Detection and various environmental factors of antibiotic resistance gene horizontal transfer

How micro-/nano-plastics influence the horizontal transfer of antibiotic resistance genes - A review

Plastic debris such as microplastics (MPs) and nanoplastics (NPTs), along with antibiotic resistance genes (ARGs), are pervasive in the environment and are recognized as significant global health and ecological concerns. Micro-/nano-plastics (MNPs) have been demonstrated to favor the spread of ARGs by enhancing the frequency of horizontal gene transfer (HGT) through various pathways. This paper comprehensively and systematically reviews the current study with focus on the influence of plastics on the HGT of ARGs. The critical role of MNPs in the HGT of ARGs has been well illustrated in sewage sludge, livestock farms, constructed wetlands and landfill leachate. A summary of the performed HGT assay and the underlying mechanism of plastic-mediated transfer of ARGs is presented in the paper. MNPs could facilitate or inhibit HGT of ARGs, and their effects depend on the type, size, and concentration. This review provides a comprehensive insight into the effects of MNPs on the HGT of ARGs, and offers suggestions for further study. Further research should attempt to develop a standard HGT assay and focus on investigating the impact of different plastics, including the oligomers they released, under real environmental conditions on the HGT of ARGs.

Seasonal dynamics of antibiotic resistance genes and mobile genetic elements in a subtropical coastal ecosystem: Implications for environmental health risks

Antibiotic resistance poses a considerable global public health concern, leading to heightened rates of illness and mortality. However, the impact of seasonal variations and environmental factors on the health risks associated with antibiotic resistance genes (ARGs) and their assembly mechanisms is not fully understood. Based on metagenomic sequencing, this study investigated the antibiotic resistome, mobile genetic elements (MGEs), and microbiomes in a subtropical coastal ecosystem of the Beibu Gulf, China, over autumn and winter, and explored the factors influencing seasonal changes in ARG and MGE abundance and diversity. Results indicated that ARG abundance and diversity were higher in winter than in autumn, with beta-lactam and multidrug resistance genes being the most diverse and abundant, respectively. Similarly, MGE abundance and diversity increased in winter and were strongly correlated with ARGs. In contrast, more pronounced associations between microbial communities, especially archaea, and the antibiotic resistome were observed in autumn than in winter. The co-occurrence network identified multiple interactions between MGEs and various multidrug efflux pumps in winter, suggesting a potential for ARG dissemination. Multivariate correlation analyses and path modeling indicated that environmental factors driving microbial community changes predominantly influenced antibiotic resistome assembly in autumn, while the relative importance of MGEs increased significantly in winter. These findings suggest an elevated health risk associated with antimicrobial resistance in the Beibu Gulf during winter, attributed to the dissemination of ARGs by horizontal gene transfer. The observed seasonal variations highlight the dynamic nature of antibiotic resistance dissemination in coastal ecosystems, emphasizing the need for comprehensive surveillance and management measures to address the growing threat of antimicrobial resistance in vulnerable environments.

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.

Masks As a New Hotspot for Antibiotic Resistance Gene Spread: Reveal the Contribution of Atmospheric Pollutants and Potential Risks

The consumption of disposable surgical masks (DSMs) considerably increased during the coronavirus pandemic in 2019. Herein, we explored the spread of antibiotic resistance genes (ARGs) and the potential risks of antibiotic resistant bacteria (ARB) on DSMs. At environmentally relevant concentrations, the conjugate transfer frequency (CTF) of ARGs increased by 1.34-2.37 folds by 20 μg/m3 of atmospheric water-soluble inorganic ions (WSIIs), and it increased by 2.62-2.86 folds by 80 ng/m3 of polycyclic aromatic hydrocarbons (PAHs). Total suspended particulates (TSP) further promoted the CTF in combination with WSIIs or PAHs. Under WSII and PAH exposure, gene expression levels related to oxidative stress, cell membrane, and the adenosine triphosphate (ATP) were upregulated. WSIIs predominantly induced cellular contact, while PAHs triggered ATP formation and membrane damage. Molecular dynamics simulations showed that WSIIs and PAHs reduced membrane lipid fluidity and increased membrane permeability through interactions with the phosphatidylcholine bilayer. DSM filtering performance decreased, and the CTF of ARGs increased with the wearing time. The gut simulator test showed that ARB disrupted the human gut microbial community and increased total ARG abundance but did not change the ARG abundance carried by ARB themselves. A mathematical model showed that long-term WSII and PAH exposure accelerated ARG dissemination in DSMs.

