poses a high risk to human health. Extensive use of non-antibiotic drugs contributes to antibiotic resistance genes (ARGs) transfer. However, how they affect the spread of broad-host plasmids in complex biological systems remains unknown. This study investigated the effect of metoprolol on the transfer frequency and host range of ARGs in both intrageneric and intergeneric pure culture systems, as well as in anammox microbiome. The results showed that environmental concentrations of metoprolol significantly promoted the intrageneric and intergeneric conjugative transfer. Initially, metoprolol induced excessive oxidative stress, resulting in high cell membrane permeability and bacterial SOS response. Meanwhile, more pili formation increased the adhesion and contact between bacteria, and the abundance of conjugation-related genes also increased significantly. Activation of the electron transport chain provided more ATP for this energy-consuming process. The underlying mechanism was further verified in the complex anammox conjugative system. Metoprolol induced the enrichment of ARGs and mobile genetic elements. The enhanced bacterial interaction and energy generation facilitated the high conjugative transfer frequency of ARGs. In addition, plasmid-borne ARGs tended to transfer to opportunistic pathogens. This work raises public concerns about the health and ecological risks of non-antibiotic drugs.

Critical insights into the Hormesis of antibiotic resistome in saline soil: Implications from salinity regulation

Soil is recognized as an important reservoir of antibiotic resistance genes (ARGs). However, the effect of salinity on the antibiotic resistome in saline soils remains largely misunderstood. In this study, high-throughput qPCR was used to investigate the impact of low-variable salinity levels on the occurrence, health risks, driving factors, and assembly processes of the antibiotic resistome. The results revealed 206 subtype ARGs across 10 categories, with medium-salinity soil exhibiting the highest abundance and number of ARGs. Among them, high-risk ARGs were enriched in medium-salinity soil. Further exploration showed that bacterial interaction favored the proliferation of ARGs. Meanwhile, functional genes related to reactive oxygen species production, membrane permeability, and adenosine triphosphate synthesis were upregulated by 6.9%, 2.9%, and 18.0%, respectively, at medium salinity compared to those at low salinity. With increasing salinity, the driver of ARGs in saline soils shifts from bacterial community to mobile gene elements, and energy supply contributed 28.2% to the ARGs at extreme salinity. As indicated by the neutral community model, stochastic processes shaped the assembly of ARGs communities in saline soils. This work emphasizes the importance of salinity on antibiotic resistome, and provides advanced insights into the fate and dissemination of ARGs in saline soils.

Characteristics, Performance and Microbial Response of Aerobic Granular Sludge for Treating Tetracycline Hypersaline Pharmaceutical Wastewater

Salt-tolerant aerobic granular sludge(AGS) was successfully cultivated under the dual stress of tetracycline and 2.5% salinity, resulting in an average particle size of 435.0 ± 0.5 and exhibiting a chemical oxygen demand(COD) removal rate exceeding 80%, as well as excellent sedimentation performance. The analysis of metagenomics technology revealed a significant pattern of succession in the development of AGS. The proportion of Oleiagrimonas, a type of salt-tolerant bacteria, exhibited a gradual increase and reached 38.07% after 42 days, which indicated that an AGS system based on moderate halophilic bacteria was successfully constructed. The expression levels of targeted genes were found to be reduced across the entire AGS process and formation, as evidenced by qPCR analysis. The presence of int1 (7.67 log10 gene copies g-1 in 0 d sludge sample) enabled microbes to horizontally transfer ARGs genes along the AGS formation under the double pressure of TC and 2.5% salinity. These findings will enhance our understanding of ARG profiles and the development in AGS under tetracycline pressure, providing a foundation for guiding the use of AGS to treat hypersaline pharmaceutical wastewater.

