Occurrence and distribution of antibiotic resistance genes in the sediments of the East China Sea bays

The coastal area of the East China Sea has experienced rapid urbanization and industrialization in China since 1980 s, resulting in severe pollution of its environments.Antibiotic resistance genes(ARGs) are regarded as a kind of emerging pollutant with potential high risk. The sediment samples were collected from Hangzhou Bay(HB),Xiangshan Bay(XB), and Taizhou Bay(TB) to investigate the spatial occurrence and distribution of 27 ARGs and class I integron–integrase gene(intI1) in the coastal area of the East China Sea. The PCR results showed the frequent presence of 11 ARGs and intI1 in the sediments of the three bays. The qPCR results further showed that sulfonamide resistance was the most prevalent ARG type and antibiotic target replacement and protection were the most important resistance mechanisms in the sediments. Regarding the subtype of ARGs, sulI, tetW, and dfrA13 were the most abundant ARGs, in which sulI was higher in TB(based on both the absolute and relative abundances) and dfrA13 was higher in HB(based on the relative abundances). The network analysis revealed that intI1 had significant correlations with tetC, sulI, sulII, and blaPSE-1. Oil was the key connected factor, which had positive connections with sulI, sulII, and blaPSE-1. In addition, the joint effect of heavy metals and nutrients organic pollutants might be crucial for the fate of ARGs in the coastal sediments.     

Low nutrient levels as drinking water conditions can reduce the fitness cost of efflux pump-mediated ciprofloxacin resistance in Pseudomonas aeruginosa

The long-term persistence of antibiotic resistance in the environment, especially in drinking water, is a public health concern. Expression of an efflux pump, an important mechanism of resistance to antibiotics, usually confers a fitness cost in bacteria. In this study, we aimed to determine why antibiotic resistance conferred by overexpression of an efflux pump persisted in low-nutrient environments(TOC 10 mg/L) such as drinking and source water in which antibiotic selective pressure might be very low or even absent.Competition experiments between wild-type Pseudomonas aeruginosa and ciprofloxacinresistant mutants revealed that the fitness cost of ciprofloxacin resistance significantly decreased(p 0.05) under low-nutrient(0.5 mg/L total organic carbon(TOC)) relative to high-nutrient(500 mg/L TOC) conditions. Mechanisms underlying this fitness cost were analyzed. The mexD gene expression in resistant bacteria(cip_3 strain) was significantly lower(p 0.05) in low-nutrient conditions, with 10 mg/L TOC((8.01 ± 0.82)-fold), than in high-nutrient conditions, with 500 mg/L TOC((48.89 ± 4.16)-fold). Moreover, rpoS gene expression in resistant bacteria((1.36 ± 0.13)-fold) was significantly lower(p 0.05) than that in the wild-type strain((2.78 ± 0.29)-fold) under low-nutrient conditions(10 mg/L TOC),suggesting a growth advantage. Furthermore, the difference in metabolic activity between the two competing strains was significantly smaller(p 0.05) in low-nutrient conditions(5 and 0.5 mg/L TOC). These results suggest that nutrient levels are a key factor in determining the persistence of antibiotic resistance conferred by efflux pumps in the natural environment with trace amounts or no antibiotics.     

Distribution and relationship between antimicrobial resistance genes and heavy metals in surface sediments of Taihu Lake, China

Heavy metals, pharmaceuticals, and other wastes released into the environment can significantly influence environmental antibiotic resistance. We investigated the occurrence of 22 antimicrobial resistance genes(ARGs) and 10 heavy metal concentrations, and the relationship between ARGs and heavy metals in surface sediment from seven sites of Lake Taihu. The results showed significant correlations(p 0.05) between sediment ARG levels,especially for tetracycline and sulfonamides(e.g., tet(A), tet(D), tet(E), tet(O), sul1, sul2 and int-1) and specific heavy metals(Fe, Mn, Cr, Cu, Zn, among others) in the Lake. In the surface sediments, heavy metals showed an interaction with resistance genes, but the strength of interaction was diminished with increasing depth. For most of the heavy metals, the concentration of elements in the top sediments was higher than that in other depths.Tetracycline resistance genes(tet(A), tet(B), tet(D), tet(E) and tet(O), β-lactam resistance genes(SHV, TEM, CTX, OXA and OXY) and sulfonamide resistance genes(sulA, sul1, sul2, sul3 and int-1) were detected. They showed a trend which inferred a statistically significant increase followed by decreases in the relative abundance of these ARGs(normalized to 16 S rRNA genes) with increasing depth. This study revealed that tet(A), tet(O), TEM, OXY, int-1, sul1 and sul3 were widespread in surface sediments with high abundance, indicating that these genes deserve more attention in future work.     

