Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements

Lessons and Considerations for the Creation of Universal Primers Targeting Non-Conserved, Horizontally Mobile Genes

Effective and accurate primer design is an increasingly important skill as the use of PCR-based diagnostics in clinical and environmental settings is on the rise. While universal primer sets have been successfully designed for highly conserved core genes such as 16S rRNA and characteristic genes such as dsrAB and dnaJ, primer sets for mobile, accessory genes such as multidrug resistance efflux pumps (MDREP) have not been explored. Here, we describe an approach to create universal primer sets for select MDREP genes chosen from five superfamilies (SMR, MFS, MATE, ABC and RND) identified in a model community of six members (Acetobacterium woodii, Bacillus subtilis, Desulfovibrio vulgaris, Geoalkalibacter subterraneus, Pseudomonas putida and Thauera aromatica). Using sequence alignments and in silico PCR analyses, a new approach for creating universal primers sets targeting mobile, non-conserved genes has been developed and compared to more traditional approaches used for highly conserved genes. A discussion of the potential shortfalls of the primer sets designed this way are described. The approach described here can be adapted to any unique gene set and aid in creating a wider, more robust library of primer sets to detect less conserved genes and improve the field of PCR-based screening research.IMPORTANCE Increasing use of molecular detection methods, specifically PCR and qPCR, requires utmost confidence in the results while minimizing false positives and negatives due to poor primer designs. Frequently, these detection methods are focused on conserved, core genes which limits their applications. These screening methods are being used in various industries for specific genetic targets or key organisms such as viral or infectious strains, or characteristic genes indicating the presence of key metabolic processes. The significance of this work is to improve primer design approaches to broaden the scope of detectable genes. The use of the techniques explored here will improve detection of non-conserved genes through unique primer design approaches. Additionally, the approaches here highlight additional, important information which can be gleaned during the in silico phase of primer design which will improve our gene annotations based on percent identities.

Insects, Rodents, and Pets as Reservoirs, Vectors, and Sentinels of Antimicrobial Resistance

This paper reviews the occurrence of antimicrobial resistance (AMR) in insects, rodents, and pets. Insects (e.g., houseflies, cockroaches), rodents (rats, mice), and pets (dogs, cats) act as reservoirs of AMR for first-line and last-resort antimicrobial agents. AMR proliferates in insects, rodents, and pets, and their skin and gut systems. Subsequently, insects, rodents, and pets act as vectors that disseminate AMR to humans via direct contact, human food contamination, and horizontal gene transfer. Thus, insects, rodents, and pets might act as sentinels or bioindicators of AMR. Human health risks are discussed, including those unique to low-income countries. Current evidence on human health risks is largely inferential and based on qualitative data, but comprehensive statistics based on quantitative microbial risk assessment (QMRA) are still lacking. Hence, tracing human health risks of AMR to insects, rodents, and pets, remains a challenge. To safeguard human health, mitigation measures are proposed, based on the one-health approach. Future research should include human health risk analysis using QMRA, and the application of in-silico techniques, genomics, network analysis, and ’big data’ analytical tools to understand the role of household insects, rodents, and pets in the persistence, circulation, and health risks of AMR.

Cadmium enhances conjugative plasmid transfer to a fresh water microbial community

Co-selection of antibiotic resistance genes (ARGs) by heavy metals might facilitate the spread of ARGs in the environments. Cadmium contamination is ubiquitous, while, it remains unknown the extent to which cadmium (Cd²⁺) impact plasmid-mediated transfer of ARGs in aquatic bacterial communities. In the present study, we found that Cd²⁺ amendment at sub-inhibitory concentration significantly increased conjugation frequency of RP4 plasmid from Pseudomonas putida KT2442 to a fresh water microbial community by liquid mating method. Cd²⁺ treatment (1-100 mg/L) significantly increased the cell membrane permeability and antioxidant activities of conjugation mixtures. Amendments of 10 and 100 mg/L Cd²⁺ significantly enhanced the mRNA expression levels of mating pair formation gene (trbBp) and the DNA transfer and replication gene (trfAp) due to the repression of regulatory genes (korA, korB and trbA). Phylogenetic analysis of transconjugants indicated that Proteobacteria was the dominant recipients and high concentration of Cd²⁺ treatment resulted in expanded recipient taxa. This study suggested that sub-inhibitory Cd²⁺ contamination would facilitate plasmid conjugation and contributed to the maintenance and spread of plasmid associated ARGs, and highlighted the urgent need for effective remediation of Cd²⁺ in aquatic environments.

Self-healing functionalization of sulfonated hafnium oxide and copper oxide nanocomposite for effective biocidal control of multidrug-resistant bacteria

The combination of copper and sulfonated hafnium oxide nanoparticles could be used as an alternative antimicrobial agent to combat multidrug resistant bacteria and membrane biofouling.

Intracellular versus extracellular antibiotic resistance genes in the environment: Prevalence, horizontal transfer, and mitigation strategies

Antibiotic resistance genes (ARGs) are present as both intracellular and extracellular fractions of DNA in the environment. Due to the poor yield of extracellular DNA in conventional extraction methods, previous studies have mainly focused on intracellular ARGs (iARGs). In this review, we evaluate the prevalence/persistence and horizontal transfer of iARGs and extracellular ARGs (eARGs) in different environments, and then explore advanced mitigation strategies in wastewater treatment plants (WWTPs) for preventing the spread of antibiotic resistance in the environment. Although iARGs are the main fraction of ARGs in nutrient-rich environments, eARGs are predominant in receiving aquatic environments. In such environments, natural transformation of eARGs occurs with a comparable frequency to conjugation of iARGs. Further, eARGs can be adsorbed by soil and sediments particles, protected from DNase degradation, and consequently persist longer than iARGs. Collectively, these characteristics emphasize the crucial role of eARGs in the spread of antibiotic resistance in the environment. Fate of iARGs and eARGs through advanced treatment technologies (disinfection and membrane filtration) indicates that different mitigation strategies may be required for each ARG fraction to be significantly removed. Finally, comprehensive risk assessment is needed to evaluate/compare the effect of iARGs versus eARGs in the environment.

Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies

Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.

Performance of Layer-by-Layer-Modified Multibore® Ultrafiltration Capillary Membranes for Salt Retention and Removal of Antibiotic Resistance Genes

Polyether sulfone Multibore^® ultrafiltration membranes were modified using polyelectrolyte multilayers via the layer-by-layer (LbL) technique in order to increase their rejection capabilities towards salts and antibiotic resistance genes. The modified capillary membranes were characterized to exhibit a molecular weight cut-off (at 90% rejection) of 384 Da. The zeta-potential at pH 7 was −40 mV. Laboratory tests using single-fiber modified membrane modules were performed to evaluate the removal of antibiotic resistance genes; the LbL-coated membranes were able to completely retain DNA fragments from 90 to 1500 nt in length. Furthermore, the pure water permeability and the retention of single inorganic salts, MgSO₄, CaCl₂ and NaCl, were measured using a mini-plant testing unit. The modified membranes had a retention of 80% toward MgSO₄ and CaCl₂ salts, and 23% in case of NaCl. The modified membranes were also found to be stable against mechanical backwashing (up to 80 LMH) and chemical regeneration (in acidic conditions and basic/oxidizing conditions).

