Assessment of extracellular antibiotic resistance genes (eARGs) in typical environmental samples and the transforming ability of eARG

The Origin, Function, Distribution, Quantification, and Research Advances of Extracellular DNA

In nature, DNA is ubiquitous, existing not only inside but also outside of the cells of organisms. Intracellular DNA (iDNA) plays an essential role in different stages of biological growth, and it is defined as the carrier of genetic information. In addition, extracellular DNA (eDNA) is not enclosed in living cells, accounting for a large proportion of total DNA in the environment. Both the lysis-dependent and lysis-independent pathways are involved in eDNA release, and the released DNA has diverse environmental functions. This review provides an insight into the origin as well as the multiple ecological functions of eDNA. Furthermore, the main research advancements of eDNA in the various ecological environments and the various model microorganisms are summarized. Furthermore, the major methods for eDNA extraction and quantification are evaluated.

Impact of Plastic Particles on the Horizontal Transfer of Antibiotic Resistance Genes to Bacterium: Dependent on Particle Sizes and Antibiotic Resistance Gene Vector Replication Capacities

Plastic particles impact the propagation of antibiotic resistance genes (ARGs) in environmental media, and their perturbation on the horizontal gene transfer (HGT) of ARGs is recognized as a critical influencing mechanism. However, studies concerning the influence and influencing mechanisms of plastic particles on the HGT of ARGs were limited, particularly for the effect of particle sizes and ARG vector-associated mechanisms. This study explored the impact of polystyrene (PS) particles with sizes of 75, 90, 100, 1000, and 10000 nm on the HGT (via transformation) of ARGs mediated by pUC19, pSTV29, and pBR322 plasmids into Escherichia coli cells. PS particles with sizes ≤100 nm impacted the transformation of ARGs, but large particles (1000 and 10000 nm) showed no obvious effects. Effects of PS particles on the transfer of three plasmids were vastly distinct. For pUC19 with high replication capacities, the transfer was monotonously promoted. However, for pSTV29 and pBR322 with low replication capacities, suppressing effects were observed. This was attributed to two competing mechanisms. The enhancing mechanism was that the direct interaction of PS particles with membrane lipids and the indirect effect associated with bacterial oxidative stress response induced pore formation on the cell membrane and increased membrane permeability, thus enhancing plasmid entrance. The inhibiting mechanism was that PS particles interfered with plasmid replication inside E. coli, thus decreasing the bacterial tranformation. This study deepened our understanding of the environmental dissemination of ARGs in plastic contamination.

Temporal dynamics of antibiotic resistant bacteria and antibiotic resistance genes in activated sludge upon exposure to starvation

The activated sludge represents a huge reservoir for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Owing to the wastewater fluctuation, annual maintenance and storage requirement, the activated sludge in wastewater treatment plants (WWTPs) may suffer from substrate deficiency (i.e., starvation). Whereas the starvation has been confirmed to regulate the antibiotic resistance in numerous pure bacteria, its impacts on the antibiotic resistance in activated sludge remain unclear. Here, the dynamics of sulfonamide and tetracycline ARB and corresponding ARGs in three forms including intracellular ARGs (iARGs), adsorbed extracellular ARGs (aeARGs) and free extracellular ARGs (feARGs) in activated sludge upon exposure to starvation were investigated. The results showed that, among the different electron donors (i.e., carbon, nitrogen and phosphate), carbon starvation could effectively reduce the absolute abundance of ARB and aeARGs by up to 1.68 lgs and 2.62 lgs, respectively, and released a small amount of feARGs in wastewater with the maximum value of 1.1 × 10⁵ copies/mL due to the high degree of sludge cell lysis and DNA adsorption/degradation. For the different acceptor conditions (that is, alternating anaerobic-aerobic, anaerobic, anoxic and aerobic), the anaerobic-aerobic starvation obviously mitigated the absolute abundance of ARB, aeARGs and iARGs by 0.71 lgs, 3.41 lgs and 1.35 lgs, respectively, via the substantial sludge cell lysis and DNA degradation. These findings demonstrated the response patterns and mechanisms of bacterial resistance in activated sludge to starvation stress, and thus provide clues to control the risk of antibiotic resistance in WWTPs by the starvation strategy.

Intra-/extra-cellular antibiotic resistance responses to sewage sludge composting and salinization of long-term compost applied soils

Municipal sewage sludge, a reservoir of antibiotic resistance genes (ARGs), is usually composted as fertilizer for agricultural application especially in arid and semi-arid areas. The evolution patterns of intracellular ARGs (iARGs) and extracellular ARGs (eARGs) during composting and their responses to soil salinization after long-term compost application kept unclear previously, which were systematically studied in the current study. The variation and dissemination risk of eARGs and iARGs with the salinization of farmland soils was also evaluated. Extra/intra-cellular ARGs relative abundance varied drastically through composting process. Generally, the relative abundance of the cell-free eARGs (f-eARGs) and the cell-adsorbed eARGs (a-eARGs) were 4.62 and 3.54 folds (median) higher than that of iARGs, respectively, during the entire composting process, which held true even before the sludge composting (false discovery rate, FDR p < 0.05). There was no significant difference in relative abundance between f-eARGs and a-eARGs. The relative abundance of eARGs gradually decreased with composting time but was relatively higher than iARGs. It was worth noting that iARGs rebounded in the maturation phase. However, an over ten-year application of the eARG-rich compost led to much more severe contamination of iARGs than eARGs in soil. Soil salinization caused remarkable rise of eARGs by 943.34-fold (FDR p < 0.05). The variation of ARGs during composting and soil salinization was closely related to the change of microbial community structure. In compost, the bacterial communities mainly interacting with ARGs were the Firmicutes (54 unique and 35 shared core genera); and the bacterial communities playing major roles in ARGs during soil salinization were Proteobacteria (116 unique and 53 shared core genera) and Actinobacteria (52 unique and 27 shared core genera). These findings are important for assessing the transmission risk of ARGs in compost application to farmland in arid and semi-arid areas.

Antibiotic resistant bacteria and genes in wastewater treatment plants: From occurrence to treatment strategies

This study aims to discuss the following: (1) occurrence and proliferation of antibiotic resistance in wastewater treatment plants (WWTPs); (2) factors influencing antibiotic resistance bacteria and genes in WWTPs; (3) tools to assess antibiotic resistance in WWTPs; (4) environmental contamination of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) from WWTPs; (5) effects of ARB and ARGs from WWTPs on human health; and (6) treatment strategies. In general, resistant and multi-resistant bacteria, including Enterobacteriaceae, Pseudomonas aeruginosa, and Escherichia coli, exist in various processes of WWTPs. The existence of ARB and ARGs results from the high concentration of antibiotics in wastewater, which promote selective pressures on the local bacteria present in WWTPs. Thus, improving wastewater treatment technology and avoiding the misuse of antibiotics is critical to overcoming the threat of proliferation of ARBs and ARGs. Numerous factors can affect the development of ARB and ARGs in WWTPs. Abiotic factors can affect the bacterial community dynamics, thereby, affecting the applicability of ARB during the wastewater treatment process. Furthermore, the organic loads and other nutrients influence bacterial survival and growth. Specifically, molecular methods for the rapid characterization and detection of ARBs or their genes comprise DNA sequencing, real-time PCR, simple and multiplex PCR, and hybridization-based technologies, including micro- and macro-arrays. The reuse of effluent from WWTPs for irrigation is an efficient method to overcome water scarcity. However, there are also some potential environmental risks associated with this practice, such as increase in the levels of antibiotic resistance in the soil microbiome. Human mortality rates may significantly increase, as ARB can lead to resistance among several types of antibiotics or longer treatment times. Some treatment technologies, such as anaerobic and aerobic treatment, coagulation, membrane bioreactors, and disinfection processes, are considered potential techniques to restrict antibiotic resistance in the environment.

From Farm to Fork: Streptococcus suis as a Model for the Development of Novel Phage-Based Biocontrol Agents

Bacterial infections of livestock threaten the sustainability of agriculture and public health through production losses and contamination of food products. While prophylactic and therapeutic application of antibiotics has been successful in managing such infections, the evolution and spread of antibiotic-resistant strains along the food chain and in the environment necessitates the development of alternative or adjunct preventive and/or therapeutic strategies. Additionally, the growing consumer preference for "greener" antibiotic-free food products has reinforced the need for novel and safer approaches to controlling bacterial infections. The use of bacteriophages (phages), which can target and kill bacteria, are increasingly considered as a suitable measure to reduce bacterial infections and contamination in the food industry. This review primarily elaborates on the recent veterinary applications of phages and discusses their merits and limitations. Furthermore, using Streptococcus suis as a model, we describe the prevalence of prophages and the anti-viral defence arsenal in the genome of the pathogen as a means to define the genetic building blocks that are available for the (synthetic) development of phage-based treatments. The data and approach described herein may provide a framework for the development of therapeutics against an array of bacterial pathogens.