Deciphering the pathogenic risks of microplastics as emerging particulate organic matter in aquatic ecosystem

Microplastics are accumulating rapidly in aquatic ecosystems, providing habitats for pathogens and vectors for antibiotic resistance genes (ARGs), potentially increasing pathogenic risks. However, few studies have considered microplastics as particulate organic matter (POM) to elucidate their pathogenic risks and underlying mechanisms. Here, we performed microcosm experiments with microplastics and natural POM (leaves, algae, soil), thoroughly investigating their distinct effects on the community compositions, functional profiles, opportunistic pathogens, and ARGs in Particle-Associated (PA) and Free-Living (FL) bacterial communities. We found that both microplastics and leaves have comparable impacts on microbial community structures and functions, enriching opportunistic pathogens and ARGs, which may pose potential environmental risks. These effects are likely driven by their influences on water properties, including dissolved organic carbon, nitrate, DO, and pH. However, microplastics uniquely promoted pathogens as keystone species and further amplified their capacity as hosts for ARGs, potentially posing a higher pathogenic risk than natural POM. Our research also emphasized the importance of considering both PA and FL bacteria when assessing microplastic impacts, as they exhibited different responses. Overall, our study elucidates the role and underlying mechanism of microplastics as an emerging POM in intensifying pathogenic risks of aquatic ecosystems in comparison with conventional natural POM.

The escalating threat of human-associated infectious bacteria in surface aquatic resources: Insights into prevalence, antibiotic resistance, survival mechanisms, detection, and prevention strategies

Anthropogenic activities and climate change profoundly impact water quality, leading to a concerning increase in the prevalence and abundance of bacterial pathogens across diverse aquatic environments. This rise has resulted in a growing challenge concerning the safety of water sources, particularly surface waters and marine environments. This comprehensive review delves into the multifaceted challenges presented by bacterial pathogens, emphasizing threads to human health within ground and surface waters, including marine ecosystems. The exploration encompasses the intricate survival mechanisms employed by bacterial pathogens and the proliferation of antimicrobial resistance, largely driven by human-generated antibiotic contamination in aquatic systems. The review further addresses prevalent pathogenic bacteria, elucidating associated risk factors, exploring their eco-physiology, and discussing the production of potent toxins. The spectrum of detection techniques, ranging from conventional to cutting-edge molecular approaches, is thoroughly examined to underscore their significance in identifying and understanding waterborne bacterial pathogens. A critical aspect highlighted in this review is the imperative for real-time monitoring of biomarkers associated with waterborne bacterial pathogens. This monitoring serves as an early warning system, facilitating the swift implementation of action plans to preserve and protect global water resources. In conclusion, this comprehensive review provides fresh insights and perspectives, emphasizing the paramount importance of preserving the quality of aquatic resources to safeguard human health on a global scale.

Understanding Stimulation of Conjugal Gene Transfer by Nonantibiotic Compounds: How Far Are We?

A myriad of nonantibiotic compounds is released into the environment, some of which may contribute to the dissemination of antimicrobial resistance by stimulating conjugation. Here, we analyzed a collection of studies to (i) identify patterns of transfer stimulation across groups and concentrations of chemicals, (ii) evaluate the strength of evidence for the proposed mechanisms behind conjugal stimulation, and (iii) examine the plausibility of alternative mechanisms. We show that stimulatory nonantibiotic compounds act at concentrations from 1/1000 to 1/10 of the minimal inhibitory concentration for the donor strain but that stimulation is always modest (less than 8-fold). The main proposed mechanisms for stimulation via the reactive oxygen species/SOS cascade and/or an increase in cell membrane permeability are not unequivocally supported by the literature. However, we identify the reactive oxygen species/SOS cascade as the most likely mechanism. This remains to be confirmed by firm molecular evidence. Such evidence and more standardized and high-throughput conjugation assays are needed to create technologies and solutions to limit the stimulation of conjugal gene transfer and contribute to mitigating global antibiotic resistance.

Fate and removal of fluoroquinolone antibiotics in mesocosmic wetlands: Impact on wetland performance, resistance genes and microbial communities

The fate of fluoroquinolone antibiotics norfloxacin and ofloxacin were investigated in mesocosmic wetlands, along with their effects on nutrients removal, antibiotic resistance genes (ARGs) and epiphytic microbial communities on Hydrilla verticillate using bionic plants as control groups. Approximately 99% of norfloxacin and ofloxacin were removed from overlaying water, and H. verticillate inhibited fluoroquinolones accumulation in surface sediments compared to bionic plants. Partial least squares path modeling showed that antibiotics significantly inhibited the nutrient removal capacity (0.55) but had no direct effect on plant physiology. Ofloxacin impaired wetland performance more strongly than norfloxacin and more impacted the primary microbial phyla, whereas substrates played the most decisive role on microbial diversities. High antibiotics concentration shifted the most dominant phyla from Proteobacteria to Bacteroidetes and inhibited the Xenobiotics biodegradation function, contributing to the aggravation in wetland performance. Dechloromonas and Pseudomonas were regarded as the key microorganisms for antibiotics degradation. Co-occurrence network analysis excavated that microorganisms degrade antibiotics mainly through co-metabolism, and more complexity and facilitation/reciprocity between microbes attached to submerged plants compared to bionic plants. Furthermore, environmental factors influenced ARGs mainly by altering the community dynamics of differential bacteria. This study offers new insights into antibiotic removal and regulation of ARGs accumulation in wetlands with submerged macrophyte.

Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach

The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.