Metagenomic insights into the nitrogen metabolism, antioxidant pathway, and antibiotic resistance genes of activated sludge from a sequencing batch reactor under tetracycline stress

Tetracycline is prevalent in wastewater treatment plants and poses a potential threat to biological nitrogen removal under long-term exposure. In the present study, the influence of different tetracycline concentrations on the nitrogen removal, bioactivity response, and the spread of antibiotic resistance genes (ARGs) was assessed in sequencing batch reactor (SBR). The nitrogen removal efficiency, nitrification rate, and denitrification rate and their corresponding enzymatic activities gradually decreased with an increase in tetracycline concentration from 0.5 to 15 mg/L. The remarkable toxicity induced by tetracycline led to a significant increase in the peroxidation and the response of antioxidant system, as evidenced by strengthened antioxidant enzymatic activity and abundant genes (SOD12, katG, PXDN, gpx, and apx). Tetracycline addition significantly inhibited the ammonia-oxidizing bacterium Nitrosomonas and functional genes (amoA, amoB, and amoC). The presence of tetracycline decreased the abundance of citrate synthase and genes (CS, IDH3, and acnA) and interfered with carbon source metabolism, leading to impaired bioactivity and treatment performance. In addition, the presence of tetracycline induces diversity and differences in ARGs. The results provide reliable basic data for a deeper understanding of the effects of tetracycline on the nitrogen removal performance of bioreactors and provide a theoretical basis to build a promising strategy for relieving antibiotic-caused process fluctuations.

Performance of sewage sludge treatment for the removal of antibiotic resistance genes: Status and prospects

Wastewater treatment plants (WWTPs) receive wastewater containing antibiotic resistant bacteria (ARB) and antibiotic resistant genes (ARGs), which are predominant contributors to environmental pollution in water and soil. Of these sources, sludge is a more significant contributor than effluent. Knowing how sludge treatment affects the fate of ARGs is vital for managing the risk of these genes in both human and natural environments. This review therefore discusses the sources and transmission of ARGs in the environment and highlights the risks of ARGs in sludge. The effects of co-existing constituents (heavy metals, microplastics, etc.) on sludge and ARGs during treatment are collated to highlight the difficulty of treating sludge with complex constituents in ARGs. The effects of various sludge treatment methods on the abundances of ARGs in sludge and in soil from land application of treated sludge are discussed, pointing out that the choice of sludge treatment method should take into account various potential factors, such as soil and soil biology in subsequent land application. This review offers significant insights and explores the abundances of ARGs throughout the process of sludge treatment and disposal. Unintentional addition of antibiotic residues, heavy metals, microplastics and organic matter in sludge could significantly increase the abundance and reduce the removal efficiency of ARGs during treatment, which undoubtedly adds a barrier to the removal of ARGs from sludge treatment. The complexity of the sludge composition and the diversities of ARGs have led to the fact that no effective sludge treatment method has so far been able to completely eliminate the ecological risk of ARGs. In order to reduce risks resulting by transmission of ARGs, technical and management measures need to be implemented.

Comparative resistome analysis of Aeromonas species in aquaculture reveals antibiotic resistance patterns and phylogeographic distribution

The overuse of antibiotics in aquaculture drives the emergence of multi-drug-resistant bacteria, and antibiotic-resistant genes (ARGs) can be disseminated to other bacteria through vertical- and horizontal gene transfer (VGT and HGT) under selective pressure. Profiling the antibiotic resistome and understanding the global distribution of ARGs constitutes the first step in developing a control strategy. Hence, this study utilized extensive genomic data from hundreds of Aeromonas strains in aquaculture to profile resistome patterns and explores their association with isolation year, country, and species characteristics. Overall, ∼400 Aeromonas genomes were used to predict the ARGs from A. salmonicida, A. hydrophila, A. veronii, A. media, and A. sobria. ARGs such as sul1, tet(A), and tet(D), which display a similar proportion of positive strains among species, were subjected to phylodynamic and phylogeographic analyses. More than a hundred ARGs were identified, some of which exhibited either species-specific or non-species-specific patterns. A. salmonicida and A. media were found to have a higher proportion of species-specific ARGs than other strains, which might lead to more distinct patterns of ARG acquisition. Overall, ∼25% of strains have either sul1, tet(A), or tet(D) gene(s), but no significant difference was observed in the proportion of positive strains by species. Phylogeographic analysis revealed that the abundant numbers of sul1, tet(A), and/or tet(D) introduced in a few East Asian and North American countries could spread to both adjacent and faraway countries. In recent years, the proportions of these ARGs have dramatically increased, particularly in strains sourced from aquatic environments, suggesting control is required of the overuse of antibiotics in aquaculture. The findings of this research offer significant insights into the global dissemination of ARGs.

