Risks of antibiotic resistance genes and antimicrobial resistance under chlorination disinfection with public health concerns

Ferrate(VI) promotes inactivation of antibiotic-resistant bacteria and chlorine-resistant bacteria in water

The increasing problem of antibiotic resistance has garnered significant global attention. As a novel water treatment agent with strong oxidizing, disinfecting, and bactericidal properties, ferrate(VI) holds promise for inactivating antibiotic-resistant bacteria (ARB) and chlorine-resistant bacteria. The results showed that complete inactivation of ARB (10⁵ CFU/mL) was achieved when the ferrate(VI) concentration was 10 μM and the treatment duration was 5 min. For higher concentrations of ARB (108 CFU/mL), it was also possible to reduce the concentration by 1.73 log units. The concentration of Acinetobacter baylyi ADP1 was also reduced by 1.77 log units. Additionally, the absolute abundance of antibiotic resistance genes (ARGs), including aphA, blaTEM, and tetA, was significantly reduced. Ferrate(VI) was rapidly consumed in the early stages of treatment, undergoing a stepwise reduction process that generated high-valent Fe intermediates and reactive oxygen species (ROS), both of which contributed to bacterial inactivation. Throughout the reaction, •O2- played a dominant role in bacterial inactivation, with H₂O₂ acting synergistically and •OH contributing at later stages, leading to ROS overload, severe cellular damage, and enhanced membrane disruption. This study confirmed that ferrate(VI) could effectively inactivate ARB and chlorine-tolerant bacteria, and reduce the abundances of ARGs.

Pre-chlorination in source water endows ARB with resistance to chlorine disinfection in drinking water treatment

Chlorine disinfection is widely used to ensure biosafety of drinking water. However, antibiotic resistance bacteria (ARB) and antibiotic resistance genes (ARGs) are often detected in treated drinking water. The impact of chlorine disinfection on the abundance of ARGs in drinking water is currently contradictory. Some studies suggested that chlorine disinfection could reduce the abundance of ARGs, while others had found that chlorine disinfection increased the abundance of ARGs. Pre-chlorination is widely applied in raw water to kill the algae cells in source water Pump Station. Different distances between the source water Pump Station and the drinking water treatment plants (DWTPs) resulted in different degrees of residual chlorine decay in the incoming raw water. This study found that the abundance of ARGs in drinking water would be increased during chlorine disinfection when the chlorine concentration in raw water was higher (> 0.2 mg/L). On the contrary, chlorine disinfection would decrease the abundance of ARGs in drinking water when the chlorine concentration in raw water was lower (< 0.09 mg/L). Pre-chlorination in source water with sub-lethal concentration could allow ARB to adapt to the chlorine environment in advance, endowing ARB with chlorine resistance, which resulted in ineffective removal of ARB and increased ARGs abundance during subsequent chlorine disinfection. High abundance of chlorine and antibiotics co-resistance bacteria in raw water was the main reason for the increase in ARGs abundance in chlorine treated drinking water. It should be noticed that, pre-chlorination treatment in source water would increase the difficulty of removing ARGs in subsequent chlorine disinfection process.

Molecularly Imprinted Titanium Dioxide: Synthesis Strategies and Applications in Photocatalytic Degradation of Antibiotics from Marine Wastewater: A Review

Antibiotic residues in the marine environment pose a serious threat to ecosystems and human health, and there is an urgent need to develop efficient and selective pollution control technologies. Molecular imprinting technology (MIT) provides a new idea for antibiotic pollution control with its specific recognition and targeted removal ability. However, traditional titanium dioxide (TiO2) photocatalysts have limited degradation efficiency and lack of selectivity for low concentrations of antibiotics. This paper reviews the preparation strategy and modification means of molecularly imprinted TiO2 (MI-TiO2) and its composites and systematically explores its application mechanism and performance advantages in marine antibiotic wastewater treatment. It was shown that MI-TiO2 significantly enhanced the selective degradation efficiency of antibiotics such as tetracyclines and sulfonamides through the enrichment of target pollutants by specifically imprinted cavities, combined with the efficient generation of photocatalytic reactive oxygen species (ROS). In addition, emerging technologies such as magnetic/electric field-assisted catalysis and photothermal synergistic effect further optimized the recoverability and stability of the catalysts. This paper provides theoretical support for the practical application of MI-TiO2 in complex marine pollution systems and looks forward to its future development in the field of environmental remediation.

Chlorination-induced spread of antibiotic resistance genes in drinking water systems

Chlorine, the most widely utilized disinfectant for drinking water globally, has recently been implicated in facilitating the spread of antibiotic resistance genes (ARGs), raising concerns about its underestimated environmental and ecological risks. However, given the current fragmented research focus and results, a comprehensive understanding of the potential mechanisms and influencing factors behind chlorination-promoted ARGs transmission in drinking water systems is crucial. This work is the first to systematically review the variations in abundance, transmission mechanisms, influencing factors, and mitigation strategies related to ARGs during the chlorination process. The results indicated that chlorination could induce genetic mutations and promote horizontal gene transfer through multiple pathways, including increased reactive oxygen species, enhanced membrane permeability, stimulation of the SOS response, and activation of efflux pumps. In addition, this work delves into significant discoveries regarding the factors affecting ARG transmission in drinking water, such as chlorine concentration, reaction time, disinfection byproducts, pipe materials, biofilms, and the water matrix. A series of effective strategies from water source to point-of-use were proposed aimed at mitigating ARGs transmission risks in the drinking water system. Finally, we address existing challenges and outline future research directions to overcome these bottlenecks. Overall, this review aims to advance our understanding of the role of chlorination in the dissemination of ARGs and to inspire innovative research ideas for optimizing disinfection techniques, minimizing the risks of antibiotic resistance transmission, and enhancing the safety of drinking water.

Impact of low-dose free chlorine on the conjugative transfer of antibiotic resistance genes in wastewater effluents: Identifying key environmental factors for predictive modeling

Reclaimed water disinfection results in the coexistence of antibiotic resistance genes (ARGs) and low-dose free chlorine in receiving environments. However, the impact of low-dose free chlorine on ARGs conjugative transfer and the key factors influencing the transfer under complex environmental conditions remain unclear, hindering the establishment of an effective monitoring system for resistance pollution in reclaimed water. This study investigated ARGs conjugative transfer under the influence of free chlorine at environmentally relevant concentrations and key interactive factors using machine learning models. The results showed that low-dose free chlorine (0.05-0.3 mg/L) promoted ARGs conjugative transfer, with 0.15 mg/L having a greater promoting effect than free chlorine concentrations of 0.05 and 0.3 mg/L. Additionally, different exposure patterns of low-dose chlorine affected ARGs conjugative transfer, with intermittent exposure posing a higher risk of ARGs dissemination. SVM linear model performed best in predicting ARGs conjugative transfer (RMSE=0.012, R2=0.975), and the SHapley Additive Explanations (SHAP) method revealed that key factors such as HCO3-, SAA, NO3-, and HA had positive SHAP values, indicating a positive influence on ARGs transfer under low-dose chlorine, making them the key features for predicting the ARGs conjugative transfer under the low-dose chlorine exposure. This study also revealed potential mechanisms of ARGs transfer under continuous low-dose free chlorine exposure, including intracellular reactive oxygen species (ROS), enzyme activity, cell membrane permeability, and gene expression. The integration of the machine learning model and post-hoc interpretation methods clarified the key drivers of ARGs conjugative transfer in reclaimed water-replenished environments, providing new insights for the safe reuse of reclaimed water and the development of river monitoring indicators.

