Purification of aquaculture wastewater by macrophytes and biofilm systems: Efficient removal of trace antibiotics and enrichment of antibiotic resistance genes

The purification performance of aquaculture wastewater and the risk of antibiotic resistance genes (ARGs) dissemination in wetlands dominated by macrophytes remain unclear. Here, the purification effects of different macrophytes and biofilm systems on real aquaculture wastewater were investigated, as well as the distribution and abundance of ARGs. Compared to the submerged macrophytes, artificial macrophytes exhibited higher removal rates of TOC (58.80 ± 5.04 %), TN (74.50 ± 2.50 %), and TP (77.33 ± 11.66 %), and achieved approximately 79.92 % removal of accumulated trace antibiotics in the surrounding water. Additionally, the biofilm microbial communities on the surface of artificial macrophytes exhibited higher microbial diversity with fewer antibiotic-resistant bacteria (ARB) enrichment from the surrounding water. The absolute abundance of ARGs (sul1, sul2, and intI1) in the mature biofilm to be one to two orders of magnitude higher than that in the water. Although biofilms could decrease ARGs in the surrounding water by enriching ARB, the intricate network structure of biofilms further facilitated the proliferation of ARB and the dissemination of ARGs in water. Network analysis suggested that Proteobacteria and Firmicutes phyla were dominant and potential carriers of ARGs, contributing 69.00 % and 16.70 %, respectively. Our findings highlight that macrophytes and biofilm systems have great performance on aquaculture wastewater purification, but with high risk of ARGs.

Insights into the global freshwater virome

Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.

Chicken liver is a potential reservoir of bacteriophages and phage-derived particles containing antibiotic resistance genes

Poultry meat production is one of the most important agri‐food industries in the world. The selective pressure exerted by widespread prophylactic or therapeutic use of antibiotics in intensive chicken farming favours the development of drug resistance in bacterial populations. Chicken liver, closely connected with the intestinal tract, has been directly involved in food‐borne infections and found to be contaminated with pathogenic bacteria, including Campylobacter and Salmonella. In this study, 74 chicken livers, divided into sterile and non‐sterile groups, were analysed, not only for microbial indicators but also for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Both bacteria and phages were detected in liver tissues, including those dissected under sterile conditions. The phages were able to infect Escherichia coli and showed a Siphovirus morphology. The chicken livers contained from 10³ to 10⁶ phage particles per g, which carried a range of ARGs (bla_TEM, bla_CTx‐M‐1, sul1, qnrA, armA and tetW) detected by qPCR. The presence of phages in chicken liver, mostly infecting E. coli, was confirmed by metagenomic analysis, although this technique was not sufficiently sensitive to identify ARGs. In addition, ARG‐carrying phages were detected in chicken faeces by qPCR in a previous study of the group. Comparison of the viromes of faeces and liver showed a strong coincidence of species, which suggests that the phages found in the liver originate in faeces. These findings suggests that phages, like bacteria, can translocate from the gut to the liver, which may therefore constitute a potential reservoir of antibiotic resistance genes.

Antibiotic resistance in the viral fraction of dairy products and a nut-based milk

Phages, the most abundant biological entities in the biosphere, can carry different bacterial genes, including those conferring antibiotic resistance. In this study, dairy products were analyzed by qPCR for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Eleven ARGs were identified in 50 samples of kefir, yogurt, milk, fresh cheese and nut-based milk (horchata), purchased from local retailers in Barcelona. Propagation experiments showed that at least some of the phages isolated from these samples infected Escherichia coli WG5, which was selected as the host strain because it does not contain prophages or ARGs in its genome. Electron microscopy revealed that the phage particles showed morphologies compatible with the Myoviridae and Siphoviridae families. Our results show that dairy products contain ARGs within infectious phage particles and may therefore serve as a reservoir of ARGs that can be mobilized to susceptible hosts, both in the food matrix and in the intestinal tract after ingestion.

