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1.
Huan Jing Ke Xue ; 42(4): 1939-1945, 2021 Apr 08.
Artículo en Chino | MEDLINE | ID: mdl-33742829

RESUMEN

In order to study the effects of chlorine dioxide (ClO2) disinfection on the super antibiotic resistance genes (SARGs), the final effluents before and after chlorine dioxide were sampled throughout one year in a wastewater treatment plant (WWTP). The bacteria and extracellular nucleic acid were collected using microporous membrane filtration and nucleic acid adsorption particles, respectively. A total of 9 SARGs was detected through a quantitative real-time polymerase chain reaction (qPCR). The results revealed that both intracellular and extracellular NDM-1, MCR-1, and MEC-A could be positively detected in the samples. Overall, ClO2 disinfection enhanced the relative abundance of the iSARGs (P<0.05), exhibiting a seasonal pattern, and increasing in the spring, summer, and autumn. In spring, it improved the most, up to twice the abundance. No SARGs were detected positive in the winter, either intracellularly or extracellularly. There was no significant variation in the concentrations of eSARGs before and after ClO2 disinfection. Therefore, ClO2 disinfection cannot effectively remove iSARGs and eSARGs in the final effluent from the WWTP.


Asunto(s)
Compuestos de Cloro , Desinfectantes , Purificación del Agua , Antibacterianos/farmacología , Cloro , Compuestos de Cloro/farmacología , Desinfectantes/farmacología , Desinfección , Farmacorresistencia Microbiana/genética , Óxidos/farmacología
2.
Huan Jing Ke Xue ; 42(2): 749-760, 2021 Feb 08.
Artículo en Chino | MEDLINE | ID: mdl-33742869

RESUMEN

Emerging contaminants including antibiotics and antibiotic resistance genes (ARGs) have been frequently detected in drinking water resources. In this study, the occurrence of antibiotics and ARGs in various environmental matrices in representative drinking water sources in Jiangsu Province and their influencing factors were explored. Five representative drinking water sources in northern, central, and southern Jiangsu were selected. Water, surface sediment, and epilithic biofilm samples were harvested near the water intakes of each water resource in December 2018 and June 2019. The concentrations and abundances of ten antibiotics, one integrase gene intl1, and seven common ARGs were measured. The results suggest that the concentrations of the target antibiotics and ARGs are relatively low compared to previously reported data in China and elsewhere in the world. The target antibiotics were detected in all of the water sources. The concentrations of sulfonamides in the water, surface sediment, and epilithic biofilm ranged from not found (NF) to 37.4 ng·L-1, NF to 47.3 ng·g-1, and NF to 3759.1 ng·g-1, respectively; the concentrations of quinolones in three matrices were NF-5.3 ng·L-1, 0.4-32.5 ng·g-1, and NF-4220.9 ng·g-1, respectively. The detection rates of the ARGs including sul 1, sul2, tetW, and tetQ were 100%, among which the sulfonamides sul1 and sul2 showed the highest abundance. The absolute abundances of sul1 in the three matrices were 2.48×106 copies·L-1, 3.54×107 copies·g-1, and 1.44×109 copies·g-1, respectively. The abundances of ARGs in the sediments and epilithic biofilms were comparable, and were much higher than in the water body. The phyla Bacteroidetes, Proteobacteris, Firmicutes, Verrucobacteria, and Actinomycetes have proven potential hosts for ARGs and might play an important role in the transmission and diffusion of resistance genes. This study offers baseline information on the presence of antibiotics and ARGs in the drinking water sources of Jiangsu Province, providing a significant theoretical basis for ARGs pollution control and safety guidelines for drinking water resources.