Dynamics, gene transfer, and ecological function of intracellular and extracellular DNA in environmental microbiome

Extracellular DNA (eDNA) and intracellular DNA (iDNA) extensively exist in both terrestrial and aquatic environment systems and have been found to play a significant role in the nutrient cycling and genetic information transmission between the environment and microorganisms. As inert DNA sequences, eDNA is able to present stability in the environment from the ribosome enzyme lysis, therein acting as the historical genetic information archive of the microbiome. As a consequence, both eDNA and iDNA can shed light on the functional gene variety and the corresponding microbial activity. In addition, eDNA is a ubiquitous composition of the cell membrane, which exerts a great impact on the resistance of outer stress from environmental pollutants, such as heavy metals, antibiotics, pesticides, and so on. This study focuses on the environmental dynamics and the ecological functions of the eDNA and iDNA from the perspectives of environmental behavior, genetic information transmission, resistance to the environmental contaminants, and so on. By reviewing the status quo and the future vista of the e/iDNAs research, this article sheds light on exploring the ecological functioning of the e/iDNAs in the environmental microbiome.

Differential variations of intracellular and extracellular antibiotic resistance genes between treatment units in centralized sewage sludge treatment plants

Centralized sludge treatment plants (CSTPs) are implicated as strong hotspots of antibiotic resistance genes (ARGs). However, the knowledge gap on the fate of intracellular and extracellular ARGs (iARGs and eARGs), and the functionality of resistant hosts limit risk assessment and management of CSTP resistome. Here, the flow of iARGs and eARGs across treatment units and analyses of ARG hosts were systematically explored in three full-scale CSTPs using quantitative metagenomic approaches. We found that 29% of sludge ARGs could be removed, with iARGs being dominant in the produced biosolids. The treatment process significantly affected the variations of iARG and eARG abundance while no significant difference in composition between iARGs and eARGs was observed in CSTPs. 15% of 295 recovered genomes were identified as antibiotic-resistant hosts, among which Actinobacteriota tended to encode multiple resistance. The key functions of ARG hosts were relative to the biological organic removal (e.g., carbohydrates). There also existed relationships between certain resistance mechanisms and functional traits, indicating that ARGs might take part in the physiological process of microorganisms in the sludge treatment. These findings provide important insight into the differential resistome variations and host functionality, which would be crucial in the management of antibiotic resistance in CSTPs.

Comprehensive insights into profiles and bacterial sources of intracellular and extracellular antibiotic resistance genes in groundwater

Antibiotic resistance genes (ARGs), especially last-resort ARGs (LARGs), are receiving extensive attention as emerging environmental contaminants in groundwater. However, their prevalent intracellular and extracellular patterns and bacterial sources in groundwater remain unclear. Herein, groundwater samples were collected in Tianjin, and characterized based on the profiles of intracellular ARGs (iARGs) and extracellular ARGs (eARGs), as well as the resident bacterial communities and extracellular DNA (eDNA)-releasing bacterial communities. The quantitative real-time PCR assays showed that eARGs presented fewer subtypes than iARGs and generally displayed lower detection frequencies than the corresponding iARGs. Similarly, LARGs exhibited lower detection frequencies than common ARGs, but the total abundance showed no significant differences between them. Genes vanA and bla_VIM were the observed dominant LARGs, and aadA was the observed common ARG independent of location inside or outside the bacteria. Furthermore, the top 10 phyla showed much difference between the main eDNA-releasing bacteria and the dominant resident bacteria. Proteobacteria was the predominant resident bacterial phyla while dominating the source of eDNA in groundwater. Despite representing a minor portion of the abundance in the resident bacteria, Actinobacteriota, Acidobacteriota, and Chloroflex surprisingly accounted for a large majority of eDNA release. Co-occurrence patterns among persistent ARGs, the resident bacteria, and eDNA-releasing bacteria revealed that the dominant common iARG aadA and intracellular LARGs bla_VIM and vanA had significant positive correlations with Methylobacterium_Methylorubrum and Shewanella. Meanwhile, the dominant extracellular LARG bla_VIM may be released by bacteria belonging to at least five genera, including Ellin6067, Bifidobacterium, Blautia, Veillonella, and Dechloromonas. Collectively, the findings of this study extend our understanding regarding the distribution of ARGs and their bacterial sources in groundwater, and indicate the serious pollution of LARGs in groundwater, which poses potential risks to public health.

Leaching risks of antibiotic resistance genes in urban underlying surface sediments during the simulated stormwater runoff and its controls

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, no available literature could be found on ARGs leaching from urban underlying surface sediments during stormwater runoff. In this study, surface sediments from commercial public squares around Nanjing (China) was selected for the investigation of target ARGs leaching kinetics, showing that absolute abundances of target ARGs desorption reached at the equilibrium during leaching time of 120-240min with all of the desorption efficiencies about 30%, indicating that there would be low proportion of leaching ARGs in the total ARGs migrating with runoff during rainfall events. Five target ARGs leaching including intI1 (clinic), strA, strB, tetM and tetX can be better described by the pseudo-second-order equation, while qacEdelta1 leaching can be better described by the pseudo-first-order equation, and the leaching for both sul1 and sul2 can be well described by the pseudo-first-order and pseudo-second-order equations. The effects of environmental factors including S/L ratios, pH values and water temperatures indicated that leaching efficiencies of target ARGs enhanced significantly with the increase of S/L ratios and water temperatures, but decreased with the increase of pH values. The transmission experiments after the simulated solar irradiation and heat implied that both large solar UV irradiation (30W/m²) and high temperature (40℃) were conducive to conjugation and transformation frequencies of ARGs. Furthermore, both high Cao and medium PAM levels could be effective for blocking ARGs transmission in the leachate from underlying surface sediments.

Antibiotic-resistant bacteria and antibiotic resistance genes in uranium mine: Distribution and influencing factors

Both heavy metals and radiation could affect the proliferation and dissemination of emerging antibiotic resistance pollutants. As an environmental medium rich in radioactive metals, the profile of antibiotic resistance in uranium mine remains largely unknown. A uranium mine in Guangdong province, China was selected to investigate the distribution and influencing factors of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) including intracellular ARGs (iARGs), adsorbed-extracellular ARGs (aeARGs), and free extracellular ARGs (feARGs). The result indicated that sulfonamide and tetracycline ARB could be generally detected in mining area with the absolute concentrations of 7.70 × 10²-5.18 × 10⁵ colony forming unit/g. The abundances of aeARGs in mine soil were significantly higher than those of iARGs (p < 0.05), highlighting the critical contribution of aeARGs to ARGs spread. The feARGs in mine drainage and its receiving river were abundant (3.38 × 10⁴-1.86 × 10⁷ copies/mL). ARB, aeARGs, and iARGs may correlate with nitrogen species and heavy metals (e.g., U and Mn), and feARGs presented a significant correlation with chemical oxygen demand (p < 0.05). These findings demonstrate the occurrence of ARB and ARGs in uranium mine for the first time, thereby contributing to the assessment and control of the ecological risk of antibiotic resistance in radioactive environments.

Deciphering changes in the abundance of intracellular and extracellular antibiotic resistance genes and mobile genetic elements under anaerobic fermentation: Driven by bacterial community

Antibiotic resistance genes (ARGs) are considered to be a new environmental pollutant and the removal of ARGs from swine manure by anaerobic fermentation was a crucial topic. This research discusses effects of initial pH values (3, 5, 7, 11) on intracellular and extracellular ARGs (iARGs and eARGs) as well as mobile genetic elements (MGEs) during anaerobic fermentation of swine manure had been examined. The initial pH during fermentation was found to be acidic (pH 3 and 5) in results, which was conducive to the removal of six eARGs and seven iARGs. Similarly, intracellular and extracellular MGEs were effectively eliminated with an initial pH of 3 and 5. The abundance of MGEs and four ARGs were enriched with an initial pH of 7 and 11. Acidic conditions can greatly deduce the diversity as well as abundance of the microbial community, ensuing removal of MEGs and ARGs. These findings are critical for risk assessment and management of ARGs.