Unveiling the occurrence, hosts and mobility potential of antibiotic resistance genes in the deep ocean

As emerging microbial contaminants, antibiotic resistance genes (ARGs) are widely reported in the neritic zone. However, the profiles of ARGs in the deep ocean have not yet been fully resolved. In this study, the distribution, hosts, and mobility potential of ARGs at different water depths in the Western Pacific (WP) were investigated and compared to those in Bohai Sea (BH) waters using environmental parameter measurements, amplicon sequencing, metagenomic assembly and binning approaches. Our results showed that the top eight most abundant known ARG types in WP and BH waters were multidrug (39.85%), peptide (14.98%), aminoglycoside (11.33%), macrolide-lincosamide-streptogramin (MLS, 4.06%), tetracycline (3.74%), beta-lactam (3.12%), fluoroquinolone (1.79%) and rifamycin (1.24%). The ARGs observed in mesopelagic and bathypelagic waters were abundant and diverse as those observed in neritic waters, indicating that deep-sea water could be another environmental reservoir for ARGs. For deep-sea ARGs, members from classes Gammaproteobacteria (70%) and Alphaproteobacteria (21.1%) were the most important potential hosts. In addition, mobile genetic element analysis suggested that the ARG migration potential in dee sea water (> 1000 m) was relatively high. Overall, our findings expanded the understanding of ARGs in deep seawater and provided guidance for ARG pollution control and risk prediction.

Bacteriophage therapy in aquaculture: current status and future challenges

The escalation of antibiotic resistance has revitalized bacteriophage (phage) therapy. Recently, phage therapy has been gradually applied in medicine, agriculture, food, and environmental fields due to its distinctive features of high efficiency, specificity, and environmental friendliness compared to antibiotics. Likewise, phage therapy also holds great promise in controlling pathogenic bacteria in aquaculture. The application of phage therapy instead of antibiotics to eliminate pathogenic bacteria such as Vibrio, Pseudomonas, Aeromonas, and Flavobacterium and to reduce fish mortality in aquaculture has been frequently reported. In this context, the present review summarizes and analyzes the current status of phage therapy in aquaculture, focusing on the key parameters of phage application, such as phage isolation, selection, dosage, and administration modes, and introducing the strategies and methods to boost efficacy and restrain the emergence of resistance. In addition, we discussed the human safety, environmental friendliness, and techno-economic practicability of phage therapy in aquaculture. Finally, this review outlines the current challenges of phage therapy application in aquaculture from the perspectives of phage resistance, phage-mediated resistance gene transfer, and effects on the host immune system.

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.

Viral Community and Virus-Associated Antibiotic Resistance Genes in Soils Amended with Organic Fertilizers

Antibiotic resistance is a global health concern. Long-term organic fertilization can influence the antibiotic resistome of agricultural soils, posing potential risks to human health. However, little is known about the contribution of viruses to the dissemination of antibiotic resistance genes (ARGs) in this context. Here, we profiled the viral communities and virus-associated ARGs in a long-term (over 10 years) organic fertilized field by viral metagenomic analysis. A total of 61,520 viral populations (viral operational taxonomic units, vOTUs) were retrieved, of which 21,308 were assigned at the family level. The viral community structures were significantly correlated with the bacterial community structures (P < 0.001) and the dosage of applied sewage sludge (r² = 0.782). A total of 16 unique ARGs were detected in soil viromes, and the number of virus-associated ARG subtypes was higher in sewage sludge treatments (except for 1 SS) than others. The network analysis showed that the application of the organic fertilizer increased the bacteria-virus interactions, suggesting that the chances of ARG exchange between viruses and their hosts may increase. Overall, our results provide a novel understanding about virus-associated ARGs and factors affecting the profile of viral community in fertilized soil.

Virome studies of food production systems: time for 'farm to fork' analyses

The food industry is under increasing pressure to produce high quality, traceable and minimally processed foods that are produced using sustainable approaches and ingredients. In line with the latter, there is an increased pressure for plant-based products to replace animal-derived products. Until recently, research efforts have mainly focused on dairy and meat products owing to their economic importance. The shift towards plant-based diets and food production requires a corresponding shift in research efforts to define the microbial requirements for and composition of (novel) plant-based foods, the (micro)organisms that are beneficial to such production systems, and the abundance and role of (bacterio)phages in shaping the microbial landscape of these foods. In this review, we explore current efforts in the area of virome analysis of foods and food production environments and highlight the need for more unified approaches to understand the contribution of phages in food safety and quality, and to develop novel tools to enhance the traceability of foods.