Asunto(s)
Antibacterianos , Agua Potable , Antibacterianos/análisis , China , Agua Potable/análisis , Farmacorresistencia Microbiana/genética , Genes Bacterianos/genética , Recursos Hídricos
3.
Huan Jing Ke Xue ; 42(2): 761-765, 2021 Feb 08.
Artículo en Chino | MEDLINE | ID: mdl-33742870

RESUMEN

Antibiotic resistance genes (ARGs) are considered emerging contaminants posing an increasing threat to the ecological environment and global human health. Profiling ARGs in tailings ponds is essential to better understand their spatial and temporal dynamics. In this study, high-throughput quantitative polymerase chain reaction (PCR) techniques were used to investigate the occurrence, diversity, abundance, and distribution of ARGs in a tailings pond. A total of 97, 52, 44, and 56 ARGs were detected in WK0, WK1, WK2, and HS, respectively, with 11, 6, 3, and 6 mobile genetic elements (MGEs) also being detected, respectively. The absolute abundance of ARGs in the pond water ranged from 6.39×107 to 1.75×108 copies·L-1. Additionally, the abundance of MGEs were higher than ARGs in WK1 and WK2, indicating the potential for horizontal gene transfer (HGT). Furthermore, Cu, TOC, and MGEs were significantly associated with ARGs. Indeed, redundancy analysis (RDA) revealed that Cu, TOC, and MGEs explained 61.64% of the alteration of the ARG profiles, implying their potential roles in the spread and evolution of ARGs in tailings ponds.


Asunto(s)
Antibacterianos , Estanques , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Genes Bacterianos/genética , Humanos
4.
Huan Jing Ke Xue ; 42(2): 850-859, 2021 Feb 08.
Artículo en Chino | MEDLINE | ID: mdl-33742879

RESUMEN

Four antibiotics[azithromycin (AZM), sulfamethoxazole (SMZ), ciprofloxacin (CIP), and tetracycline (TCY)], and the antibiotic resistance genes (ARGs)[sulfonamides (sul1 and sul2), tetracyclines (tetX and tetM), quinolones (qnrS and qnrD), macrolides (ermB), and 16S rDNA] were selected as target compounds. Artificial ecosystems were constructed with combinations of two emergent plants and Microcystis aeruginosa (Acorus calamus+Cordyceps, algae+Cordyceps, algae+Acorus calamus, and algae+Acorus calamus+Cordyceps) in an indoor-simulated river system. Throughout the artificial ecosystems, changes in antibiotic concentrations and other pollution indicators (i.e., COD, NH4+-N, TP, and TN) were monitored in different media (the aqueous phase, sediment phase, and in plants), and the distribution and removal of ARGs in aqueous and sediment phases were explored. Removal of the target compounds was calculated based on mass balance, and the correlation between ARG abundance and environmental factors in the aqueous and sediment phases was analyzed. The results showed that the constructed artificial ecosystem achieved removal rates of COD, NH4+-N, TP, and TN ranging from 60.2% to 74.8%, 63.4% to 77.4%, 64.0% to 73.2%, and 46.8% to 54.8%, respectively. The antibiotics in the aqueous phase were notably removed and the artificial ecosystem 'algae+Acorus calamus+Cordyceps' achieved the best removal efficiency for the four antibiotics. Removal rates of the antibiotics in the sediment phase were ranked in the order TCY>CIP>AZM>SMZ; the removal efficiency of TCY in the 'algae+Acorus calamus+Cordyceps' system reached up to 53.5%. The total removal rates of antibiotics obtained by the ecosystems were ranked in the following order:algae+Acorus calamus+Cordyceps > algae+Cordyceps > algae+Acorus calamus > Acorus calamus+Cordyceps. Removal of the four ARGs was very efficient and was higher in the aqueous phase than in the sediment phase. Correlations between the ARGs, the other pollution indicators, and the antibiotics were variable; tetX and environmental factors were correlated in the aqueous phase, while AZM and its corresponding ARGs were not significantly correlated in the sediment phase. The results showed that ARGs can be targeted under corresponding antibiotic pressure and other types of environmental pressure. In the study system, the concentrations of antibiotics did not directly affect the transmission of ARGs. Overall, this study shows that artificial ecosystems constructed with emergent plants and Microcystis aeruginosa can be effective at purifying water and reducing the environmental risks of antibiotics in urban rivers.