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

In the One Health context, wastewater treatment plants (WWTPs) are central to safeguarding water resources. Nonetheless, many questions remain about their effectiveness in preventing antimicrobial resistance (AMR) dissemination. Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in intracellular DNA (iDNA) extracted from WWTP influents and effluents. The role of extracellular free DNA (exDNA) in wastewater is mostly overlooked. This study analyzed the transfer of ARGs and MGEs in a full-scale Nereda® reactor removing nutrients with aerobic granular sludge. We tracked the composition and fate of the iDNA and exDNA pools of influent, sludge, and effluent samples. Metagenomics was used to profile the microbiome, resistome, and mobilome signatures of iDNA and exDNA extracts. Selected ARGs and MGEs were analyzed by qPCR. From 2,840 ARGs identified, the genes arr-3 (2%), tetC (1.6%), sul1 (1.5%), oqxB (1.2%), and aph(3")-Ib (1.2%) were the most abundant among all sampling points and bioaggregates. Pseudomonas, Acinetobacter, Aeromonas, Acidovorax, Rhodoferax, and Streptomyces populations were the main potential hosts of ARGs in the sludge. In the effluent, 478 resistance determinants were detected, of which 89% were from exDNA potentially released by cell lysis during aeration in the reactor. MGEs and multiple ARGs were co-localized on the same extracellular genetic contigs. Total intracellular ARGs decreased 3-42% due to wastewater treatment. However, the ermB and sul1 genes increased by 2 and 1 log gene copies mL^-1, respectively, in exDNA from influent to effluent. The exDNA fractions need to be considered in AMR surveillance, risk assessment, and mitigation strategies.

Cascade Filtration With PCR Detection and Field-Flow-Fractionation Online With ICP-MS for the Characterization of DNA Interaction With Suspended Particulate Matter

The variety of applied antibiotics in animal and human medicine results in the release, development, and spread of relevant numbers of antibiotic resistance genes (ARGs) in the environment. The majority of ARGs are present in intracellular forms (in bacteria). Neglected aspects are extracellular variants of ARGs (eARGs) and their fragments, which have been detected in surface-water samples and sediments. The stability of eARGs is expected to be low; however, binding to particulate matter is likely to improve their stability and also affect their transport and dissemination behavior. Few studies have investigated DNA particle interactions, mostly via indirect characterization of adduct formation in model systems but not in real environmental matrices. Therefore, our study aims at a novel approach for direct characterization of desoxyribonucleic acid (DNA) particle interactions using both cascade filtration and field-flow fractionation. Cascade filtration with quantitative polymerase chain reaction (qPCR) detection indicated retention of ARGs on filters with much larger pore sizes supporting the hypothesis of ARG-particle interactions. However, artifacts from membrane clogging or DNA–membrane interaction cannot be excluded. Consequently, asymmetric flow field-flow fractionation was investigated as an alternative separation technique with the advantage of particle separation in a thin channel, reducing the risk of artifacts. The key method parameters, membrane composition, molecular weight cut off, and carrier composition, were systematically investigated using a calf-thymus DNA-spiked surface-water sample as a model. The results clearly showed a shift in the elution time of clay particles suggesting the presence of DNA–clay adducts. Multi-element detection by inductively coupled plasma mass spectrometry (ICP-MS) enabled monitoring of clay via the Al, Fe, and Si signals and DNA via the P signal. Matching peak profiles for the new fraction in the fractograms of the ARG and DNA-spiked water sample support adduct formation. Further evidence was provided by a novel post-channel filtration approach for the separation of free DNA from DNA–clay adducts.

Profile of Bacterial Community and Antibiotic Resistance Genes in Typical Vegetable Greenhouse Soil

The use of vegetable greenhouse production systems has increased rapidly because of the increasing demand for food materials. The vegetable greenhouse production industry is confronted with serious environmental problems, due to their high agrochemical inputs and intensive utilization. Besides this, antibiotic-resistant bacteria, carrying antibiotic-resistance genes (ARGs), may enter into a vegetable greenhouse with the application of animal manure. Bacterial communities and ARGs were investigated in two typical vegetable-greenhouse-using counties with long histories of vegetable cultivation. The results showed that Proteobacteria, Firmicutes, Acidobacteria, Chloroflexi, and Gemmatimonadetes were the dominant phyla, while aadA, tetL, sul1, and sul2 were the most common ARGs in greenhouse vegetable soil. Heatmap and principal coordinate analysis (PCoA) demonstrated that the differences between two counties were more significant than those among soils with different cultivation histories in the same county, suggesting that more effects on bacterial communities and ARGs were caused by soil type and manure type than by the accumulation of cultivation years. The positive correlation between the abundance of the intI gene with specific ARGs highlights the horizontal transfer potential of these ARGs. A total of 11 phyla were identified as the potential hosts of specific ARGs. Based on redundancy analysis (RDA), Ni and pH were the most potent factors determining the bacterial communities, and Cr was the top factor affecting the relative abundance of the ARGs. These results might be helpful in drawing more attention to the risk of manure recycling in the vegetable greenhouse, and further developing a strategy for practical manure application and sustainable production of vegetable greenhouses.

Critical review of antibiotic resistance genes in the atmosphere

We conducted a critical review to establish what is known about the sources, characteristics, and dissemination of ARGs in the atmosphere. We identified 52 papers that reported direct measurements of bacterial ARGs in air samples and met other inclusion criteria. The settings of the studies fell into the following categories: urban, rural, hospital, industrial, wastewater treatment plants (WWTPs), composting and landfill sites, and indoor environments. Certain genes were commonly studied and generally abundant: sul1, intI1, β-lactam ARGs, and tetracycline ARGs. Abundances of total ARGs varied by season and setting, with air in urban areas having higher ARG abundance than rural areas during the summer and vice versa during the winter. There was greater consistency in the types and abundances of ARGs throughout the seasons in urban areas. Human activity within indoor environments was also linked to increased ARG content (abundance, diversity, and concentration) in the air. Several studies found that human exposure to ARGs through inhalation was comparable to exposure through drinking water or ingesting soil. Detection of ARGs in air is a developing field, and differences in sampling and analysis methods reflect the many possible approaches to studying ARGs in air and make direct comparisons between studies difficult. Methodologies need to be standardized to facilitate identification of the dominant ARGs in the air, determine their major sources, and quantify the role of atmospheric transport in dissemination of ARGs in the environment. With such knowledge we can develop better policies and guidelines to limit the spread of antimicrobial resistance.

Polyethylene terephthalate microplastic fibers increase the release of extracellular antibiotic resistance genes during sewage sludge anaerobic digestion

Microplastic fibers (MFs), as the most frequently detected microplastic shape in sewage sludge, have posed emerging concern for sludge treatment and disposal. However, the effect of MFs on antibiotic resistance genes (ARGs), especially extracellular ARGs (eARGs) during sludge treatment remains far from explicit. Therefore, this study investigated the potential impact of MFs on eARGs during sludge anaerobic digestion (AD), a commonly used sludge treatment method, through long-term operation. The qPCR results showed that both absolute and relative abundances of eARGs increased with the MFs exposure during sludge AD. The average absolute and relative abundances of eight tested eARGs in the AD reactor with the highest MFs dosage (170 items/gTS) were 1.70 and 2.15 times higher than those in the control AD reactor. The metagenomics results further comfirmed the increase of eARGs abundance during sludge anaerobic digestion after MFs exposure and the enhancement did not show significant selectivity. The identification of the potential hosts of eARGs suggested the host numbers of eARGs also increased with MFs exposure, which may suggest enhanced horizonal transformation as a result of increased eARGs. Further exploring the mechansims showed that the genes involved in type IV secretion system was upregulated after MFs exposure, suggesting the active release of eARGs was enhanced with MFs exposure. In contrast, the MFs may not affect the passive release of eARGs as its impact on cell membrance damage was insignificant. The enhanced eARGs in sludge AD process may further accelerate the transport of ARGs in environment, which should be considered during sludge treatment and disposal.

Fates of quaternary ammonium compound resistance genes and the corresponding resistant strain in partial nitrification/anammox system under pressure of hexadecyl trimethyl ammonium chloride

Hexadecyl trimethyl ammonium chloride (ATMAC-C16) is a kind of quaternary ammonium compound (QACs) which is extensively consumed as disinfectants, antimicrobials and surfactants. Here, the partial nitrification/anammox (PN/A) system was exposed to different levels of ATMAC-C16 (0-10 mg/L) and the main objective was to reveal the long-term microbiological responses of PN/A system to ATMAC-C16, importantly, explore the tolerance of PN/A to ATMAC-C16 and the key resistant strain. Nitrogen removal efficiency was influenced by environmental and extreme levels of ATMAC-C16 through mainly affecting the anammox (hzsB) gene. Two types of anammox, Candidatus Jettenia and Candidatus Kuenenia, were enriched under the pressure of ATMAC-C16, which allowed PN/A system to maintain good nitrogen removal performance. ATMAC-C16 might cause the hormesis of entire microbial population in PN/A system, leading to the enhancement of cell viability. ATMAC-C16 decreased the relative abundances of most antibiotics resistance genes (ARGs) but significantly enriched QACs resistance genes (QRGs). The tolerance of PN/A system to ATMAC-C16 might be strengthened by inducing the efflux pumps encoding genes (qacH-01/02). Microbial hosts dynamic and co-selection mechanism among ARGs and QRGs resulted in the opposite trends of qacEdeltal-01/02 and qacH-01/02. Pseudoxanthomonas mexicana was identified as the ATMAC-C16 resistant strain, and its resistance to 10 mg/L ATMAC-C16 might not only obtain by capturing the qacH gene, but also benefit from its own efflux pump system. Therefore, from the perspective of the transmission of resistance genes, especially for QRGs, the spread risk of QRGs and ATMAC-C16 resistant strain in PN/A technique should be taken seriously.

