The association of the emergence of bacterial resistance to clinical environments is common; however, aquatic environments, especially the polluted ones, also play a key role in this regard. Aquatic environments can act as facilitator for the exchange of mobile elements, responsible for resisting antibiotics. They even may stimulate the emergence and selection of these elements through contaminants or the natural competition between bacterial phyla. Currently there is a large number of highly-reliable resistance genes, which is selected in aquatic environments, mostly due to several types of pollution, such as the mcr-1 gene that causes resistance to one of the antibiotics, available in the market, namely colistin. Thus, the present review aims to show a range of impacts capable of selecting bacterial resistance in the environment, thus clarifying this environment's role in dispersion of resistance.

Sediment samples from three coastal sites - two beach resorts (Beach 1 and Beach 2 sites) and an area lying between an oil refinery and a river estuary (Estuarine site) - were analyzed for antibiotic- and heavy metal (HM)-resistant enterococci.A total of 123 enterococci, 36 E. faecium, 34 E. casseliflavus, 33 E. hirae, 5 E. faecalis, 3 E. durans, 3 E. gallinarum, and 9 Enterococcus spp, were recovered. Strains resistant to erythromycin, tetracycline and quinupristin/dalfopristin (Q/D) were recovered from all sites, whereas multidrug-resistant isolates were recovered only from “Beach 2” (14%) and “Estuarine” (3.7%). As regards HM resistance, the strains showed a high frequency (68%) of cadmium and/or copper resistance and uniform susceptibility to mercury. The prevalence of cadmium-resistant strains was significantly higher among erythromycin-resistant than among erythromycin-susceptible strains. A significant association between cadmium or copper resistance and Q/D resistance was also observed at “Estuarine” site. The levels of the two HMs in sediment from all sites were fairly low, ranging from 0.070 to 0.126 μg/g, for cadmium and from 1.00 to 7.64 μg/g for copper. Mercury was always undetectable. These findings are consistent with reports that low HM concentrations may contribute to co-selection of antibiotic-resistant bacterial strains, including enterococci.

With the rapid development of urbanization and industrialization, the peri-urban areas are often the sites for waste dumps, which may exacerbate the occurrence and spread of antibiotic resistance from waste to soil bacteria. However, the profiles of antibiotic resistomes and the associated factors influencing their dissemination in peri-urban areas have not been fully explored. Here, we characterized the antibiotic resistance genes (ARGs) in peri-urban arable and pristine soils in four seasons at the watershed scale, by using high-throughput qPCR. ARGs in peri-urban soils were diverse and abundant, with a total of 222 genes were detected in the peri-urban soil samples. The arable soil harbored more diverse ARGs compared to the pristine soils, and nearly all the ARGs detected in the pristine soils were also detected in the farmlands. A random forest prediction showed that the overall patterns of ARGs clustered closely with the landuse type. Mantel test and partial redundancy analysis indicated that bacterial community variation is a major contributor to antibiotic resistome alteration. Significant positive correlation was found between the abundance of ARGs and mobile genetic elements (MGEs), suggesting potential mobility of ARGs in peri-urban areas. Our results extend knowledge of the resistomes compositions in peri-urban areas, and suggest that anthropogenic activities driving its spatial and temporal distribution.

High abundances of antibiotic-resistant pathogenic bacteria (ARPB) and antibiotic resistance genes (ARGs) in agricultural soil-plant systems have become serious threats to human health and environmental safety. Therefore, it is crucial to develop targeted technology to control existing antibiotic resistance (AR) contamination and potential dissemination in soil-plant systems. In this work, polyvalent bacteriophage (phage) therapy and biochar amendment were applied separately and in combination to stimulate ARPB/ARG dissipation in a soil-lettuce system. With combined application of biochar and polyvalent phage, the abundance of Escherichia coli K-12 (tetR) and Pseudomonas aeruginosa PAO1 (ampR + fosR) and their corresponding ARGs (tetM, tetQ, tetW, ampC, and fosA) significantly decreased in the soil after 63 days' incubation (p < 0.05). Similar results for endophytic K-12 and PAO1, and ARGs, were also obtained in lettuce tissues following combined treatment. Additionally, high throughput sequencing revealed that biochar and polyvalent phage synergetically improved the structural diversity and functional stability of the indigenous bacterial communities in soil and the endophytic ones in lettuce. Hence, this work proposes a novel biotechnology that combines biochar amendment and polyvalent phage therapy to achieve targeted inactivation of ARPB, which stimulates ARG dissipation in soil-lettuce systems.