Asunto(s)
Antibacterianos , Ríos , Farmacorresistencia Microbiana/genética , Ecosistema , Genes Bacterianos/genética , Aguas Residuales/análisis
5.
Sci Total Environ ; 764: 142907, 2021 Apr 10.
Artículo en Inglés | MEDLINE | ID: mdl-33757248

RESUMEN

Antibiotics are continuously released into aquatic environments and ecosystems where they accumulate, which increases risks from the transmission of antibiotic resistance genes (ARGs). However, it is difficult to completely remove antibiotics by conventional biological methods, and during such treatment, ARGs may spread via the activated sludge process. Easy-to-biodegrade food have been reported to improve the removal of toxic pollutants, and therefore, this study investigated whether such co-substrates may also decrease the abundance of ARGs and their transferal. This study investigated amoxicillin (AMO) degradation using 0-100 mg/L acetate sodium as co-substrate in a sequencing biological reactor. Proteobacteria, Bacteroidetes, and Actinobacteria were identified as dominant phyla for AMO removal and mineralization. Furthermore, acetate addition increased the abundances of adeF and mdsC as efflux resistance genes, which improved microbial resistance, the coping ability of AMO toxicity, and the repair of the damage from AMO. As a result, acetate addition contributed to almost 100% AMO removal and stabilized the chemical oxygen demand (~20 mg/L) in effluents when the influent AMO fluctuated from 20 to 100 mg/L. Moreover, the total abundance of ARGs decreased by approximately ~30%, and the proportion of the most dominant antibiotic resistance bacteria Proteobacteria decreased by ~9%. The total abundance of plasmids that encode ARGs decreased by as much as ~30%, implying that the ARG spreading risks were alleviated. In summary, easy-to-biodegrade food contributed to the simultaneous elimination of antibiotics and ARGs in an activated sludge process.


Asunto(s)
Antibacterianos , Aguas del Alcantarillado , Amoxicilina , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Ecosistema , Genes Bacterianos , Aguas Residuales
6.
J Environ Sci (China) ; 103: 12-19, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33743895

RESUMEN

Antibiotic resistance genes (ARGs) as emergence contaminations have spread widely in the water environment. Wild fish may be recipients and communicators of ARGs in the water environment, however, the distribution and transmission of ARGs in the wild fish and relevant water environment were rarely reported. Here, we have profiled ARGs and bacterial communities in wild freshwater fish and relevant water in a peri-urban river using high-throughput qPCR and 16S rRNA gene sequence. A total of 80 and 220 unique ARG subtypes were identified in fish and water samples. Fish and water both showed significant ARG seasonal variations (P < 0.05). The highest absolute abundance of ARGs in fish and water occurred in summer (1.32 × 109 copies per g, on average) and autumn (9.04 × 106 copies per mL), respectively. In addition, the bipartite network analysis showed that 9 ARGs and 1 mobile genetic element continuously shared in fish and water. Furthermore, bacteria shared in fish and water were found to significantly correlate with shard ARGs. The findings demonstrate that bacteria and ARGs in fish and water could interconnect and ARGs might transfer between fish and water using bacteria as a spreading medium.


Asunto(s)
Microbioma Gastrointestinal , Ríos , Animales , Antibacterianos/análisis , Farmacorresistencia Microbiana/genética , Genes Bacterianos , ARN Ribosómico 16S/genética , Agua
7.
Bioresour Technol ; 329: 124924, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33691205

RESUMEN

For exploring the impact of temperature on antibiotic resistant genes (ARGs) during sludge anaerobic digestion (AD), the dynamic variations of sludge ARGs, plasmid ARGs, and cell-free ARGs in mesophilic (25 °C and 35 °C) and thermophilic (55 °C) digesters were investigated. The study revealed that the abundance of sludge ARGs and plasmid ARGs in thermophilic sludge AD was significantly lower than that in mesophilic digesters, while the cell-free ARGs abundance of the thermophilic digesters was similar to mesophilic digesters. Higher archaea abundance, lower bacteria abundance, and different microbial community were found in thermophilic digesters compared to that of mesophilic ones. Firmicutes might be a main group of potential hosts of ARGs in sludge AD. The distinct microbial community was the main contributor to the low ARGs abundance in thermophilic sludge AD. Thermophilic operation at 55 °C rather than mesophilic operation is more conducive to control ARGs in sludge anaerobic digestion.