The genome of Symbiodiniaceae-associated Stutzerimonas frequens CAM01 reveals a broad spectrum of antibiotic resistance genes indicating anthropogenic drift in the Palk Bay coral reef of south-eastern India

An increase in antibiotic pollution in reef areas will lead to the emergence of antibiotic-resistant bacteria, leading to ecological disturbances in the sensitive coral holobiont. This study provides insights into the genome of antibiotics-resistant Stutzerimonas frequens CAM01, isolated from Favites-associated Symbiodiniaceae of a near-shore polluted reef of Palk Bay, India. The draft genome contains 4.67 Mbp in size with 52 contigs. Further genome analysis revealed the presence of four antibiotic-resistant genes, namely, adeF, rsmA, APH (3")-Ib, and APH (6)-Id that provide resistance by encoding resistance-nodulation-cell division (RND) antibiotic efflux pump and aminoglycoside phosphotransferase. The isolate showed resistance against 73% of the antibiotics tested, concurrent with the predicted AMR genes. Four secondary metabolites, namely Aryl polyene, NRPS-independent-siderophore, terpenes, and ectoine were detected in the isolate, which may play a role in virulence and pathogenicity adaptation in microbes. This study provides key insights into the genome of Stutzerimonas frequens CAM01 and highlights the emergence of antibiotic-resistant bacteria in coral reef ecosystems.

Potential of direct granulation and organic loading rate tolerance of aerobic granular sludge in ultra-hypersaline environment

Salt-tolerant aerobic granular sludge (SAGS) technology has shown potentials in the treatment of ultra-hypersaline high-strength organic wastewater. However, the long granulation period and salt-tolerance acclimation period are still bottlenecks that hinder SAGS applications. In this study, "one-step" development strategy was used to try to directly cultivate SAGS under 9% salinity, and the fastest cultivation process was obtained under such high salinity compared to the previous papers with the inoculum of municipal activated sludge without bioaugmentation. Briefly, the inoculated municipal activated sludge was almost discharged on Day 1-10, then fungal pellets appeared and it gradually transitioned to mature SAGS (particle size of ∼4156 μm and SVI₃₀ of 57.8 mL/g) from Day 11 to Day 47 without fragmentation. Metagenomic revealed that fungus Fusarium played key roles in the transition process probably because it functioned as structural backbone. RRNPP and AHL-mediated systems might be the main QS regulation systems of bacteria. TOC and NH₄⁺-N removal efficiencies maintained at ∼93.9% (after Day 11) and ∼68.5% (after Day 33), respectively. Subsequently, the influent organic loading rate (OLR) was stepwise increased from 1.8 to 11.7 kg COD/m³·d. It was found that SAGS could maintain intact structure and low SVI₃₀ (< 55 mL/g) under 9% salinity and the OLR of 1.8-9.9 kg COD/m³·d with adjustment of air velocity. TOC and NH₄⁺-N (TN) removal efficiencies could maintain at ∼95.4% (below OLR of 8.1 kg COD/m³·d) and ∼84.1% (below nitrogen loading rate of 0.40 kg N/m³·d) in ultra-hypersaline environment. Halomonas dominated the SAGS under 9% salinity and varied OLR. This study confirmed the feasibility of direct aerobic granulation in ultra-hypersaline environment and verified the upper OLR boundary of SAGS in ultra-hypersaline high-strength organic wastewater treatment.