Biogas residue and organic manure are frequently used for crop planting. However, the evaluation of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs) and bacterial community before their applications to fields is still lacking. This study monitored the variations of bacteria resistant to sulfadiazine, tetracycline and norfloxacin, 57 resistance genes for sulfonamides, tetracyclines and fluoroquinolones as well as the bacterial community during the 28-day aerobic storage of biogas residue and organic manure by using viable plate counts, high-throughput qPCR and Illumina MiSeq sequencing methods. Then two storage conditions, incubator (25 °C) and natural environment, were used to assess the responses of ARB and ARGs to the environmental factors. Results showed that a total of 35 and 21 ARGs were detected in biogas residue and organic manure, respectively. ARB and ARGs were enriched up to 8.01-fold in biogas residue after the 28-day storage, but varied in a narrow range during the storage of organic manure. Compared with the incubator condition, the proliferation of ARB and ARGs in biogas residue under the natural condition was relatively inhibited by the varied and complicated environmental factors. However, we found that there was no significant difference of ARB and ARGs in organic manure between the incubator and natural conditions. Bacterial community was also shifted during the storage of biogas residue, especially Bacteroidetes_VC2.1_Bac22, Aequorivita, Luteimonas and Arenimonas. Network analysis revealed that the relationship in biogas residue was much more complicated than that in organic manure, which ultimately resulted in large successions of ARB and ARGs during the short-term storage of biogas residue. Therefore, we suggest that further measures should be taken before the application of biogas residue to fields.

Antibiotic resistance is an increasingly important environmental pollutant with direct consequences for human health. Identification of environmental sources of antibiotic resistance genes (ARGs) makes it possible to follow their evolution and prevent their entry into the clinical setting. ARGs have been found in environmental sources exogenous to the original source and previous studies have shown that these genes are capable of being transferred from livestock to humans. Due to the nature of farming and the slaughter of ruminants for food, humans interact with these animals in close proximity, and for this reason it is important to consider the risks to human health. In this study, we characterised the ARG populations in the ovine rumen, termed the resistome. This was done using the Comprehensive Antibiotic Resistance Database (CARD) to identify the presence of genes conferring resistance to antibiotics within the rumen. Genes were successfully mapped to those that confer resistance to a total of 30 different antibiotics. Daptomycin was identified as the most common antibiotic for which resistance is present, suggesting that ruminants may be a source of daptomycin ARGs. Colistin resistance, conferred by the gene pmrE, was also found to be present within all samples, with an average abundance of 800 counts. Due to the high abundance of some ARGs (against daptomycin) and the presence of rare ARGs (against colistin), we suggest further study and monitoring of the rumen resistome as a possible source of clinically relevant ARGs.

Trace elements (TEs) availability, biochemical activity and functional gene diversity was studied in a Cu-contaminated soil, revegetated for six years with a mixed stand of willow, black poplar, and false indigo-bush, and amended or not with compost plus dolomitic limestone (OMDL). The OMDL amendment significantly reduced Cu and As availability and soil toxicity, and increased the biochemical activity and microbial functional diversity assessed with the GEOCHIP technique, as compared to the unamended soil (Unt). The OMDL soil showed significantly higher abundance of 25 functional genes involved in decomposition organic compounds, and 11, 3 and 11 functional genes involved in the N, P and S biogeochemical cycles. Functional gene abundance was positively correlated with nutrient contents but negatively correlated with Cu availability and soil toxicity. The abundance of microbial functional genes encoding for resistance to various TEs also increased, possibly due to the microbial proliferation and lower Cu exposure in the presence of high total soil Cu concentration. Genes encoding for antibiotic resistance due to the co-occurrence of TEs and antibiotic resistant genes on genetic mobile elements. Overall, phytomanagement confirmed its potential to restore the biological fertility and diversity of a severely Cu-contaminated soil, but the increase of TEs and antibiotic resistant gene abundances deserve attention in future studies.