Role played by the environment in the emergence and spread of antimicrobial resistance (AMR) through the food chain

The role of food-producing environments in the emergence and spread of antimicrobial resistance (AMR) in EU plant-based food production, terrestrial animals (poultry, cattle and pigs) and aquaculture was assessed. Among the various sources and transmission routes identified, fertilisers of faecal origin, irrigation and surface water for plant-based food and water for aquaculture were considered of major importance. For terrestrial animal production, potential sources consist of feed, humans, water, air/dust, soil, wildlife, rodents, arthropods and equipment. Among those, evidence was found for introduction with feed and humans, for the other sources, the importance could not be assessed. Several ARB of highest priority for public health, such as carbapenem or extended-spectrum cephalosporin and/or fluoroquinolone-resistant Enterobacterales (including Salmonella enterica), fluoroquinolone-resistant Campylobacter spp., methicillin-resistant Staphylococcus aureus and glycopeptide-resistant Enterococcus faecium and E. faecalis were identified. Among highest priority ARGs bla CTX -M, bla VIM, bla NDM, bla OXA -48-like, bla OXA -23, mcr, armA, vanA, cfr and optrA were reported. These highest priority bacteria and genes were identified in different sources, at primary and post-harvest level, particularly faeces/manure, soil and water. For all sectors, reducing the occurrence of faecal microbial contamination of fertilisers, water, feed and the production environment and minimising persistence/recycling of ARB within animal production facilities is a priority. Proper implementation of good hygiene practices, biosecurity and food safety management systems is very important. Potential AMR-specific interventions are in the early stages of development. Many data gaps relating to sources and relevance of transmission routes, diversity of ARB and ARGs, effectiveness of mitigation measures were identified. Representative epidemiological and attribution studies on AMR and its effective control in food production environments at EU level, linked to One Health and environmental initiatives, are urgently required.

Temporal Resistome and Microbial Community Dynamics in an Intensive Aquaculture Facility with Prophylactic Antimicrobial Treatment

Excessive use of antimicrobials in aquaculture is concerning, given possible environmental ramifications and the potential contribution to the spread of antimicrobial resistance (AR). In this study, we explored seasonal abundance of antimicrobial resistance genes and bacterial community composition in the water column of an intensive aquaculture pond stocked with Silver Carp (Hypophthalmichthys molitrix) prophylactically treated with sulfamethoprim (25% sulfadiazine; 5% trimethoprim), relative to an adjacent unstocked reservoir. Bacterial community composition was monitored using high-throughput sequencing of 16S rRNA gene amplicons in eight sampling profiles to determine seasonal dynamics, representing principal stages in the fish fattening cycle. In tandem, qPCR was applied to assess relative abundance of selected antimicrobial resistance genes (sul1, sul2, dfrA1, tetA and blaTEM) and class-1 integrons (int1). Concomitantly, resistomes were extrapolated from shotgun metagenomes in representative profiles. Analyses revealed increased relative abundance of sulfonamide and tetracycline resistance genes in fishpond-03, relative to pre-stocking and reservoir levels, whereas no significant differences were observed for genes encoding resistance to antimicrobials that were not used in the fishpond-03. Seasons strongly dictated bacterial community composition, with high abundance of cyanobacteria in summer and increased relative abundance of Flavobacterium in the winter. Our results indicate that prophylactic use of sulfonamides in intensive aquaculture ponds facilitates resistance suggesting that prophylactic use of these antimicrobials in aquaculture should be restricted.

Revealing antimicrobial resistance in stormwater with MinION

Discharge of urban stormwater containing organic matter, heavy metals and sometime human feces, to the natural aquatic reservoirs without any treatment is not only an environmental problem. It can lead to prevalence of antibiotic resistant bacteria in stormwater systems and transmission of antibiotic resistance genes to the environment. We performed antibiotic resistome identification and virus detection in stormwater samples from Stockholm, using publicly available metagenomic sequencing MinION data. A MinION platform offers low-cost, precise environmental metagenomics analysis. 37 groups of antibiotic resistant bacteria (ARB), 11 resistance types with 26 resistance mechanisms - antibiotic resistance genes (ARGs) giving tolerance to the aminoglycoside, beta-lactams, fosmidomycin, MLS, multidrug and vancomycin were identified using ARGpore pipeline. The majority of the identified bacteria species were related to the natural environment such as soil and were not dangerous to human. Alarmingly, human pathogenic bacteria carrying resistance to antibiotics currently used against them (Bordetella resistant to macrolides and multidrug resistant Propionibacterium avidum) were also found in the samples. Most abundant viruses identified belonged to Caudovirales and Herpesvirales and they were not carrying ARGs. Unlike the virome, resistome and ARB were not unique for stormwater sampling points. This results underline the need for extensive monitoring of the microbial community structure in the urban stormwater systems to assess antimicrobial resistance spread.