Metagenomic and network analyses decipher profiles and co-occurrence patterns of antibiotic resistome and bacterial taxa in the reclaimed wastewater distribution system

Metagenomic and network analyses were applied to decipher the profiles and co-occurrence of resistome and microbial taxa in the reclaimed wastewater distribution system, including reclaimed wastewater and two types of biofilms, i.e., surface layer biofilms and inner layer biofilms. The effects of chlorination, UV irradiation and no disinfection treatment on ARG relative abundance and composition were systemically investigated. The reclaimed wastewater possesses more diverse and abundant ARGs than biofilms and total ARG relative abundance followed the order of reclaimed wastewater samples > surface layer biofilms > inner layer biofilms. Multidrug, bacitracin, sulfonamide, aminoglycoside, beta-lactam, and macrolide-lincosamide-streptogramin resistance genes were the six most dominant ARG types and their sum accounted for 90.1 %-96.0 % of the total ARG relative abundance in different samples. Beta-lactam resistance gene was the discriminative ARG type for reclaimed wastewater. Bacitracin resistance gene and bacA were the discriminative ARG type and subtype for biofilms. Chlorination significantly reduced ARG relative abundance in the reclaimed wastewater. Nevertheless, it could not reduce ARG relative abundance in biofilms. Regarding to the total ARG profiles, there were no obvious increasing or decreasing trends over time during one year period. Co-occurrence results revealed twenty-six genera were deduced as the potential hosts of twenty-two ARG subtypes.

Critical insight into the fate of antibiotic resistance genes during biological treatment of typical biowastes

Antibiotic resistance genes (ARGs) in biowaste, such as livestock manure and excess activated sludge, pose potential threat to human and ecological health when applied to agricultural fields. Biological treatment approaches, such as thermophilic composting/vermicomposting and anaerobic digestion, widely adopted to stabilize biowaste have demonstrated significant effects on the fate of ARGs. However, the influence of these biological treatments on ARGs is not known. This review summarizes the occurrence of ARGs in biowaste and the impact of thermophilic composting, vermicomposting, and anaerobic digestion on the fate of ARGs with discussion on factors, including substrate properties, pretreatments, additives, and operational parameters, associated with ARGs during biological treatment of biowaste. Finally, this review explores the research implications and proposes new avenues in the field of biological treatment of organic waste.

High-throughput characterization of the expressed antibiotic resistance genes in sewage sludge with transcriptional analysis

Antibiotic resistance genes (ARGs) are emerging micro-pollutants that pose potential threats to environments and humans. Sewage sludge from wastewater is an important source for ARGs and current studies mainly focus on their existence in microbial genomes. However, little is known about which ARGs are expressed even though ARGs expression remains a better proxy for functional activity. In this study, the expressed ARGs in sewage sludge were characterized by high-throughput quantitative PCR (296 primer sets) combined with transcriptional analysis. A total of 202 ARG transcripts were detected and their abundances ranged from 3.1 × 10⁹ to 1.2 × 10¹⁰ copies/g dry weight. The sum abundance of five most abundant ARG transcripts (qacEdelta1-02, sul2, qacEdelta1-01, aadA2-03, tetX) exhibited a linear correlation with the total abundance of ARG transcripts (R² = 0.88, p < 10^-4), suggesting that these genes could be regarded as indicators to quantitatively predict the total abundance of expressed ARGs. Dynamics of expressed ARGs were observed with lower abundances in summer and winter than those in other seasons (p < 0.05, Kruskal-Wallis test). Variation partitioning analysis indicated that the shift in bacterial community structures induced by changes in environmental attributes might be the main driver for the dynamics of expressed ARGs. Results of this study provided new insights into the ARGs in sewage sludge.

Study of the generation and diffusion of bioaerosol under two aeration conditions

Given that studies on actual sewage treatment plants are often affected by environmental conditions, it is challenging to clearly understand the associated bioaerosol generation and diffusion characteristics during the aeration process. Therefore, to enhance understanding in this regard, in this study, bioaerosol generator was used to simulate bioaerosol generation and diffusion under two aeration modes, i.e., bubble bottom aeration and brush surface aeration. The total concentration range of culturable bacteria in the bioaerosol produced by bubble bottom aeration and that produced by brush surface aeration were 300-3000 CFU/m³. Under bubble bottom aeration, the generated bioaerosol was symmetrically distributed around the source point, whereas under brush surface aeration, it was primarily distributed in the forward direction of the rotating brush surface. These bioaerosols from bubble bottom aeration predominantly consisted of particles with sizes below 3.3 μm, particularly those with sizes in the range 1.1-2.1 μm. On the contrary, the bioaerosols produced via brush surface aeration predominantly consisted of particles with sizes above 3.3 μm. The distribution characteristics of population structure in the two aeration modes were consistent with the distribution characteristics of concentration in the corresponding models. Additionally, the results showed that when the aeration process is unaffected by environmental conditions (particle matters, wind direct, wind speed, etc.), the bioaerosol components originate primarily from the parent sewage or sludge, and do not diffuse far from the source point. Therefore, source reduction (capping or sealing) can be recommended as the primary control strategy for bioaerosols in sewage treatment plants. The adoption of such measures will significantly limit the diffusion of bioaerosols, thereby reducing the potential risks associated with human exposure.

The role of mobile genetic elements in organic micropollutant degradation during biological wastewater treatment

Wastewater treatment plants (WWTPs) are crucial for producing clean effluents from polluting sources such as hospitals, industries, and municipalities. In recent decades, many new organic compounds have ended up in surface waters in concentrations that, while very low, cause (chronic) toxicity to countless organisms. These organic micropollutants (OMPs) are usually quite recalcitrant and not sufficiently removed during wastewater treatment. Microbial degradation plays a pivotal role in OMP conversion. Microorganisms can adapt their metabolism to the use of novel molecules via mutations and rearrangements of existing genes in new clusters. Many catabolic genes have been found adjacent to mobile genetic elements (MGEs), which provide a stable scaffold to host new catabolic pathways and spread these genes in the microbial community. These mobile systems could be engineered to enhance OMP degradation in WWTPs, and this review aims to summarize and better understand the role that MGEs might play in the degradation and wastewater treatment process. Available data about the presence of catabolic MGEs in WWTPs are reviewed, and current methods used to identify and measure MGEs in environmental samples are critically evaluated. Finally, examples of how these MGEs could be used to improve micropollutant degradation in WWTPs are outlined. In the near future, advances in the use of MGEs will hopefully enable us to apply selective augmentation strategies to improve OMP conversion in WWTPs.

Co-occurrence of multidrug resistance, β-lactamase and plasmid mediated AmpC genes in bacteria isolated from river Ganga, northern India

Wastewater effluents released in surface water provides suitable nutrient rich environment for the growth and proliferation of antibiotic resistant bacteria (ARB) and genes (ARG). Consequently, bacterial resistance has highly evolved over the recent years and diversified that each antibiotic class is inhibited by a distinct mechanism. In the present study, the prevalence of Multidrug resistant (MDR), extended spectrum β-lactamases (ESBL) and plasmid mediated Amp-C producing strains was analyzed in 28 surface water samples collected near domestic effluent discharge sites in river Ganga located across 11 different geographical indices of Uttar Pradesh, India. A total of 243 bacterial strains with different phenotypes were isolated. Among 243 isolates, 206 (84.77%) exhibited MDR trait displaying maximum resistance towards β-lactams (P = 78.19%; AMX = 72.84%), glycopeptides (VAN = 32.92%; TEI = 79.42%), cephalosporins (CF = 67.90%; CFX = 38.27%), and lincosamides (CD = 78.18%) followed by sulfonamide, macrolide and tetracycline. ESBL production was confirmed in 126 (51.85%) isolates that harbored the genes: blaTEM (95.24%), blaSHV (22.22%), blaOXA (11.90%) and blaCTX-M group (14.28%). The presence of plasmid mediated AmpC was detected only in 6.17% of isolates. The existence of such pathogenic strains in the open environment generates an urgent need for incorporating stringent measures to reduce the antibiotic consumption and hence its release.