Asunto(s)
Antibacterianos , Aguas del Alcantarillado , Anaerobiosis , Antibacterianos/farmacología , Bacterias/genética , Farmacorresistencia Microbiana/genética , Temperatura
8.
Water Res ; 195: 116979, 2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-33690012

RESUMEN

Zero valent iron (ZVI) has been previously documented to attenuate the propagation of antibiotic resistance genes (ARGs) in microbes, while how ZVI affects the evolution of ARGs remains unclear. Herein, we investigated the influences of ZVI on ARGs dissemination in anaerobic bioreactor treating oxytetracycline (tet) containing wastewater, by deciphering the roles of iron homeostasis and regulatory effects. A net reduction of tet gene targets ranging from 0.75 to 1.88 and 0.67 to 2.08 log unit in intracellular and extracellular DNA was achieved at the optimal dosage of 5 g/L ZVI, whereas 20 g/L ZVI made no effects on ARGs reduction. The reduced ARGs abundance by ZVI was directly related to the inhibited horizontal transfer of ARGs and decreased proliferation of resistant strains (mainly Paludibacter and WCHB1-32). The potential mechanisms included the increased antioxidant capacity, the depressed efflux pump system and the weakened energy driving force by Fur regulon in microbes (especially for Cloacibacterium and Dechloromonas). The negligible influence of 20 g/L ZVI on ARGs reduction was ascribed to the iron-catalyzed oxidative damage and reduced physiological activity. This study firstly illustrated the potential relationships among activation of iron uptake regulator leading to protection against oxidative stress, alternation of physiological metabolisms and reduction of ARGs dissemination. This work extents our understanding about the priority of ZVI in mitigating ARGs proliferation and sheds light on its potential application in wastewater treatment plants.


Asunto(s)
Antibacterianos , Hierro , Anaerobiosis , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Homeostasis
9.
Bioresour Technol ; 330: 124970, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33735726

RESUMEN

Currently, anaerobic sludge digestion (ASD) is considered not only for treating residual sewage sludge and energy recovery but also for the reduction of antibiotic resistance genes (ARGs). The current review highlights the reasons why antibiotic resistant bacteria (ARB) and ARGs exist in ASD and how ASD performs in the reduction of ARB and ARGs. ARGs and ARB have been detected in ASD with some reports indicating some of the ARGs can be completely removed during the ASD process, while other studies reported the enrichment of ARB and ARGs after ASD. This paper reviews the performance of ASD based on operational parameters as well as environmental chemistry. More studies are needed to improve the performance of ASD in reducing ARGs that are difficult to handle and also differentiate between extracellular (eARGs) and intracellular ARGs (iARGs) to achieve more accurate quantification of the ARGs.


Asunto(s)
Genes Bacterianos , Aguas del Alcantarillado , Anaerobiosis , Antagonistas de Receptores de Angiotensina , Inhibidores de la Enzima Convertidora de Angiotensina , Antibacterianos/farmacología , Bacterias/genética , Digestión , Farmacorresistencia Microbiana/genética , Aguas Residuales
10.
Bioresour Technol ; 330: 124945, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33735733

RESUMEN

The influence of copper ion (Cu2+) on anaerobic ammonium oxidation (anammox) performance and microbial community structures after oxytetracycline (OTC) stress recovery were assessed. Experimental results demonstrated that anammox performance were stressed by 1.0 mg L-1 Cu2+ and inhibitions were reversible with total nitrogen removal rate higher than 3.08 ± 0.2 kg N m-3 d-1. The residual OTC in the anammox sludge could combine with Cu2+ introduced and thereby retarded inhibition on performance in the presence of 2.0 mg L-1 Cu2+. Moreover, the positive relation of dominant bacterium Ca. Anammoxoglobus with the abundance of functional genes and parts of antibiotic resistance genes were observed, suggesting that regain of performance was the results of the gradual domestication of latent resistant species after inhibition. This investigation reveals new insights into resistance of anammox performance for Cu2+ and OTC.