Effects of long-term microplastic pollution on soil heavy metals and metal resistance genes: Distribution patterns and synergistic effects

Heavy metals (HMs) and microplastics (MPs) are two emerging factors threatening global food security. Whether long-term MPs pollution will affect the distribution of HMs and their resistance genes (MRGs) in soil is unknown. Here, metagenomic approach was used to decipher the fate of MRGs in cropland soils with long-term film MPs residues. Similar distribution pattern of MRGs was formed in long-term film MPs contaminated soil. A total of 202 MRG subtypes were detected, with resistance genes for Multimetal, Cu, and As being the most prevalent type of MRGs. MRGs formed a modular distribution of five clusters centered on MRGs including ruvB in long-term film MPs contaminated soil. MRGs also formed tight co-occurrence networks with mobile genetic elements (MGEs: integrons, insertions and plasmids). Redundancy analysis showed that HMs together with microbial communities and MGEs affected the distribution of MRGs in soil. Thirteen genera including Pseudomonas were identified as potential hosts for MRGs and MGEs. The research provides preliminary progress on the synergistic effect of HMs and MPs in affecting soil ecological security. The synergistic effect of MPs and HMs needs to be considered in the remediation of contaminated soils.

Para-chloro-meta-xylenol reshaped the fates of antibiotic resistance genes during sludge fermentation: Insights of cell membrane permeability, bacterial structure and biological pathways

The occurrence of para-chloro-meta-xylenol (PCMX, as largely consumed antimicrobial chemicals) in waste activated sludge (WAS) would pose environmental risks for WAS utilization. This study revealed that PCMX principally prompted the abundances and diversity of antibiotic resistance genes (ARGs), particularly for the multidrug- genes (i.e., acrB and mexW), and reshaped the resistance mechanism categories during WAS fermentation process. The genotype and phenotype results indicated that PCMX upregulated abundances of transposase and increased cell permeability via disrupting WAS structure, which further facilitated the horizontal transfer of ARGs. The network and correlation analysis among ARGs, mobile genetic elements (MGEs) and genera (i.e., Sphingopyxis and Pseudoxanthomonas) verified that PCMX enriched the potential ARGs hosts associated with multidrug resistance mechanism. Also, PCMX upregulated the genes involved in ARGs-associated metabolic pathways, such as two-component (i.e., phoP and vcaM) and quorum sensing systems (i.e., lasR and cciR), which determined the ARGs proliferation via multidrug efflux pump and outer membrane proteins, and facilitated the recognition between ARGs hosts. Variance partitioning analysis (VPA) implied that the shift of microbial community contributed predominantly to the dissemination of ARGs. These findings unveiled the environmental behaviors and risks of exogenous pollutants in WAS with insightful understanding, which could guide the WAS utilization for resource recovery.

Fate of antibiotic resistance genes (ARGs) in wastewater treatment plant: Preliminary study on identification before and after ultrasonication

This study collected sludge samples from four different sections of a local wastewater treatment plant in Mikkeli, Finland, for antibiotic resistance genes (ARGs) analysis. Here, we examine the seven representative ARGs in sludge, encoding erythromycin (ermB), tetracycline (tetA, tetC, tetQ, tetW) and sulphonamide (sul1) to check abundance before and after ultrasonication. The class 1 integron (intl1) was also observed as an indicator of antibiotic resistance and horizontal gene transmission. The pre-treatment condition included 10 min of ultrasonication (US) for the sludge sample before freeze-drying. The droplet digital PCR system was used to assess the ARGs from the samples, and it was found that ARGs were not effectively eliminated by pre-treatment. After ultrasonication, tetA, tetC and tetQ did not show any variation but tetW showed 20 copies/ng of lower abundance in digested sludge than raw sludge, and a similar abundance was found in dewatered sludge. For MBR sludge, only ermB showed 1000 copies/ng higher abundance compared to the raw sample and surprisingly it did not show the presence of any other types of ARG. This study provides an overview of the appearance of ARGs in regional municipal sludge for further research reflection.