Treatment Processes for Microbial Resistance Mitigation: The Technological Contribution to Tackle the Problem of Antibiotic Resistance

Advances generated in medicine, science, and technology have contributed to a better quality of life in recent years; however, antimicrobial resistance has also benefited from these advances, creating various environmental and health problems. Several determinants may explain the problem of antimicrobial resistance, such as wastewater treatment plants that represent a powerful agent for the promotion of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG), and are an important factor in mitigating the problem. This article focuses on reviewing current technologies for ARB and ARG removal treatments, which include disinfection, constructed wetlands, advanced oxidation processes (AOP), anaerobic, aerobic, or combined treatments, and nanomaterial-based treatments. Some of these technologies are highly intensive, such as AOP; however, other technologies require long treatment times or high doses of oxidizing agents. From this review, it can be concluded that treatment technologies must be significantly enhanced before the environmental and heath problems associated with antimicrobial resistance can be effectively solved. In either case, it is necessary to achieve total removal of bacteria and genes to avoid the possibility of regrowth given by the favorable environmental conditions at treatment plant facilities.

Localized effect of treated wastewater effluent on the resistome of an urban watershed

Background

Wastewater treatment is an essential tool for maintaining water quality in urban environments. While the treatment of wastewater can remove most bacterial cells, some will inevitably survive treatment to be released into natural environments. Previous studies have investigated antibiotic resistance within wastewater treatment plants, but few studies have explored how a river’s complete set of antibiotic resistance genes (the “resistome") is affected by the release of treated effluent into surface waters.

Results

Here we used high-throughput, deep metagenomic sequencing to investigate the effect of treated wastewater effluent on the resistome of an urban river and the downstream distribution of effluent-associated antibiotic resistance genes and mobile genetic elements. Treated effluent release was found to be associated with increased abundance and diversity of antibiotic resistance genes and mobile genetic elements. The impact of wastewater discharge on the river’s resistome diminished with increasing distance from effluent discharge points. The resistome at river locations that were not immediately downstream from any wastewater discharge points was dominated by a single integron carrying genes associated with resistance to sulfonamides and quaternary ammonium compounds.

Conclusions

Our study documents variations in the resistome of an urban watershed from headwaters to a major confluence in an urban center. Greater abundances and diversity of antibiotic resistance genes are associated with human fecal contamination in river surface water, but the fecal contamination effect seems to be localized, with little measurable effect in downstream waters. The diverse composition of antibiotic resistance genes throughout the watershed suggests the influence of multiple environmental and biological factors.

Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

A multitude of factors, such as drug misuse, lack of strong regulatory measures, improper sewage disposal, and low-quality medicine and medications, have been attributed to the emergence of drug resistant microbes. The emergence and outbreaks of multidrug resistance to last-line antibiotics has become quite common. This is further fueled by the slow rate of drug development and the lack of effective resistome surveillance systems. In this review, we provide insights into the recent advances made in computational approaches for the surveillance of antibiotic resistomes, as well as experimental formulation of combinatorial drugs. We explore the multiple roles of antibiotics in nature and the current status of combinatorial and adjuvant-based antibiotic treatments with nanoparticles, phytochemical, and other non-antibiotics based on synergetic effects. Furthermore, advancements in machine learning algorithms could also be applied to combat the spread of antibiotic resistance. Development of resistance to new antibiotics is quite rapid. Hence, we review the recent literature on discoveries of novel antibiotic resistant genes though shotgun and expression-based metagenomics. To decelerate the spread of antibiotic resistant genes, surveillance of the resistome is of utmost importance. Therefore, we discuss integrative applications of whole-genome sequencing and metagenomics together with machine learning models as a means for state-of-the-art surveillance of the antibiotic resistome. We further explore the interactions and negative effects between antibiotics and microbiomes upon drug administration.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.

The highly selective detecting of antibiotics and support of noble metal catalysts by a multifunctional Eu-MOF

Designing novel multifunctional rare-earth metal-organic frameworks (MOFs) has attracted intensive attention. In particular, employing such materials for sensing or catalytic reactions is still very challenging. Here, a new 3D porous Eu(iii)-MOF, [Eu(cppa)(OH)]·xS (denoted as CTGU-19, S = solvent molecule, CTGU = China Three Gorges University), was synthesized by using 5-(4-carboxyphenyl)picolinic acid (H2cppa) as an organic ligand, and it shows a 3D (3,12)-connected topological net with the point symbol (420·628·818)(43)4, constructed from cubane-shaped tetranuclear europium building units. Interestingly, CTGU-19 can be used as a highly sensitive luminescent sensor to identify ornidazole (ODZ) and nitrofurantoin (NFT) at different excitation wavelengths. This result represents the first example of a lanthanide-metal-organic-framework (Eu-MOF) that can be employed as a discriminating fluorescent probe to recognize ODZ and NFT at different excitation wavelengths. Furthermore, after loading CTGU-19 with Ag and/or Au nanoparticles, the composites exhibit efficient catalytic performance for reducing 2-/3-/4-nitrophenols (2-/3-/4-NP), in which the unit mass reduction rate constants of Ag0.8Au0.2@CTGU-19 for 2-NP, 3-NP, and 4-NP reach 68.8, 53.80, and 52.34 s-1 g-1, respectively.

Antibiotic Resistance in Recreational Waters: State of the Science

Ambient recreational waters can act as both recipients and natural reservoirs for antimicrobial resistant (AMR) bacteria and antimicrobial resistant genes (ARGs), where they may persist and replicate. Contact with AMR bacteria and ARGs potentially puts recreators at risk, which can thus decrease their ability to fight infections. A variety of point and nonpoint sources, including contaminated wastewater effluents, runoff from animal feeding operations, and sewer overflow events, can contribute to environmental loading of AMR bacteria and ARGs. The overall goal of this article is to provide the state of the science related to recreational exposure and AMR, which has been an area of increasing interest. Specific objectives of the review include (1) a description of potential sources of antibiotics, AMR bacteria, and ARGs in recreational waters, as documented in the available literature; (2) a discussion of what is known about human recreational exposures to AMR bacteria and ARGs, using findings from health studies and exposure assessments; and (3) identification of knowledge gaps and future research needs. To better understand the dynamics related to AMR and associated recreational water risks, future research should focus on source contribution, fate and transport-across treatment and in the environment; human health risk assessment; and standardized methods.

Measuring Environmental Exposure to Enteric Pathogens in Low-Income Settings: Review and Recommendations of an Interdisciplinary Working Group

Infections with enteric pathogens impose a heavy disease burden, especially among young children in low-income countries. Recent findings from randomized controlled trials of water, sanitation, and hygiene interventions have raised questions about current methods for assessing environmental exposure to enteric pathogens. Approaches for estimating sources and doses of exposure suffer from a number of shortcomings, including reliance on imperfect indicators of fecal contamination instead of actual pathogens and estimating exposure indirectly from imprecise measurements of pathogens in the environment and human interaction therewith. These shortcomings limit the potential for effective surveillance of exposures, identification of important sources and modes of transmission, and evaluation of the effectiveness of interventions. In this review, we summarize current and emerging approaches used to characterize enteric pathogen hazards in different environmental media as well as human interaction with those media (external measures of exposure), and review methods that measure human infection with enteric pathogens as a proxy for past exposure (internal measures of exposure). We draw from lessons learned in other areas of environmental health to highlight how external and internal measures of exposure can be used to more comprehensively assess exposure. We conclude by recommending strategies for advancing enteric pathogen exposure assessments.