Research progress on the origin, fate, impacts and harm of microplastics and antibiotic resistance genes in wastewater treatment plants

Previous studies reported microplastics (MPs), antibiotics, and antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). There is still a lack of research progress on the origin, fate, impact and hazards of MPs and ARGs in WWTPs. This paper fills a gap in this regard. In our search, we used "microplastics", "antibiotic resistance genes", and "wastewater treatment plant" as topic terms in Web of Science, checking the returned results for relevance by examining paper titles and abstracts. This study mainly explores the following points: (1) the origins and fate of MPs, antibiotics and ARGs in WWTPs; (2) the mechanisms of action of MPs, antibiotics and ARGs in sludge biochemical pools; (3) the impacts of MPs in WWTPs and the spread of ARGs; (4) and the harm inflicted by MPs and ARGs on the environment and human body. Contaminants in sewage sludge such as MPs, ARGs, and antibiotic-resistant bacteria enter the soil and water. Contaminants can travel through the food chain and thus reach humans, leading to increased illness, hospitalization, and even mortality. This study will enhance our understanding of the mechanisms of action among MPs, antibiotics, ARGs, and the harm they inflict on the human body.

Current examining methods and mathematical models of horizontal transfer of antibiotic resistance genes in the environment

The increasing prevalence of antibiotic resistance genes (ARGs) in the environment has garnered significant attention due to their health risk to human beings. Horizontal gene transfer (HGT) is considered as an important way for ARG dissemination. There are four general routes of HGT, including conjugation, transformation, transduction and vesiduction. Selection of appropriate examining methods is crucial for comprehensively understanding characteristics and mechanisms of different HGT ways. Moreover, combined with the results obtained from different experimental methods, mathematical models could be established and serve as a powerful tool for predicting ARG transfer dynamics and frequencies. However, current reviews of HGT for ARG spread mainly focus on its influencing factors and mechanisms, overlooking the important roles of examining methods and models. This review, therefore, delineated four pathways of HGT, summarized the strengths and limitations of current examining methods, and provided a comprehensive summing-up of mathematical models pertaining to three main HGT ways of conjugation, transformation and transduction. Finally, deficiencies in current studies were discussed, and proposed the future perspectives to better understand and assess the risks of ARG dissemination through HGT.

Regulation of quorum sensing for the manipulation of conjugative transfer of antibiotic resistance genes in wastewater treatment system

The emergence and transmission of antibiotic resistance genes (ARGs) through plasmid-mediated conjugation has become a significant worldwide public health threat. Biofilms are widely recognized as the primary reservoirs for ARGs, providing favorable conditions for horizontal gene transfer. Quorum sensing (QS) plays a critical role in bacterial biofilm formation, which further influences the spread of bacterial resistance. In this study, we examined the effects of vanillin, a QS inhibitor (QSI), at subinhibitory concentrations (sub-MICs) ranging from 0 - 0.1 g/L, on the transfer of ARGs between Escherichia coli and Pseudomonas aeruginosa. Our findings indicated that vanillin at sub-MICs inhibited the conjugative transfer frequency of the RP4 plasmid. This inhibition was supported by the downregulation of plasmid transfer genes. The suppression of conjugation can mainly be attributed to the inhibition of biofilm formation, the synthesis of extracellular polymeric substances (EPS), and the secretion of virulence factors, all of which are regulated by the bacterial QS system. On the other hand, the levels of ROS and cell membrane permeability were not primary explanations for this phenomenon. Furthermore, vanillin also reduced the conjugative transfer frequency of ARGs in wastewater effluent, providing a potential approach to alleviate bacterial resistance in water environments. These findings underscore the regulatory role of QSI in controlling ARGs transfer and have significant implications for manipulating the dissemination of bacterial resistance in the environment.

Effect of biochar on the fate of antibiotic resistant genes and integrons in compost amended agricultural soil

The persistence and transmission of emerging pollutants such as antibiotic resistance genes (ARGs) via mobile genetic elements (MGEs) have caused concern to scientific community. Composting practises are often adapted for the reduction of organic waste or to enhance fertility in agriculture soil but its continuous usage has posed a potential risk of increased abundance of ARGs in soil. Thus, the present study scrutinises the emerging risk of ARGs and MGEs in agriculture soil and its potential mitigation using biochar owing to its proven environmental sustainability and performance. After 30 days incubation, ARG distribution of SulI, SulII, dfrA1, dfrA12, tetA, flor, and ErmA was 50, 37.5, 37.5, 62.5, 42.11, 62.5, and 52.63% in control samples whereas it was 5, 15.78, 21.05, 15.79, 10.53, 21.05, and 31.58%, respectively, for biochar amended samples. Similarly, IntI1 and IntI2 in control and biochar amended samples were 18.75 and 6.25% and 10.53 and 5.26%, respectively. Principal component analysis (PCA) factor suggests that biochar amendment samples showed enhanced value for pH, organic matter, and organic carbon over control samples. Furthermore, Pearson's correlation analysis performed between detected ARGs and MGEs demonstrated the positive and significant correlation at p < 0.05 for both control and biochar amended samples.

Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

Innovative Biomedical and Technological Strategies for the Control of Bacterial Growth and Infections

Antibiotics comprise one of the most successful groups of pharmaceutical products. Still, they have been associated with developing bacterial resistance, which has become one of the most severe problems threatening human health today. This context has prompted the development of new antibiotics or co-treatments using innovative tools to reverse the resistance context, combat infections, and offer promising antibacterial therapy. For the development of new alternatives, strategies, and/or antibiotics for controlling bacterial growth, it is necessary to know the target bacteria, their classification, morphological characteristics, the antibiotics currently used for therapies, and their respective mechanisms of action. In this regard, genomics, through the sequencing of bacterial genomes, has generated information on diverse genetic resources, aiding in the discovery of new molecules or antibiotic compounds. Nanotechnology has been applied to propose new antimicrobials, revitalize existing drug options, and use strategic encapsulating agents with their biochemical characteristics, making them more effective against various bacteria. Advanced knowledge in bacterial sequencing contributes to the construction of databases, resulting in advances in bioinformatics and the development of new antimicrobials. Moreover, it enables in silico antimicrobial susceptibility testing without the need to cultivate the pathogen, reducing costs and time. This review presents new antibiotics and biomedical and technological innovations studied in recent years to develop or improve natural or synthetic antimicrobial agents to reduce bacterial growth, promote well-being, and benefit users.

Distribution of Antibiotic Resistance in a Mixed-Use Watershed and the Impact of Wastewater Treatment Plants on Antibiotic Resistance in Surface Water

The aquatic environment has been recognized as a source of antibiotic resistance (AR) that factors into the One Health approach to combat AR. To provide much needed data on AR in the environment, a comprehensive survey of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues was conducted in a mixed-use watershed and wastewater treatment plants (WWTPs) within the watershed to evaluate these contaminants in surface water. A culture-based approach was used to determine prevalence and diversity of ARB in surface water. Low levels of AR Salmonella (9.6%) and Escherichia coli (6.5%) were detected, while all Enterococcus were resistant to at least one tested antibiotic. Fewer than 20% of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (17.3%) and carbapenem-resistant Enterobacteriaceae (CRE) (7.7%) were recovered. Six ARGs were detected using qPCR, primarily the erythromycin-resistance gene, ermB. Of the 26 antibiotics measured, almost all water samples (98.7%) had detectable levels of antibiotics. Analysis of wastewater samples from three WWTPs showed that WWTPs did not completely remove AR contaminants. ARGs and antibiotics were detected in all the WWTP effluent discharges, indicating that WWTPs are the source of AR contaminants in receiving water. However, no significant difference in ARGs and antibiotics between the upstream and downstream water suggests that there are other sources of AR contamination. The widespread occurrence and abundance of medically important antibiotics, bacteria resistant to antibiotics used for human and veterinary purposes, and the genes associated with resistance to these antibiotics, may potentially pose risks to the local populations exposed to these water sources.

Oxytetracycline and heavy metals promote the migration of resistance genes in the intestinal microbiome by plasmid transfer

Horizontal gene transfer (HGT) has been considered the most important pathway to introduce antibiotic resistance genes (ARGs), which seriously threatens human health and biological security. The presence of ARGs in the aquatic environment and their effect on the intestinal micro-ecosystem of aquatic animals can occur easily. To investigate the HGT potential and rule of exogenous ARGs in the intestinal flora, a visual conjugative model was developed, including the donor of dual-fluorescent bacterium and the recipient of Xenopus tropicalis intestinal microbiome. Some common pollutants of oxytetracycline (OTC) and three heavy metals (Zn, Cu and Pb) were selected as the stressor. The multi-techniques of flow cytometry (FCM), scanning electron microscopy (SEM), atomic force microscopy (AFM), single-cell Raman spectroscopy with sorting (SCRSS) and indicator analysis were used in this study. The results showed that ARG transfer could occur more easily under stressors. Moreover, the conjugation efficiency mainly depended on the viability of the intestinal bacteria. The mechanisms of OTC and heavy metal stressing conjugation included the upregulation of ompC, traJ, traG and the downregulation of korA gene. Moreover, the enzymatic activities of SOD, CAT, GSH-PX increased and the bacterial surface appearance also changed. The predominant recipient was identified as Citrobacter freundi by SCRSS, in which the abundance and quantity of ARG after conjugation were higher than those before. Therefore, since the diversity of potential recipients in the intestine are very high, the migration of invasive ARGs in the microbiome should be given more attention to prevent its potential risks to public health.

Response of viable bacteria to antibiotics in aerobic granular sludge: Resistance mechanisms and behaviors, bacterial communities, and driving factors

The assessment of antimicrobial resistance (AMR) risk by DNA-based techniques mainly relies on total bacterial DNA. In this case, AMR risk recognition is restricted to the genotype level, lacking crucial phenotypic information, such as the distribution of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in dead and viable bacteria. This limitation hinders the recognition of AMR behavior. Herein, based on propidium monoazide (PMA) shielding method, this work firstly quantified the intracellular ARGs/MGEs in viable and dead bacteria, and the impact of viable bacteria composition on the formation of intracellular/extracellular polymeric substance-related /cell-free ARGs (i/e/cARGs) and MGEs (i/e/cMGEs) in aerobic granular sludge (AGS). The shielding efficiency of PMA against dead bacteria was optimized to be as high as 97.5% when the MLSS of AGS was 2.0 g/L. Under antibiotic stimulation, 29.0% ∼ 49.0% of iARGs/iMGEs were carried by viable bacteria, and the remaining proportion were carried by dead bacteria. 18 out of the top 20 dominant genera showed a change in abundance by more than 1% after PMA treatment. 29 viable hosts were identified to associate with 52 iARGs, of which 28 and 15 hosts were also linked to 40 eARGs and 26 cARGs. Also, partial least-squares path model and variance partitioning analysis disclosed that viable bacteria and i/e/cMGEs had a positive effect on i/e/cARGs, with both contributing as much as 64.5% to the total ARGs enrichment. These results better visualized the AMR risk carried by viable bacteria and the categories of viable hosts. This work provides a novel insight into analyzing the actual AMR risk and viable hosts, helping to the reduction and control of AMR in wastewater treatment plants.