Metagenomic insights into the rapid recovery mechanisms of prokaryotic community and spread of antibiotic resistance genes after seawater disinfection

Disinfectants, such as bleaching powder, are widely employed in marine aquaculture worldwide to control the bacterial pathogens and eliminate antibiotic resistance genes (ARGs). Nevertheless, the rapid recovery of prokaryotic community compositions (PCCs) after disinfection may significantly influence the overall efficacy of disinfection. Presently, little is known about the rapid recovery mechanisms of PCCs and its impact on the removal of ARGs in seawater. In this study, 16S rRNA gene sequencing and metagenomic analysis were used to address the above concerns through simulating the disinfection process in aquaculture. The results showed that recovery of PCCs began within 16 h. The underlying mechanisms of the rapid recovery of PCCs were the synergistic interactions between microbes and the residues of disinfection-resistant bacteria (DRB). Disinfection resistance genes (DRGs) related to efflux pump serve as the primary molecular foundation providing DRB to resist disinfection. Among the 78 annotated ARGs, only 10 ARGs exhibited a significant decrease (P < 0.05) after 72 h, implying the ineffective removal of ARGs by bleaching powder. Furthermore, bacterial co-resistance to disinfectants and antibiotics was observed. Genome analysis of two highly resistant DRB from Pseudomonadaceae revealed that both DRB carried 16 DRGs, aiding the recovery of PCCs and the spread of ARGs. These findings provide novel insights in the mechanisms of the rapid recovery of PCCs and bacterial co-resistance to disinfectants and antibiotics, which can be crucial for the management of pathogens and antibiotic resistance in seawater.

Antibiotic resistance genes profile of selected drinking water treatment plants in South Africa as impacted by different treatment stages

Water treatment plants treat raw water making it suitable for consumption. Treatment stages are linked to the quality status of the treatment. The classes of antibiotic resistance genes as impacted by treatment stages remain under explored. We report the classes of antibiotic resistance genes (ARGs) from shotgun metagenomes as influenced by treatment stages.

Modified activated carbon material-assisted electrochemical disinfection effectively inactivate antibiotic-resistant bacteria

ABSTRACTThe production and widespread transmission of antibiotic-resistant bacteria (ARB) pose an emerging threat to global public health. Electrochemical disinfection (ED) is an environmentally friendly disinfection technology widely utilized to inactivate ARB. This study explored the effect of modified activated carbon material (MACM) assisted ED on multi-ARB inactivation and the regeneration ability. The established ED technique was proven to be effective in inactivating multi-resistant ARB. Specifically, a 5-log ARB removal was achieved within 30 min treatment of MACM-assisted ED at 2.5 V. Additionally, no ARB regrowth was observed, indicating a permanent inactivation of ARB. The high level of reactive chlorine induced by MACM electrolysis was stressful to the ARB. Reactive chlorine led to overproduction of reactive oxygen species and damage of cell membranes in cells, accelerating the inactivation of ARB. Conclusively, the MACM-assisted ED method demonstrated efficient performance for ARB inactivation, implying this method is a promising alternative to traditional disinfection methods in countering ARB transmission.

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

Antibiotic resistance and resistome risks of inhalable bioaerosols at aeration tank of a full-scale wastewater treatment plant

Antibiotic resistome could be aerosolized under wastewater aeration processes, however, their seasonal variation, mobility, hosts, aerosolization behavior, and risk, are largely unknown. Herein, the antibiotic resistant pollution associated with fine particulate matter (PM2.5) from the actual aeration tank (AerT), was analyzed using metagenomic assembly. The antibiotic resistance of AerT-PM2.5 was characterized by significant seasonality. Antibiotic resistance genes (ARGs) in AerT-PM2.5, exhibited higher enrichment and mobility and were harbored more by pathogens than those in upwind-PM2.5, regardless of sampling season. Mobile ARGs were mainly flanked by transposase. Totally, 18 pathogenic antibiotic-resistant bacteria (PARB) carried more than one ARG, including 9 PARB with multiple ARG types. Although wastewater exerted a dominant source contribution for the airborne ARGs (47.31-55.56 %) and PARB (46.18-64.32 %), aeration endowed differential aerosolization capacity for various ARGs and PARB from wastewater. Airborne antibiotic resistome was mainly determined by bacterial community and indirectly influenced by meteorological conditions (i.e., relative humidity). Higher PM2.5-borne resistome risk was observed in AerT than upwind, and the most serious resistome risk of AerT-PM2.5 was found in winter. This study emphasizes the importance of wastewater aeration processes in emission of airborne antibiotic resistome and offers referenced information for mitigating air pollution in wastewater treatment plants.

Water chlorination increases the relative abundance of an antibiotic resistance marker in developing sourdough starters

Multiple factors explain the proper development of sourdough starters. Although the role of raw ingredients and geography, among other things, have been widely studied recently, the possible effect of air quality and water chlorination on the overall bacterial communities associated with sourdough remains to be explored. Here, using 16S rRNA amplicon sequencing, we show that clean, filtered-air severely limited the presence of lactic acid bacteria in sourdough starters, suggesting that surrounding air is an important source of microorganisms necessary for the development of sourdough starters. We also show that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, using targeted sequencing, which offers a higher resolution, we found that the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic-resistance genes in spoilage and pathogenic bacteria, increased significantly with the level of water chlorination. Although our results suggest that water chlorination might not impact sourdough starters at a deep phylogenetic level, they indicate that it can favor the spread of genetic elements associated with spoilage bacteria.

IMPORTANCE

Proper development of sourdough starters is critical for making tasty and healthy bread. Although many factors contributing to sourdough development have been studied, the effect of water chlorination on the bacterial communities in sourdough has been largely ignored. Researchers used sequencing techniques to investigate this effect and found that water chlorination at levels commonly found in drinking water systems has a limited impact on the overall bacterial communities developing in sourdough starters. However, they discovered that water chlorination could increase the abundance of integron 1, a genetic mechanism responsible for the horizontal exchange of antibiotic resistance genes in spoilage and pathogenic bacteria. This suggests that water chlorination could favor the growth of key spoilage bacteria and compromise the quality and safety of the bread. These findings emphasize the importance of considering water quality when developing sourdough starters for the best possible bread.