Membrane Fouling Inversely Impacts Intracellular and Extracellular Antibiotic Resistance Gene Abundances in the Effluent of an Anaerobic Membrane Bioreactor

Anaerobic membrane bioreactors (AnMBRs) can significantly reduce the release of antibiotic resistance elements to the environment. The purpose of this study was to elucidate the role of membrane fouling layers (biofilms) in mitigating the release of intracellular and extracellular antibiotic resistance genes (iARGs and eARGs) from an AnMBR. The AnMBR was equipped with three membrane modules, each exhibiting a different level of fouling. Results showed that the absolute abundance of ARGs decreased gradually in the suspended biomass during operation of the AnMBR. Normalized abundances of targeted ARGs and intI1 were found to be significantly higher in the fouling layers compared to the suspended biomass, implying adsorption or an increased potential for horizontal gene transfer of ARGs in the biofilm. Effluent ARG data revealed that the highly fouled (HF) membrane significantly reduced the absolute abundance of eARGs. However, the HF membrane effluent concomitantly had the highest absolute abundance of iARGs. Nevertheless, total ARG abundance (sum of iARG and eARG) in the effluent of the AnMBR was not impacted by the extent of fouling. These results suggest a need for a combination of different treatment technologies to effectively prevent antibiotic resistance proliferation associated with these two ARG fractions.

Achieving simultaneous nitrogen and antibiotic removal in one-stage partial nitritation-Anammox (PN/A) process

Partial nitritation-Anammox (PN/A) process has been recognized as a sustainable process for biological nitrogen removal. Although various antibiotics have been ubiquitously detected in influent of wastewater treatment plants, little is known whether functional microorganisms in the PN/A process are capable of biodegrading antibiotics. This study aimed to investigate simultaneous nitrogen and antibiotic removal in a lab-scale one-stage PN/A system treating synthetic wastewater containing a widely-used antibiotic, sulfadiazine (SDZ). Results showed that maximum total nitrogen (TN) removal efficiency of 86.1% and SDZ removal efficiency of 95.1% could be achieved when treating 5 mg/L SDZ under DO conditions of 0.5-0.6 mg/L. Compared to anammox bacteria, ammonia-oxidizing bacteria (AOB) made a major contribution to SDZ degradation through their cometabolic pathway. A strong correlation between amoA gene and SDZ removal efficiency was found (p < 0.01). In addition, the degradation products of SDZ did not exhibit any inhibitory effects on Escherichia coli. The findings suggest that it is promising to apply the PN/A process to simultaneously remove antibiotics and nitrogen from contaminated wastewater.

Long-term responses of antibiotic resistance genes under high concentration of enrofloxacin, sulfadiazine and triclosan in aerobic granular sludge system

It is worth to reveal the long-term responses of antibiotic resistance genes (ARGs) in aerobic granular sludge (AGS) system exposed to high level enrofloxacin (ENR), sulfadiazine (SDZ) and triclosan (TCS). In present study, ppm level ENR, SDZ and TCS were added into three AGS reactors, respectively. ARGs in ENR and SDZ systems showed trends of increasing first and then decreasing, which were contrary to that in TCS system. 80%, 56% and 40% ARGs in ENR, SDZ and TCS systems, respectively, were enriched after loading, but several ARGs still kept high enrichment values after the withdrawn of loadings. The dominant bacteria in ENR (Flavobacterium), SDZ (Candidatus_Competibacter and Defluviicoccus) and TCS (Defluviicoccus) systems might contribute to the reductions of ARGs. IntI1 altered the overall ARGs profiles through horizontal gene transfer. The interactions of bacterial communities and environmental factors might be responsible for the different ARGs patterns in ENR, SDZ and TCS systems.

Antibiotic-contaminated wastewater irrigated vegetables pose resistance selection risks to the gut microbiome

Wastewater reuse in food crop irrigation has led to agroecosystem pollution concerns and human health risks. However, there is limited attention on the relationship of sub-lethal antibiotic levels in vegetables and resistance selection. Most risk assessment studies show non-significant toxicity, but overlook the link between antibiotics in crops and propagation of gut microbiome resistance selection. The review highlights the risk of antibiotics in treated water used for irrigation, uptake, and accumulation in edible vegetable parts. Moreover, it elucidates the risks to the adaptive resistance selection of the gut microbiome from sub-lethal antibiotic levels, as a result of dietary contaminated vegetables. Experiments have reported that bacterial resistance selection is possible at concentrations that are several hundred-folds lower than lethal effect levels on susceptible cells. Consequently, mutants selected at low antibiotic levels, such as those from vegetables, are fitter and more resistant compared to those selected at high concentrations. Necessary standardization, such as the development of minimum acceptable antibiotic limits allowable in food crop irrigation water, with a focus on minimum selection concentration, and not only toxicity, has been proposed. Wastewater irrigation offers environmental benefits and can contribute to food security, but it has non-addressed risks. Research gaps, future perspectives, and frameworks of mitigating the potential risks are discussed.

The environmental contribution to the dissemination of carbapenem and (fluoro)quinolone resistance genes by discharged and reused wastewater effluents: The role of cellular and extracellular DNA

Wastewater treatment plants (WWTPs) are major reservoirs and sources for the dissemination of antibiotic resistance into the environment. In this study, the population dynamics of two full-scale WWTPs was characterized along different sampling points, including the reused effluents, in both cellular and extracellular DNA samples. The analysis was performed by high throughput sequencing targeting the 16S rRNA V4 gene region and by three in-house TaqMan multiplex qPCR assays that detect and quantify the most clinically relevant and globally distributed carbapenem (bla) and (fluoro)quinolone (qnr) resistance genes. The obtained results identify the biological treatment as the crucial step on tailoring the wastewater bacterial community, which is thereafter maintained in both discharged and reused effluents. The influent bacterial community does not alter the WWTP core community, although it clearly contributes for the introduction and spread of antibiotic resistance to the in-house bacteria. The presence of high concentrations of bla and qnr genes was not only detected in the wastewater influents and discharged effluents, but also in the reused effluents, which therefore represent another gateway for antibiotic resistant bacteria and genes into the environment and directly to the human populations. Moreover, and together with the study of the cellular DNA, it was described for the first time the role of the extracellular DNA in the dissemination of carbapenem and (fluoro)quinolone resistance, as well as the impact of the wastewater treatment process on this DNA fraction. Altogether, the results prove that the current wastewater treatments are inefficient in the removal of antibiotic resistant bacteria and genes and reinforce that targeted treatments must be developed and implemented at full-scale in the WWTPs for wastewater reuse to become a safe and sustainable practice, able to be implemented in areas such as agricultural irrigation.

Occurrence of Fluoroquinolones and Sulfonamides Resistance Genes in Wastewater and Sludge at Different Stages of Wastewater Treatment: A Preliminary Case Study

This study identified differences in the prevalence of antibiotic resistance genes (ARGs) between wastewater treatment plants (WWTPs) processing different proportions of hospital and municipal wastewater as well as various types of industrial wastewater. The influence of treated effluents discharged from WWTPs on the receiving water bodies (rivers) was examined. Genomic DNA was isolated from environmental samples (river water, wastewater and sewage sludge). The presence of genes encoding resistance to sulfonamides (sul1, sul2) and fluoroquinolones (qepA, aac(6′)-Ib-cr) was determined by standard polymerase chain reaction (PCR). The effect of the sampling season (summer – June, fall – November) was analyzed. Treated wastewater and sewage sludge were significant reservoirs of antibiotic resistance and contained all of the examined ARGs. All wastewater samples contained sul1 and aac(6′)-lb-cr genes, while the qepA and sul2 genes occurred less frequently. These observations suggest that the prevalence of ARGs is determined by the type of processed wastewater. The Warmia and Mazury WWTP was characterized by higher levels of the sul2 gene, which could be attributed to the fact that this WWTP processes agricultural sewage containing animal waste. However, hospital wastewater appears to be the main source of the sul1 gene. The results of this study indicate that WWTPs are significant sources of ARGs, contributing to the spread of antibiotic resistance in rivers receiving processed wastewater.