Abundance, diversity, and host assignment of total, intracellular, and extracellular antibiotic resistance genes in riverbed sediments

Human health risk assessment for environmental antibiotic resistant microbes requires not only quantifying the abundance of antibiotic resistance genes (ARGs) in environmental matrices, but also understanding their hosts and genetic context. Further, differentiating ARGs in intracellular and extracellular DNA (iDNA and eDNA) fractions may help refine our understanding of ARG transferability. The objectives of this study were to understand the (O1) abundance and diversity of extracellular, intracellular, and total ARGs along a land use gradient and (O2) impact of bioinformatics pipeline on the assignment of putative hosts for the ARGs observed in the different DNA fractions. Sediment samples were collected along a land use gradient in the Raritan River, New Jersey, USA. DNA was extracted to separate eDNA and iDNA and qPCR was performed for select ARGs and the 16S rRNA gene. Shotgun metagenomic sequencing was performed on DNA extracts for the different DNA fractions. ARG hosts were assigned via two different bioinformatic pipelines: network analysis of raw reads versus assembly. Results of the two pipelines were compared to evaluate their performance in terms of number and diversity of linkages and accuracy of in silico matrix spike host assignments. No differences were observed in the 16S rRNA gene normalized sul1 concentrations between the DNA fractions. The overall microbial community structure was more similar for iDNA and total DNA compared to eDNA and generally clustered by sampling site. ARGs associated with mobile genetic elements increased in iDNA for the downstream sites. Regarding host assignment, the raw reads pipeline via network analysis identified 247 ARG hosts as compared to 53 hosts identified by assembly pipeline. Other comparisons between the pipelines were made including ARG assignment to taxa containing waterborne pathogens and practical considerations regarding processing time.

Deciphering the extracellular and intracellular antibiotic resistance genes in multiple environments reveals the persistence of extracellular ones

The extracellular and intracellular antibiotic resistance genes (eARGs and iARGs) together constitute the entire resistome in environments. However, the systematic analysis of eARGs and iARGs was still inadequate. Three kinds of environments, i.e., livestock manure, sewage sludge, and lake sediment, were analyzed to reveal the comprehensive characteristics of eARGs and iARGs. Based on the metagenomic data, the diversities, relative abundances, and compositions of eARGs and iARGs were similar. The extracellular and intracellular integrons and insertion sequences (ISs) also did not show any significant differences. However, the degree and significance of the correlation between total relative abundances of integrons/ISs and ARGs were lower outside than inside the cells. Gene cassettes carried by class 1 integron were amplified in manure and sludge samples, and sequencing results showed that the identified ARGs extracellularly and intracellularly were distinct. By analyzing the genetic contexts, most ARGs were found located on chromosomes. Nevertheless, the proportion of ARGs carried by plasmids increased extracellularly. qPCR was employed to quantify the absolute abundances of sul1, sul2, tetO, and tetW, and their extracellular proportions were found highest in sludge samples. These findings together raised the requirements of considering eARGs and iARGs separately in terms of risk evaluation and removal management.

Risk of horizontal transfer of intracellular, extracellular, and bacteriophage antibiotic resistance genes during anaerobic digestion of cow manure

The fate of intracellular antibiotic resistance genes (iARGs), extracellular ARGs (eARGs) and bacteriophage ARGs (bARGs) during anaerobic digestion (AD) of cow manure is unclear. Thus, the characteristics of iARGs, eARGs and bARGs during mesophilic AD (MAD) and thermophilic AD (TAD) of cow manure were investigated. The absolute abundances of iARGs decreased by 69.82% after TAD. After MAD and TAD, the total absolute abundances of eARGs increased by 63.5 times and 67.6 times, respectively, whereas those of the bARGs increased by 47.60% and 59.22%. eARGs were mainly derived from the non-specific lysis of Firmicutes, Bacteroidetes, while bacteriophages had a wide range of hosts. The variations in iARGs, eARGs and bARGs were affected by the microbial hosts but also directly driven by physicochemical factors (e.g., pH). Overall, the findings of this study revealed that there may be a risk of eARGs and bARGs disseminating during the AD of cow manure.

Using biochar to strengthen the removal of antibiotic resistance genes: Performance and mechanism

In this study, the excess activated sludge was used for pyrolysis to produce biochar with Ce modification. The removal process and mechanism of ampicillin resistance gene (ARG_Amp) by biochar was investigated. The results showed that when pyrolyzing the excess sludge at 400 °C, the organic components in the sludge could be partially pyrolyzed and complexed with Ce. By accepting electrons from phenol or quinone, persistent free radicals (PFRs) were formed on the surface of biochar. On the optimized conditions with the initial ARG_Amp concentration of 41.43 mg/L, the removal ratios of ARG_Amp by adsorption, PFRs, hydroxyl free radicals (·OH) by adding H₂O₂ were 28.37%, 8.26%, and 27.56%. No melted DNA was detected in the treated samples. The oxidation process by PFRs and ·OH can directly destroy the ARG_Amp structure. The phosphodiester bond in the base stacking structure and the phosphate bond in the nucleotide are the possible action sites of PFRs. Treated ARG_Amp products were in the form of base pair residues or short-chain double helix structures. ·OH can be added to the bases of nucleotide molecules to form highly active free radical adducts. They can initiate molecular dehydrogenation and intermolecular proton transfer, resulting in oxidation of the base to the scission of the phosphate sugar backbone.

Extracellular polymeric substances (EPS) associated extracellular antibiotic resistance genes in activated sludge along the AAO process: Distribution and microbial secretors

Wastewater treatment plants (WWTPs) are important sources of antibiotic resistance genes (ARGs). Increasing attention has been paid to extracellular ARGs in cell-free form due to their horizontal gene transfer via transformation. However, the fate of the adsorbed form of extracellular ARGs that exist in extracellular polymeric substances (EPS) of activated sludge in WWTP remains largely unknown. Herein, seven EPS-associated ARGs along the anaerobic-anoxic-aerobic (AAO) process were quantified using quantitative polymerase chain reaction. Results show that the absolute abundances of EPS-associated ARGs were 0.69-4.52 logs higher than those of cell-free ARGs. There was no significant difference in the abundances of EPS-associated ARGs along the AAO process. Among these target genes, the abundances of EPS-associated sul genes were higher than those of EPS-associated tet and bla genes. Proteobacteria and Bacteroidetes were identified as the major secretors of EPS-associated ARGs, and they may play an important role in the proliferation of extracellular ARGs. Moreover, the transformation efficiencies of EPS-associated ARGs were 3.55-4.65 logs higher than those of cell-free ARGs, indicating that EPS-associated ARGs have higher environmental risks. These findings have advanced our understanding of EPS-associated ARGs and are useful for the control and risk assessment of ARGs in WWTPs.

UV-aging of microplastics increases proximal ARG donor-recipient adsorption and leaching of chemicals that synergistically enhance antibiotic resistance propagation

Despite growing attention to environmental pollution by microplastics (MP), the effects of MP aging on bacterial horizontal gene transfer (HGT) have not been systematically investigated. Here, we used UV-aged polystyrene microplastics (PS-MPs) to investigate how aging affects antibiotic resistance genes (ARGs) transfer efficiency from various ARG vectors to recipient bacteria. The adsorption capacity of MP₂₀ (20-day UV-aged PS-MPs) towards E. coli (harboring plasmid-borne bla_TEM-1), plasmid pET29 (harboring bla_NDM-1) and phage lambda (carrying the aphA1 ARG) increased by 6.6-, 5.2- and 8.3-fold, respectively, relative to pristine PS-MPs (MP₀), due to increased specific surface area and affinity for these ARG vectors. Moreover, MP₂₀ released more organic compounds (TOC 1.6 mg/g-MP₂₀, versus 0.2 mg/g-MP₀ in 4 h) -possibly depolymerization byproducts (verified by GC-MS), which induced intracellular ROS generation, increased cell permeability and upregulated HGT associated genes. Accordingly, MP₂₀ enhanced ARG transfer frequency from E. coli, plasmid pET29 and phage lambda (relative to MP₀) by 1.3-, 4.7- and 3.5-fold, respectively. The Bliss independence model infers that higher bacterial adsorption and exposure to chemicals released during MP aging synergistically enhanced ARG transfer. This underscores the need to assess the significance of this overlooked phenomenon to the environmental dissemination of antibiotic resistance and other HGT processes.