Asunto(s)
Microbiota , Oxitetraciclina , Anaerobiosis , Antibacterianos/farmacología , Reactores Biológicos , Cobre , Farmacorresistencia Microbiana/genética , Nitrógeno , Oxidación-Reducción , Oxitetraciclina/farmacología , Aguas del Alcantarillado
11.
BMC Bioinformatics ; 22(1): 117, 2021 Mar 10.
Artículo en Inglés | MEDLINE | ID: mdl-33691615

RESUMEN

BACKGROUND: Metagenomics is gaining attention as a powerful tool for identifying how agricultural management practices influence human and animal health, especially in terms of potential to contribute to the spread of antibiotic resistance. However, the ability to compare the distribution and prevalence of antibiotic resistance genes (ARGs) across multiple studies and environments is currently impossible without a complete re-analysis of published datasets. This challenge must be addressed for metagenomics to realize its potential for helping guide effective policy and practice measures relevant to agricultural ecosystems, for example, identifying critical control points for mitigating the spread of antibiotic resistance. RESULTS: Here we introduce AgroSeek, a centralized web-based system that provides computational tools for analysis and comparison of metagenomic data sets tailored specifically to researchers and other users in the agricultural sector interested in tracking and mitigating the spread of ARGs. AgroSeek draws from rich, user-provided metagenomic data and metadata to facilitate analysis, comparison, and prediction in a user-friendly fashion. Further, AgroSeek draws from publicly-contributed data sets to provide a point of comparison and context for data analysis. To incorporate metadata into our analysis and comparison procedures, we provide flexible metadata templates, including user-customized metadata attributes to facilitate data sharing, while maintaining the metadata in a comparable fashion for the broader user community and to support large-scale comparative and predictive analysis. CONCLUSION: AgroSeek provides an easy-to-use tool for environmental metagenomic analysis and comparison, based on both gene annotations and associated metadata, with this initial demonstration focusing on control of antibiotic resistance in agricultural ecosystems. Agroseek creates a space for metagenomic data sharing and collaboration to assist policy makers, stakeholders, and the public in decision-making. AgroSeek is publicly-available at https://agroseek.cs.vt.edu/ .


Asunto(s)
Farmacorresistencia Microbiana/genética , Microbiología Ambiental , Genes Bacterianos , Metadatos , Metagenómica , Ecosistema , Internet , Metagenoma , Programas Informáticos
12.
Environ Pollut ; 276: 116704, 2021 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-33652188

RESUMEN

Antibiotic resistance genes (ARGs) are emerging contaminants in the environment and have been highlighted as a worldwide environmental and health concern. As important participants in the biogeochemical cycles, mangrove ecosystems are subject to various anthropogenic disturbances, and its microbiota may be affected by various contaminants such as ARGs. This study selected 13 transects of mangrove-covered areas in Hainan, China for sediment sample collection. The abundance and diversity of ARGs and mobile genetic elements (MGEs) were investigated using high-throughput quantitative polymerase chain reaction (HT-qPCR), and high-throughput sequencing was used to study microbial structure and diversity. A total of 179 ARGs belonging to 9 ARG types were detected in the study area, and the detection rates of vanXD and vatE-01 were 100%. The abundance of ARGs was 8.30 × 107-6.88 × 108 copies per g sediment (1.27 × 10-2-3.39 × 10-2 copies per 16S rRNA gene), which was higher than similar studies, and there were differences in the abundance of ARGs in these sampling transects. The multidrug resistance genes (MRGs) accounted for the highest proportion (69.0%), which indicates that the contamination of ARGs in the study area was very complicated. The ARGs significantly positively correlated with MGEs, which showed that the high level of ARGs was related to its self-enhancement. The dominant bacteria at the genus level were Desulfococcus, Clostridium, Rhodoplanes, Bacillus, Vibrio, Enterococcus, Sedimentibacter, Pseudoalteromonas, Paracoccus, Oscillospira, Mariprofundus, Sulfurimonas, Aminobacterium, and Novosphingobium. There was a significant positive correlation between 133 bacterial genera and some ARGs. Chthoniobacter, Flavisolibacter, Formivibrio, Kaistia, Moryella, MSBL3, Perlucidibaca, and Zhouia were the main potential hosts of ARGs in the sediments of Hainan mangrove area, and many of these bacteria are important participants in biogeochemical cycles. The results contribute to our understanding of the distribution and potential hosts of ARGs and provide a scientific basis for the protection and management of Hainan mangrove ecosystem.