Molecular profiling of multidrug-resistant river water isolates: insights into resistance mechanism and potential inhibitors

Polluted waters are an important reservoir for antibiotic resistance genes and multidrug-resistant bacteria. This report describes the microbial community, antibiotic resistance genes, and the genetic profile of extended spectrum β-lactamase strains isolated from rivers at, Pune, India. ESBL-producing bacteria isolated from diverse river water catchments running through Pune City were characterized for their antibiotic resistance. The microbial community and types of genes which confer antibiotic resistance were identified followed by the isolation of antibiotic-resistant bacteria on selective media and their genome analysis. Four representative isolates were sequenced using next generation sequencing for genomic analysis. They were identified as Pseudomonas aeruginosa, Escherichia coli, and two isolates were Enterobacter cloacae. The genes associated with the multidrug efflux pumps, such as tolC, macA, macB, adeL, and rosB, were detected in the isolates. As MacAB-TolC is an ABC type efflux pump responsible for conferring resistance in bacteria to several antibiotics, potential efflux pump inhibitors were identified by molecular docking. The homology model of their MacB protein with that from Escherichia coli K12 demonstrated structural changes in different motifs of MacB. Molecular docking of reported efflux pump inhibitors revealed the highest binding affinity of compound MC207-110 against MacB. It also details the potential efflux pump inhibitors that can serve as possible drug targets in drug development and discovery.

Sonophotocatalytic disinfection of Shigella species under visible light irradiation: Insights into its molecular mechanism, antibacterial resistance and biofilm formation

Microbial contamination of water is one of the major sources of many diseases worldwide. Evolution of antibacterial resistance (ABR) alongside the caveats in most of the water treatment methods causes the severity of the current problem extremely vexing. This calls for an urgent need to develop new treatment methods aiming to reduce the microbial as well as ABR load in the environment. Herein, we successfully developed a visible light assisted sonophotocatalysis (SPC) using Fe/ZnO nanoparticles (NPs) for the disinfection of Shigella dysenteriae. A consortia containing S. dysenteriae and S. flexineri was also completely disinfected using SPC. Growth conditions of S. dysenteriae like growth phases and growth temperaturehad different outcomes on the overall efficacy of SPC. Compared with catalysts such as ZnO and TiO₂, Fe/ZnO resulted in better disinfection. Multi-ROS production, mostly containing h⁺ and O₂· radicals, due to the electron displacement in the catalyst and acoustic cavitation was identified as the factors behind bacterial lethality. The ROS produced was found to interfere with the metabolic activities of S. dysenteriae by causing membrane perturbation. We identified DNA damage inside the cells and the subsequent release of intracellular components. The compositional changes in the fatty acid makeup of the cells were altered as a result of SPC and few fatty acid markers indicating the stress posed by SPC were also identified. Loss of ABR in S. dysenteriae was also recorded post SPC treatment. Abatement in the biofilm forming ability of the injured bacterial cells was also recorded, proving the extremity of stress induced by SPC. Hence, the excellent efficacy of SPC in disinfecting bacteria is proposed for tertiary water treatment applications.

Environmental resistome risks of wastewaters and aquatic environments deciphered by shotgun metagenomic assembly

In this paper, we deciphered the core resistome disseminating from hospital wastewater to the aquatic environment by characterising the resistome, plasmidome, mobilome and virulome using metagenomic analysis. This study also elucidated different environmental resistome risks using shotgun-metagenomic assembly. The results showed that clinically relevant taxa were found in assessed matrices (Salmonella spp., Acinetobacter spp, Escherichia-Shigella spp., Pseudomonas spp., Staphylococcus spp. and Vibrio spp.). For the plasmidome, we found 249 core plasmidome sequences that were shared among all assessed matrices. The core mobilome of 2424 mobile genetic elements shared among all assessed matrices was found. Regarding the virulome, we found 148 core virulence factors shared among all assessed samples, and the core virulome content was consistently shared across the most abundant bacterial genera. Although influent of wastewater showed considerable higher relative bacterial abundance (P = 0.008), hospital wastewater showed significant higher environmental resistome risk scores against all other assessed matrices, with an average of 46.34% (P = 0.001). These results suggest hospital wastewater, effluent and sewage sludge should be subjected to stringent mitigating measures to minimise such dissemination.

Identification of Selected Antibiotic Resistance Genes in Two Different Wastewater Treatment Plant Systems in Poland: A Preliminary Study

Antibiotic resistance is a growing problem worldwide. The emergence and rapid spread of antibiotic resistance determinants have led to an increasing concern about the potential environmental and public health endangering. Wastewater treatment plants (WWTPs) play an important role in this phenomenon since antibacterial drugs introduced into wastewater can exert a selection pressure on antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Therefore, WWTPs are perceived as the main sources of antibiotics, ARB and ARG spread in various environmental components. Furthermore, technological processes used in WWTPs and its exploitation conditions may influence the effectiveness of antibiotic resistance determinants’ elimination. The main aim of the present study was to compare the occurrence of selected tetracycline and sulfonamide resistance genes in raw influent and final effluent samples from two WWTPs different in terms of size and applied biological wastewater treatment processes (conventional activated sludge (AS)-based and combining a conventional AS-based method with constructed wetlands (CWs)). All 13 selected ARGs were detected in raw influent and final effluent samples from both WWTPs. Significant ARG enrichment, especially for tet(B, K, L, O) and sulIII genes, was observed in conventional WWTP. The obtained data did not show a clear trend in seasonal fluctuations in the abundance of selected resistance genes in wastewaters.

Fluoroquinolone Resistance and Virulence Properties Among Wastewater Aeromonas caviae Isolates

The study provides data on antibiotic resistance as well as the virulence characteristics of Aeromonas caviae isolated from raw and treated wastewater. The isolates were identified as A. caviae by 16S rRNA gene sequencing. In the analyzed strains, high frequency for the following genes was observed: aac(6')-Ib-cr, qnrB, and qnrD. The presence of qnrA and ogxB genes was not found in any strain. The higher frequency of the investigated genes was observed in strains from raw wastewater (RW). The strains of A. caviae showed multiple antibiotic resistance evaluated by the disk diffusion method. Multiple antibiotic resistance indices ranged from 0.36 to 0.69. Susceptibility to six heavy metals (Cd⁺², Zn⁺², Cu⁺², Co⁺², Mn⁺², and Ni⁺²) was recorded for all the isolates. The order of metal resistance of A. caviae was Co > Cu > Zn > Cd > Ni > Mn. All the strains of A. caviae showed β-hemolytic activity. Enzymes of amylase, cellulase, and lipase were produced by all isolates. Only the strains from RW had the ability to form biofilms and showed motility. The obtained results indicate that wastewater is a potential source and/or reservoir of virulent and multidrug-resistant A. caviae as "high-risk isolates."

Comparison of novel functionalized nanofiber forward osmosis membranes for application in antibacterial activity and TRGs rejection

Antibiotic resistance genes (ARGs) are serious pollutants in municipal sewage treatment plants and may cause significant harm to ecological systems, microbial fouling is also inevitable in membrane process. Herein, novel forward osmosis (FO) membranes made of electrospun nanofibers (TFN0) and further impregnated with titanium dioxide (TiO₂) (TFN1) nanoparticles and titanium dioxide/silver composite nanoparticles (TiO₂/AgNPs) (TFN2). The FO membranes were used to compare the antimicrobial performance and rejection of tetracycline-resistant genes (TRGs). Characterizations revealed that the TiO₂/AgNPs were evenly scattered in the polysulfone (PSf) nanofibers and resulted in a TFN2 membrane that exhibited excellent physicochemical properties, filtration, and antibiofouling performance in real wastewater. The cell viability analysis revealed that the antibacterial effect of the TFN2 membranes was significantly better than that of TFN1, as indicated by about 65 % of E. coli cells killed after contact with the TFN2 membrane. TFN2 membranes had greater rejection rates of TRB and TRGs than TFN1. The TRG permeation rates of the TFN2 membrane in the FO mode (active layer facing the feed solution) were 39.62 % and 33.02 % lower than the TFN0 and TFN1 membranes, respectively. FO membranes modified by the TiO₂/AgNPs nanocomposites hold promise to remove ARGs and pathogens from wastewater treatment plant effluents.