Experimental appraisal and numerical modelling of chlorine demand and decay in a typical drinking water distribution network in South Africa

Safe drinking water requires sound monitoring and maintenance of residual chlorine within drinking water distribution networks (DWDNs) to suppress possible microbial regrowth. However, in the developing world, DWDNs face unique challenges, including aging infrastructure, water pipes laid near or even aboveground thus exposing water to high temperature fluctuations, and relatively high organic loads. Therefore, safely maintaining sustainable residual chlorine levels and restricting the problems of hazardous disinfection by-products (DBPs) formation and of antimicrobial resistance (AMR), both tracing back to extensive chlorination, is a difficult exercise in those settings. Here, the temperature dependent bulk chlorine decay, i.e., the rate at which chlorine residual is consumed, was estimated for a typical DWDN system in South Africa. To this end, experimental assays were performed and a mathematical model was developed to predict chlorine levels within the DWDN under study. A direct relationship (R2 = 0.99) between bulk chlorine decay and initial chlorine dosage was identified, with bulk chlorine decay following the first-order decay model. The bulk chlorine decay rate coefficient (Kb) and the reaction constant with the pipe walls (Kw) were experimentally estimated, with the first being the main chlorine consumer and the latter only slightly contributing to chlorine decay. EPANET was used to simulate the chlorine concentrations within the examined DWDN, while residual chlorine concentrations were modelled using COMSOL. The software programs were calibrated and validated using experimental results. The optimum liquid chlorine dosage was 5 mg L-1, and this could maintain residual levels at 0.5 mg L-1 for 3500 min in the water distribution tanks. Yet, the residual chlorine levels at the distal end of the DWDN were below the recommended safety limits, suggesting the need for chlorine booster stations to supplement residual chlorine rather than further increasing chlorine initial dosages which will lead to unsafe chlorine levels at the proximal points and inevitably will increase DBPs in drinking water. This relatively high chlorine dosage reflects the overall poor quality of the raw water that feeds the drinking water treatment plant under study, which is consistent with the poor water quality of surface water in South Africa. Overall, this methodology can be replicated in DWDNs in South Africa and across the developing world, where similar challenges persist and ensure safe drinking water but not at the expense of DBPs formation and possibly AMR spreading.

Fomite disinfection using spray systems: A computational multi-physics framework

Disinfecting inanimate objects or materials carrying infectious agents, i.e., fomites, using spray systems reduces healthcare-associated infections in medical settings and community-acquired infections in non-medical environments. However, an accurate prediction of such systems is challenging as these systems embrace multi-physics phenomena depending on several parameters. Therefore, this paper presents a computational modeling-based multi-physics framework to evaluate the performance and effectiveness of spray systems employed in disinfecting fomites with non-porous hydrophilic surfaces. The framework includes four key phases: (i) atomizing the liquid disinfectant jet into the disinfectant droplets; (ii) interactions between disinfectant droplets and the surrounding air; (iii) impingements created by the disinfectant droplets on the fomite surface; (iv) interactions between the disinfectant depositions and pathogens causing fomite disinfection. The accuracy of the framework is evaluated using two sets of experimental data on the reduction of viable Bacillus atrophaeus spores over an 1800-second period. The results show that the framework can predict fomite disinfection via spray systems, with the deviations from the measured data being 2.73% and 2.38%. By presenting a detailed perception of the dynamics involved in fomite disinfection, this framework has the potential to improve public health practices and lead to the development of more effective and targeted disinfection strategies in diverse settings.

Land use conversion to uplands significantly increased the risk of antibiotic resistance genes in estuary area

Land use conversion in estuary wetlands may affect the transmission of antibiotic resistance genes (ARGs), while the risk rank of the ARGs and the change of clinically relevant ARGs under various land-use types are not well understood. This study used metagenomics to reveal the diversity and abundance of ARGs across five distinct land uses: reed wetland, tidal flat, grassland, agricultural land and fallow land, as well as their distribution and potential health risks. Results showed that high numbers of ARG subtypes and classes were detected irrespective of land-use types, notably higher in agricultural land (144 ARG subtypes). The most shared ARG subtypes were multidrug resistance genes across all the land uses (29 subtypes, 4.7 × 10-2-1.5 × 10-1 copies per 16S rRNA gene copy). Proteobacteria and Actinobacteria were primary ARG hosts, with 18 and 15 ARGs were found in both of them, respectively. The ARG subtype mdtB was the most dominant clinical ARG detected with 90 % amino acid identity. The change of ARGs exhibited a consistent trend across land uses in terms of health risk ranks, with the highest observed in fallow land and the lowest in reed wetland. This study reveals the distribution pattern of ARGs across various land-use types, and enhances our understanding of the potential health risks associated with ARGs in the context of coastal wetland conversion in estuary areas.

Optimized Antibiotic Resistance Genes Monitoring Scenarios Promote Sustainability of Urban Water Cycle

Dissemination of antibiotic resistance genes (ARGs) in urban water bodies has become a significant environmental and health concern. Many approaches based on real-time quantitative PCR (qPCR) have been developed to offer rapid and highly specific detection of ARGs in water environments, but the complicated and time-consuming procedures have hindered their widespread use. Herein, we developed a facile one-step approach for rapid detection of ARGs by leveraging the trans-cleavage activity of Cas12a and recombinase polymerase amplification (RPA). This efficient method matches the sensitivity and specificity of qPCR and requires no complex equipment. The results show a strong correlation between the prevalence of four ARG markers (ARGs: sul1, qnrA-1, mcr-1, and class 1 integrons: intl1) in tap water, human urine, farm wastewater, hospital wastewater, municipal wastewater treatment plants (WWTPs), and proximate natural aquatic ecosystems, indicating the circulation of ARGs within the urban water cycle. Through monitoring the ARG markers in 18 WWTPs in 9 cities across China during both peak and declining stages of the COVID epidemic, we found an increased detection frequency of mcr-1 and qnrA-1 in wastewater during peak periods. The ARG detection method developed in this work may offer a useful tool for promoting a sustainable urban water cycle.

Deciphering soil resistance and virulence gene risks in conventional and organic farming systems

Organic farming is a sustainable agricultural practice emphasizing natural inputs and ecological balance, and has garnered significant attention for its potential health and environmental benefits. However, a comprehensive evaluation of the emergent contaminants, particularly resistance and virulence genes within organic farming system, remains elusive. Here, a total of 36 soil samples from paired conventional and organic vegetable farms were collected from Jiangsu province, China. A systematic metagenomic approach was employed to investigate the prevalence, dispersal capability, pathogenic potential, and drivers of resistance and virulence genes across both organic and conventional systems. Our findings revealed a higher abundance of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) in organic farming system, with ARGs exhibiting a particularly notable increase of 10.76% compared to the conventional one. Pathogens such as Pseudomonas aeruginosa, Escherichia coli, and Mycobacterium tuberculosis were hosts carrying all four gene categories, highlighting their potential health implications. The neutral community model captured 77.1% and 71.9% of the variance in community dynamics within the conventional and organic farming systems, respectively, indicating that stochastic process was the predominant factor shaping gene communities. The relative smaller m value calculated in organic farming system (0.021 vs 0.023) indicated diminished gene exchange with external sources. Moreover, farming practices were observed to influence the resistance and virulence gene landscape by modifying soil properties, managing heavy metal stress, and steering mobile genetic elements (MGEs) dynamics. The study offers insights that can guide agricultural strategies to address potential health and ecological concerns.

Metabolic response of bacterial community to sodium hypochlorite and ammonia nitrogen affected the antibiotic resistance genes in pipelines biofilm

The biofilm is important for the antibiotic resistance genes (ARGs) propagation in drinking water pipelines. This study investigated the influence of chlorine disinfection and ammonia nitrogen on the ARGs in pipelines biofilm using metagenomic and metabolomics analysis. Chlorine disinfection reduced the relative abundance of unclassified_c_Actinobacteria, Acidimicrobium, and Candidatus_Pelagibacter to 394-430 TPM, 114-123 TPM, and 49-54 TPM, respectively. Correspondingly, the ARGs Saur_rpoC_DAP, macB, and mfd was reduced to 8-12 TPM, 81-92 TPM and 30-35 TPM, respectively. The results of metabolomics suggested that chlorine disinfection suppressed the pathways of ABC transporters, fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and biosynthesis of amino acids. These pathways were related to the cell membrane integrality and extracellular polymeric substances (EPS) secretion. Chlorine disinfection induced the decrease of EPS-related genes, resulting in the lower relative abundance of bacterial community and their antibiotic resistance. However, added approximately 0.5 mg/L NH3-N induced up-regulation of these metabolic pathways. In addition, NH3-N addition increased the relative abundance of enzymes related to inorganic and organic nitrogen metabolic pathway significantly, such as ammonia monooxygenase, glutamine synthetase, and glutamate synthase. Due to the EPS protection and nitrogen metabolism, the relative abundance of the main bacterial genera and the related ARGs increased to the level equal to that in pipelines biofilm with no disinfection. Therefore, NH3-N reduced the ARGs removal efficiency of chlorine disinfection. It is necessary to take measures to improve the removal rate of NH3-N and ARGs for preventing their risks in drinking water.

