Diversity and potential environmental risks of DNA viruses on international ships' ballast water at Shanghai port, China.

The misuse of antibiotics causes antibiotic resistance genes (ARGs) in bacteria to be gradually enriched by environmental selection, resulting in increased tolerance and resistance in bacteria to antibiotics. Ballast water is a mobile carrier for the global transfer of bacteria and genes, thus posing a certain risk of ARGs spreading into the global ocean. Therefore, it is important to investigate the current status of ARGs in ballast water, as well as control the abundance of ARGs. Herein, we attempt to comprehensively summarize the distribution and abundance of ARGs in ballast water from different sea areas and analyze the influencing factors (such as physical factors, chemical factors, temperature, pH, etc.) on the distribution of ARGs. Furthermore, we seek to review the changes in ARGs after differential disinfection technology treatment in ballast water (including chlorination, ultraviolet, ozone, and free radical technology), especially the enhancing effect of subinhibitory concentrations of disinfectants on ARGs transfer. Overall, we believe this review can serve as a guide for future researchers to establish a more reasonable standard of ballast water discharge that considers the pollution of ARGs and provide new insight into the risk of vertical and horizontal ARG transfer in ballast water after disinfection.

There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.

Spatial distribution, source identification, and environmental risk of antibiotic resistance genes in the lower reaches of the Yangtze River

Occurrence and spatial distribution of antibiotic resistance genes in the Bohai Sea and Yellow Sea areas, China

Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach.

Temporal variations, distribution, and dissemination of antibiotic resistance genes and changes of bacterial communities in a biofloc-based zero-water-exchange mariculture system

The overuse of antibiotics in livestock farms is general, leading to a wide distribution of antibiotic resistance genes (ARGs) in aquatic environment adjacent to livestock farms. However, researches of the distribution and types of ARGs in aquatic environment of China are still in the initial stage. In this study, wastewater and surface water samples were collected from 12 livestock farms (four pig farms, four cattle farms, and four chicken farms) in Jiangsu Province of China. The prevalence, abundance, and distribution of 22 ARGs were investigated, which were categorized into six groups, including nine tetracyclin resistance genes, three sulfonamides resistance genes, three quinolone resistance genes, two macrolide resistance genes, three aminoglycoside resistance genes, and two multidrug resistance genes, employing quantitative real-time PCR (qPCR). The results suggested that all of the 22 ARGs were detected in samples. Sul1, sul2, and tetM were the most abundant with the average concentration of 3.84 × 10(1) copies/16S recombinant RNA (rRNA) gene copies, 1.62 × 10(1) copies/16S rRNA gene copies, 2.33 × 10(1) copies/16S rRNA gene copies, respectively. Principle component analysis revealed that the comprehensive pollution of ARGs in northern Jiangsu was more serious. ARGs in wastewater were more abundant when compared to that in surface water. A preliminary study regarding the fate of ARGs after an aerobiotic process showed that tetA, tetC, sul1, sul2, oqxB, and qnrS were significantly increased. And, among the tetracycline resistance genes, the efflux pump genes were enriched while the ribosomal protection protein encoding genes were decreased in the aerobiotic process. The prevalance of ARGs in water environment is of concern; more surveillance is required to determine the pollution level and pattern of antibiotic resistance genes.

Distribution of antibiotic resistance genes in soil amended using Azolla imbricata and its driving mechanisms.

In many parts of the world, shipping-related emissions have already exceeded or are expected to soon exceed those from land-based sources. Shipping emissions can be reduced substantially by using some of the same technologies being applied to land-based sources, including cleaner engines and fuels, exhaust control methods, and operational modifications. Various ports are testing the feasibility of these mechanisms with varying degrees of success. What is perhaps most greatly needed is expedited creation of better regulations at all levels, from the International Maritime Organization to port city authorities.

The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) have attracted great concerns worldwide. Wastewater treatment plants (WWTPs) are reservoirs of ARGs while wastewater/sludge treatment processes are considered as important means to control these emerging biological pollutants. However, the full profiles of ARGs in WWTPs or the removal efficiency of ARGs by wastewater/sludge treatment process was not well characterized yet. Thus, the major tasks in this study were (1) to reveal the broad-spectrum profiles of ARGs in WWTPs; (2) to investigate the removal efficiencies of ARGs using wastewater/sludge treatment process; (3) to examine the differences and similarities of ARGs in samples from WWTPs and other environments; (4) to develop an efficient platform for examination on the broad-spectrum profiles of environmental ARGs through metagenomic analysis.
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\nActivated sludge is an important segment for harboring ARGs and horizontal gene transfer of ARGs among different microbial communities. Existence of six-lactam resistance genes were found through PCR and qPCR approaches in activated sludge collected from 15 WWTPs in East Asia and North America. Abundances of these resistance genes ranged from 5.34×101 copies/ng DNA to 5.49×104 copies/ng DNA. Broad-spectrum profiles of ARGs in activated sludge from a local WWTP in a period of four years were investigated through metagenomic analysis. A total of 16 ARGs types were detected. During the 4-year period, a descending trend of total ARGs abundance was found but the abundances of _-lactam and quinolone resistance genes increased. Moreover, resistance genes of tetracycline, sulfonamide and vancomycin showed seasonal variation.
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\nMetagenomic analysis was also applied to study the fate of ARGs in wastewater/sludge treatment processes in a full-scale municipal WWTP. Results suggested that 99.82% of ARGs in influent could be removed by wastewater treatment process while only 20.70% of ARGs could be removed in sludge anaerobic digestion. The distribution of ARGs in WWTP was significantly correlated with six genera and five of which included potential pathogens.
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\nEffect of temperature on ARGs removal from activated sludge by anaerobic digestion was examined through metagenomic analysis. No significant change was found for the removal efficiency of total ARGs using bench-scale thermophilic or mesophilic anaerobic digestion reactor. But results suggested that more ARGs subtypes can be effectively removed by anaerobic digestion under mesophilic condition.
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\nARGs profiles in 10 typical environments, including different sections in WWTPs, river water, drinking water, soils, sediments and faeces from livestock and human, were revealed through metagenomic analysis. Generally the total ARGs abundances in different environments increased with the impacts of anthropogenic activities. Co-occurrence of ARGs subtypes in different environments was studied using network analysis, tetM and aminoglycoside resistance genes were recognized as the indicators to estimate the abundances of other co-occurred ARGs subtypes.
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\nThe processes in metagenomic analysis were improved to shorten the analysis time and simplify the classification of ARGs-like sequences. Error and redundant sequences were removed from the widely used reference database of ARGs. A structured database was then constructed to realize the automatic classification of ARGs in metagenomic data. A hybrid alignment process was optimized for rapid ARGs or other specific functional genes annotation as well.

Antibiotic resistance genes might serve as new indicators for wastewater contamination of coastal waters: Spatial distribution and source apportionment of antibiotic resistance genes in a coastal bay

Microbial communities and mobile genetic elements determine the variations of antibiotic resistance genes for a continuous year in the urban river deciphered by metagenome assembly

The effect of extracellular polymeric substances on the distribution and transmission of antibiotic resistance genes treating antibiotic wastewater via microbial electrolysis cells

Diverse bacterial hosts and potential risk of antibiotic resistomes in ship ballast water revealed by metagenomic binning

Vessel transport of antibiotic resistance genes across oceans and its implications for ballast water management