ARGDIT: a validation and integration toolkit for Antimicrobial Resistance Gene Databases

MOTIVATION

Antimicrobial resistance is currently one of the main challenges in public health due to the excessive use of antimicrobials in medical treatments and agriculture. The advancements in high-throughput next-generation sequencing and development of bioinformatics tools allow simultaneous detection and identification of antimicrobial resistance genes (ARGs) from clinical, food and environment samples, to monitor the prevalence and track the dissemination of these ARGs. Such analyses are however reliant on a comprehensive database of ARGs with accurate sequence content and annotation. Most of the current ARG databases are therefore manually curated, but this is a time-consuming process and the resulting curation errors could be hard to detect. Several secondary ARG databases consolidate contents from different source ARG databases, and hence modifications in the primary databases might not be propagated and updated promptly in the secondary ARG databases.

RESULTS

To address these problems, a validation and integration toolkit called ARGDIT was developed to validate ARG database fidelity, and merge multiple primary ARG databases into a single consolidated secondary ARG database with optional automated sequence re-annotation. Experimental results demonstrated the effectiveness of this toolkit in identifying errors such as sequence annotation typos in current ARG databases and generating an integrated non-redundant ARG database with structured annotation. A toolkit-oriented workflow is also proposed to minimize the efforts in validating, curating and merging multiple ARG protein or coding sequence databases. Database developers therefore benefit from faster update cycles and lower costs for database maintenance, while ARG pipeline users can easily evaluate the reference ARG database quality.

AVAILABILITY AND IMPLEMENTATION

ARGDIT is available at https://github.com/phglab/ARGDIT.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Accumulation of sulfonamide resistance genes and bacterial community function prediction in microbial fuel cell-constructed wetland treating pharmaceutical wastewater

Microbial fuel cell constructed wetlands (CW-MFCs) with different circuit operation conditions and hydraulic retention time (HRT) were constructed to evaluate their ability to remove and accumulate pharmaceutical and personal care products (PPCPs) (sulfadiazine (SDZ), carbamazepine (CBZ), naproxen (NPX) and ibuprofen (IBP)) during four months running process. The abundance level of corresponding sulfonamide antibiotic resistance genes (ARGs) was also investigated. The results showed that closed circuit operation of CW-MFC contributed to the decrease in mass loading of COD, NH₄⁺-N, PPCPs, and wastewater toxicity in the effluent. Additionally, closed circuit operation with low HRT contributed to enhancing selected PPCP mass accumulation on electrodes by electro-adsorption, and thus the higher sulfonamide ARG abundance was detected in the electrodes and effluent. Moreover, the composition of bacteria was greatly influenced by the mass accumulation of PPCPs revealed by redundancy analysis results. Procrustes analysis results further demonstrated that bacterial community contributed greatly to the ARGs profiles. Therefore, ARGs with their host bacteria revealed by network analysis were partially deposited on electrode substrates, and thus ARGs were effectively accumulated on electrodes. Function analysis of the bacterial community from PICRUSt predicted metagenomes revealed that closed circuit mode enhanced the abundances of the function genes of metabolic and the multiple ARGs, suggesting that closed circuit operation exhibited positive effects on metabolic process and ARG accumulation in CW-MFC system.

Characteristics of and variation in airborne ARGs among urban hospitals and adjacent urban and suburban communities: A metagenomic approach

Environmental antibiotic resistance genes (ARGs) have received much attention, while the characteristics of ARGs carried by particulate matter (PM) as a function of urban functional region are almost unknown. In this study, ARGs carried by PM_2.5 and PM₁₀ in an urban hospital, a nearby urban community and the nearest suburban community were detected using metagenomics. In total, 643 ARG subtypes belonging to 22 different ARG types were identified. The chloramphenicol exporter gene, sul1, bacA, and lnuA were the most abundant ARG subtypes in all air samples. The hospital exhibited higher ARG abundance and richness than the nearby communities. ARG profiles depended on functional region: hospital and suburban samples clustered separately, and samples from the nearby urban community interspersed among them. The representation of multidrug and quinolone resistance genes decayed with distance from the hospital to the urban community to the suburban community, indicating that hospital PM may be a hotspot for ARGs encoding proteins conferring multidrug and quinolone resistance. Airborne ARGs carried by PM in the hospital environment were more closely associated with clinically important pathogens than were those in nearby communities. In particular, carbapenemase genes, including bla_NDM,bla_KPC,bla_IMP,bla_VIM,and bla_OXA-48, were discovered in hospital PM. In the suburban community, crAssphage, a human host-specific bacteriophage, was applied to predict ARG abundance and found to be enriched due to anthropogenic pollution but showed no clear evidence for ARG selection. In the hospital and the nearby urban community, the drivers of ARGs were complex. Our results highlighted that PM ARGs were closely related to human activities and revealed a potential hotspot, which could provide new evidence for further research and consequently mitigate the formation of airborne ARGs and transfer risks.

Isolation, nucleotide sequencing and genomic comparison of a Novel SXT/R391 ICE mobile genetic element isolated from a municipal wastewater environment

Integrative Conjugative Elements (ICE’s) of the SXT/R391 family have largely been detected in clinical or environmental isolates of Gammaproteobacteria, particularly Vibrio and Proteus species. As wastewater treatment plants accumulate a large and diverse number of such species, we examined raw water samples taken from a municipal wastewater treatment plant initially using SXT/R391 family integrase gene-specific PCR probes to detect the presence of such elements in a directed approach. A positive amplification occurred over a full year period and a subsequent Restriction Fragment Length Polymorphism (RFLP) analysis revealed a very limited diversity in the treatment plant examined. Samples demonstrating positive amplification were cultured using Vibrio and Proteus selective media and PCR amplification tracking was utilized to monitor SXT/R391-ICE family containing strains. This screening procedure resulted in the isolation and identification of a Proteus mirabilis strain harbouring an ICE. Whole-genome sequencing of this ICE containing strain using Illumina sequencing technology revealed a novel 81 kb element that contained 75 open reading frames on annotation but contained no antibiotic or metal resistance determinants. Comparative genomics revealed the element contained a conserved ICE core with one of the insertions containing a novel bacteriophage defence mechanism. This directed isolation suggests that ICE elements are present in the environment without apparent selective pressure but may contain adaptive functions allowing survival in particular environments such as municipal wastewater which are reservoirs for large bacterial phage populations.