Cell-Free DNA: An Underestimated Source of Antibiotic Resistance Gene Dissemination at the Interface Between Human Activities and Downstream Environments in the Context of Wastewater Reuse

The dissemination of antimicrobial resistance (AMR) is one of the biggest challenges faced by mankind in the public health domains. It is currently favored by a lack of confinement between waste disposal and food production in the environmental compartment. To date, much effort has been devoted into the elucidation and control of cell-associated propagation of AMR. However, substantial knowledge gaps remain on the contribution of cell-free DNA to promote horizontal transfers of resistance genes in wastewater and downstream environments. Cell free DNA, which covers free extracellular DNA (exDNA) as well as DNA encapsulated in vesicles or bacteriophages, can persist after disinfection and promote gene transfer in the absence of physical and temporal contact between a donor and recipient bacteria. The increasing water scarcity associated to climatic change requires developing innovative wastewater reuse practices and, concomitantly, a robust evaluation of AMR occurrence by implementing treatment technologies able to exert a stringent control on AMR propagation in downstream environments exposed to treated or non-treated wastewater. This necessarily implies understanding the fate of ARGs on various forms of cell-free DNA, especially during treatment processes that are permissive to their formation. We propose that comprehensive approaches, investigating both the occurrence of ARGs and their compartmentalization in different forms of cellular or cell-free associated DNA should be established for each treatment technology. This should then allow selecting and tuning technologies for their capacity to limit the propagation of ARGs in any of their forms.

Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce

New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).

Viruses as key reservoirs of antibiotic resistance genes in the environment

Antibiotic resistance is a rapidly growing health care problem globally and causes many illnesses and deaths. Bacteria can acquire antibiotic resistance genes (ARGs) by horizontal transfer mediated by mobile genetic elements, where the role of phages in their dissemination in natural environments has not yet been clearly resolved. From metagenomic studies, we showed that the mean proportion of predicted ARGs found in prophages (0-0.0028%) was lower than those present in the free viruses (0.001-0.1%). Beta-lactamase, from viruses in the swine gut, represented 0.10 % of the predicted genes. Overall, in the environment, the ARG distribution associated with viruses was strongly linked to human activity, and the low dN/dS ratio observed advocated for a negative selection of the ARGs harbored by the viruses. Our network approach showed that viruses were linked to putative pathogens (Enterobacterales and vibrionaceae) and were considered key vehicles in ARG transfer, similar to plasmids. Therefore, these ARGs could then be disseminated at larger temporal and spatial scales than those included in the bacterial genomes, allowing for time-delayed genetic exchanges.

Comprehensive insights into the key components of bacterial assemblages in pharmaceutical wastewater treatment plants

Due to complexity and variety of pharmaceutical wastewater composition, little is known as for functionally important microflora of pharmaceutical wastewater treatment plants (pWWTPs). We compared bacterial composition and diversity of pWWTPs (27 sludge samples collected from 12 full-scale pWWTPs) with those of other industrial (iWWTPs) (27 samples) and municipal wastewater treatment plants (mWWTPs) (27 samples) through meta-analysis based on 16S rRNA gene amplicon sequencing, and identified putatively important organisms and their ecological correlations. Non-metric multidimensional scaling indicated that the pWWTPs, iWWTPs and mWWTPs showed distinctive differences in bacterial community composition (P < 1e-04), and the pWWTPs had significantly lower bacterial diversity than the mWWTPs (P < 1e-06). Thermotogae and Synergistetes phyla only strictly dominated in the pWWTPs, and 26, 30 and 6 specific genera were identified in the pWWTPs, mWWTPs and iWWTPs, respectively. Totally, 15 and 1300 OTUs were identified as core and occasional groups, representing 23.2% and 66.2% of the total read abundance of the pWWTPs, respectively. Permutational multivariate analysis of variance revealed that the bacterial components were clearly clustered corresponding to the types of pharmaceutical wastewater, and a total of 129 local specific OTUs were identified in the pWWTPs, among which anticancer antibiotics pWWTPs had the highest number of specific OTUs (40 ones). Co-occurrence network revealed that the species dominating in the same type of pWWTPs tended to co-occur much more frequently than theoretical random expectation. The results may extend our knowledge regarding the ecological status and correlation of the key microflora in pWWTPs.