Deciphering the dynamics and driving mechanisms of high-risk antibiotic resistome in size-fractionated bacterial community during drinking water chlorination via metagenomic analysis

To reveal the impact of chlorination on the high-risk resistome in size-fractionated bacterial community, we employed metagenomic approaches to decipher dynamics of high-risk antibiotic resistance genes (ARGs) and driving mechanisms in the free-living and particle-associated fractions within a full-scale drinking water treatment system. Our results revealed that chlorination significantly increased the relative abundance of high-risk ARGs in the free-living fraction to 0.33 ± 0.005 copies/cell (cpc), bacitracin and chloramphenicol resistance types were major contributors. Furthermore, chlorination significantly increased the relative abundance of mobile genetic elements (MGEs) in the free-living fraction, while decreasing it in the particle-associated fraction. During chlorination, size-fractionated bacterial communities varied considerably. Multiple statistical analyses highlighted the pivotal role of the bacterial community in altering high-risk ARGs in both the free-living and particle-associated fractions, while MGEs had a more pronounced impact on high-risk ARGs in the free-living fraction. Specifically, the enrichment of pathogenic hosts, such as Comamonas and Pseudomonas, led to an increase in the abundance of high-risk ARGs. Concurrently, MGEs exhibited significant correlations with high-risk ARGs, indicating the potential of horizontal transfer of high-risk ARGs. These findings provide novel insights for mitigating antibiotic resistance risk by considering different bacterial fractions and respective risk ranks in drinking water.

Occurrences and implications of pathogenic and antibiotic-resistant bacteria in different stages of drinking water treatment plants and distribution systems

Different stages of drinking water treatment plants (DWTPs) play specific roles in diverse contaminants' removal present in natural water sources. Although the stages are recorded to promote adequate treatment of water, the occurrence of pathogenic bacteria (PB) and antibiotic-resistant bacteria (ARB) in the treated water and the changes in their diversity and abundance as it passed down to the end users through the drinking water distribution systems (DWDSs), is a great concern, especially to human health. This could imply that the different stages and the distribution system provide a good microenvironment for their growth. Hence, it becomes pertinent to constantly monitor and document the diversity of PB and ARB present at each stage of the treatment and distribution system. This review aimed at documenting the occurrence of PB and ARB at different stages of treatment and distribution systems as well as the implication of their occurrence globally. An exhaustive literature search from Web of Science, Science-Direct database, Google Scholar, Academic Research Databases like the National Center for Biotechnology Information, Scopus, and SpringerLink was done. The obtained information showed that the different treatment stages and distribution systems influence the PB and ARB that proliferate. To minimize the human health risks associated with the occurrence of these PB, the present review, suggests the development of advanced technologies that can promote quick monitoring of PB/ARB at each treatment stage and distribution system as well as reduction of the cost of environomics analysis to promote better microbial analysis.

Potential Causes of Spread of Antimicrobial Resistance and Preventive Measures in One Health Perspective-A Review

Antimicrobial resistance, referring to microorganisms' capability to subsist and proliferate even when there are antimicrobials is a foremost threat to public health globally. The appearance of antimicrobial resistance can be ascribed to anthropological, animal, and environmental factors. Human-related causes include antimicrobial overuse and misuse in medicine, antibiotic-containing cosmetics and biocides utilization, and inadequate sanitation and hygiene in public settings. Prophylactic and therapeutic antimicrobial misuse and overuse, using antimicrobials as feed additives, microbes resistant to antibiotics and resistance genes in animal excreta, and antimicrobial residue found in animal-origin food and excreta are animals related contributive factors for the antibiotic resistance emergence and spread. Environmental factors including naturally existing resistance genes, improper disposal of unused antimicrobials, contamination from waste in public settings, animal farms, and pharmaceutical industries, and the use of agricultural and sanitation chemicals facilitatet its emergence and spread. Wildlife has a plausible role in the antimicrobial resistance spread. Adopting a one-health approach involving using antimicrobials properly in animals and humans, improving sanitation in public spaces and farms, and implementing coordinated governmental regulations is crucial for combating antimicrobial resistance. Collaborative and cooperative involvement of stakeholders in public, veterinary and ecological health sectors is foremost to circumvent the problem effectively.

Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement

The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.

Chlorine disinfection modifies the microbiome, resistome and mobilome of hospital wastewater - A nanopore long-read metagenomic approach

The aim of the present study was to analyze changes in the microbiome, resistome, and mobilome of hospital wastewater (HWW) induced by disinfection with chlorine compounds. Changes in bacterial communities and specific antibiotic resistance genes (ARGs) in HWW were determined with the use of a nanopore long-read metagenomic approach. The main hosts of ARGs in HWW were identified, and the mobility of resistance mechanisms was analyzed. Special attention was paid to the prevalence of critical-priority pathogens in the HWW microbiome, which pose the greatest threat to human health. The results of this study indicate that chlorine disinfection of HWW can induce significant changes in the structure of the total bacterial population and antibiotic resistant bacteria (ARB) communities, and that it can modify the resistome and mobilome of HWW. Disinfection favored the selection of ARGs, decreased their prevalence in HWW, while increasing their diversity. The mobility of the HWW resistome increased after disinfection. Disinfection led to the emergence of new drug resistance mechanisms in previously sensitive bacterial taxa. In conclusion, this study demonstrated that HWW disinfected with low (sublethal) concentrations of free chlorine significantly contributes to the mobility and transfer of drug resistance mechanisms (including critical mechanisms) between bacteria (including pathogens).