Metagenomic Profiles of Antibiotic Resistance Genes in Activated Sludge, Dewatered Sludge and Bioaerosols

Wastewater treatment plants (WWTPs) have been considered hotspots for the development and dissemination of antibiotic resistance in the environment. Although researchers have reported a significant increase in bioaerosols in WWTPs, the associated bacterial taxa, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) remain relatively unknown. In this study, we have investigated the abundance and occurrences of ARGs and MGEs, as well as the bacterial community compositions in activated sludge (AS), dewatered sludge (DS) and bioaerosols (BA) in a WWTP. In total, 153 ARG subtypes belonging to 19 ARG types were identified by the broad scanning of metagenomic profiles obtained using Illumina HiSeq. The results indicated that the total occurrences and abundances of ARGs in AS and DS samples were significantly higher than those in BA samples (p < 0.05). However, some specific ARG types related to sulfonamide, tetracycline, macrolide resistance were present in relatively high abundance in BA samples. Similar to many other full-scale WWTPs, the Proteobacteria (58%) and Bacteroidetes (18%) phyla were dominant in the AS and DS samples, while the Firmicutes (25%) and Actinobacteria (20%) phyla were the most dominant in the BA samples. Although the abundance of genes related to plasmids and integrons in bioaerosols were two to five times less than those in AS and DS samples, different types of MGEs were observed in BA samples. These results suggest that comprehensive analyses of resistomes in BA are required to better understand the emergence of both ARGs and MGEs in the wastewater treatment process due to the significant increase of scientific attention toward bioaerosols effects.

Metagenomic analysis of an urban resistome before and after wastewater treatment

Determining the effect of wastewater treatment in water resistome is a topic of interest for water quality, mainly under re-use and One-Health perspectives. The resistome, the plasmidome, and the bacterial community composition of samples from influents and treated effluents from a wastewater treatment plant located in Northern Portugal were studied using metagenomic techniques. Wastewater treatment contributed to reduce the abundance of resistance genes and of plasmid replicons, coinciding with a decline in the number of intrinsic resistance genes from Enterobacteriaceae, as well as with a reduction in the relative abundance of Firmicutes and Proteobacteria after treatment. These taxons comprise bacterial pathogens, including those belonging to the ESKAPE group, which encompasses bacteria with the highest risk of acquiring antibiotic resistance, being the most relevant hosts of resistance genes acquired through horizontal gene transfer. Our results support that wastewater treatment efficiently removes the hosts of antibiotic resistance genes and, consequently, the harboured antibiotic resistance genes. Principal component analysis indicates that the resistome and the bacterial composition clustered together in influent samples, while did not cluster in final effluent samples. Our results suggest that wastewater treatment mitigates the environmental dissemination of urban resistome, through the removal of the hosts harbouring mobile resistance genes.

Potential risks of antibiotic resistant bacteria and genes in bioremediation of petroleum hydrocarbon contaminated soils

Bioremediation represents a sustainable approach to remediating petroleum hydrocarbon contaminated soils. One aspect of sustainability includes the sourcing of nutrients used to stimulate hydrocarbon-degrading microbial populations. Organic nutrients such as animal manure and sewage sludge may be perceived as more sustainable than conventional inorganic fertilizers. However, organic nutrients often contain antibiotic residues and resistant bacteria (along with resistance genes and mobile genetic elements). This is further exacerbated since antibiotic resistant bacteria may become more abundant in contaminated soils due to co-selection pressures from pollutants such as metals and hydrocarbons. We review the issues surrounding bioremediation of petroleum-hydrocarbon contaminated soils, as an example, and consider the potential human-health risks from antibiotic resistant bacteria. While awareness is coming to light, the relationship between contaminated land and antibiotic resistance remains largely under-explored. The risk of horizontal gene transfer between soil microorganisms, commensal bacteria and/or human pathogens needs to be further elucidated, and the environmental triggers for gene transfer need to be better understood. Findings of antibiotic resistance from animal manures are emerging, but even fewer bioremediation studies using sewage sludge have made any reference to antibiotic resistance. Resistance mechanisms, including those to antibiotics, have been considered by some authors to be a positive trait associated with resilience in strains intended for bioremediation. Nevertheless, recognition of the potential risks associated with antibiotic resistant bacteria and genes in contaminated soils appears to be increasing and requires further investigation. Careful selection of bacterial candidates for bioremediation possessing minimal antibiotic resistance as well as pre-treatment of organic wastes to reduce selective pressures (e.g., antibiotic residues) are suggested to prevent environmental contamination with antibiotic-resistant bacteria and genes.

Characterization of antibiotic resistance genes and bacterial community in selected municipal and industrial sewage treatment plants beside Poyang Lake

Sewage treatment plants (STPs) are significant reservoirs of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Municipal STPs (MSTPs) and industrial STPs (ISTPs) are the two most important STP types in cities. In this study, the ARGs, mobile genetic elements (MGEs), and bacterial communities of selected STPs, including two MSTPs and one ISTP, in the vicinity of Poyang Lake were comprehensively investigated through high-throughput qPCR and high-throughput Illumina sequencing. The results showed that the profiles of ARGs, MGEs and bacteria differed between the ISTP and the two MSTPs, most likely due to differences in influent water quality, such as the Pb that characterized in the ISTP's influent. The longer hydraulic retention times (HRTs) of the two MSTPs than of the ISTP may also have accounted for the different profiles. Thus, a prolonged HRT in the CASS process seems to allow a more extensive removal of ARGs and bacteria in ISTPs with similar treatment process. By providing comprehensive insights into the characteristics of ARGs, MGEs and the bacterial communities of the selected MSTPs and ISTP, our study provides a scientific basis for controlling the propagation and diffusion of ARGs and ARB in different types of STPs.

Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes

Antibiotic or antimicrobial resistance (AR) facilitated by the vertical and/or horizontal transfer of antibiotic resistance genes (ARGs), is a serious global health challenge. While traditionally associated with pathogens in clinical environments, it is becoming increasingly clear that non-clinical environments may also be reservoirs of ARGs. The recent improvements in rapid and affordable next generation sequencing technologies along with sophisticated bioinformatics platforms has the potential to revolutionize diagnostic microbiology and microbial surveillance. Through the study and characterization of ARGs in bacterial genomes and complex metagenomes, we are now able to reveal the genetic scope of AR in single bacteria and complex communities, and obtain important insights into AR dynamics at species, population and community levels, providing novel epidemiological and ecological perspectives. A suite of bioinformatics pipelines and ARG databases are currently available for genomic and metagenomic data analyses. However, different platforms may significantly vary and therefore, it is crucial to choose the tools that are most suitable for the specific analysis being conducted. This review provides a detailed account of available bioinformatics platforms for identification and characterization of ARGs and associated genetic elements within single bacterial isolates and complex environmental samples. It focuses primarily on currently available ARG databases, employing a comprehensive benchmarking pipeline to identify ARGs in four bacterial genomes (Aeromonas salmonicida, Bacillus cereus, Burkholderia sp. and Escherichia coli) and three shotgun metagenomes (human gut, poultry litter and soil) providing insight into which databases should be used for different analytical scenarios.

Unravelling kinetic and microbial responses of enriched nitrifying sludge under long-term exposure of cephalexin and sulfadiazine

Wastewater treatment plants (WWTPs) have been identified as one of the reservoirs of antibiotics. Although nitrifying bacteria have been reported to be capable of degrading various antibiotics, there are very few studies investigating long-term effects of antibiotics on kinetic and microbial responses of nitrifying bacteria. In this study, cephalexin (CFX) and sulfadiazine (SDZ) were selected to assess chronic impacts on nitrifying sludge with stepwise increasing concentrations in two independent bioreactors. The results showed that CFX and SDZ at an initial concentration of 100 μg/L could be efficiently removed by enriched nitrifying sludge, as evidenced by removal efficiencies of more than 88% and 85%, respectively. Ammonia-oxidizing bacteria (AOB) made a major contribution to the biodegradation of CFX and SDZ via cometabolism, compared to limited contributions from heterotrophic bacteria and nitrite-oxidizing bacteria. Chronic exposure to CFX (≥30 μg/L) could stimulate ammonium oxidation activity in terms of a significant enhancement of ammonium oxidation rate (p < 0.01). In contrast, the ammonium oxidation activity was inhibited due to exposure to 30 μg/L SDZ (p < 0.01), then it recovered after long-term adaption under exposure to 50 and 100 μg/L SDZ. In addition, 16S rRNA gene amplicon sequencing revealed that the relative abundance of AOB decreased distinctly from 23.8% to 28.8% in the control phase (without CFX or SDZ) to 14.2% and 10.8% under exposure to 100 μg/L CFX and SDZ, respectively. However, the expression level of amoA gene was up-regulated to overcome this adverse impact and maintain a stable and efficient removal of both ammonium and antibiotics. The findings in this study shed a light on chronic effects of antibiotic exposure on kinetic and microbial responses of enriched nitrifying sludge in WWTPs.