Electrochemical flow-through disinfection reduces antibiotic resistance genes and horizontal transfer risk across bacterial species

Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), as emerging pollutants, are released into environment, increasing the risk of horizontal gene transfer (HGT). However, a limited number of studies quantified the effects of ARB disinfection on the HGT risk. This study investigated the inactivation of E. coli 10667 (sul) and the release and removal of ARGs using an electrochemical flow-through reactor (EFTR). Furthermore, the transfer frequencies and potential mechanisms of HGT after disinfection were explored using non-resistant E. coli GMCC 13373 as the recipient and E. coli DH5α carrying plasmid RP4 as the donor. A threshold of current density (0.25 mA/cm²) was observed to destroy cells and release intracellular ARGs (iARGs) to increase extracellular ARGs (eARGs) concentration. The further increase in the current density to 1 mA/cm² resulted in the decline of eARGs concentration due to the higher degradation rate of eARGs than the release rate of iARGs. The performance of ARGs degradation and HGT frequency by EFTR were compared with those of conventional disinfection processes, including chlorination and ultraviolet radiation (UV). A higher ARGs degradation (83.46%) was observed by EFTR compared with that under chlorination (10.23%) and UV (27.07%). Accordingly, EFTR reduced the HGT frequency (0.69) of released ARGs into the recipient (Forward transfer), and the value was lower than that by chlorination (2.69) and UV (1.73). Meanwhile, the surviving injured E. coli 10667 (sul) with increased cell permeability was transferred by plasmid RP4 from the donor (Reverse transfer) with a higher frequency of 0.33 by EFTR compared with that under chlorination (0.26) and UV (0.16). In addition, the sul3 gene was the least resistant to EFTR than sul1 and sul2 gene. These findings provide important insights into the mechanism of HGT between the injured E. coli 10667 (sul) and environmental bacteria. EFTR is a promising disinfection technology for preventing the spread of antibiotic resistance.

Dead but Not Forgotten: How Extracellular DNA, Moisture, and Space Modulate the Horizontal Transfer of Extracellular Antibiotic Resistance Genes in Soil

Antibiotic-resistant bacteria and the spread of antibiotic resistance genes (ARGs) pose a serious risk to human and veterinary health. While many studies focus on the movement of live antibiotic-resistant bacteria to the environment, it is unclear whether extracellular ARGs (eARGs) from dead cells can transfer to live bacteria to facilitate the evolution of antibiotic resistance in nature. Here, we use eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to track the movement of eARGs to live P. stutzeri cells via natural transformation, a mechanism of horizontal gene transfer involving the genomic integration of eARGs. In sterile, antibiotic-free agricultural soil, we manipulated the eARG concentration, soil moisture, and proximity to eARGs. We found that transformation occurred in soils inoculated with just 0.25 μg of eDNA g^-1 soil, indicating that even low concentrations of soil eDNA can facilitate transformation (previous estimates suggested ∼2 to 40 μg eDNA g^-1 soil). When eDNA was increased to 5 μg g^-1 soil, there was a 5-fold increase in the number of antibiotic-resistant P. stutzeri cells. We found that eARGs were transformed under soil moistures typical of terrestrial systems (5 to 30% gravimetric water content) but inhibited at very high soil moistures (>30%). Overall, this work demonstrates that dead bacteria and their eARGs are an overlooked path to antibiotic resistance. More generally, the spread of eARGs in antibiotic-free soil suggests that transformation allows genetic variants to establish in the absence of antibiotic selection and that the soil environment plays a critical role in regulating transformation. IMPORTANCE Bacterial death can release eARGs into the environment. Agricultural soils can contain upwards of 10⁹ ARGs g^-1 soil, which may facilitate the movement of eARGs from dead to live bacteria through a mechanism of horizontal gene transfer called natural transformation. Here, we track the spread of eARGs from dead, antibiotic-resistant Pseudomonas stutzeri cells to live antibiotic-susceptible P. stutzeri cells in sterile agricultural soil. Transformation increased with the abundance of eARGs and occurred in soils ranging from 5 to 40% gravimetric soil moisture but was lowest in wet soils (>30%). Transformants appeared in soil after 24 h and persisted for up to 15 days even when eDNA concentrations were only a fraction of those found in field soils. Overall, our results show that natural transformation allows eARGs to spread and persist in antibiotic-free soils and that the biological activity of eDNA after bacterial death makes environmental eARGs a public health concern.

Spatial behavior and source tracking of extracellular antibiotic resistance genes in a chlorinated drinking water distribution system

Antibiotic resistance genes (ARGs) are receiving increasing concerns due to the antibiotic resistance crisis. Nevertheless, little is known about the spatial behavior and sources of extracellular ARGs (eARGs) in the chlorinated drinking water distribution systems (DWDSs). Here, tap water was continuously collected to reveal the occurrence of both eARGs and intracellular ARGs (iARGs) along a chlorinated DWDS. Afterward, the correlation between eARGs, eDNA-releasing communities, and communities of planktonic bacteria was further analyzed. The eARG concentration decreased significantly, whereas the proportion of vanA and bla_NDM-1 increased. Further, the diversity of the eDNA-releasing community increased markedly with increasing distance from the drinking water treatment plant (DWTP). Moreover, the dominant eDNA-releasing bacteria shifted from Acinetobacter, Pseudomonas, and Methylobacterium-Methylorubrum in finished water from the DWTP to Bacteroides, Faecalibacterium, Staphylococcus, and Parabacteroides in the DWDS. In terms of eARG source, thirty genera were significantly correlated with seven types of eARGs that resulted from the lysis of dead planktonic bacteria and detached biofilms. Conversely, the iARGs concentration increased, whereas the biodiversity of the planktonic bacteria community decreased in the sampling points along the DWDSs. Our findings provide critical insights into the spatial behavior and sources of eARGs, highlighting the health risks associated with ARGs in DWDSs.

Unveil the role of dissolved and sedimentary metal(loid)s on bacterial communities and metal resistance genes (MRGs) in an urban river of the Qinghai-Tibet Plateau

Though metal resistance genes (MRGs) are of global concern in aquatic ecosystems, the underlying factors responsible for MRGs dissemination, especially in urban rivers on the vulnerable Qinghai-Tibet Plateau, are rarely known. Here, we collected 64 samples including water and sediments during the wet and dry seasons and effluents from six wastewater treatment plants (WWTPs) during the dry season and measured 50 metal(loid)s, 60 bacterial phyla, and 259 MRGs. We observed the distinct difference of metal(loid)s, bacterial communities, and MRGs between water and sediments and the great seasonal changes in metal(loid)s and bacterial communities instead of MRGs. Thirty-one metal(loid)s were detectable in the water, with relatively low concentrations and no significant effects on the planktonic bacterial communities and MRGs. Interestingly, the WWTPs effluent partially promoted the prevalence of dissolved metal(loid)s, bacterial communities, and MRGs along the river. In the sediments, the average concentrations of 17 metal(loid)s exceeded their corresponding background levels in this region and strongly influenced the bacterial communities and the MRGs. Sedimentary Hg and Cd, mainly sourced from the intensive animal husbandry, were the major pollutants causing ecological risks and largely shaped their corresponding resistomes. Moreover, we found that bacterial communities predominantly determined the variation of MRGs in both water and sediments. Metagenome-assembled genomes further reveals the widespread co-occurrence of MRGs and antibiotic resistance genes (ARGs) in MRG hosts. Our study highlighted the concern of effluents discharged from WWTPs and emphasized the importance of controlling the anthropogenic inputs of sedimentary metal(loid)s in the plateau river ecosystems.

Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas

Environmental contamination by heavy metals (HMs) poses several indirect risks to human health, including the co-spreading of genetic traits conferring resistance to both HMs and antibiotics among micro-organisms. Microbial antibiotic resistance (AR) acquisition is enhanced at sites anthropogenically polluted by HMs, as well as in remote systems naturally enriched in HMs, such as hydrothermal vents in the deep sea. However, to date, the possible role of hydrothermal vents at shallower water depths as hot spots of microbial AR gain and spreading has not been tested, despite the higher potential risks associated with the closer vicinity of such ecosystems to coasts and human activities. In this work, we collected waters and sediments at the Panarea shallow-water hydrothermal vents, testing the presence of culturable marine bacteria and their sensitivity to antibiotics and HMs. All of the bacterial isolates showed resistance to at least one antibiotic and one HM and, most notably, 80% of them displayed multi-AR on average to 12 (min 8, max 15) different antibiotics, as well as multi-HM tolerance. We show that our isolates displayed high similarity (≥99%) to common marine bacteria, affiliating with Actinobacteria, Gammaproteobacteria, Alphaproteobacteria and Firmicutes, and all displayed wide growth ranges for temperature and salinity during in vitro physiological tests. Notably, the analysis of the genomes available in public databases for their closest relatives highlighted the lack of genes for AR, posing new questions on the origin of multi-AR acquisition in this peculiar HM-rich environment. Overall, our results point out that shallow-water hydrothermal vents may contribute to enhance AR acquisition and spreading among common marine bacteria in coastal areas, highlighting this as a focus for future research.

A new modelling framework for assessing the relative burden of antimicrobial resistance in aquatic environments

The infections caused by antibiotic resistant bacteria (ARB) can lead to higher medical costs, prolonged hospital stays, and increased mortality compared to bacteria that are susceptible to antibiotics. Challenges exist in quantifying the potential risk/burden associated with antimicrobial resistance (AMR) as there is a lack of dose-response models available for pathogens which are resistant to antibiotics, in addition to the fact that very little is known regarding the health risks posed by antibiotic resistant genes (ARG). In this paper, we proposed a new modelling framework to evaluate the relative burden of AMR in natural aquatic environments. With this framework, an AMR burden score for each sample was calculated based on burden coefficients assigned for each ARB and ARG, as well as weighted burdens for the separate ARBs and ARGs components. The method developed in this study was applied to assess the relative burden of AMR in local aquatic environments with different land uses at different seasons. The collected filed data were used to verify the applicability of the proposed relative burden assessment method. Through the established method, the spatial and temporal hotspots of AMR were identified, which could provide useful information to agencies for better control and management of AMR emergence in natural aquatic environments.

Biochar effectively inhibits the horizontal transfer of antibiotic resistance genes via transformation

The rapid spread of antibiotic resistance genes (ARGs) has posed a risk to human health. Here, the effects of biochar (BC) on the horizontal transfer of ARG-carrying plasmids to Escherichia coli via transformation were systematically investigated. BC could significantly inhibit the transformation of ARGs and the inhibition degree increased with pyrolysis temperature. Rice straw-derived BC showed a stronger inhibitory effect on the transformation of ARGs than that of peanut shell-derived BC from the same pyrolysis temperature. The inhibitory effect of BC from low pyrolysis temperature (300 ℃) was mainly caused by BC dissolutions, while it was mainly attributed to BC solids for high pyrolysis temperature (700 ℃) BC. BC dissolutions could induce intramolecular condensation and even agglomeration of plasmids, hindering their transformation into competent bacteria. The cell membrane permeability was slightly decreased in BC dissolutions, which might also contribute to the inhibitory effect. Plasmid can be adsorbed by BC solids and the adsorption increased with BC pyrolysis temperature. Meanwhile, BC-adsorbed plasmid could hardly be transformed into E. coli. BC solids could also deactivate E. coli and thereby inhibit their uptake of ARGs. These findings provide a way using BC to limit the spread of ARGs in the environment.

Implications for mitigation of antibiotic resistance: Differential response of intracellular and extracellular antibiotic resistance genes to sludge fermentation coupled with thermal hydrolysis

Thermal hydrolysis pretreatment (THP) can effectively remove the antibiotic resistance genes (ARGs) from sewage sludge, but the rebounding effects in the subsequent anaerobic fermentation are often observed. The purpose of this study was to elucidate the distribution and fate of intracellular and extracellular ARGs (iARGs and eARGs) in the sludge acidogenic fermentation process coupled with THP. Our results revealed that THP significantly reduced the absolute abundance of total ARGs in raw sludge but increased eARGs by 0.3-1.4 log units under practical conditions (140 °C for 30 min). There is no significant difference in the removal of total ARGs between the two acidogenic fermenters receiving raw and hydrolyzed sludge, with iARGs prevailing in the produced biosolids. The succession of bacterial community and the co-occurrence relationships among ARG type, mobile genetic elements and bacterial taxa were observed, suggesting a phylogenetic basis for the iARGs patterns in fermented sludge. However, eARGs were susceptible to biodegradation with a half-life of 2.34 h and they contributed limitedly to the ARGs propagation through transformation. These findings suggest an emphasis on the mitigation of iARGs during the acidogenic fermentation of sludge, which would be achieved by lowering the richness and physicochemical destruction of potential hosts.

Effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of antibiotic resistance genes in water environments: A review

Antibiotic resistance has created obstacles in the treatment of infectious diseases with antibiotics. The horizontal transfer of antibiotic resistance genes (ARGs) can exacerbate the dissemination of antibiotic resistance in water environments. In addition to antibiotic selective pressure, multiple non-antibiotic factors can affect the horizontal transfer of ARGs. Herein, we seek to comprehensively review the effects and relevant mechanisms of non-antibiotic factors on the horizontal transfer of ARGs in water environments, especially contaminants from human activities and water treatment processes. Four pathways have been identified to accomplish horizontal gene transfer (HGT), i.e., conjugation, transformation, transduction, and vesiduction. Changes in conjugative frequencies by non-antibiotic factors are mainly related to their concentrations, which conform to hormesis. Relevant mechanisms involve the alteration in cell membrane permeability, reactive oxygen species, SOS response, pilus, and mRNA expression of relevant genes. Transformation induced by extracellular DNA may be more vulnerable to non-antibiotic factors than other pathways. Except bacteriophage infection, the effects of non-antibiotic factors on transduction exhibit many similarities with that of conjugation. Given the secretion of membrane vesicles stimulated by non-antibiotic factors, their effects on vesiduction can be inferred. Furthermore, contaminants from human activities at sub-inhibitory or environmentally relevant concentrations usually promote HGT, resulting in further dissemination of antibiotic resistance. The horizontal transfer of ARGs is difficult to be inhibited by individual water treatment processes (e.g., chlorination, UV treatment, and photocatalysis) unless they attain sufficient intensity. Accordingly, the synergistic application containing two or more water treatment processes is recommended. Overall, we believe this review can elucidate the significance for risk assessments of contaminants from human activities and provide insights into the development of environment-friendly and cost-efficient water treatment processes to inhibit the horizontal transfer of ARGs.

The air-borne antibiotic resistome: Occurrence, health risks, and future directions

Antibiotic resistance comprising of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) is an emerging problem causing global human health risks. Several reviews exist on antibiotic resistance in various environmental compartments excluding the air-borne resistome. An increasing body of recent evidence exists on the air-borne resistome comprising of antibiotic resistance in air-borne bioaerosols from various environmental compartments. However, a comprehensive review on the sources, dissemination, behavior, fate, and human exposure and health risks of the air-borne resistome is still lacking. Therefore, the current review uses the source-pathway-receptor-impact-mitigation framework to investigate the air-borne resistome. The nature and sources of antibiotic resistance in the air-borne resistome are discussed. The dissemination pathways, and environmental and anthropogenic drivers accounting for the transfer of antibiotic resistance from sources to the receptors are highlighted. The human exposure and health risks posed by air-borne resistome are presented. A health risk assessment and mitigation strategy is discussed. Finally, future research directions including key knowledge gaps are summarized.

eDNA Inactivation and Biofilm Inhibition by the PolymericBiocide Polyhexamethylene Guanidine Hydrochloride (PHMG-Cl)

The choice of effective biocides used for routine hospital practice should consider the role of disinfectants in the maintenance and development of local resistome and how they might affect antibiotic resistance gene transfer within the hospital microbial population. Currently, there is little understanding of how different biocides contribute to eDNA release that may contribute to gene transfer and subsequent environmental retention. Here, we investigated how different biocides affect the release of eDNA from mature biofilms of two opportunistic model strains Pseudomonas aeruginosa ATCC 27853 (PA) and Staphylococcus aureus ATCC 25923 (SA) and contribute to the hospital resistome in the form of surface and water contaminants and dust particles. The effect of four groups of biocides, alcohols, hydrogen peroxide, quaternary ammonium compounds, and the polymeric biocide polyhexamethylene guanidine hydrochloride (PHMG-Cl), was evaluated using PA and SA biofilms. Most biocides, except for PHMG-Cl and 70% ethanol, caused substantial eDNA release, and PHMG-Cl was found to block biofilm development when used at concentrations of 0.5% and 0.1%. This might be associated with the formation of DNA–PHMG-Cl complexes as PHMG-Cl is predicted to bind to AT base pairs by molecular docking assays. PHMG-Cl was found to bind high-molecular DNA and plasmid DNA and continued to inactivate DNA on surfaces even after 4 weeks. PHMG-Cl also effectively inactivated biofilm-associated antibiotic resistance gene eDNA released by a pan-drug-resistant Klebsiella strain, which demonstrates the potential of a polymeric biocide as a new surface-active agent to combat the spread of antibiotic resistance in hospital settings.

