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.

Heavy metal contamination poses grave risks to all kinds of life. The fastest growing automotive, electroplating, and battery industries release the most common heavy metal, Nickel, into the environment, which has lethal impacts on human health. Our research aims to find Ni-resistant bacteria in the metal-contaminated soil that have a great potential for removing Ni from the environment. Attempts have been made to extract and characterize Ni-resistant bacteria from automobile and electroplating industry waste-contaminated soil using serial dilution, streak plating, and various morphological, biochemical, and genetic techniques. The maximum tolerable concentration of Ni and other heavy elements, such as cadmium, lead, and aluminium for the selected isolate, was investigated using the UV-Vis spectrophotometric method. Additionally, the bacterial strain's ability to remove Ni was assessed using an atomic absorption spectrophotometer.  The current research reveals a novel strain of Kluyvera cryocrescens that could withstand Ni, Cd, Pb, Al, and combinations of these heavy metals. The maximum tolerance concentration of K. cryocrescens M7 for Ni, Cd, Pb, and Al was found to be 150 ppm, 200 ppm, 1000 ppm, and 150 ppm, respectively. Additionally, it was also observed that the bacterial strain could remove Ni by 29.57%, 35.36%, 48.41%, 46.91%, and 44.88% after 12, 24, 48, 72, and 96 hours, respectively. The strain has also exhibited resistance to vancomycin, ampicillin, carbenicillin, and streptomycin. This research discovered a novel bacterial strain, K. cryocrescens M7 that may be beneficial for removing heavy metals, particularly Ni, from metal-contaminated soil.

Sewage treatment plants (STPs) are considered as “hotspots” for the emergence and proliferation of antibiotic resistance. However, the impact of heavy metals contamination on dispersal of antibiotic resistance in STPs is poorly understood. This study simultaneously investigated the effect of removal of metal and antibiotic resistance as well as mobile elements at different treatment units of STPs in Delhi, India. Results showed that treatment technologies used in STPs were inefficient for the complete removal of metal and antibiotic resistance, posing an ecological risk of co-selection of antibiotic resistance. The strong correlations were observed between heavy metals, metal and antibiotic resistance, and integrons, implying that antibiotic resistance may be exacerbated in the presence of heavy metals via integrons, and that metal and antibiotic resistance share a common or closely associated mechanism. We quantified an MRG rcnA, conferring resistance to Co and Ni, and identified that it was more abundant than all MRGs, ARGs, integrons, and 16S rRNA, suggesting rcnA could be important in antibiotic resistance dissemination in the environment. The associations between heavy metals, metal and antibiotic resistance, and integrons highlight the need for additional research to better understand the mechanism of co-selection as well as to improve the removal efficacy of current treatment systems.

Thermokarst lakes form as the results of ice-rich permafrost thawing and act as important water resources in cold regions. However, the distributions of antibiotic resistance genes (ARGs) in thermokarst lakes are far less studied. Using metagenomic sequencing approach, we provided the first study to document ARGs in thermokarst lakes of the Yellow River Source Area on the Qinghai-Tibet Plateau (QTP). The results revealed that both sediment and water of the thermokarst lakes harbor diverse ARGs. Multidrug resistance genes were the most diverse, while rifamycin resistance genes were the most abundant with rpoB2 and rpoB genes having the highest proportion. Sediment samples contained more ARGs than water samples, but their composition differed between the two types of samples. However, the composition variations of sediment and water ARGs were closely correlated. The Sorensen dissimilarities of ARGs were controlled by strong turnover processes in sediment samples, and by turnover and nestedness in water samples. High contributions of nestedness were found between sediment and water samples. Moreover, ARGs in water had more significant relationships with environmental variables than that in sediment. Given the role of thermokarst lakes as important water resources in permafrost landscape, as well as intensifying influences of climate change and anthropogenetic activities, thermokarst lakes could bring potential ARG risks, warranting further investigation and evaluation.

Antimicrobial resistance genes (ARGs) and virulence factor genes (VFGs) constitute a serious threat to public health, and climate change has been predicted to affect the increase in bacterial pathogens harboring ARGs and VFGs. However, studies on bacterial pathogens and their ARGs and VFGs in permafrost region have received limited attention. In this study, a metagenomic approach was applied to a comprehensive survey to detect potential ARGs, VFGs, and pathogenic antibiotic resistant bacteria (PARB) carrying both ARGs and VFGs in the active layer and permafrost. Overall, 70 unique ARGs against 18 antimicrobial drug classes and 599 VFGs classified as 38 virulence factors were detected in the Arctic permafrost region. Eight genes with mobile genetic elements (MGEs) carrying ARGs were identified; most MGEs were classified as phages. In the metagenome-assembled genomes, the presence of 15 PARB was confirmed. The soil profile showed that the transcripts per million (TPM) values of ARGs and VFGs in the sub-soil horizon were significantly lower than those in the top soil horizon. Based on the TPM value of each gene, major ARGs, VFGs, and these genes in PARB from the Arctic permafrost region were identified and their distribution was confirmed. The major host bacteria for ARGs and VFGs and PARB were identified. A comparison of the percentage identity distribution of ARGs and VFGs to reference databases indicated that ARGs and VFGs in the Arctic soils differ from previously identified genes. Our results may help understand the characteristics and distribution of ARGs, VFGs, and these genes in PARB in the Arctic permafrost region. This findings suggest that the Arctic permafrost region may serve as potential reservoirs for ARGs, VFGs, and PARB. These genes could pose a new threat to human health if they are released by permafrost thawing owing to global warming and propagate to other regions.