Inactivation of chlorine-resistant bacteria (CRB) via various disinfection methods: Resistance mechanism and relation with carbon source metabolism

With the widespread use of chlorine disinfection, chlorine-resistant bacteria (CRB) in water treatment systems have gained public attention. Bacterial chlorine resistance has been found positively correlated with extracellular polymeric substance (EPS) secretion. In this study, we selected the most suitable CRB controlling method against eight bacterial strains with different chlorine resistance among chloramine, ozone, and ultraviolet (UV) disinfection, analyzed the resistance mechanisms, clarified the contribution of EPS to disinfection resistance, and explored the role of carbon source metabolism capacity. Among all the disinfectants, UV disinfection showed the highest disinfection capacity by achieving the highest average and median log inactivation rates for the tested strains. For Bacillus cereus CR19, the strain with the highest chlorine resistance, 40 mJ/cm2 UV showed a 1.90 log inactivation, which was much higher than that of 2 mg-Cl2/L chlorine (0.67 log), 2 mg-Cl2/L chloramine (1.68 log), and 2 mg/L ozone (0.19 log). Meanwhile, the UV resistance of the bacteria did not correlate with EPS secretion. These characteristics render UV irradiation the best CRB controlling disinfection method. Chloramine was found to have a generally high inactivation efficiency for bacteria with high chlorine-resistance, but a low inactivation efficiency for low chlorine-resistant ones. Although EPS consumed up to 56.7% of chloramine which an intact bacterial cell consumed, EPS secretion could not explain chloramine resistance. Thus, chloramine is an acceptable CRB control method. Similar to chlorine, ozone generally selected high EPS-secreting bacteria, with EPS consuming up to 100% ozone. Therefore, ozone is not an appropriate method for controlling CRB with high EPS secretion. EPS played an important role in all types of disinfection resistance, and can be considered the main mechanism for bacterial chlorine and ozone disinfection resistance. However, as EPS was not the main resistance mechanism in UV and chloramine disinfection, CRB with high EPS secretion were inactivated more effectively. Furthermore, carbon source metabolism was found related to the multiple resistance of bacteria. Those with low carbon source metabolism capacity tended to have higher multiple resistance, especially to chlorine, ozone, and UV light. Distinctively, among the tested gram-negative bacteria, in contrast to other disinfectants, chloramine resistance was negatively correlated with EPS secretion and positively correlated with carbon source metabolism capacity, suggesting a special disinfection mechanism.

Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure

Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.

Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly

Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.

Functional immune boosters; the herb or its dead microbiome? Antigenic TLR4 agonist MAMPs found in 65 medicinal roots and algae's

Background

Humans have been consuming medicinal plants (as herbs/ spices) to combat illness for centuries while ascribing beneficial effects predominantly to the plant/phytochemical constituents, without recognizing the power of obligatory resident microorganism' communities (MOCs) (live/dead bacteria, fungus, yeast, molds etc.) which remain after industrial microbial reduction methods. Very little is known about the taxonomic identity of residual antigenic microbial associated molecular patterns (MAMPs) debris in our botanical over the counter (OTC) products, which if present would be recognized as foreign (non-self) antigenic matter by host pattern recognition receptors (PRRs) provoking a host immune response; this the basis of vaccine adjuvants. As of today, only few research groups have removed the herbal MAMP biomass from herbs, all suggesting that immune activation may not be from the plant but rather its microbial biomass; a hypothesis we corroborate.

Purpose

The purpose of this work was to conduct a high through put screening (HTPS) of over 2500 natural plants, OTC botanical supplements and phytochemicals to elucidate those with pro-inflammatory; toll like receptor 4 (TLR4) activating properties in macrophages.

Study Design

The HTPS was conducted on RAW 264.7 cells vs. lipopolysaccharide (LPS) E. coli 0111:B4, testing iNOS / nitric oxide production ( NO 2 - ) as a perimeter endpoint. The data show not a single drug/chemical/ phytochemical and approximately 98 % of botanicals to be immune idle (not effective) with only 65 pro-inflammatory (hits) in a potency range of LPS. Method validation studies eliminated the possibility of false artifact or contamination, and results were cross verified through multiple vendors/ manufacturers/lot numbers by botanical species. Lead botanicals were evaluated for plant concentration of LPS, 1,3:1,6-β-glucan, 1,3:1,4-β-D-glucan and α-glucans; where the former paralleled strength in vitro. LPS was then removed from plants using high-capacity endotoxin poly lysine columns, where bioactivity of LPS null "plant" extracts were lost. The stability of E.Coli 0111:B4 in an acid stomach mimetic model was confirmed. Last, we conducted a reverse culture on aerobic plate counts (APCs) from select hits, with subsequent isolation of gram-negative bacteria (MacConkey agar). Cultures were 1) heat destroyed (retested/ confirming bioactivity) and 2) subject to taxonomical identification by genetic sequencing 18S, ITS1, 5.8 s, ITS2 28S, and 16S.

Conclusion

The data show significant gram negative MAMP biomass dominance in A) roots (e.g. echinacea, yucca, burdock, stinging nettle, sarsaparilla, hydrangea, poke, madder, calamus, rhaponticum, pleurisy, aconite etc.) and B) oceanic plants / algae's (e.g. bladderwrack, chlorella, spirulina, kelp, and "OTC Seamoss-blends" (irish moss, bladderwrack, burdock root etc), as well as other random herbs (eg. corn silk, cleavers, watercress, cardamom seed, tribulus, duckweed, puffball, hordeum and pollen). The results show a dominance of gram negative microbes (e.g. Klebsilla aerogenes, Pantoae agglomerans, Cronobacter sakazakii), fungus (Glomeracaea, Ascomycota, Irpex lacteus, Aureobasidium pullulans, Fibroporia albicans, Chlorociboria clavula, Aspergillus_sp JUC-2), with black walnut hull, echinacea and burdock root also containing gram positive microbial strains (Fontibacillus, Paenibacillus, Enterococcus gallinarum, Bromate-reducing bacterium B6 and various strains of Clostridium).

Conclusion

This work brings attention to the existence of a functional immune bioactive herbal microbiome, independent from the plant. There is need to further this avenue of research, which should be carried out with consideration as to both positive or negative consequences arising from daily consumption of botanicals highly laden with bioactive MAMPS.

Plants against cancer: the immune-boosting herbal microbiome: not of the plant, but in the plant. Basic concepts, introduction, and future resource for vaccine adjuvant discovery

The presence of microorganism communities (MOCs) comprised of bacteria, fungi, archaea, algae, protozoa, viruses, and the like, are ubiquitous in all living tissue, including plant and animal. MOCs play a significant role in establishing innate and acquired immunity, thereby influencing susceptibility and resistance to disease. This understanding has fostered substantial advancements in several fields such as agriculture, food science/safety, and the development of vaccines/adjuvants, which rely on administering inactivated-attenuated MOC pathogens. Historical evidence dating back to the 1800s, including reports by Drs Busch, Coley, and Fehleisen, suggested that acute febrile infection in response to "specific microbes" could trigger spontaneous tumor remission in humans. This discovery led to the purposeful administration of the same attenuated strains, known as "Coley's toxin," marking the onset of the first microbial (pathogen) associated molecular pattern (MAMPs or PAMPs)-based tumor immunotherapy, used clinically for over four decades. Today, these same MAMPS are consumed orally by billions of consumers around the globe, through "specific" mediums (immune boosting "herbal supplements") as carriers of highly concentrated MOCs accrued in roots, barks, hulls, sea algae, and seeds. The American Herbal Products Association (AHPA) mandates microbial reduction in botanical product processing but does not necessitate the removal of dead MAMP laden microbial debris, which we ingest. Moreover, while existing research has focused on the immune-modulating role of plant phytochemicals, the actual immune-boosting properties might instead reside solely in the plant's MOC MAMP laden biomass. This assertion is logical, considering that antigenic immune-provoking epitopes, not phytochemicals, are known to stimulate immune response. This review explores a neglected area of research regarding the immune-boosting effects of the herbal microbiome - a presence which is indirectly corroborated by various peripheral fields of study and poses a fundamental question: Given that food safety focuses on the elimination of harmful pathogens and crop science acknowledges the existence of plant microbiomes, what precisely are the immune effects of ingesting MAMPs of diverse structural composition and concentration, and where are these distributed in our botanicals? We will discuss the topic of concentrated edible MAMPs as acid and thermally stable motifs found in specific herbs and how these would activate cognate pattern recognition receptors (PPRs) in the upper gut-associated lymphoid tissue (GALT), including Peyer's patches and the lamina propria, to boost antibody titers, CD8+ and CD4+ T cells, NK activity, hematopoiesis, and facilitating M2 to M1 macrophage phenotype transition in a similar manner as vaccines. This new knowledge could pave the way for developing bioreactor-grown/heat-inactivated MOC therapies to boost human immunity against infections and improve tumor surveillance.

