Emergence Of Antibiotic Resistance Genes Research Articles

Prevalence of antibiotic resistance genes in drinking water and biofilms: The correlation with the microbial community and opportunistic pathogens

The emergence of antibiotic resistance genes (ARGs) and opportunistic pathogens (OPs) in drinking water system posed potential risks to human health. However, the occurrence of ARGs and OPs in drinking water biofilms is still at its infancy. In this study, we investigated the occurrence of ARGs and OPs in both water and biofilm samples from a drinking water system, and the correlation between ARGs and microbial communities was analyzed. The quantitative PCR results showed that the drinking water treatment process effectively decreased the absolute abundances of ARGs. However, the relative concentration of ARGs did not show a significant difference between raw water and treated water samples. Compared with bulk water and tap water samples, biofilms had higher relative abundances of ARGs. 16 S Illumina Miseq sequencing results showed that microbial communities of biofilms were distinguished with water samples. Meanwhile, qPCR results of OPs also showed that biofilms had higher relative abundances of OPs compared with water samples. Furthermore, the Spearman correlation analysis indicated that Dechloromonas, Desulfovibrio, Methylobacterium and Propionivibrio correlated well with the relative abundance of ARGs. The absolute concentrations of OPs and ARGs also showed a significant correlation. Results of this study suggest that biofilms could serve as the reservoirs for the spread of ARGs and the interaction between biofilms and bulk water requires further research.

Online searching platform for the antibiotic resistome in bacterial tree of life and global habitats.

Metagenomic analysis reveals that antibiotic-resistance genes (ARGs) are widely distributed in both human-associated and non-human-associated habitats. However, it is difficult to equally compare ARGs between samples without a standard method. Here, we constructed a comprehensive profile of the distribution of potential ARGs in bacterial tree of life and global habitats by investigating ARGs in 55 000 bacterial genomes, 16 000 bacterial plasmid sequences, 3000 bacterial integron sequences and 850 metagenomes using a standard pipeline. We found that >80% of all known ARGs are not carried by any plasmid or integron sequences. Among potential mobile ARGs, tetracycline and beta-lactam resistance genes (such as tetA, tetM and class A beta-lactamase gene) distribute in multiple pathogens across bacterial phyla, indicating their clinical relevance and importance. We showed that class 1 integrases (intI1) display a poor linear relationship with total ARGs in both non-human-associated and human-associated environments. Furthermore, both total ARGs and intI1 genes show little correlation with the degree of anthropogenicity. These observations highlight the need to differentiate ARGs of high clinical relevance. This profile is published on an online platform (ARGs-OSP, http://args-osp.herokuapp.com/) as a valuable resource for the most challenging topics in this field, i.e. the risk, evolution and emergence of ARGs.

Occurrence of antibiotics and antibiotic resistance genes and their correlations in lower Yangtze River, China

The overuse and misuse of antibiotics could promote the emergence of antibiotic resistance genes (ARGs) and pose a potential risk to human health and the ecological environment. In this study, fifteen antibiotics and their corresponding ARGs in water, sediment and sewage treatment plant (STP) effluent were analysed to investigate their occurrence and correlation in the Yangtze River (Jiangsu section) for the first time. The concentrations of erythromycin-H2O (EM-H2O) (2.08–30 ng L−1) and ofloxacin (OFL) (290–8400 ng kg−1) were the highest in the water and sediment, respectively, and EM-H2O and clarithromycin (CLA) posed the highest risks to aquatic organisms. The concentrations of antibiotics in STP effluent were significantly higher (p < 0.05) than those in the water. Norfloxacin (NOR) was the most predominant antibiotic, with low removal efficiency (−38%-51%), in STPs; the concentration of NOR in the STP effluent was 4–6 orders of magnitude higher than that in the water. Moreover, the concentrations of antibiotics and their corresponding ARG abundance in downstream were higher than those in upstream, suggesting that STPs with high concentration levels might be an important source of river contamination. Additionally, the concentrations of antibiotics and the abundance of ARGs might increase after the sewage treatment process. The results also showed the prevalence of sul1 and sul2 in all the sampling sites. Significant correlations (p < 0.0001) were detected between int1 and sul1 and sul2, which resulted from the contribution of int1 to the propagation of ARGs. Overall, this study demonstrated the prevalence of antibiotics and ARGs and their inconsistent correlations in the Yangtze River (Jiangsu section) and provides support for further investigation of the occurrence and spread of antibiotics and ARGs.