Phage particles harboring antibiotic resistance genes in fresh-cut vegetables and agricultural soil

Bacteriophages are ubiquitously distributed prokaryotic viruses that are more abundant than bacteria. As a consequence of their life cycle, phages can kidnap part of their host's genetic material, including antibiotic resistance genes (ARGs), which released phage particles transfer in a process called transduction. The spread of ARGs among pathogenic bacteria currently constitutes a serious global health problem. In this study, fresh vegetables (lettuce, spinach and cucumber), and cropland soil were screened by qPCR for ten ARGs (bla_TEM, bla_CTX-M-1 group, bla_CTX-M-9 group, bla_OXA-48, bla_VIM, mecA, sul1, qnrA, qnrS and armA) in their viral DNA fraction. The presence of ARGs in the phage DNA was analyzed before and after propagation experiments in an Escherichia coli host strain to evaluate the ability of the phage particles to infect a host. ARGs were found in the phage DNA fraction of all matrices, although with heterogeneous values. ARG prevalence was significantly higher in lettuce and soil, and the most common overall were β-lactamases. After propagation experiments, an increase in ARG densities in phage particles was observed in samples of all four matrices, confirming that part of the isolated phage particles were infectious. This study reveals the abundance of free, replicative ARG-containing phage particles in vegetable matrices and cropland soil. The particles are proposed as vehicles for resistance transfer in these environments, where they can persist for a long time, with the possibility of generating new resistant bacterial strains. Ingestion of these mobile genetic elements may also favor the emergence of new resistances, a risk not previously considered.

Detection of Bacteriophage Particles Containing Antibiotic Resistance Genes in the Sputum of Cystic Fibrosis Patients

Cystic fibrosis (CF) is a chronic disease in which the bacterial colonization of the lung is linked to an excessive inflammatory response that leads to respiratory failure. The microbiology of CF is complex. Staphylococcus aureus is the first bacterium to colonize the lungs in 30% of pediatric CF patients, and 80% of adult patients develop a chronic Pseudomonas aeruginosa infection, but other microorganisms can also be found. The use of antibiotics is essential to treat the disease, but antibiotic performance is compromised by resistance mechanisms. Among various mechanisms of transfer of antibiotic resistance genes (ARGs), the recently been reported bacteriophages are the least explored in clinical settings. To determine the role of phages in CF as mobile genetic elements (MGEs) carrying ARGs, we evaluated their presence in 71 CF patients. 71 sputum samples taken from these patients were screened for eight ARGs (bla_TEM, bla_CTX-M-1-group, bla_CTX-M-9-group, bla_OXA-48, bla_VIM, mecA, qnrA, and qnrS) in the bacteriophage DNA fraction. The phages found were also purified and observed by electron microscopy. 32.4% of CF patients harbored ARGs in phage DNA. β-lactamase genes, particularly bla_VIM and bla_TEM, were the most prevalent and abundant, whereas mecA, qnrA, and qnrS were very rare. Siphoviridae phage particles capable of infecting P. aeruginosa and Klebsiella pneumoniae were detected in CF sputum. Phage particles harboring ARGs were found to be abundant in the lungs of both CF patients and healthy individuals and could contribute to the colonization of multiresistant strains.

Metagenomic analysis of antibiotic resistance genes in coastal industrial mariculture systems

The overuse of antibiotics has posed a propagation of antibiotic resistance genes (ARGs) in aquaculture systems. This study firstly explored the ARGs profiles of the typical mariculture farms including conventional and recirculating systems using metagenomics approach. Fifty ARGs subtypes belonging to 21 ARGs types were identified, showing the wide-spectrum profiles of ARGs in the coastal industrial mariculture systems. ARGs with multiple antibiotics resistance have emerged in the mariculure systems. The co-occurrence pattern between ARGs and microbial taxa showed that Proteobacteria and Bacteroidetes were potential dominant hosts of ARGs in the industrial mariculture systems. Typical nitrifying bacteria such as Nitrospinae in mariculture systems also carried with some resistance genes. Relative abundance of ARGs in fish ponds and wastewater treatment units was relatively high. The investigation showed that industrial mariculture systems were important ARGs reservoirs in coastal area, indicating the critical role of recirculating systems in the terms of ARGs pollution control.