Asunto(s)
Antibacterianos , Genes Bacterianos , Antibacterianos/farmacología , Bacterias/genética , China , Farmacorresistencia Microbiana/genética , Humanos , Islas , ARN Ribosómico 16S
13.
Sci Total Environ ; 770: 145399, 2021 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-33736375

RESUMEN

Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.


Asunto(s)
Estiércol , Microbiota , Animales , Antibacterianos/farmacología , Farmacorresistencia Microbiana/genética , Granjas , Genes Bacterianos , Metagenómica , Microbiota/genética , ARN Ribosómico 16S , Suelo , Microbiología del Suelo
14.
Ecotoxicol Environ Saf ; 214: 112070, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33652361

RESUMEN

In line with sustainable development principles and in order to combat climate change, which contributes to progressive soil depletion, various solutions are being sought to use treated sewage sludge as a soil amendment to improve soil quality and enrich arable soils with adequate amounts of biogenic compounds. This review article focuses on the effects of the agricultural use of biosolids on the environment. The article reviews the existing knowledge on selected emerging contaminants in treated sewage sludge and describes the impact of these pollutants on the environment and living organisms based on 183 publications selected from over 16,000 papers on related topics published over the last ten years. This study deals not only with chemical contaminants but also genetic determinants of resistance to these compounds. Current research has questioned the agricultural use of biosolids due to the presence of mutual interactions between antibiotics, heavy metals, the genetic determinants of resistance (antibiotic resistance genes - ARGs and heavy metal resistance genes - HMRGs) and non-steroidal anti-inflammatory drugs as well as the risks associated with their transfer to the environment. This study emphasizes the need for more extensive legal regulations that account for other pollutants of environmental concern (PEC), particularly in countries where sewage sludge is applied in agriculture most extensively. Future research should focus on more effective methods of eliminating PEC from sewage sludge, especially from the sludge that is used to fertilize agricultural land, because even small amounts of these micropollutants can have serious implications for the health and life of humans and animals.


Asunto(s)
Agricultura , Aguas del Alcantarillado/química , Contaminantes del Suelo/análisis , Eliminación de Residuos Líquidos/métodos , Animales , Antibacterianos , Productos Agrícolas , Farmacorresistencia Microbiana/genética , Contaminantes Ambientales , Humanos , Metales Pesados/análisis , Suelo/química
15.
Sci Total Environ ; 772: 145516, 2021 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-33571766

RESUMEN

Mining activities are known to generate a large amount of mine tailings and acid mine drainage which contain varieties of heavy metals. Heavy metals play an important role in co-selection for bacterial antibiotic resistance. However, the characteristics of antibiotic resistance genes (ARGs) in mining-affected water environments are still unclear. Here we investigated the pollution of metals, profiles of ARGs, mobile genetic elements (MGEs) and microbial community in mining-affected surface water and groundwater. The results showed that in the tested water samples, the concentrations of Zn and Mn were the highest, and Ni was the lowest. Higher abundances of ARGs with great proportion of sulfonamides, chloramphenicols and tetracyclines resistance genes were found in mining-affected water when compared with those without mining activities. Additionally, there were positive correlations between heavy metals (especially Ni, Zn and Mn) and these ARGs. Linear regression analysis suggested that MGEs were positively correlated with ARGs. In addition, total phosphorus was correlated with ARGs (p < 0.05). The microbial community was different between the mining-affected water and the reference (p < 0.05). Proteobacteria, Bacteroidetes and Actinobacteria were dominant phyla in the surface water and groundwater. Network analysis showed that many ARGs were significantly associated with these dominant bacteria, which suggested they might be potential hosts for these ARGs. These findings provide a clear evidence that the mining activities in the study area had a significant impact on surface water and groundwater to different degrees.