Horizontal transfer and driving factors of extended-spectrum β-lactamase-producing resistance genes in mice intestine after the ingestion of contaminated water

Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli (E. coli) has been identified in various water environments, posing a serious risk to public health. However, whether and how ESBL-producing genes in water-derived E. coli can spread among mammalian gut microbiota via drinking water is largely unclear. To address this problem, horizontal transfer characterization of ESBL-producing genes in mice gut microbiota was determined after the oral ingestion of contaminated water by ESBL-producing E. coli, and then the driving factors were comprehensively examined from multiple different perspectives. The results showed that water-borne ESBL-producing E. coli can colonize in the mice intestine, the ESBL-producing genes can horizontally spread among gut microbiota, and the recipient bacteria include opportunistic pathogens Klebsiella pneumoniae and Salmonella enterica. This horizontal spread may be attributed to the intestinal micro-environment changes caused by the ingestion of contaminated water by ESBL-producing E. coli. These changes, including gut microbiota diversity, increased levels of inflammatory response and reactive oxygen species, cell membrane permeability, and expression levels of conjugative transfer-related genes, are all major driving factors for horizontal transfer of ESBL-producing genes in mice gut microbiota. Our findings highlight the potential for ESBL-producing E. coli to spread resistance genes to mammalian gut microbiota during ingestion of contaminated water.

Anaerobic sludge digestion elevates dissemination risks of bacterial antibiotic resistance in effluent supernatant

Anaerobic digestion following a variety of pretreatments is a promising technique for the reduction of excess sludge in municipal wastewater treatment plants (MWWTPs), and eliminations of possible pathogens, viruses, protozoa, and other disease-causing organisms. Notwithstanding a rapidly increasing health concern of antibiotic resistant bacteria (ARB) in MWWTPs, dissemination risks of ARB in anaerobic digestion processes are still poorly understood, especially in the digested supernatant. Taking the representative ARB with respect to the common tetracycline-, sulfamethoxazole-, clindamycin- and ciprofloxacin resistance, we investigated the compositions of ARB in the sludge and supernatant, and quantified their variations along the entire anaerobic sludge digestion process following ultrasonication-, alkali-hydrolysis- and alkali-ultrasonication pretreatments, respectively. Results showed that the abundance of ARB was diminished by up to 90% from the sludge along anaerobic digestion coupling with the pretreatments. Surprisingly, pretreatments clearly boosted the abundance of specific ARB (e.g., 2.3 × 10² CFU/mL of tetracycline-resistant bacteria) in the supernatant that otherwise remained relatively low value of 0.6 × 10² CFU/mL from the direct digestion. Measurements of the soluble-, loosely-bound- and tightly-bound extracellular polymeric substances components revealed a gradually intensified destruction of the sludge aggregates along the entire anaerobic digestion processes, which could be likely responsible to the increase of the ARB abundance in the supernatant. Furthermore, analysis of the bacterial community components showed that the ARB populations were strongly correlated with the occurrence of Bacteroidetes, Patescibacteria, and Tenericutes. Interestingly, intensified conjugal transfer (0.015) of antibiotic resistance genes (ARGs) was observed upon returning of the digested supernatant to the biological treatment system. It implies the likelihood of ARGs spreading and subsequent ecological risks upon anaerobic digestion towards reducing excess sludge, and therefore requires further attentions for the excess sludge treatments especially of supernatant.

Comparative Metagenomic and Metatranscriptomic Analyses Reveal the Response of Black Soldier Fly (Hermetia illucens) Larvae Intestinal Microbes and Reduction Mechanisms to High Concentrations of Tetracycline

Black soldier fly (Hermetia illucens L) larvae (BSFL) possess remarkable antibiotic degradation abilities due to their robust intestinal microbiota. However, the response mechanism of BSFL intestinal microbes to the high concentration of antibiotic stress remains unclear. In this study, we investigated the shift in BSFL gut microbiome and the functional genes that respond to 1250 mg/kg of tetracycline via metagenomic and metatranscriptomic analysis, respectively. The bio-physiological phenotypes showed that the survival rate of BSFL was not affected by tetracycline, while the biomass and substrate consumption of BSFL was slightly reduced. Natural BSFL achieved a 20% higher tetracycline degradation rate than the germ-free BSFL after 8 days of rearing. Metagenomic and metatranscriptomic sequencing results revealed the differences between the entire and active microbiome. Metatranscriptomic analysis indicated that Enterococcus, Vagococcus, Providencia, and Paenalcaligenes were the active genera that responded to tetracycline. Furthermore, based on the active functional genes that responded to tetracycline pressure, the response mechanisms of BSFL intestinal microbes were speculated as follows: the Tet family that mediates the expression of efflux pumps expel tetracycline out of the microbes, while tetM and tetW release it from the ribosome. Eventually, tetracycline was degraded by deacetylases and novel enzymes. Overall, this study provides novel insights about the active intestinal microbes and their functional genes in insects responding to the high concentration of antibiotics.

Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It initiates the acquisition of exogenous genes and propagates antimicrobial resistance alongside vertical and conjugative transfers. We combined mixed-culture biotechnology and Hi-C sequencing to elucidate the transformation of wastewater microorganisms with a synthetic plasmid encoding GFP and kanamycin resistance genes, in the mixed culture of chemostats exposed to kanamycin at concentrations representing wastewater, gut and polluted environments (0.01-2.5-50-100 mg L^-1). We found that the phylogenetically distant Gram-negative Runella (102 Hi-C links), Bosea (35), Gemmobacter (33) and Zoogloea (24) spp., and Gram-positive Microbacterium sp. (90) were transformed by the foreign plasmid, under high antibiotic exposure (50 mg L^-1). In addition, the antibiotic pressure shifted the origin of aminoglycoside resistance genes from genomic DNA to mobile genetic elements on plasmids accumulating in microorganisms. These results reveal the power of Hi-C sequencing to catch and surveil the transfer of xenogenetic elements inside microbiomes.

Phthalates Promote Dissemination of Antibiotic Resistance Genes: An Overlooked Environmental Risk

Plastics-microorganism interactions have aroused growing environmental and ecological concerns. However, previous studies concentrated mainly on the direct interactions and paid little attention to the ecotoxicology effects of phthalates (PAEs), a common plastic additive that is continuously released and accumulates in the environment. Here, we provide insights into the impacts of PAEs on the dissemination of antibiotic resistance genes (ARGs) among environmental microorganisms. Dimethyl phthalate (DMP, a model PAE) at environmentally relevant concentrations (2-50 μg/L) significantly boosted the plasmid-mediated conjugation transfer of ARGs among intrageneric, intergeneric, and wastewater microbiota by up to 3.82, 4.96, and 4.77 times, respectively. The experimental and molecular dynamics simulation results unveil a strong interaction between the DMP molecules and phosphatidylcholine bilayer of the cell membrane, which lowers the membrane lipid fluidity and increases the membrane permeability to favor transfer of ARGs. In addition, the increased reactive oxygen species generation and conjugation-associated gene overexpression under DMP stress also contribute to the increased gene transfer. This study provides fundamental knowledge of the PAE-bacteria interactions to broaden our understanding of the environmental and ecological risks of plastics, especially in niches with colonized microbes, and to guide the control of ARG environmental spreading.

Antibiotic resistance in soil-plant systems: A review of the source, dissemination, influence factors, and potential exposure risks

As an emerging environmental contaminant, the widespread of antibiotic resistance has caused a series of environmental issues and human health concerns. A load of antibiotic residues induced by agricultural practices have exerted selective pressure to bacterial communities in the soil-plant system, which facilitated the occurrence and dissemination of antibiotic resistance genes (ARGs) through horizontal gene transfer. As a result, the enrichment of ARGs within crops at harvest under the influence of food ingestion could lead to critical concerns of public health. In this review, the prevalence and dissemination of antibiotic resistance in the soil-plant system are highlighted. Moreover, different underlying mechanisms and detection methods for ARGs transfer between the soil environment and plant compartments are summarized and discussed. On the other hand, a wide range of influencing factors for the transfer and distribution of antibiotic resistance within the soil-plant system are also presented and discussed. In response to exposure of antibiotic residues and resistomes, corresponding hazard identification assessments have been summarized, which could provide beneficial guides of the toxicological tolerance for the general population. Finally, further research priorities for detection and management ARGs spread are also suggested.

Design of a stable ethanologenic bacterial strain without heterologous plasmids and antibiotic resistance genes for efficient ethanol production from concentrated dairy waste

Engineering sustainable bioprocesses that convert abundant waste into fuels is pivotal for efficient production of renewable energy. We previously engineered an Escherichia coli strain for optimized bioethanol production from lactose-rich wastewater like concentrated whey permeate (CWP), a dairy effluent obtained from whey valorization processes. Although attractive fermentation performances were reached, significant improvements are required to eliminate recombinant plasmids, antibiotic resistances and inducible promoters, and increase ethanol tolerance. Here, we report a new strain with chromosomally integrated ethanologenic pathway under the control of a constitutive promoter, without recombinant plasmids and resistance genes. The strain showed extreme stability in 1-month subculturing, with CWP fermentation performances similar to the ethanologenic plasmid-bearing strain. We then investigated conditions enabling efficient ethanol production and sugar consumption by changing inoculum size and CWP concentration, revealing toxicity- and nutritional-related bottlenecks. The joint increase of ethanol tolerance, via adaptive evolution, and supplementation of small ammonium sulphate amounts (0.05% w/v) enabled a fermentation boost with 6.6% v/v ethanol titer, 1.2 g/L/h rate, 82.5% yield, and cell viability increased by three orders of magnitude. Our strain has attractive features for industrial settings and represents a relevant improvement in the existing ethanol production biotechnologies.