Is Genetic Mobilization Considered When Using Bacteriophages in Antimicrobial Therapy?

The emergence of multi-drug resistant bacteria has undermined our capacity to control bacterial infectious diseases. Measures needed to tackle this problem include controlling the spread of antibiotic resistance, designing new antibiotics, and encouraging the use of alternative therapies. Phage therapy seems to be a feasible alternative to antibiotics, although there are still some concerns and legal issues to overcome before it can be implemented on a large scale. Here we highlight some of those concerns, especially those related to the ability of bacteriophages to transport bacterial DNA and, in particular, antibiotic resistance genes.

Aquarium Viromes: Viromes of Human-Managed Aquatic Systems

An aquarium ecosystem is home to many animal species providing conditions similar to native aquatic habitats but under highly controlled management. With a growing interest in understanding the interaction of microbiomes and resident animal health within aquarium environments, we undertook a metagenomic survey of viromes in seven aquarium systems with differing physicochemical and resident animal profiles. Our results show that a diverse array of viruses was represented in aquarium viromes, many of which were widespread in different aquarium systems (27 common viral families in all of the aquarium systems). Most viromes were dominated by DNA phages of the order Caudovirales as commonly found in other aquatic environments with average relative abundance greater than 64%. The composition and structure of aquarium viromes were associated with controlled system parameters, including nitrate, salinity, and temperature as well as resident animal profiles, indicating the close interaction of viromes with aquarium management practices. Furthermore, finding human associated viruses in a touch exhibit suggested that exposure of aquarium systems to human contact may lead to introduction of human cutaneous viruses into aquaria. This is consistent with the high abundance of skin microflora on the palms of healthy individuals and their detection in recreational waters, such as swimming pools. Lastly, assessment of antibiotic resistance genes (ARGs) in aquarium viromes revealed a unique signature of ARGs in different aquarium systems with trimethoprim being the most common. This is the first study to provide vital information on viromes and their unique relationships with management practices in a human-built and controlled aquarium environment.

Viromes As Genetic Reservoir for the Microbial Communities in Aquatic Environments: A Focus on Antimicrobial-Resistance Genes

Despite studies of viromes isolated from aquatic environments are becoming increasingly frequent, most of them are limited to the characterization of viral taxonomy. Bacterial reads in viromes are abundant but the extent to which this genetic material is playing a role in the ecology of aquatic microbiology remains unclear. To this aim, we developed of a useful approach for the characterization of viral and microbial communities of aquatic environments with a particular focus on the identification of microbial genes harbored in the viromes. Virus-like particles were isolated from water samples collected across the Lambro River, from the spring to the high urbanized Milan area. The derived viromes were analyzed by shotgun metagenomic sequencing looking for the presence, relative abundance of bacterial genes with particular focus on those genes involved in antimicrobial resistance mechanisms. Antibiotic and heavy metal resistance genes have been identified in all virome samples together with a high abundance of reads assigned to cellular processes and signaling. Virome data compared to those identified in the microbiome isolated from the same sample revealed differences in terms of functional categories and their relative abundance. To verify the role of aquatic viral population in bacterial gene transfer, water-based mesocosms were perturbed or not perturbed with a low dose of tetracycline. The results obtained by qPCR assays revealed variation in abundance of tet genes in the virome and microbiome highlighting a relevant role of viral populations in microbial gene mobilization.

Phages in the Human Body

Bacteriophages, viruses that infect bacteria, have re-emerged as powerful regulators of bacterial populations in natural ecosystems. Phages invade the human body, just as they do other natural environments, to such an extent that they are the most numerous group in the human virome. This was only revealed in recent metagenomic studies, despite the fact that the presence of phages in the human body was reported decades ago. The influence of the presence of phages in humans has yet to be evaluated; but as in marine environments, a clear role in the regulation of bacterial populations could be envisaged, that might have an impact on human health. Moreover, phages are excellent vehicles of genetic transfer, and they contribute to the evolution of bacterial cells in the human body by spreading and acquiring DNA horizontally. The abundance of phages in the human body does not pass unnoticed and the immune system reacts to them, although it is not clear to what extent. Finally, the presence of phages in human samples, which most of the time is not considered, can influence and bias microbiological and molecular results; and, in view of the evidences, some studies suggest that more attention needs to be paid to their interference.