Asunto(s)
Antibacterianos , Agua Subterránea , Antibacterianos/análisis , Farmacorresistencia Microbiana/genética , Genes Bacterianos , Agua
16.
Ecotoxicol Environ Saf ; 213: 111981, 2021 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-33592372

RESUMEN

Environmental pollution due to resistance genes from livestock manure has become a serious issue that needs to be resolved. However, little studies focused on the removal of resistance genes in simultaneous processing of livestock feces and urine. This study investigated the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and class 1 integron-integrase gene (intI1) during thermophilic fermentation of swine manure in an ectopic fermentation system (EFS), which has been regarded as a novel system for efficiently treating both feces and urine. The abundances of MRGs and tetracycline resistance genes were 34.44-97.71% lower in the EFS. The supplementation of heavy metals significantly increased the abundance of intI1, with the enhancement effect of copper being more prominent than that of zinc. The highest abundances of resistance genes and intI1 were observed at high Cu levels (A2), indicating that Cu can increase the spreading of resistance genes through integrons. Network analysis revealed the co-occurrence of ARGs, MRGs, and intI1, and these genes potentially shared the same host bacteria. Redundancy analysis showed that the bacterial community explained most of the variations in ARGs, and environmental factors had influences on ARGs abundances by modulating the bacterial community composition. The decreased Sphingomonas, Comamonas, Acinetobacter, Lactobacillus, Bartonella, Rhizobium, and Bacteroides were mainly responsible for the reduced resistance genes. These results demonstrate that EFS can reduce resistance genes in simultaneous processing of livestock feces and urine.


Asunto(s)
Farmacorresistencia Microbiana/genética , Fermentación/fisiología , Genes Bacterianos , Estiércol/microbiología , Metales Pesados/análisis , Animales , Antibacterianos/análisis , Bacterias/efectos de los fármacos , Cobre , Integrones , Ganado , Estiércol/análisis , Porcinos , Tetraciclina/farmacología
17.
Ecotoxicol Environ Saf ; 213: 112011, 2021 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-33592374

RESUMEN

Denitrification play an important role in nitrogen cycle and is affected by veterinary drugs entering agricultural soils. In the present study, the effects of copper and florfenicol on denitrification, related antibiotic resistance and environmental variables were characterized using real-time quantitative PCR (qPCR) and amplicon sequencing in a short-term (30 d) soil model experiment. Drug additions significantly decreased the nirS gene abundance (P < 0.05) but maximized the abundance of gene nirK in soil containing florfenicol and moderate copper levels (150 mg kg-1). Surprisingly, copper additions decreased the fexB gene abundance, however, the abundance of gene pcoD significantly increased in soils containing florfenicol, moderate copper levels (150 mg kg-1), and florfenicol and low copper levels (30 mg kg-1), respectively (P < 0.05). Overall, the nirK-type community composition was more complex than that of nirS-type but Proteobacteria predominated (> 90%) in both communities. Correlation analysis indicated that the gene abundance of fexB was highly correlated with NH4+-N (P < 0.05) and NO3--N (P < -0.01), and floR gene abundance was positively correlated with nirK (P < 0.01). Besides, the abundance of nirS-type genera Bradyrhizobium and Pseudomonas were obviously related to total organic matter (TOM), total nitrogen (TN) or total phosphorus (TP) (P < 0.05), while the abundance of nirK-type Rhizobium, Sphingomonas and Bosea showed a significantly correlated with TOM, TN or copper contents (P < 0.05). Taken together, copper and florfenicol contamination increased the possibility of durg resistance genes spread in agricultural soils through nitrogen transformation.