Factors and Mechanisms Influencing Conjugation In Vivo in the Gastrointestinal Tract Environment: A Review

The emergence and spread of antibiotic resistance genes (ARGs) have imposed a serious threat on global public health. Horizontal gene transfer (HGT) via plasmids is mainly responsible for the spread of ARGs, and conjugation plays an important role in HGT. The conjugation process is very active in vivo and its effect on the spreading of ARGs may be underestimated. In this review, factors affecting conjugation in vivo, especially in the intestinal environment, are summarized. In addition, the potential mechanisms affecting conjugation in vivo are summarized from the perspectives of bacterial colonization and the conjugation process.

High-pressure processing effect on conjugal antibiotic resistance genes transfer in vitro and in the food matrix among strains from starter cultures

This study analyzed the effect of high-pressure processing (HPP) on the frequency of conjugal gene transfer of antibiotic resistance genes among strains obtained from starter cultures. Gene transfer ability was analyzed in vitro and in situ in the food matrix. It was found that the transfer of aminoglycoside resistance genes did not occur after high-pressure treatment, either in vitro or in situ. After exposure to HPP, the transfer frequencies of tetracycline, ampicillin and chloramphenicol resistance genes increased significantly compared to the control sample, both in vitro and in situ. The frequency of resistance genes transfer in the food matrix in the pressurized samples did not differ significantly from the in vitro transfer rate. Minimum Inhibitory Concentrations (MICs) for these antibiotics determined for transconjugants were lower or equal to MICs determined for the donors. No significant differences were observed between the MIC values determined for the transconjugants obtained in vitro and in situ. The results suggest that HPP may contribute to the spread of antibiotic resistance. This points to the need to verify starter cultures strains for their antibiotic resistance and pressurization parameters to avoid spreading antibiotic resistance genes.

The prevalence of potential pathogens in ballast water and sediments of oceangoing vessels and implications for management

Ballast water and sediments can serve as prominent vectors for the widespread dispersal of pathogens between geographically distant areas. However, information regarding the diversity and distribution of the bacterial pathogens in ballast water and sediments is highly limited. In this study, using high-throughput sequencing and quantitative PCR, we investigated the composition and abundance of potential pathogens, and their associations with indicator microorganisms. We accordingly detected 48 potential bacterial pathogens in the assessed ballast water and sediments, among which there were significant differences in the compositions and abundances of pathogenic bacterial communities characterizing ballast water and sediments. Rhodococcus erythropolis, Bacteroides vulgatus, and Vibrio campbellii were identified as predominant pathogens in ballast water, whereas Pseudomonas stutzeri, Mycobacterium paragordonae, and Bacillus anthracis predominated in ballast sediments. Bacteroidetes, Vibrio alginolyticus, Vibrio parahaemolyticus, and Escherichia coli were generally detected with median values of 8.54 × 10³-1.22 × 10⁷ gene copies (GC)/100 mL and 1.16 × 10⁷-3.97 × 10⁹ GC/100 g in ballast water and sediments, respectively. Notably, the concentrations of Shigella sp., Staphylococcus aureus, and V. alginolyticus were significantly higher in ballast sediments than in the water. In addition, our findings tend to confirm that the indicator species specified by the International Maritime Organization (IMO) might underestimate the pathogen risk in the ballast water and sediments, as these bacteria were unable to predict some potential pathogens assessed in this study. In summary, this study provides a comprehensive insight into the spectrum of the potential pathogens that transferred by ship ballast tanks and emphasizes the need for the implementation of IMO convention on ballast sediment management.

Pharmaceuticals and Personal Care Products in the Environment with Emphasis on Horizontal Transfer of Antibiotic Resistance Genes

Pharmaceuticals and personal care products (PPCPs) discharged into environment has several adverse impacts. PPCPs are widely utilised for veterinary as well as cosmetic and personal health reasons. These are members of the expanding class of substances known as Contaminants of Emerging Concern (CECs). Antibiotic resistance in the environment and garbage generated by PPCP endanger life. The World Health Organisation (WHO) now recognises antibiotic resistance as a significant global health problem due to the expected increase in mortality caused by it. In the past ten years, mounting data has led experts to believe that the environment has a significant impact on the development of resistance. For human diseases, the external environment serves as a source of resistance genes. It also serves as a major pathway for the spread of resistant bacteria among various habitats and human populations. Large-scale DNA sequencing methods are employed in this thesis to better comprehend the dangers posed by environmental antibiotic resistance. The quantification of the number is an important step in this process. Metagenomic measurement of the number of antibiotic resistance genes in various contexts is a crucial step in this process. However, it’s also crucial to put this data into a broader context by integrating things like taxonomic information, antibiotic concentrations, and the genomic locations of found resistance genes.

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.