Effect and mechanism of quorum sensing on horizontal transfer of multidrug plasmid RP4 in BAC biofilm

The widespread emergence of antibiotic resistance genes (ARGs) in drinking water systems endangers human health, and may be exacerbated by their horizontal gene transfer (HGT) among microbiota. In our previous study, Quorum sensing (QS) molecules produced by bacteria from biological activated carbon (BAC) biofilms were demonstrated to influence the transfer efficiency of a model conjugative plasmid, here RP4. In this study, we further explored the effect and mechanism of QS on conjugation transfer. The results revealed that Acyl-homoserine lactones producing (AHL-producing) bacteria isolated from BAC biofilm play a role in the propagation of ARGs. We selected several quorum sensing inhibitors (QSIs) to study their effects on AHL-producing bacteria, including the formation of biofilm and the regulating effect on conjugation transfer. In addition, the possible molecular mechanisms for AHLs that promote conjugative transfer were attributable to enhancing the mRNA expression, which involved altered expressions of conjugation-related genes. We also found that QSIs could inhibit conjugative transfer by downregulating the conjugation-relevant genes. We believe that this is the first insightful exploration of the mechanism by which AHLs will facilitate and QSIs will inhibit the conjugative transfer of ARGs. These results provide creative insight into ARG pollution control that involves blocking QS during BAC treatment in drinking water systems.

The impact and mechanism of quaternary ammonium compounds on the transmission of antibiotic resistance genes.

The emergence of antibiotic resistance genes (ARGs) in microbes can be largely attributed to the abuse and misuse of antibiotics and biocides. Quaternary ammonium compounds (QACs) have been used worldwide as common disinfectants and detergents; however, their potential impact on the spread and diffusion of ARGs is still unknown. In this study, we detected the QAC resistance gene (qacEΔ1), the 1 integron gene (intI1), and 12 ARGs (sul1, sul2, cfr, cml, fexA, tetA, tetG, tetQ, tetX, ermB, blaTEM, and dfrA1) in 48 water samples from three watersheds by quantitative PCR (qPCR). We investigated the evolution of bacterial antibiotic resistance under QAC and antibiotic environmental pressures by long-term continuous culture. In addition, five QACs were selected to investigate the effect of QAC on the efficiency of conjugation transfer. The changes in bacterial cell membrane and production of reactive oxygen species (ROS) were detected by flow cytometry, revealing the mechanism by which QAC affects the spread of antibiotic resistance. Our results showed that the QAC resistance gene was ubiquitous in watersheds and it had significant correlation with intI1 and seven ARGs (r = 0.999, p < 0.01). QACs could increase the resistance of bacteria to multiple antibiotics. Furthermore, all five QACs promoted the conjugation transfer of the RP4 plasmid; the optimal concentration of QACs was about 10-1-10-2mg/L and their transfer efficiencies were between 1.33 × 10-6 and 8.87 × 10-5. QACs enhanced membrane permeability of bacterial cells and stimulated bacteria to produce ROS, which potentially promoted the transfer of plasmids between bacteria. In conclusion, this study demonstrated that QACs may facilitate the evolution and gene transfer of antibiotic resistance gene among microbiome.

Oral Beta-Lactamase Protects the Canine Gut Microbiome from Oral Amoxicillin-Mediated Damage

Antibiotics damage the gut microbiome, which can result in overgrowth of pathogenic microorganisms and emergence of antibiotic resistance. Inactivation of antibiotics in the small intestine represents a novel strategy to protect the colonic microbiota. SYN-004 (ribaxamase) is a beta-lactamase formulated for oral delivery intended to degrade intravenously administered beta-lactam antibiotics in the gastrointestinal (GI) tract. The enteric coating of ribaxamase protects the enzyme from stomach acid and mediates pH-dependent release in the upper small intestine, the site of antibiotic biliary excretion. Clinical benefit was established in animal and human studies in which ribaxamase was shown to degrade ceftriaxone in the GI tract, thereby preserving the gut microbiome, significantly reducing Clostridioides difficile disease, and attenuating antibiotic resistance. To expand ribaxamase utility to oral beta-lactams, delayed release formulations of ribaxamase, SYN-007, were engineered to allow enzyme release in the lower small intestine, distal to the site of oral antibiotic absorption. Based on in vitro dissolution profiles, three SYN-007 formulations were selected for evaluation in a canine model of antibiotic-mediated gut dysbiosis. Dogs received amoxicillin (40 mg/kg, PO, TID) +/- SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were measured after the first and last antibiotic doses and gut microbiomes were evaluated using whole genome shotgun sequence metagenomics analyses of fecal DNA prior to and after antibiotic treatment. Serum amoxicillin levels did not significantly differ +/- SYN-007 after the first dose for all SYN-007 formulations, while only one SYN-007 formulation did not significantly reduce systemic antibiotic concentrations after the last dose. Gut microbiomes of animals receiving amoxicillin alone displayed significant loss of diversity and emergence of antibiotic resistance genes. In contrast, for animals receiving amoxicillin + SYN-007, microbiome diversities were not altered significantly and the presence of antibiotic resistance genes was reduced. These data demonstrate that SYN-007 diminishes amoxicillin-mediated microbiome disruption and mitigates emergence and propagation of antibiotic resistance genes without interfering with antibiotic systemic absorption. Thus, SYN-007 has the potential to protect the gut microbiome by inactivation of beta-lactam antibiotics when administered by both oral and parenteral routes and to reduce emergence of antibiotic-resistant pathogens.