Antibiotic resistance genes (ARGs) and virulence factors (VFs) are critical threats to human health. Their abundance in aquatic ecosystems is maintained and enhanced via selection driven by environmental xenobiotics. However, their activity and expression in these environments under xenobiotic stress remains unknown. Here ARG and VF expression profiles were examined in aquatic microcosms under ciprofloxacin, glyphosate and sertraline hydrochloride treatment. Ciprofloxacin increased total expression of ARGs, particularly multidrug resistance genes. Total expression of ARGs and VFs decreased significantly under glyphosate and sertraline treatments. However, in opportunistic human pathogens, these agents increased expression of both ARGs and VFs. Xenobiotic pollutants, such as the compounds we tested here, have the potential to disrupt microbial ecology, promote resistance, and increase risk to human health. This study systematically evaluated the effects of environmental xenobiotics on transcription of ARGs and VFs, both of which have direct relevance to human health. Transcription of such genes has been overlooked in previous studies.

Antibiotic resistance genes (ARGs) are abundantly shed in feces. Thus, it is crucial to identify their host sources so that ARG pollution can be effectively mitigated and aquatic ecosystems can be properly conserved. Here, spatiotemporal variations and sources of ARGs in the Longjiang watershed of South China were investigated by linking them with microbial source tracker (MST) indicators. The most frequently detected ARGs (>90%) were sulI, sulII, blaTEM, tetW, ermF, and the mobile element intI1. Spatial distribution analyses showed that tributaries contributed significantly more sulI, sulII, and ermF contamination to the Longjiang watershed than the main channel. MST indicator analysis revealed that the Longjiang watershed was contaminated mainly by human fecal pollution. Livestock- and poultry-associated fecal pollution significantly declined after the swine fever outbreak. The occurrence of most ARGs is largely explained by human fecal pollution. In contrast, pig fecal pollution might account for the prevalence of tetO. Moreover, combined human-pig fecal pollution contributed to the observed blaNDM₋₁ distribution in the Longjiang watershed. Subsequent analysis of the characteristics of MST markers disclosed that the relatively lower specificities of BacHum and Rum-2-Bac may lead to inaccurate results of tracking ARG pollution source. The present study determined spatiotemporal variations and ARG origins in the Longjiang watershed by combining MST markers. It also underscored the necessity of using multiple MST markers simultaneously to identify and characterize ARG pollution sources accurately.

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, there were little data on the diversity and distribution of ARGs associated with road sediments transported in runoff. The investigation of ARGs diversity showed that sulfonamide resistance genes (sul2 and sul3) occupied 61.7%–82.3% of total ARGs in runoff. The analysis of ARGs distribution in particulate matter (PM) implied that both tetQ and trbC existed mainly in PM with size of 150–300 μm, but other ARGs and mobile genetic elements (MGEs) were dominant in PM with size <75 μm. The discussion of potential hosts indicated that target genes (ermF, blaOXA1/blaOXA30, ermC, qnrA, sul2, tnpA-01, intI2, tetW, intI1, sul3, trbC) had the strongest subordinate relationship with Proteobacteria at phylum level and Enterobacter at genus level. The effect evaluation of ARGs distribution suggested that 13 kinds of ARGs were positively correlated with Pr/PS and Zeta potential, resulting in the more ARGs in PM with smaller size (<75 μm).

The high antibiotic resistance gene (ARGs) contents in livestock manure pose a potential risk to environment and human health. The heap composting with an ambient temperature and thermophilic composting are two methods for converting livestock manure into fertilizer. This study investigated the variations in ARGs and mobile genetic elements (MGEs) and revealed potential mechanisms for ARGs removal using the two composting methods. The ARGs abundance were enriched by 44-fold in heap composting, among them, the macrolide-resistance genes increased significantly. On the contrary, the ARGs were removed by 92% in thermophilic composting, among them, tetracycline-resistance genes decreased by 97%. The bacterial hosts of ARGs were associated with the variations of ARGs and MGEs. The tetO was correlated with the most diverse bacteria in heap composting, and Bacteroidetes was the major host bacteria. While tetT was correlated with the most diverse bacteria in thermophilic composting, and Proteobacteria was the major host bacteria. Structural equation models showed that the enrichment of ARGs in heap composting was mainly correlated with bacterial communities, whereas, the removal of ARGs in thermophilic composting was directly affect by MGEs. Composting temperature directly affected the variations in ARGs. Higher and lower temperatures significantly decreased and increased, respectively, ARGs and MGEs abundance levels.

Seas and oceans are a global reservoir of antibiotic resistance genes (ARGs). Only a few studies investigated the dynamics of ARGs along the water column of the Black Sea, a unique environment, with a peculiar geology, biology and history of anthropogenic pollution. In this study, we analyzed metagenomic data from two sampling campaigns (2013 and 2019) collected across three different sites in the Western Black Sea at depths ranging from 5 to 2000 m. The data were processed to annotate ARGs, metal resistance genes (MRGs) and integron integrase genes. The ARG abundance was significantly higher in the deep water layers and depth was the main driver of beta-diversity both for ARGs and MRGs. Moreover, ARG and MRG abundances strongly correlated (r = 0.95). The integron integrase gene abundances and composition were not influenced by the water depth and did not correlate with ARGs. The analysis of the obtained MAGs showed that some of them harbored intI gene together with several ARGs and MRGs, suggesting the presence of multidrug resistant bacteria and that MRGs and integrons could be involved in the selection of ARGs. These results demonstrate that the Black Sea is not only an important reservoir of ARGs, but also that they accumulate in the deep water layers where co-selection with MRGs could be assumed as a relevant mechanism of their persistence.