Cu(II) assisted peroxymonosulfate for antibiotic resistant bacteria inactivation: A potential disinfection technology in swimming pool

Alternative disinfection technology to chlorination is required to control the risk of antibiotic resistance in swimming pools. In this study, copper ions (Cu(II)), which often exist in swimming pools as algicides, were used to activate peroxymonosulfate (PMS) for the inactivation of ampicillin-resistant E. coli. Cu(II) and PMS showed synergistic effects on E. coli inactivation in weak alkaline conditions, obtaining 3.4 log inactivation in 20 min with 10 μM Cu(II) and 100 μM PMS at pH 8.0. Quenching experiments indicated that radicals (i.e., OH and SO₄^-) were not the main disinfectors for E. coli inactivation. Based on the structure of Cu(II) and density functional theory calculations, the Cu(II)-PMS complex (Cu(H₂O)₅SO₅) was recommended as the active species for E. coli inactivation. Under the experimental conditions, the PMS concentration had a greater influence on E. coli inactivation than the Cu(II) concentration, possibly because increasing PMS concentration accelerates ligand exchange reaction and facilitates active species generation. By forming hypohalous acids, halogen ions could improve the disinfection efficiency of Cu(II)/PMS. The addition of HCO₃^- concentration (from 0 to 1.0 mM) and humic acid (0.5 and 1.5 mg/l) did not significantly inhibit the E. coli inactivation. The feasibility of adding PMS to waters containing Cu(II) for the inactivation of antibiotic-resistant bacteria was validated in actual swimming pool waters, where 4.7 log inactivation of E. coli was achieved in 60 min.

Fergusonite-type rare earth niobates ANbO4 (A = Nd, Sm, and Eu) as electrode modifiers: deep insights into A site variations towards bifunctional electrochemical sensing applications

Lanthanide orthoniobates, LnNbO₄ (Ln = Nd, Sm, and Eu), are a domineering class of binary metal oxides with significant catalytic behavior and effective charge transfer ability, acting as eminent candidates to be explored as electrode materials. However, niobates have limitations to be used in sensing platforms due to the complicated synthetic procedures, which have been addressed in this study by proposing a facile hydrothermal tactic based on in situ homoleptic complex formation. All three niobates are isostructural with the monoclinic form of fergusonite structure, which was confirmed by XRD studies. The impact of the A site variation in the fergusonite crystal was verified by FTIR spectroscopy analysis, and the elemental composition was determined by XPS studies. FESEM with EDX spectroscopy obviously proved the morphological differences. Furthermore, a LnNbO₄-modified GCE was employed to detect pharmaceutical pollutants, namely, furazolidone (FZD) and dimetridazole (DMZ). Cyclic voltammetry studies were used to optimize the parameters of the sensing platform, and differential pulse voltammetry was performed to obtain the detection limits and linear range. SmNbO₄/GCE exhibited superior performance to other electrodes with a wide linear range of 0.01 μM to 264 μM and LOD values of 4 nM and 2 nM for FZD and DMZ, respectively. Finally, the feasibility of the proposed electrode in real-time analysis was studied by extending the voltammetry experiment to saliva and water samples.

Bacterial drug-resistance and viability phenotyping upon disinfectant exposure revealed by single-nucleotide resolved-allele specific isothermal RNA amplification

Disinfectant abuse poses a risk of bacterial evolution against stresses, especially during the coronavirus disease 2019 (COVID-19) pandemic. However, bacterial phenotypes, such as drug resistance and viability, are hard to access quickly. Here, we reported an allele specific isothermal RNA amplification (termed AlleRNA) assay, using an isothermal RNA amplification technique, i.e., nucleic acid sequence-based amplification (NASBA), integrated the amplification refractory mutation system (ARMS), involving the use of sequence-specific primers to allow the amplification of the targets with complete complementary sequences. AlleRNA assay enables rapid and simultaneous detection of the single nucleotide polymorphism (SNP) (a detection limit, a LOD of 0.5 % SNP) and the viability (a LOD of 80 CFU) of the quinolone resistant Salmonella enterica. With the use of AlleRNA assay, we found that the quinolone resistant S. enterica exhibited higher survival ability during exposure toquaternary ammonium salt, 75 % ethanol and peracetic acid, which might be attributed to the upregulation of stress response-associated genescompared with the susceptible counterparts. Additionally, the AlleRNA assay indicated the potential risk in a high-frequency occurrence of viable but nonculturable (VBNC) quinolone resistant S. enterica induced by disinfectants due to the depression of ATP biosynthesis. The excessive usage of disinfectants during the COVID-19 pandemic should be carefully evaluated due to the latent threat to ecological and human health.

Occupational exposure in swine farm defines human skin and nasal microbiota

Anthropogenic environments take an active part in shaping the human microbiome. Herein, we studied skin and nasal microbiota dynamics in response to the exposure in confined and controlled swine farms to decipher the impact of occupational exposure on microbiome formation. The microbiota of volunteers was longitudinally profiled in a 9-months survey, in which the volunteers underwent occupational exposure during 3-month internships in swine farms. By high-throughput sequencing, we showed that occupational exposure compositionally and functionally reshaped the volunteers’ skin and nasal microbiota. The exposure in farm A reduced the microbial diversity of skin and nasal microbiota, whereas the microbiota of skin and nose increased after exposure in farm B. The exposure in different farms resulted in compositionally different microbial patterns, as the abundance of Actinobacteria sharply increased at expense of Firmicutes after exposure in farm A, yet Proteobacteria became the most predominant in the volunteers in farm B. The remodeled microbiota composition due to exposure in farm A appeared to stall and persist, whereas the microbiota of volunteers in farm B showed better resilience to revert to the pre-exposure state within 9 months after the exposure. Several metabolic pathways, for example, the styrene, aminobenzoate, and N-glycan biosynthesis, were significantly altered through our PICRUSt analysis, and notably, the function of beta-lactam resistance was predicted to enrich after exposure in farm A yet decrease in farm B. We proposed that the differently modified microbiota patterns might be coordinated by microbial and non-microbial factors in different swine farms, which were always environment-specific. This study highlights the active role of occupational exposure in defining the skin and nasal microbiota and sheds light on the dynamics of microbial patterns in response to environmental conversion.

Conjugation-mediated transfer of antibiotic resistance genes influenced by primary soil components and underlying mechanisms

Soil is the main natural reservoir of antibiotic resistant bacteria and antibiotic resistance genes (ARGs). Their dissemination and proliferation were largely motivated by conjugative transfer, while the influence of soil components on bacterial conjugative transfer and the underlying mechanisms remain poorly understood. In the present study, two Escherichia coli strains were exposed to soil minerals (quartz, kaolinite and montmorillonite) and organic matters (humic acid, biochar and soot) respectively to investigate their impact on ARGs conjugation. The results showed that quartz had no significant effect on conjugation; montmorillonite promoted the growth of the donor, but inhibited the recipient and conjugant; kaolinite and three organic matters significantly promoted the production of conjugant, while biochar promoted and then inhibited it with time prolong. Within the range of bacterial concentration involved in this study, the concentration of conjugant increased with the ratio of the concentration of donor and recipient (R_D/R), indicating that the variation of conjugant production was mainly mediated by changing R_D/R. Further observation of biochar treatment group showed that the bacterial responses such as cell membrane permeability, cell surface hydrophobicity and biofilm formation ability shifted with the exposure time, which might be a potential factor affecting conjugative transfer. Collectively, our findings suggest that the type and exposure time of soil components jointly affected conjugation, while the change of R_D/R and related bacterial responses are the main underlying mechanisms.

Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic

Antimicrobial resistance is recognized as one of the greatest public health concerns. It is becoming an increasingly threat during the COVID-19 pandemic due to increasing usage of antimicrobials, such as antibiotics and disinfectants, in healthcare facilities or public spaces. To explore the characteristics of airborne antibiotic resistome in public transport systems, we assessed distribution and health risks of airborne antibiotic resistome and microbiome in railway stations before and after the pandemic outbreak by culture-independent and culture-dependent metagenomic analysis. Results showed that the diversity of airborne antibiotic resistance genes (ARGs) decreased following the pandemic, while the relative abundance of core ARGs increased. A total of 159 horizontally acquired ARGs, predominantly confering resistance to macrolides and aminoglycosides, were identified in the airborne bacteria and dust samples. Meanwhile, the abundance of horizontally acquired ARGs hosted by pathogens increased during the pandemic. A bloom of clinically important antibiotic (tigecycline and meropenem) resistant bacteria was found following the pandemic outbreak. 251 high-quality metagenome-assembled genomes (MAGs) were recovered from 27 metagenomes, and 86 genera and 125 species were classified. Relative abundance of ARG-carrying MAGs, taxonomically assigned to genus of Bacillus, Pseudomonas, Acinetobacter, and Staphylococcus, was found increased during the pandemic. Bayesian source tracking estimated that human skin and anthropogenic activities were presumptive resistome sources for the public transit air. Moreover, risk assessment based on resistome and microbiome data revealed elevated airborne health risks during the pandemic.

Leveraging risk assessment for foodborne outbreak investigations: The Quantitative Risk Assessment-Epidemic Curve Prediction Model

Root cause analysis can be used in foodborne illness outbreak investigations to determine the underlying causes of an outbreak and to help identify actions that could be taken to prevent future outbreaks. We developed a new tool, the Quantitative Risk Assessment-Epidemic Curve Prediction Model (QRA-EC), to assist with these goals and applied it to a case study to investigate and illustrate the utility of leveraging quantitative risk assessment to provide unique insights for foodborne illness outbreak root cause analysis. We used a 2019 Salmonella outbreak linked to melons as a case study to demonstrate the utility of this model (Centers for Disease Control and Prevention [CDC], 2019). The model was used to evaluate the impact of various root cause hypotheses (representing different contamination sources and food safety system failures in the melon supply chain) on the predicted number and timeline of illnesses. The predicted number of illnesses varied by contamination source and was strongly impacted by the prevalence and level of Salmonella contamination on the surface/inside of whole melons and inside contamination niches on equipment surfaces. The timeline of illnesses was most strongly impacted by equipment sanitation efficacy for contamination niches. Evaluations of a wide range of scenarios representing various potential root causes enabled us to identify which hypotheses, were likely to result in an outbreak of similar size and illness timeline to the 2019 Salmonella melon outbreak. The QRA-EC framework can be adapted to accommodate any food-pathogen pairs to provide insights for foodborne outbreak investigations.

Effect of graphene and graphene oxide on antibiotic resistance genes during copper-contained swine manure anaerobic digestion

Copper is an important selectors for antibiotic resistance genes (ARGs) transfer because of metal-antibiotic cross-resistance and/or coresistance. Due to carbon-based materials' good adsorption capacity for heavy metals, graphene and graphene oxide have great potential to reduce ARGs abundance in the environment with copper pollution. To figure out the mechanics, this study investigated the effects of graphene and graphene oxide on the succession of ARGs, mobile genetic elements (MGEs), heavy metal resistance genes (HMRGs), and bacterial communities during copper-contained swine manure anaerobic digestion. Results showed that graphene and graphene oxide could reduce ARGs abundance in varying degrees with the anaerobic reactors that contained a higher concentration of copper. Nevertheless, graphene decreased the abundance of ARGs more effectively than graphene oxide. Phylum-level bacteria such as Firmicutes, Bacteroidetes, Spirochaetes, and Verrucomicrobiaat were significantly positively correlated with most ARGs. Network and redundancy analyses demonstrated that alterations in the bacterial community are one of the main factors leading to the changes in ARGs. Firmicutes, Bacteroidetes, and Spirochaetes were enriched lower in graphene reactor than graphene oxide in anaerobic digestion products, which may be the main reason that graphene is superior to graphene oxide in reduced ARGs abundance. Additionally, ARGs were close to HMRGs than MGEs in the treatments with graphene, the opposite in graphene oxide reactors. Therefore, we speculate that the reduction of HMRGs in graphene may contribute to the result that graphene is superior to graphene oxide in reduced ARGs abundance in anaerobic digestion.

Distribution and migration of antibiotic resistance genes, as well as their correlation with microbial communities in swine farm and its surrounding environments

The prevalence and correlation of antibiotic resistance genes (ARGs) in pig farm wastewater treatment plants (WWTPs) and surrounding environment were investigated using metagenomics and real time quantitative PCR (q-PCR). The hosts of ARGs were also studied in this study. The abundance of ARGs decreased significantly in the anoxic/oxic (A/O) process and disinfection tank of WWTPs. New ARGs emerged in wastewater that passed though the anaerobic reactor. The abundances of ARGs in the soils and water near pig farm were 10- and 35-fold higher than those in the control, respectively. The abundance of ARGs in wells near pig farm were an order of magnitude higher than that in the control. Similarly, a high abundance of ARGs was detected in swine manure. After composting, most of the ARGs were eliminated, but sul1 increased 10.5-fold. A high-throughput analysis revealed that the pig farm altered the microbial community structure in the surrounding environment, with 52% and 37% of the operational taxonomic units (OTUs) endemic to the soil and water samples near pig farm in comparison with these data in the control, respectively. The phyla Proteobacteria, Choroflexi, and Actinobacteriota dominated the water and soil samples. In addition, three pathogenic genera were found in the surrounding soil and water samples. A metagenomic analysis identified 14 types of ARGs (>1%), with the highest proportion of multidrug ARGs at 47%. A total of 28 subtypes of ARGs were detected (>1%), with macB the most prevalent. The correlation analysis revealed that several key phyla, including Proteobacteria, Actinobacteria and Acidobacteria, were the main potential hosts and posed a positive correlation with the ARGs. Efflux pumps (60-66%) were the primary resistance mechanism, and each resistance mechanism was distributed in similar proportions in the microbial community.