Enhanced propagation of intracellular and extracellular antibiotic resistance genes in municipal wastewater by microplastics

Microplastics (MPs) are an emerging global concern as they are abundant in the environment and can act as vectors of various contaminants. However, whether and how MPs can be vectors of antibiotic resistance genes (ARGs), especially extracellular ARGs (eARGs), remains far from explicit. This study addresses the adsorption of both intracellular ARGs (iARGs) and eARGs by four types of MPs in municipal wastewater, and then explores the potential horizontal gene transfer of iARGs and eARGs exposed to MPs. Results indicate that though MPs significantly adsorbed both iARGs and eARGs, eARGs were adsorbed with a significantly higher fold enrichment (2.0-5.0 log versus 2.0-3.3 log) and rate (0.0056 min^-1 versus 0.0037 min^-1) than iARGs. While all four types of MPs adsorbed ARGs, polypropylene MPs showed the highest adsorption capacity for ARGs. Background constituents such as humic acid and antibiotics significantly inhibited adsorption of iARGs, but not eARGs on MPs. The presence of sodium chloride didn't significantly affect adsorption of iARGs or eARGs. The adsorption of ARGs was well explained by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) interaction energy profile. Higher eARG adsorption was attributed to a lower energy barrier between MPs and eARGs than that between MPs and iARGs. Exposure to MPs enhanced horizontal gene transfer of both iARGs and eARGs by 1.5 and 2.0 times, respectively. The improved contact potential between donors and recipients, as well as the increased cell permeability of recipients induced the improved horizontal gene transfer by MPs. This study underscores the need to address ARG propagation through adsorption to MPs.

Fates of intracellular and extracellular antibiotic resistance genes during the cattle farm wastewater treatment process

Cattle farm wastewater, as a significant reservoir for antibiotic resistance genes (ARGs), has received wide attention. Intracellular and extracellular ARGs (iARGs and eARGs) were detected during wastewater treatment, including solid-liquid separation, anaerobic regulation, upflow anaerobic sludge blanket (UASB) digestion, an anoxic-oxic-anoxic-oxic (A²O²) process, a membrane bioreactor (MBR), and ozone disinfection. Ten abundant ARGs were chosen as the target ARGs according to metagenomic sequencing. The concentrations of the total target iARGs and eARGs were 6.12 × 10⁷ and 3.24 × 10⁶ copy numbers/mL in raw wastewater, and then 3.79 × 10³ and 3.95 × 10⁵ copy numbers/mL in final effluent, because UASB, A²O², MBR and ozone disinfection can gradually reduce the concentrations of most ARGs. The concentrations of ARGs were positively correlated with almost all wastewater quality indicators. Positive correlation was also observed between iARGs and Bacteroidetes, Firmicutes and Spirochaetes, indicating that the bacteria in these three phyla might be the main hosts of ARGs. Wastewater quality indicators and bacterial community composition affected the distribution and removal of ARGs during cattle wastewater treatment.

Metagenomic and Recombination Analyses of Antimicrobial Resistance Genes from Recreational Waters of Black Sea Coastal Areas and Other Marine Environments Unveil Extensive Evidence for Their both Intrageneric and Intergeneric Transmission across Genetically Very Diverse Microbial Communities

Microbial communities of marine coastal recreation waters have become large reservoirs of AMR genes (ARGs), contributing to the emergence and transmission of various zoonotic, foodborne and other infections that exhibit resistance to various antibiotics. Thus, it is highly imperative to determine ARGs assemblages as well as mechanisms and trajectories of their transmission across these microbial communities for our better understanding of the evolutionary trends of AMR (AMR). In this study, using metagenomics approaches, we screened for ARGs in recreation waters of the Black Sea coastal areas of the Batumi City (Georgia). Also, a large array of the recombination detection algorithms of the SplitsTree, RDP4, and GARD was applied to elucidate genetic recombination of ARGs and trajectories of their transmission across various marine microbial communities. The metagenomics analyses of sea water samples, obtained from across the above marine sites, could identify putative ARGs encoding for multidrug resistance efflux transporters mainly from the Major Facilitator and Resistance Nodulation Division superfamilies. The data, generated by SplitsTree (fit ≥95.619; bootstrap values ≥ 95; Phi p ≤ 0.0494), RDP4 (p ≤ 0.0490), and GARD, provided strong statistical evidence not only for intrageneric recombination of these ARGs, but also for their intergeneric recombination across fairly large and diverse microbial communities of marine environment. These bacteria included both human pathogenic and nonpathogenic species, exhibiting collectively the genera of Vibrio, Aeromonas, Synechococcus, Citromicrobium, Rhodobacteraceae, Pseudoalteromonas, Altererythrobacter, Erythrobacter, Altererythrobacter, Marivivens, Xuhuaishuia, and Loktanella. The above nonpathogenic bacteria are strongly suggested to contribute to ARGs transmission in marine ecosystems.

Fate of antibiotic resistance genes in industrial-scale rapid composting of pharmaceutical fermentation residue: The role implications of microbial community structure and mobile genetic elements

Composting is an effective technology to recycle organic solid waste as a green resource. However, pharmaceutical fermentation residue (PFR) contains a variety of pollutants, such as residual drug and antibiotic resistance genes (ARGs), which limits the green cycle of using PFR as a resource. To promote the green recycling of PFR, this study evaluated the characteristics of abundance and the response relationship of ARGs during the process of rapid composting. Different rapid composting samples were collected, and DNA was extracted from each sample. The absolute abundance of ARGs was quantified using quantitative PCR, and the microbial community structure was identified using high-throughput sequencing. The results showed that ermB, ermF, tetM and tetQ were reduced by 89.55%, 15.10%, 89.55%, and 82.30% respectively, and only sul2 increased by approximately 5-fold. Mobile genetic elements (MGEs) directly affected the changes in abundance of ARGs. As typical MGEs, intl1 and intl2 decreased by 3.40% and 54.32%, respectively. Potential host microorganisms important factors that affected ARGs and MGEs. A network analysis indicated that the potential host microorganisms were primarily distributed in Firmicutes and Proteobacteria at the phylum level. The pH and content of water-extractable sulfur were physicochemical parameters that substantially affected the abundance of potential host microorganisms through redundancy analysis. Industrial-scale rapid composting could reduce the number of ARGs and shorten the composting cycle, which merits its popularization and application.

What Is the Role of the Environment in the Emergence of Novel Antibiotic Resistance Genes? A Modeling Approach

It is generally accepted that intervention strategies to curb antibiotic resistance cannot solely focus on human and veterinary medicine but must also consider environmental settings. While the environment clearly has a role in transmission of resistant bacteria, its role in the emergence of novel antibiotic resistance genes (ARGs) is less clear. It has been suggested that the environment constitutes an enormous recruitment ground for ARGs to pathogens, but its extent is practically unknown. We have constructed a model framework for resistance emergence and used available quantitative data on relevant processes to identify limiting steps in the appearance of ARGs in human pathogens. We found that in a majority of possible scenarios, the environment would only play a minor role in the emergence of novel ARGs. However, the uncertainty is enormous, highlighting an urgent need for more quantitative data. Specifically, more data is most needed on the fitness costs of ARG carriage, the degree of dispersal of resistant bacteria from the environment to humans, and the rates of mobilization and horizontal transfer of ARGs. This type of data is instrumental to determine which processes should be targeted for interventions to curb development and transmission of ARGs in the environment.

Initial behaviors and removal of extracellular plasmid gene in membrane bioreactor

Extracellular antibiotic resistance genes (eARG) are considered to play an important role in spread of antimicrobial resistance (AMR) in wastewater treatment and water environment. Membrane bioreactor (MBR) reportedly has better removal of ARGs in wastewater than conventional activated sludge process. However, removal of eARG is possibly limited because eARG is small to pass through microfiltration (MF) membranes. To evaluate potential removal of eARG in MBR, this study aimed to understand the initial behaviors of eARG received in MBR. The recombinant plasmid with artificial marker gene was spiked in lab-scale MBR to trace fate of eARG in MBR. Among 10 ¹⁰ copies/L of the spiked gene, 2.6 × 10⁹ copies/L was adsorbed on sludge particles at 6 h after spiking, while only 2.2 × 10⁸-3.6 × 10⁸ copies/L of the spiked gene was remained but constant in sludge liquid phase from 6 until 48 h. This result suggests that adsorption on sludge particles served as the main mechanism to govern the initial fate of eARG in MBR. Meanwhile, the spiked gene concentrations in membrane permeate was lower than sludge liquid phase and decreased overtime, suggesting retention of eARG in membrane filtration. Total LRV of the spiked extracellular gene were 3.4 ± 0.8 log at 48 h after spiking. LRV by adsorption corresponded to 1.7 ± 0.7 log constantly since 3 h after spiking, while LRV by membrane filtration increased from 0 to 1.7 ± 0.6 log. Linear correlation of LRV by membrane filtration with transmembrane pressure (TMP) suggested that foulant deposition on membrane governs removal of eARG by membrane filtration in MBR.