Detection of an Enterococcus faecium Carrying a Double Copy of the PoxtA Gene from Freshwater River, Italy

Oxazolidinones are valuable antimicrobials that are used to treat severe infections due to multidrug-resistant (MDR) Gram-positive bacteria. However, in recent years, a significant spread of clinically relevant linezolid-resistant human bacteria that is also present in animal and environmental settings has been detected and is a cause for concern. This study aimed to investigate the presence, genetic environments, and transferability of oxazolidinone resistance genes in enterococci from freshwater samples. A total of 10 samples were collected from a river in Central Italy. Florfenicol-resistant enterococci were screened for the presence of oxazolidinone resistance genes by PCR. Enterococcus faecium M1 was positive for the poxtA gene. The poxtA transfer (filter mating and aquaria microcosm assays), localization (S1-PFGE/hybridization), genetic context, and clonality of the isolate (WGS) were analyzed. Two poxtA copies were located on the 30,877-bp pEfM1, showing high-level identity and synteny to the pEfm-Ef3 from an E. faecium collected from an Italian coastal area. The isolate was able to transfer the poxtA to enterococcal recipients both in filter mating and aquaria microcosm assays. This is-to the best of our knowledge-the first detection of an enterococcus carrying a linezolid resistance gene from freshwater in Italy.

Metabolic characteristics and markers in viable but nonculturable state of Pseudomonas aeruginosa induced by chlorine stress

Many Gram-negative pathogens enter the viable but nonculturable (VBNC) state to resist external environmental stress (such as disinfection). However, little is known about the metabolic properties, especially for the metabolic markers, of VBNC bacteria, which impedes the development of efficient disinfection technologies and causes more potential health risks. In this study, we analyzed the metabolic characteristics of chlorine stress-induced VBNC Pseudomonas aeruginosa at the population and single-cell levels. The overall metabolic activity of VBNC bacteria showed a downward trend, but the glyoxylate cycle, fatty acid and glycerophospholipid metabolism pathways were up-regulated. Based on the metabolic profiles of VBNC bacteria, nine metabolic markers (pyruvate, glyoxylate, guanine, glutamate, sn glycero-3-phos-phocholine, fatty acid, D-alanine, glutathione, N-Butanoyl-D-homoserine lactone) were determined. The results of single-cell Raman spectroscopy showed that the metabolic activity of VBNC bacteria was significantly reduced, but showed more significant metabolic heterogeneity. The redshift of the Raman peaks of ¹⁵N and ¹³C labeled VBNC bacteria was significantly weaker than that of the culturable bacteria, suggesting that the VBNC bacteria have a reduced ability to synthesize proteins, nucleotides, phospholipids, and carbohydrates. The result of this study can help to better understand the metabolic mechanisms and energy management strategy of VBNC bacteria, to achieve precise identification and effective control of VBNC bacteria.

Coconut shell and its biochar as fertilizer amendment applied with organic fertilizer: Efficacy and course of actions on eliminating antibiotic resistance genes in agricultural soil

Biomass amendments have numerous benefits in reducing antibiotic resistance genes (ARGs) in the soil environment. However, there are debatable outcomes regarding the effect of raw biomass and its pyrolytic biochar on ARGs, and the exploration of the influence mechanism is still in infancy. Herein, we investigated the changes in soil ARGs under the organic fertilizer application with coconut shell and its biochar. The results showed that the coconut shell biochar could effectively diminish ARGs, with 61.54% reduction in target ARGs, which was higher than that adding raw coconut shells (p < 0.05). Structural equation modeling indicated that ARGs were significantly affected by changes in environmental factors, mainly by modulating bacterial communities. Neutral community model and network analysis demonstrated that the coconut shell biochar can restrict the species dispersal, thereby mitigating the spread of ARGs. Also, coconut shell biochar exhibited strong adsorption, with a large specific surface area (476.66 m²/g) and pores (pore diameter approximately 1.207 nm, total pore volume: 0.2451 m³/g), which markedly enhanced soil heterogeneity that created a barrier to limit the resistant bacteria proliferation and ARGs propagation. The outcome gives an approach to control the development of ARGs after organic fertilizer application into soil.

Bacteriophages: Underestimated vehicles of antibiotic resistance genes in the soil

Bacteriophages (phages), the most abundant biological entities on Earth, have a significant effect on the composition and dynamics of microbial communities, biogeochemical cycles of global ecosystems, and bacterial evolution. A variety of antibiotic resistance genes (ARGs) have been identified in phage genomes in different soil samples. Phages can mediate the transfer of ARGs between bacteria via transduction. Recent studies have suggested that anthropogenic activities promote phage-mediated horizontal gene transfer events. Therefore, the role of phages in the dissemination of ARGs, which are a potential threat to human health, may be underestimated. However, the contribution of phages to the transfer of ARGs is still poorly understood. Considering the growing and wide concerns of antibiotic resistance, phages should be considered a research focus in the mobile resistome. This review aimed to provide an overview of phages as vehicles of ARGs in soil. Here, we summarized the current knowledge on the diversity and abundance of ARGs in soilborne phages and analyzed the contribution of phages to the horizontal transfer of ARGs. Finally, research deficiencies and future perspectives were discussed. This study provides a reference for preventing and controlling ARG pollution in agricultural systems.