Occurrence of antibiotics and antibiotic resistance genes in a typical estuary aquaculture region of Hangzhou Bay, China

The widespread use of antibiotics in aquaculture can potentially lead to the emergence of antibiotic resistance genes (ARGs) and threaten human health by entering the food chain. To assess the environmental risk posed by antibiotics in China, the spatial-temporal distribution and correlation of 8 antibiotics based on the abundance of 11 ARGs in water sources, pond water, and sediment in 8 ponds were determined. The results indicated that sul1 was the predominant ARG in water sources and pond water, and tetC was the most in the sediment. A trend of increasing abundance of ARGs was observed with increased rearing density and pond age. Compared to monoculture, shrimp culture integrated with different trophic levels of fish farming could influence the abundance of ARGs. There was also a significant correlation between the abundance of ARGs and antibiotic concentration in the sediment, while no correlation was observed in water sources and pond water.

Screening of tropical estuarine water in south-west coast of India reveals emergence of ARGs-harboring hypervirulent Escherichia coli of global significance.

The goal of this study was to investigate the involvement of a tropical Indian estuary in the emergence of antibiotic resistance genes (ARGs)-harboring hypervirulent E. coli of global significance. A total of 300 E. coli isolates was tested for antibiotic susceptibility to β-lactams, aminoglycosides, chloramphenicol, quinolones, sulphonamides, tetracyclines, and trimethoprim. The E. coli isolates were screened for the presence of antibiotic resistance genes (blaTEM, blaCTX-M, tetA, tetB, sul1, sul2, strA, aphA2, catI, dhfr1, and dhfr7), integrase (int1, int2, and int3), Shiga toxin genes (stx1 and stx2) and extraintestinal virulence genes (papAH, papC, sfa/focDE, kpsMT II, and iutA). The highest prevalence of antibiotic resistance was observed for ampicillin, followed by tetracycline, and nalidixic acid. Among E. coli isolates, 64% were resistant to at least one of the 15 antibiotics tested, and approximately 40% were multiple antibiotic-resistant (MAR). More than 40% (n = 122) of E. coli isolates had ARGs. Integrase 1 (int1) was found in 7.6% of E. coli isolates. Among E. coli isolates, 16.3% (n = 49) were extraintestinal pathogenic E. coli (ExPEC), and approximately 34.6% (n = 17) of ExPEC had ARGs. A hypervirulent ARGs-harboring STEC was isolated. The prevalence of Shiga toxin-producing E. coli (STEC) was low (n = 1). The prevalence of ARGs-harboring pathogenic E. coli isolates was higher in stations close to the City (urban area), than that of other stations. ERIC-PCR (enterobacterial repetitive intergenic consensus sequence polymerase chain reaction) analysis revealed a high degree of genetic diversity among the ARGs-harboring E. coli isolates. The results demonstrate a high prevalence of ARGs-harboring E. coli in estuarine water and confirm the need for a better wastewater treatment facility and proper control measures to reduce the discharge of sewage and wastewater into the aquatic environments.

Plasmid-Mediated Quinolone Resistance Genes and Antibiotic Residues in Wastewater and Soil Adjacent to Swine Feedlots: Potential Transfer to Agricultural Lands

Background: Inappropriate use of antibiotics in swine feed could cause accelerated emergence of antibiotic resistance genes, and agricultural application of swine waste could spread antibiotic resistance genes to the surrounding environment.Objectives: We investigated the distribution of plasmid-mediated quinolone resistance (PMQR) genes from swine feedlots and their surrounding environment.Methods: We used a culture-independent method to identify PMQR genes and estimate their levels in wastewater from seven swine feedlot operations and corresponding wastewater-irrigated farm fields. Concentrations of (fluoro)quinolones in wastewater and soil samples were determined by ultra-performance liquid chromatography–electrospray tandem mass spectrometry.Results: The predominant PMQR genes in both the wastewater and soil samples were qnrD, qepA, and oqxB, whereas qnrS and oqxA were present only in wastewater samples. Absolute concentrations of all PMQR genes combined ranged from 1.66 × 107 to 4.06 × 108 copies/mL in wastewater and 4.06 × 106 to 9.52 × 107 copies/g in soil. Concentrations of (fluoro)quinolones ranged from 4.57 to 321 ng/mL in wastewater and below detection limit to 23.4 ng/g in soil. Significant correlations were found between the relative abundance of PMQR genes and (fluoro)quinolone concentrations (r = 0.71, p = 0.005) and the relative abundance of PMQR genes in paired wastewater and agricultural soil samples (r = 0.91, p = 0.005).Conclusions: Swine feedlot wastewater may be a source of PMQR genes that could facilitate the spread of antibiotic resistance. To our knowledge, this is the first study to examine the occurrence of PMQR genes in animal husbandry environments using a culture-independent method.