Metagenomics analysis of antibiotic resistance genes, the bacterial community and virulence factor genes of fouled filters and effluents from household water purifiers in drinking water

The aim of this study was to explore the influence and removal of household water purifiers (HWPs) on emerging contaminants in drinking water, and their distribution characteristics. The antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs) and bacterial communities were profiled in the fouled filters, influents, and effluents from HWPs with five steps of filtration after 150 days operation, using metagenomics. The results showed that the diversity of dominant species in Poly Propylene 1 μm (PP1) and nanofiltration membrane (NM) was significantly higher than that in other filters. Post-activated carbon (AC) was used to detect low species richness or diversity, and the highest proportion of dominant species, which contributes to the greater microbial risk of HWPs effluents in drinking water. The number of dominant bacterial genera in the filters disinfected with chloramine was higher than that in the same group disinfected with chlorine. The bacterial species richness or diversity in water was reduced by the purification of HWPs because the filter elements effectively trapped a variety of microorganisms. The relative abundance of Antibiotic efflux in the effluents of chlorinated and chloraminated HWPs was 5.58 × 10-3 and 4.60 × 10-3, respectively, which was the main resistance mechanism. High abundance of VFGs was found in HWPs effluents and the relative abundance of aggressive VFGs was significantly higher than those of defensive VFGs. Based on the co-occurrence results, 243 subtypes of ARGs co-occurred with VFGs, and a variety of bacteria were thought to be possible ARGs hosts, which indicated that the host bacteria of VFGs in HWP effluents had a stronger attack ability. The effluent of HWPs with only filtration processes is exposed to the risk of ARGs and VFGs. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.

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.

Inactivation of Bacteria and Residual Antimicrobials in Hospital Wastewater by Ozone Treatment

The emergence and spread of antimicrobial resistance (AMR) has become a persistent problem globally. In this study, an ozone treatment facility was established for an advanced hospital wastewater treatment in a core hospital facility in an urban area in Japan to evaluate the inactivation of antimicrobial-resistant bacteria and antimicrobials. Metagenomic DNA-seq analysis and the isolation of potential extended-spectrum β-lactamase (ESBL)-producing bacteria suggested that ozone exposure for at least 20 min is required for the adequate inactivation of DNA and ESBL-producing bacteria. Escherichia coli and Klebsiella species were markedly susceptible to 20-min ozone exposure, whereas Raoultella ornithinolytica and Pseudomonas putida were isolated even after an 80-min exposure. These ozone-resistant bacteria might play a pivotal role as AMR reservoirs in the environment. Nine antimicrobials (ampicillin, cefdinir, cefpodoxime, ciprofloxacin, levofloxacin, clarithromycin, chlortetracycline, minocycline, and vancomycin) were detected at 373 ng/L to 27 μg/L in the hospital wastewater, and these were removed (96–100% removal) after a 40-min treatment. These results facilitate a comprehensive understanding of the AMR risk posed by hospital wastewater and provides insights for devising strategies to eliminate or mitigate the burden of antimicrobial-resistant bacteria and the flow of antimicrobials into the environment. To the best of our knowledge, this is the first report on the implementation of a batch-type, plant-scale ozone treatment system in a hospital facility to execute and evaluate the inactivation of drug-resistant bacteria and antimicrobials.

Neglected resistance risks: Cooperative resistance of antibiotic resistant bacteria influenced by primary soil components

Various antibiotic resistant bacteria (ARB) can thrive in soil and resist such environmental pressures as antibiotics through cooperative resistance, thereby promoting ARB retention and antibiotic resistance genes transmission. However, there has been finite knowledge in regard to the mechanisms and potential ecological risks of cooperative resistance in soil microbiome. In this study, soil minerals and organic matters were designed to treat a mixture of two Escherichia coli strains with different antibiotic resistance (E. coli DH5α/pUC19 and E. coli XL2-Blue) to determine how soil components affected cooperative resistance, and Luria-Bertani plates containing two antibiotics were used to observe dual-drug resistant bacteria (DRB) developed via cooperative resistance. Results showed quartz, humic acid, and biochar promoted E. coli XL2-Blue with high fitness costs, whereas kaolin, montmorillonite, and soot inhibited both strains. Using fluorescence microscope and PCR, it was speculated DRB could resist the antibiotic pressure via E. coli XL2-Blue coating E. coli DH5α/pUC19. E. coli DH5α/pUC19 dominated cooperative resistance. Correlation analysis and scanning electron microscope images indicated soil components influenced cooperative resistance. Biochar promoted cooperative resistance by increasing intracellular reactive oxygen species, thereby reducing the dominant strain concentration required for DRB development. Kaolin inhibited cooperative resistance the most, followed by soot and montmorillonite.

Does Chlorination Promote Antimicrobial Resistance in Waterborne Pathogens? Mechanistic Insight into Co-Resistance and Its Implication for Public Health

Chemical agents including chlorine and antibiotics are used extensively to control infectious microorganisms. While antibiotics are mainly used to treat bacterial infections, chlorine is widely used for microbial inactivation in the post-secondary disinfection steps of water treatment. The extensive use of these agents has been acknowledged as a driving force for the expansion of antimicrobial resistance (AMR) and has prompted discourse on their roles in the evolution and proliferation of resistant pathogens in the aquatic milieus. We live in a possible “post-antibiotic” era when resistant microbes spread at startling levels with dire predictions relating to a potential lack of effective therapeutic antibacterial drugs. There have been reports of enhancement of resistance among some waterborne pathogens due to chlorination. In this context, it is pertinent to investigate the various factors and mechanisms underlying the emergence and spread of resistance and the possible association between chlorination and AMR. We, therefore, reflect on the specifics of bacterial resistance development, the mechanisms of intrinsic and acquired resistance with emphasis on their environmental and public health implications, the co-selection for antibiotic resistance due to chlorination, biofilm microbiology, and multidrug efflux activity. In-depth knowledge of the molecular basis of resistance development in bacteria will significantly contribute to the more rational utilization of these biocidal agents and aid in filling identified knowledge gap toward curbing resistance expansion.

Evaluation of the Correspondence between the Concentration of Antimicrobials Entering Sewage Treatment Plant Influent and the Predicted Concentration of Antimicrobials Using Annual Sales, Shipping, and Prescriptions Data

The accuracy and correspondence between the measured concentrations from the survey and predicted concentrations on the basis of the three types of statistical antimicrobial use in Japan was evaluated. A monitoring survey of ten representative antimicrobials: ampicillin (APL), cefdinir (CDN), cefpodoxime proxetil (CPXP), ciprofloxacin (CFX), clarithromycin (CTM), doxycycline (DCL), levofloxacin (LFX), minocycline (MCL), tetracycline (TCL), and vancomycin (VMC), in the influent of sewage treatment plant (STP) located in urban areas of Japan, was conducted. Then, the measured values were verified in comparison with the predicted values estimated from the shipping volumes, sales volumes, and prescription volumes based on the National Database of Health Insurance Claims and Specific Health Checkups of Japan (NDB). The results indicate that the correspondence ratios between the predicted concentrations calculated on the basis of shipping and NDB volumes and the measured concentrations (predicted concentration/measured concentration) generally agreed for the detected concentration of antimicrobials in the STP influent. The correspondence ratio on the basis of shipping volume was, for CFX, 0.1; CTM, 2.9; LFX, 0.5; MCL, 1.9; and VMC, 1.7, and on the basis of NDB volume the measured concentration was CFX, 0.1; CTM, 3.7; DCL, 0.4; LFX, 0.7; MCL, 1.9; TCL, 0.6; and VMC, 1.6. To our knowledge, this is the first report to evaluate the accuracy of predicted concentrations based on sales, shipping, NDB statistics and measured concentrations for antimicrobials in the STP influent.