Fate of antibiotics and antibiotic resistance genes in a full-scale restaurant food waste treatment plant: Implications of the roles beyond heavy metals and mobile genetic elements

Is our food safe and free of the crisis of antibiotics and antibiotic resistance(AR)?And will the derived food waste(FW) impose AR risk to the environment after biological treatment? This study used restaurant FW leachates flowing through a 200 tons-waste/day biological treatment plant as a window to investigate the fate of antibiotics and antibiotic-resistance genes(ARGs) during the acceptance and treatment of FW. Sulfonamides(sulfamethazine, sulfamethoxazole) and quinolones(ciprofloxacin, enrofloxacin, ofloxacin) were detected during FW treatment, while tetracyclines, macrolides and chloramphenicols were not observable. ARGs encoding resistance to sulfonamides, tetracyclines and macrolides emerged in FW leachates.Material flow analysis illustrated that the total amount of antibiotics(except sulfamethazine) and ARGs were constant during FW treatment processes. Both the concentration and total amount of most antibiotics and ARGs fluctuated during treatment, physical processes(screening, centrifugation, solid–liquid and oil–water separation) did not decrease antibiotic or ARGs concentrations or total levels permanently; the affiliated wastewater treatment plant appeared to remove sulfonamides and most ARGs concentrations and total amount. Heavy metals Ni,Co and Cu were important for disseminating antibiotics concentrations and MGEs for distributing ARGs concentrations. Humic substances(fulvic acids, hydrophilic fractions), C-associated and N-associated contents were essential for the distribution of the total amounts of antibiotics and ARGs. Overall, this study implied that human food might not be free of antibiotics and ARGs, and FW was an underestimated AR pool with various determinants. Nonetheless, derived hazards of FW could be mitigated through biological treatment with well-planned daily operations.     

Impacts of advanced treatment processes on elimination of antibiotic resistance genes in a municipal wastewater treatment plant

The distributions of ARGs were monitored in a WWTP in Harbin during six months. CASS had the best removal efficacy of ARGs compared to other processes in the WWTP. UV disinfection could effectively control the HGT. AGAC significantly remove ARGs and organics due to its high absorption capacity. Combination of ozone and AGAC significantly improve removal of ARGs and organics. Antibiotic resistance genes (ARGs) pose a serious threat to public health. Wastewater treatment plants (WWTPs) are essential for controlling the release of ARGs into the environment. This study investigated ARG distribution at every step in the treatment process of a municipal WWTP located in Harbin for six consecutive months. Changes in ARG distribution involved in two advanced secondary effluent treatment processes, ozonation and granular activated carbon (GAC) adsorption, were analyzed. Biological treatment resulted in the highest ARG removal (0.76–1.94 log reduction), followed by ultraviolet (UV) disinfection (less than 0.5-log reduction). Primary treatment could not significantly remove ARGs. ARG removal efficiency increased with an increase in the ozone dose below 40 mg/L. However, amorphous GAC (AGAC) adsorption with a hydraulic retention time (HRT) of 1 h showed better removal of ARGs, total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP) than ozonation at a 60 mg/L dose. UV treatment could efficiently reduce the relative ARG abundance, despite presenting the lowest efficiency for the reduction of absolute ARG abundance compared with GAC and ozone treatments. The combination of ozone and AGAC can significantly improve the removal of ARGs, TOC, TN and TP. These results indicate that a treatment including biological processing, ozonation, and AGAC adsorption is a promising strategy for removing ARGs and refractory organic substances from sewage.     

Culturomics and metagenomics: In understanding of environmental resistome

State of the art of culturomics and metagenomics to study resistome was presented. The combination of culturomics and metagenomics approaches was proposed. The research directions of antibiotic resistance study has been suggested. Pharmaceutical residues, mainly antibiotics, have been called “emerging contaminants” in the environment because of their increasing frequency of detection in aquatic and terrestrial systems and their sublethal ecological effects. Most of them are undiscovered. Both human and veterinary pharmaceuticals, including antibiotics, are introduced into the environment via many different routes, including discharges from municipal wastewater treatment plants and land application of animal manure and biosolids to fertilize croplands. To gain a comprehensive understanding of the widespread problem of antibiotic resistance, modern and scientific approaches have been developed to gain knowledge of the entire antibiotic-resistant microbiota of various ecosystems, which is called the resistome. In this review, two omics methods, i.e. culturomics, a new approach, and metagenomics, used to study antibiotic resistance in environmental samples, are described. Moreover, we discuss how both omics methods have become core scientific tools to characterize microbiomes or resistomes, study natural communities and discover new microbes and new antibiotic resistance genes from environments. The combination of the method for get better outcome of both culturomics and metagenomics will significantly advance our understanding of the role of microbes and their specific properties in the environment.     

