Metagenomic insight into the prevalence and driving forces of antibiotic resistance genes in the whole process of three full-scale wastewater treatment plants

The spread of antibiotic resistance genes (ARGs) is an emerging global health concern, and wastewater treatment plants (WWTPs), as an essential carrier for the occurrence and transmission of ARGs, deserves more attention. Based on the Illumina NovaSeq high-throughput sequencing platform, this study conducted a metagenomic analysis of 18 samples from three full-scale WWTPs to explore the fate of ARGs in the whole process (influent, biochemical treatment, advanced treatment, and effluent) of wastewater treatment. Total 70 ARG subtypes were detected, among which multidrug, aminoglycoside, tetracycline, and macrolide ARGs were most abundant. The different treatment processes used for three WWTPs were capable of reducing ARG diversity, but did not significantly reduce ARG abundance. Compared to that by denitrification filters, the membrane bioreactor (MBR) process was advantageous in controlling the prevalence of multidrug ARGs in WWTPs. Linear discriminant analysis Effect Size (LEfSe) suggested g_Nitrospira, g_Curvibacter, and g_Mycobacterium as the key bacteria responsible for differential ARG prevalence among different WWTPs. Meanwhile, adeF, sul1, and mtrA were the persistent antibiotic resistance genes (PARGs) and played dominant roles in the prevalence of ARGs. Proteobacteria and Actinobacteria were the host bacteria of majority ARGs in WWTPs, while Pseudomonas and Nitrospira were the most crucial host bacteria influencing the dissemination of critical ARGs (e.g., adeF). In addition, microbial richness was determined to be the decisive factor affecting the diversity and abundance of ARGs in wastewater treatment processes. Overall, regulating the abundance of microorganisms and key host bacteria by selecting processes with microbial interception, such as MBR process, may be beneficial to control the prevalence of ARGs in WWTPs.

Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste

The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and the potential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12 months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, the pH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.

Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting

Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM= 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.

Elucidating the role of two types of essential oils in regulating antibiotic resistance in soil

Although several approaches for reducing antibiotic resistance genes (ARGs) in soil have been proposed, the application of environmentally friendly approaches is now attracting much more attention. In the present study, two types of essential oils (EOs), namely lavender essential oil (LEO) and oregano essential oil (OEO), were selected to investigate their roles in regulating ARGs in soil. In a 28-day microcosm experiment, it was found that the different types and doses of EOs significantly changed the composition of microbial communities. The LEO treatments enriched more taxa belonging to Actinobacteria than the control, whereas the low dose of OEO reduced Actinobacteria enrichment. Besides, the control and the treatments with a high dose of LEO and OEO all significantly enriched the functional pathways related to Human Diseases, which were positively associated with ARGs. However, the low dose of these EOs helped to reduce the pathways. Because of inhibition of the functional pathways and ARG hosts, the low dose of OEO reduce the ARGs related to antibiotic efflux by 71.8% and the resistance genes to multidrug by 56.4%, but these roles did not occur in LEO treatments. These outcomes provide practical and theoretical support for the application of EOs in remediating ARG-contaminated soils.

Co-occurrence of genes for antibiotic resistance and arsenic biotransformation in paddy soils

Paddy soils are potential hotspots of combined contamination with arsenic (As) and antibiotics, which may induce co-selection of antibiotic resistance genes (ARGs) and As biotransformation genes (ABGs), resulting in dissemination of antimicrobial resistance and modification in As biogeochemical cycling. So far, little information is available for these co-selection processes and specific patterns between ABGs and ARGs in paddy soils. Here, the 16S rRNA amplicon sequencing and high-throughput quantitative PCR and network analysis were employed to investigate the dynamic response of ABGs and ARGs to As stress and manure application. The results showed that As stress increased the abundance of ARGs and mobile genetic elements (MGEs), resulting in dissemination risk of antimicrobial resistance. Manure amendment increased the abundance of ABGs, enhanced As mobilization and methylation in paddy soil, posing risk to food safety. The frequency of the co-occurrence between ABGs and ARGs, the host bacteria carrying both ARGs and ABGs were increased by As or manure treatment, and remarkably boosted in soils amended with both As and manure. Multidrug resistance genes were found to have the preference to be co-selected with ABGs, which was one of the dominant co-occurring ARGs in all treatments, and manure amendment increased the frequency of Macrolide-Lincosamide-Streptogramin B resistance (MLSB) to co-occur with ABGs. Bacillus and Clostridium of Firmicutes are the dominant host bacteria carrying both ABGs and ARGs in paddy soils. This study would extend our understanding on the co-selection between genes for antibiotics and metals, also unveil the hidden environmental effects of combined pollution.

Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient

The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.

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 pathway deserves more attention. We analyzed the ARG hosts and the resistome in lettuce rhizosphere and phyllosphere with film mulching via hybrid Illumina-Nanopore sequencing. Pseudomonas sp. 7SR1 was more abundant than other ARG hosts, accounting for 1.0% and 47.1% of the total bacteria in rhizosphere and phyllosphere, respectively. The species has flagella that can promote mobility and can excrete extracellular polymeric substances and/or surfactant-like microbial products, which benefits its colonization in the phyllosphere. Impeding the migration of Pseudomonas sp. 7SR1 via the soil-endosphere-phyllosphere pathway would be effective to further reduce ARGs in phyllosphere. Multidrug resistant genes were predominant in phyllosphere (40.3% of the total), and 87.6% of the phyllosphere ARGs were located on chromosomes, indicating relatively low horizontal gene transfer (HGT) potentials. This study provides insights into the transfer mechanism, hosts, and control strategies of phyllosphere ARGs in typical plants.

Fate of antibiotic resistance genes in farmland soil applied with three different fertilizers during the growth cycle of pakchoi and after harvesting

The increasing prevalence of antibiotic resistance genes (ARGs) in the soil environment poses a serious threat to crop safety and even public health. In this study, the fate of ARGs in the soil was investigated during the growth period of pakchoi and after harvesting with the application of different kinds of fertilizers. The result showed that increasing rate of soil ARGs during the growth period of pakchoi followed the order of composted manure > commercial fertilizer > mineral fertilizer. After harvesting, soil ARGs abundance treated with mineral fertilizer, commercial fertilizer or composted manure significantly increased by 0.63, 3.19 and 8.65 times (p < 0.05), respectively, compared with the non-fertilized soil. The ARGs abundance in the pakchoi treated with composted manure was significantly higher than that of treatments with mineral fertilizer and commercial organic fertilizer. These findings indicated the application of composted pig manure would significantly increase the pollution load of ARGs in farmland soil and plant, and also promote the proliferation of farmland ARGs. Principal component analysis suggested that bacterial communities might have a significant influence on ARGs changes during the growth period of pakchoi. Network analysis further indicated ARGs changes may be mainly related to their host bacteria (including Gammaproteobacteria, Flavobacteriia and Bacilli). The results provided a proper method and useful information on reducing transmission risk of ARGs and control the propagation of ARGs in agricultural activities.

Does lipid stress affect performance, fate of antibiotic resistance genes and microbial dynamics during anaerobic digestion of food waste?

The dissemination of antibiotic resistance genes (ARGs) in food waste (FW) disposal can pose severe threats to public health. Lipid is a primary composition in FW, while whether lipid stress can affect ARGs dynamics during anaerobic digestion (AD) process of FW is uncertain. This study focused on the impacts of lipid stress on methane production, fate of ARGs and its microbial mechanisms during AD of FW. Results showed that high lipid content increased methane yield but prolonged hydrolysis and lag time of methane production compared to AD of FW without oil. Moreover, variations of ARGs were more susceptible to lipid stress. Lipid stress could facilitate the reduction of total ARGs abundances compared to the group without oil, particularly restraining the proliferation of sul1, aadA1 and mefA in AD systems (P < 0.05). Mantel test suggested that integrons (intl1 and intl2) were significantly correlated with all detected ARGs (r: 0.33, P < 0.05), indicating that horizontal gene transfer mediated by integrons could be the driving force on ARGs dissemination. Network analysis suggested that Firmicutes, Bacteroidetes, Synergistetes and Proteobacteria were the main potential hosts of ARGs. In addition, under the lipid stress, the reduction of host bacteria was responsible for the elimination of several specific ARGs, thereby affecting ARGs profiles. These findings firstly deciphered ARGs dynamics and their driving factors responding to lipid stress during anaerobic biological treatment of FW.