Tetracyclines are a class of antimicrobials frequently found in the environment, and have promoted the proliferation of antibiotic resistance. An unanswered research question is whether tetracycline sorbed to soils is still bioavailable to bacteria and exerts selective pressure on the bacterial community for the development of antibiotic resistance. In this study, bioreporter E. coli MC4100/pTGM strain was used to probe the bioavailability of tetracycline sorbed by smectite clay, a class of common soil minerals. Batch sorption experiments were conducted to prepare clay samples with a wide range of sorbed tetracycline concentration. The bioreporter was incubated with tetracycline-sorbed clay at different clay/solution ratios and water contents, as well as using dialysis tubings to prevent the direct contact between bacterial cells and clay particles. The expression of antibiotic resistance genes from the bioreporter was measured using a flow cytometer as a measurement of bioavailability/selective pressure. The direct contact of bioreporter cells to clay surfaces represented an important pathway facilitating bacterial access to clay-sorbed tetracycline. In clay-water suspensions, reducing solution volume rendered more bacteria to attach to clay surfaces enhancing the bioavailability of clay-sorbed tetracycline. The strong fluorescence emission from bioreporter cells on clay surfaces indicated that clay-sorbed tetracycline was still bioavailable to bacteria. The formation of biofilms on clay surfaces could increase bacterial access to clay-sorbed tetracycline. In addition, desorption of loosely sorbed tetracycline into bulk solution contributed to bacterial exposure and activation of the antibiotic resistance genes. Tetracycline sorbed by soil geosorbents could exert selective pressure on the surrounding microbial communities via bacterial exposure to tetracycline in solution from desorption and to the geosorbent-sorbed tetracycline as well.

The determination of values of abundance of antibiotic resistance genes (ARGs) per mass of soil is extremely useful to assess the potential impacts of relevant sources of antibiotic resistance, such as irrigation with treated wastewater or manure application. Culture-independent methods and, in particular, quantitative PCR (qPCR), have been regarded as suitable approaches for such a purpose. However, it is arguable if these methods are sensitive enough to measure ARGs abundance at levels that may represent a risk for environmental and human health. This study aimed at demonstrating the range of values of ARGs quantification that can be expected based on currently used procedures of DNA extraction and qPCR analyses. The demonstration was based on the use of soil samples spiked with known amounts of wastewater antibiotic resistant bacteria (ARB) (Enterococcus faecalis, Escherichia coli, Acinetobacter johnsonii, or Pseudomonas aeruginosa), harbouring known ARGs, and also on the calculation of expected values determined based on qPCR.The limits of quantification (LOQ) of the ARGs (vanA, qnrS, blaTEM, blaOXA, blaIMP, blaVIM) were observed to be approximately 4 log-units per gram of soil dry weight, irrespective of the type of soil tested. These values were close to the theoretical LOQ values calculated based on currently used DNA extraction methods and qPCR procedures. The observed LOQ values can be considered extremely high to perform an accurate assessment of the impacts of ARGs discharges in soils. A key message is that ARGs accumulation will be noticeable only at very high doses. The assessment of the impacts of ARGs discharges in soils, of associated risks of propagation and potential transmission to humans, must take into consideration this type of evidence, and avoid the simplistic assumption that no detection corresponds to risk absence.

Environmental observations of antibiotics and other pharmaceuticals have received attention as indicators of an urbanizing global water cycle. When connections between environment and development of antibiotic resistance (ABR) are considered, it is increasingly important to understand the life cycle of antibiotics. Here we examined the global occurrence of erythromycin (ERY) in: 1. wastewater effluent, inland waters, drinking water, groundwater, and estuarine and coastal systems; 2. sewage sludge, biosolids and sediments; and 3. tissues of aquatic organisms. We then performed probabilistic environmental hazard assessments to identify probabilities of exceeding the predicted no-effect concentration (PNEC) of 1.0 μg L−1 for promoting ABR, based on previous modeling of minimum inhibitory concentrations and minimal selective concentrations of ERY, and measured levels from different geographic regions. Marked differences were observed among geographic regions and matrices. For example, more information was available for water matrices (312 publications) than solids (97 publications). ERY has primarily been studied in Asia, North America and Europe with the majority of studies performed in China, USA, Spain and the United Kingdom. In surface waters 72.4% of the Asian studies have been performed in China, while 85.4% of the observations from North America were from the USA; Spain represented 41.9% of the European surface water studies. Remarkably, results from PEHAs indicated that the likelihood of exceeding the ERY PNEC for ABR in effluents was markedly high in Asia (33.3%) followed by Europe (20%) and North America (17.8%). Unfortunately, ERY occurrence data is comparatively limited in coastal and marine systems across large geographic regions including Southwest Asia, Eastern Europe, Africa, and Central and South America. Future studies are needed to understand risks of ERY and other antibiotics to human health and the environment, particularly in developing regions where waste management systems and treatment infrastructure are being implemented slower than access to and consumption of pharmaceuticals is occurring.