Elimination of antibiotic resistance genes and control of horizontal transfer risk by UV-based treatment of drinking water: A mini review

Antibiotic-resistant bacteria and antibiotic resistance genes are in water bodies. UV/chlorination method is better to remove ARGs than UV or chlorination alone. Research on UV/hydrogen peroxide to eliminate ARGs is forthcoming. UV-based photocatalytic processes are effective to degrade ARGs. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have been recognized as one of the biggest public health issues of the 21st century. Both ARB and ARGs have been determined in water after treatment with conventional disinfectants. Ultraviolet (UV) technology has been seen growth in application to disinfect the water. However, UV method alone is not adequate to degrade ARGs in water. Researchers are investigating the combination of UV with other oxidants (chlorine, hydrogen peroxide (H₂O₂), peroxymonosulfate (PMS), and photocatalysts) to harness the high reactivity of produced reactive species (Clž·, ClOž·ž, Clž₂·ž⁻, žž·OH, and SOž₄ž·⁻€) in such processes with constituents of cell (e.g., deoxyribonucleic acid (DNA) and its components) in order to increase the degradation efficiency of ARGs. This paper briefly reviews the current status of different UV-based treatments (UV/chlorination, UV/H₂O₂, UV/PMS, and UV-photocatalysis) to degrade ARGs and to control horizontal gene transfer (HGT) in water. The review also provides discussion on the mechanism of degradation of ARGs and application of q-PCR and gel electrophoresis to obtain insights of the fate of ARGs during UV-based treatment processes.     

A review on anammox process for the treatment of antibiotic-containing wastewater: Linking effects with corresponding mechanisms

• Anammox is promising for nitrogen removal from antibiotic-containing wastewater. • Most antibiotics could inhibit the anammox performance and activity. • Antibiotic pressure promoted the increase in antibiotic resistance genes (ARGs). • Antibiotic-resistance mechanisms of anammox bacteria are speculated. Antibiotic is widely present in the effluent from livestock husbandry and the pharmaceutical industry. Antibiotics in wastewater usually have high biological toxicity and even promote the occurrence and transmission of antibiotic resistant bacteria and antibiotic resistance genes. Moreover, most antibiotic-containing wastewater contains high concentration of ammonia nitrogen. Improper treatment will lead to high risk to the surrounding environment and even human health. The anaerobic ammonium oxidation (anammox) with great economic benefit and good treatment effect is a promising process to remove nitrogen from antibiotic-containing wastewater. However, antibiotic inhibition has been observed in anammox applications. Therefore, a comprehensive overview of the single and combined effects of various antibiotics on the anammox system is conducted in this review with a focus on nitrogen removal performance, sludge properties, microbial community, antibiotic resistance genes and anammox-involved functional genes. Additionally, the influencing mechanism of antibiotics on anammox consortia is summarized. Remaining problems and future research needs are also proposed based on the presented summary. This review provides a better understanding of the influences of antibiotics on anammox and offers a direction to remove nitrogen from antibiotic-containing wastewater by the anammox process.     

Film mulching reduces antibiotic resistance genes in the phyllosphere of lettuce

Phyllosphere is an important reservoir of antibiotic resistance genes(ARGs), but the transfer mechanism of ARGs from soil and air to phyllosphere remains unclear. This study demonstrated that soil-air-phyllosphere was the dominant ARG transfer pathway, and blocking it by film mulching can reduce typical phyllosphere ARGs in lettuce by 80.7%-98.7%(89.5% on average). To further eliminate phyllosphere ARGs in lettuce grown with film mulching, the internal soil-endosphere-phyllosphere transfer pathw...     

Antimicrobial resistance in Escherichia coli and Salmonella spp. isolates from fresh produce and the impact to food safety

Foodborne diseases associated with fresh produce consumption have escalated worldwide, causing microbial safety of produce of critical importance. Bacteria that have increasingly been detected in fresh produce are Escherichia coli and Salmonella spp., both of which have been shown to progressively display antimicrobial resistance. The study focused on the assessment of antimicrobial resistance of these enteric bacteria from different kinds of fresh produce from various open air markets and supermarkets in the Philippines. Using the disk diffusion assay on a total of 50 bacterial isolates obtained from 410 fresh produce surveyed, monoresistance to tetracycline was observed to be the most prevalent (38%), followed by multidrug resistance to tetracycline, chloramphenicol, ciprofloxacin, and nalidixic acid (4%), and lastly by dual resistance to tetracycline and chloramphenicol (2%). Using multiplex and simplex polymerase chain reaction (PCR) assays, tetA (75%) and tetB (9%) were found in tetracycline resistant isolates, whereas catI (67%) and catIII (33%) were detected in chloramphenicol resistant isolates. Sequence analysis of gyr and par genes from the ciprofloxacin and nalidixic acid resistant isolates revealed different mutations. Based on the results, fresh produce act as a reservoir of these antibiotic resistant bacteria which may pose health threat to consumers.