Knowledge gaps in the assessment of antimicrobial resistance in surface waters

The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on (i) the risk assessment in surface waters, (ii) selective pressures contributing to its transfer and propagation and (iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.

Evaluation of the Antimicrobial Efficacy of N-Acetyl-l-Cysteine, Rhamnolipids, and Usnic Acid-Novel Approaches to Fight Food-Borne Pathogens

In the food industry, the increasing antimicrobial resistance of food-borne pathogens to conventional sanitizers poses the risk of food contamination and a decrease in product quality and safety. Therefore, we explored alternative antimicrobials N-Acetyl-l-cysteine (NAC), rhamnolipids (RLs), and usnic acid (UA) as a novel approach to prevent biofilm formation and reduce existing biofilms formed by important food-borne pathogens (three strains of Salmonella enterica and two strains of Escherichia coli, Listeria monocytogenes, Staphylococcus aureus). Their effectiveness was evaluated by determining minimum inhibitory concentrations needed for inhibition of bacterial growth, biofilm formation, metabolic activity, and biofilm reduction. Transmission electron microscopy and confocal scanning laser microscopy followed by image analysis were used to visualize and quantify the impact of tested substances on both planktonic and biofilm-associated cells. The in vitro cytotoxicity of the substances was determined as a half-maximal inhibitory concentration in five different cell lines. The results indicate relatively low cytotoxic effects of NAC in comparison to RLs and UA. In addition, NAC inhibited bacterial growth for all strains, while RLs showed overall lower inhibition and UA inhibited only the growth of Gram-positive bacteria. Even though tested substances did not remove the biofilms, NAC represents a promising tool in biofilm prevention.

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.

The Requirement of Genetic Diagnostic Technologies for Environmental Surveillance of Antimicrobial Resistance

Antimicrobial resistance (AMR) is threatening modern medicine. While the primary cost of AMR is paid in the healthcare domain, the agricultural and environmental domains are also reservoirs of resistant microorganisms and hence perpetual sources of AMR infections in humans. Consequently, the World Health Organisation and other international agencies are calling for surveillance of AMR in all three domains to guide intervention and risk reduction strategies. Technologies for detecting AMR that have been developed for healthcare settings are not immediately transferable to environmental and agricultural settings, and limited dialogue between the domains has hampered opportunities for cross-fertilisation to develop modified or new technologies. In this feature, we discuss the limitations of currently available AMR sensing technologies used in the clinic for sensing in other environments, and what is required to overcome these limitations.

Distribution of antibiotic resistance genes in the environment

The prevalence of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the microbiome is a major public health concern globally. Many habitats in the environment are under threat due to excessive use of antibiotics and evolutionary changes occurring in the resistome. ARB and ARGs from farms, cities and hospitals, wastewater treatment plants (WWTPs) or as water runoffs, may accumulate in water, soil, and air. We present a global picture of the resistome by examining ARG-related papers retrieved from PubMed and published in the last 30 years (1990-2020). Natural Language Processing (NLP) was used to retrieve 496,640 papers, out of which 9374 passed the filtering test and were further analyzed to determine the distribution and diversity of ARG subtypes. The papers revealed seven major antibiotic families together with their respective ARG subtypes in different habitats on six continents. Asia, especially China, had the highest number of ARGs related papers compared to other countries/regions/continents. ARGs belonging to multidrug, glycopeptide, and β-lactam families were the most common in reports from hospitals and sulfonamide and tetracycline families were common in reports from farms, WWTPs, water and soil. We also highlight the 'omics' tools used in resistome research, describe some factors that shape the development of resistome, and suggest future work needed to better understand the resistome. The goal was to show the global nature of ARB and ARGs in order to encourage collaborate research efforts aimed at reducing the negative impacts of antibiotic resistance on the One Health concept.

Impact of biochar-induced vertical mobilization of dissolved organic matter, sulfamethazine and antibiotic resistance genes variation in a soil-plant system

The migration risk of antibiotic and antibiotic resistance genes (ARGs) have attracted lots of attentions due to their potential threaten to public health. Strategies to reduce their vertical mobilization risk are urgently required for groundwater safety and human health. Biochar enjoys numerous interests due to its excellent sorption affinity. However, little was known about the efficacy of biochar amendment in impeding the vertical mobilization of antibiotic and ARGs. To fill this gap, a column study was carried out to investigate biochar-induced variations in the leaching behavior of dissolved organic matter (DOM), sulfamethazine (SMZ) and ARGs. Results showed that biochar addition enhanced DOM export from soil, changed its composition and impeded the vertical transport of SMZ. Biochar amendment could effectively decrease the occurrence of extracellular and intracellular sul2 in soil and impede its vertical transportation, however, it did not work out with sul1 gene. Structural equation modeling analysis demonstrated that the abundance of sul2 was significantly controlled by SMZ concentration, while the primary drivers of sul1 were SMZ concentration and DOM content. These results indicated the failure in inhibiting the vertical transfer of sul1 under biochar amendment and highlighted the important role of DOM in the leaching of soil ARGs.

Artificial sweeteners stimulate horizontal transfer of extracellular antibiotic resistance genes through natural transformation

Antimicrobial resistance has emerged as a global threat to human health. Natural transformation is an important pathway for horizontal gene transfer, which facilitates the dissemination of antibiotic resistance genes (ARGs) among bacteria. Although it is suspected that artificial sweeteners could exert antimicrobial effects, little is known whether artificial sweeteners would also affect horizontal transfer of ARGs via transformation. Here we demonstrate that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) promote transfer of ARGs via natural transformation in Acinetobacter baylyi ADP1, a model organism for studying competence and transformation. Such phenomenon was also found in a Gram-positive human pathogen Bacillus subtilis and mice faecal microbiome. We reveal that exposure to these sweeteners increases cell envelope permeability and results in an upregulation of genes encoding DNA uptake and translocation (Com) machinery. In addition, we find that artificial sweeteners induce an increase in plasmid persistence in transformants. We propose a mathematical model established to predict the long-term effects on transformation dynamics under exposure to these sweeteners. Collectively, our findings offer insights into natural transformation promoted by artificial sweeteners and highlight the need to evaluate these environmental contaminants for their antibiotic-like side effects.

Monitoring antibiotic resistance genes in wastewater treatment: Current strategies and future challenges

Antimicrobial resistance (AMR) is a growing threat to human and animal health. Progress in molecular biology has revealed new and significant challenges for AMR mitigation given the immense diversity of antibiotic resistance genes (ARGs), the complexity of ARG transfer, and the broad range of omnipresent factors contributing to AMR. Municipal, hospital and abattoir wastewater are collected and treated in wastewater treatment plants (WWTPs), where the presence of diverse selection pressures together with a highly concentrated consortium of pathogenic/commensal microbes create favourable conditions for the transfer of ARGs and proliferation of antibiotic resistant bacteria (ARB). The rapid emergence of antibiotic resistant pathogens of clinical and veterinary significance over the past 80 years has re-defined the role of WWTPs as a focal point in the fight against AMR. By reviewing the occurrence of ARGs in wastewater and sludge and the current technologies used to quantify ARGs and identify ARB, this paper provides a research roadmap to address existing challenges in AMR control via wastewater treatment. Wastewater treatment is a double-edged sword that can act as either a pathway for AMR spread or as a barrier to reduce the environmental release of anthropogenic AMR. State of the art ARB identification technologies, such as metagenomic sequencing and fluorescence-activated cell sorting, have enriched ARG/ARB databases, unveiled keystone species in AMR networks, and improved the resolution of AMR dissemination models. Data and information provided in this review highlight significant knowledge gaps. These include inconsistencies in ARG reporting units, lack of ARG/ARB monitoring surrogates, lack of a standardised protocol for determining ARG removal via wastewater treatments, and the inability to support appropriate risk assessment. This is due to a lack of standard monitoring targets and agreed threshold values, and paucity of information on the ARG-pathogen host relationship and risk management. These research gaps need to be addressed and research findings need to be transformed into practical guidance for WWTP operators to enable effective progress towards mitigating the evolution and spread of AMR.