Asunto(s)
Cobre/toxicidad , Desnitrificación/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Microbiología del Suelo , Contaminantes del Suelo/toxicidad , Tianfenicol/análogos & derivados , Agricultura , Desnitrificación/genética , Nitrógeno , Fósforo , Proteobacteria/genética , Suelo , Tianfenicol/toxicidad , Verduras
18.
Microbiome ; 9(1): 47, 2021 02 17.
Artículo en Inglés | MEDLINE | ID: mdl-33597039

RESUMEN

BACKGROUND: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity. RESULTS: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development. CONCLUSIONS: The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.


Asunto(s)
Microbiota , Moraxella/genética , Moraxella/aislamiento & purificación , Propionibacteriaceae/genética , Propionibacteriaceae/aislamiento & purificación , Piel/microbiología , Adulto , Anciano , Antibacterianos/farmacología , China/etnología , Farmacorresistencia Microbiana/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Grupos Étnicos , Femenino , Genes Bacterianos/efectos de los fármacos , Humanos , Masculino , Metagenómica , Microbiota/efectos de los fármacos , Microbiota/genética , Persona de Mediana Edad , Moraxella/efectos de los fármacos , América del Norte/etnología , Propionibacteriaceae/efectos de los fármacos , Staphylococcus/efectos de los fármacos , Staphylococcus/genética , Staphylococcus/aislamiento & purificación , Simbiosis , Adulto Joven
19.
Microbiome ; 9(1): 32, 2021 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-33517907

RESUMEN

BACKGROUND: While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors. RESULTS: Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features. CONCLUSIONS: Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.


Asunto(s)
Entorno Construido , Microbiota , Boca/microbiología , Cepillado Dental , Adolescente , Adulto , Anciano , Farmacorresistencia Microbiana/efectos de los fármacos , Farmacorresistencia Microbiana/genética , Humanos , Metagenoma/efectos de los fármacos , Metagenoma/genética , Microbiota/efectos de los fármacos , Microbiota/genética , Persona de Mediana Edad , Boca/efectos de los fármacos , Triclosán/farmacología , Adulto Joven
20.
Microbiome ; 9(1): 40, 2021 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-33557954

RESUMEN

BACKGROUND: The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs), are highly transmittable between food, water, animal, and human to mitigate the efficacy of antibiotics. Accurately identifying ARGs is thus an indispensable step to understanding the ecology, and transmission of ARGs between environmental and human-associated reservoirs. Unfortunately, the previous computational methods for identifying ARGs are mostly based on sequence alignment, which cannot identify novel ARGs, and their applications are limited by currently incomplete knowledge about ARGs. RESULTS: Here, we propose an end-to-end Hierarchical Multi-task Deep learning framework for ARG annotation (HMD-ARG). Taking raw sequence encoding as input, HMD-ARG can identify, without querying against existing sequence databases, multiple ARG properties simultaneously, including if the input protein sequence is an ARG, and if so, what antibiotic family it is resistant to, what resistant mechanism the ARG takes, and if the ARG is an intrinsic one or acquired one. In addition, if the predicted antibiotic family is beta-lactamase, HMD-ARG further predicts the subclass of beta-lactamase that the ARG is resistant to. Comprehensive experiments, including cross-fold validation, third-party dataset validation in human gut microbiota, wet-experimental functional validation, and structural investigation of predicted conserved sites, demonstrate not only the superior performance of our method over the state-of-art methods, but also the effectiveness and robustness of the proposed method. CONCLUSIONS: We propose a hierarchical multi-task method, HMD-ARG, which is based on deep learning and can provide detailed annotations of ARGs from three important aspects: resistant antibiotic class, resistant mechanism, and gene mobility. We believe that HMD-ARG can serve as a powerful tool to identify antibiotic resistance genes and, therefore mitigate their global threat. Our method and the constructed database are available at http://www.cbrc.kaust.edu.sa/HMDARG/ . Video abstract (MP4 50984 kb).


Asunto(s)
Aprendizaje Profundo , Farmacorresistencia Microbiana/genética , Genes Bacterianos/genética , Animales , Humanos , beta-Lactamasas/genética
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