Emergence and spread patterns of antibiotic resistance genes during two different aerobic granular sludge cultivation processes

The prevalence and accumulation of antibiotic resistance genes (ARGs) were frequently detected in biological wastewater treatment processes, which might cause potential health crisis to human. In present study, the fates of ARGs during two different aerobic granular sludge (AGS) cultivation processes were investigated. The results showed that traditional AGS (T-AGS) cultivation process and enhanced AGS (E-AGS) cultivation process had significant differences (P < 0.005) in ARGs shift patterns. E-AGS process had higher average relative abundance (0.280 ± 0.079) of ARGs than T-AGS process (0.130 ± 0.041), while the intensity of ARGs enrichment during E-AGS (1.52-5.29 fold) was lower than T-AGS (3.79-75.31 fold) process. TnpA and intI1 as two different types of mobile genetic elements (MGEs) carrying ARGs, were observed to contribute significantly to the horizontal gene transfer (HGT) during T-AGS (r = 0.902, P < 0.050) and E-AGS (r = 0.823, P < 0.001) processes, respectively. Higher HGT level took place and more possible potential hosts (25 hosts) harboring ARGs were detected during E-AGS process comparing with T-AGS process (17 hosts). Meanwhile, over large AGS might increase the propagation of several antibiotic deactivation ARGs, so it was not advised. Overall, whether during T-AGS or during E-AGS process which was applied in a pilot-scale sequencing batch reactor treating municipal wastewater, the accumulation and spread of ARGs were inevitable. It should be valued that some suitable pre-treatments of seed sludge should be executed, meanwhile, advanced treatment for removing of ARGs in AGS should be conducted to maintain the relative abundances of ARGs at relatively low level.

Mobile genetic elements in potential host microorganisms are the key hindrance for the removal of antibiotic resistance genes in industrial-scale composting with municipal solid waste

During the municipal solid waste (MSW) composting, antibiotic resistance genes (ARGs) could be one of the concerns to hinder the application of MSW composting. However, the understanding of enrichment and dissemination of ARGs during the industrial-scale composting is still not clear. Hence, this study aimed to investigate the ARG distributions at different stages in an industrial-scale MSW composting plant. Seven target ARGs and four target mobile genetic elements (MGEs) and bacterial communities were investigated. The abundances of ARGs and MGEs increased during two aerobic thermophilic stages, but they decreased in most ARGs and MGEs after composting. Network analysis showed that potential host bacteria of ARGs were mainly Firmicutes and Actinobacteria. The reduction of potential host bacteria was important to remove ARGs. MGEs were an important factor hindering ARG removal. Water-extractable S and pH were two main physicochemical factors in the changes of microbial community and the abundance of ARGs.

Characterization and source identification of antibiotic resistance genes in the sediments of an interconnected river-lake system

Antimicrobial resistance has been a global public health concern. The river-lake systems are one of the tightly connected terrestrial ecosystems and, appear to be reservoirs of antibiotic resistant genes (ARGs) and dispersal routes of resistant pathogens because they are easily impacted by human activities. Currently, systematic knowledge on the prevalence, transfer risk and source of ARGs in river-lake systems is largely lacking. In this study, we focused on the high-throughput profiling and source-sink relationship disentangling of ARGs in the sediments of an interconnected river-lake system (Fuhe River and its receiving Lake Baiyang in northern China). To this end, 40 surface sediments were collected for metagenomic shotgun sequencing. The profile and co-occurrence of ARGs in the sediments of the river-lake system were comprehensively characterized, as well as the mobile genetic elements (MGEs) carrying ARGs and their potential resistome dissemination risk. CrAssphage, a recently-discovered bacteriophage, was used to track human fecal pollution on the prevalence of ARGs. Meanwhile, a novel fast expectation-maximization microbial source tracking (FEAST) method was combined with linear discriminant analysis effect size method (LEfSe) for quantitatively apportioning the contribution of river sediment to the presence of ARGs in the receiving lake. Results showed abundant and diverse ARGs (24 types consisting of 510 subtypes) were detected in the sediments of the river-lake system, including some emerging ARGs such as mcr-1, tetX and carbapenemases types. Network analysis suggested non-random co-occurrence patterns of ARGs within the same type and among different types. Importantly, a number of MGE-carrying contigs were identified with jointly containing one or more ARGs, resulting in higher resistome risk potential in Lake Baiyang than many worldwide lakes. Source tracking indicated the prevalence of ARGs in the sediments of the river-lake system might be largely explained by the extent of human fecal contamination, and apportionment estimates the load transport from Fuhe River contributed more than 80% of ARGs to the receiving Lake Baiyang.

Prevalence and distribution analysis of antibiotic resistance genes in a large-scale aquaculture environment

This study examined the profiles of antibiotic resistance genes (ARGs) in water and sediments from one large-scale freshwater pond farming system. A qPCR array was used to quantify ARGs (16S, Tetx, Tetw, TetG, Intll, and Sull) and microbial community structure was analyzed by 16S rRNA gene sequencing. A large number of ARGs (2 8 8) were detected. The ARG richness of the sediments was significantly higher than that of water and an average of 15 more genes were detected (p < 0.01). Sediment samples showed significantly higher taxonomic diversity and higher abundance of Gammaproteobacteria, Betaproteobacteria, and Flavobacteria. A significant correlation was observed between antibiotic resistance genes and breeding periods. The taxonomic diversity of the samples in ponds was significantly higher than that in ditch samples (p < 0.05), suggesting that pond farming systems could act as a local reservoir to spread ARGs into aquatic environments of rural communities.

Mitigation of antibiotic resistance in a pilot-scale system treating wastewater from high-speed railway trains

Wastewater from high-speed railway trains represents a mobile reservoir of microorganisms with antibiotic resistance. It harbors abundant and diverse antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). This study investigated the removal of ARB and ARGs in a pilot-scale reactor, which consisted of an anaerobic/anoxic/oxic process, anaerobic/anoxic/aerobic process, and ozone-based disinfection to treat 1 m³/day wastewater from an electric multiple unit high-speed train. Further, the high prevalence of two mobile genetic elements (intI1 and Tn916/615) and five ARGs (tetA, tetG, qnrA, qnrS, bla_NDM-1, and ermF) was investigated using quantitative PCR. Significant positive correlations between ARGs (tetA, bla_NDM-1, and qnrA) and intI1 were identified (R² of 0.94, 0.85, and 0.70, respectively, P < 0.01). Biological treatment could significantly reduce Tn916/1545 (2.57 logs reduction) and Enterococci (2.56 logs reduction of colony forming unit (CFU)/mL), but the qnrS abundance increased (1.19 logs increase). Ozonation disinfection could further significantly decrease ARGs and Enterococci in wastewater, with a reduction of 1.67-2.49 logs and 3.16 logs CFU/mL, respectively. Moreover, food-related bacteria families which may contain opportunistic or parasitic pathogens (e.g., Moraxellaceae, Carnobacteriaceae, and Ruminococcaceae) were detected frequently. Enterococci filtered in this study shows multi-antibiotic resistance. Our study highlights the significance to mitigate antibiotic resistance from wastewater generated from high-speed railway trains, as a mobile source.