Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes

Metagenomic Profiling of Internationally Sourced Sewage Influents and Effluents Yields Insight into Selecting Targets for Antibiotic Resistance Monitoring

It has been debated whether wastewater treatment plants (WWTPs) primarily act to attenuate or amplify antibiotic resistance genes (ARGs). However, ARGs are highly diverse with respect to their resistance mechanisms, mobilities, and taxonomic hosts and therefore their behavior in WWTPs should not be expected to be universally conserved. We applied metagenomic sequencing to wastewater influent and effluent samples from 12 international WWTPs to classify the behavior of specific ARGs entering and exiting WWTPs. In total, 1079 different ARGs originating from a variety of bacteria were detected. This included ARGs that could be mapped to assembled scaffolds corresponding to nine human pathogens. While the relative abundance (per 16S rRNA gene) of ARGs decreased during treatment at 11 of the 12 WWTPs sampled and absolute abundance (per mL) decreased at all 12 WWTPs, increases in relative abundance were observed for 40% of the ARGs detected at the 12th WWTP. Also, the relative abundance of mobile genetic elements (MGE) increased during treatment, but the fraction of ARGs known to be transmissible between species decreased, thus demonstrating that increased MGE prevalence may not be generally indicative of an increase in ARGs. A distinct conserved resistome was documented in both influent and effluent across samples, suggesting that well-functioning WWTPs generally attenuate influent antibiotic resistance loads. This work helps inform strategies for wastewater surveillance of antibiotic resistance, highlighting the utility of tracking ARGs as indicators of treatment performance and relative risk reduction.

Virome and metagenomic sequencing reveal the impact of microbial inoculants on suppressions of antibiotic resistome and viruses during co-composting

Co-composting with exogenous microbial inoculant, presents an effective approach for the harmless utilization of livestock manure and agroforestry wastes. However, the impact of inoculant application on the variations of viral and antibiotic resistance genes (ARGs) remains poorly understood, particularly under varying manure quantity (low 10 % vs. high 20 % w/w). Thus, employing virome and metagenomic sequencing, we examined the influence of Streptomyces-Bacillus Inoculants (SBI) on viral communities, phytopathogen, ARGs, mobile genetic elements, and their interrelations. Our results indicate that SBI shifted dominant bacterial species from Phenylobacterium to thermotropic Bordetella, and the quantity of manure mediates the effect of SBI on whole bacterial community. Major ARGs and genetic elements experienced substantial changes with SBI addition. There was a higher ARGs elimination rate in the composts with low (∼76 %) than those with high manure (∼70 %) application. Virus emerged as a critical factor influencing ARG dynamics. We observed a significant variation in virus community, transitioning from Gemycircularvirus- (∼95 %) to Chlamydiamicrovirus-dominance. RDA analysis revealed that Gemycircularvirus was the most influential taxon in shaping ARGs, with its abundance decreased approximately 80 % after composting. Collectively, these findings underscore the role of microbial inoculants in modulating virus communities and ARGs during biowaste co-composting.

Mitigated dissemination of antibiotic resistance genes by nanoscale zero-valent iron and iron oxides during anaerobic digestion: Roles of microbial succession and regulation

Nanoscale zero-valent iron (ZVI) and the oxides have been documented as an effective approach for mitigating the dissemination of antibiotic resistance genes (ARGs) during anaerobic digestion (AD). However, the mechanism of ARGs dissemination mitigated by nanoscale ZVI and iron oxides remain unclear. Here, we investigated the influencing mechanisms of nanoscale ZVI and iron oxides on ARGs dissemination during AD. qPCR results indicated that nanoscale ZVI and iron oxides significantly declined the total ARGs abundances, and the strongest inhibiting effect was observed by 10 g/L nanoscale ZVI. Mantel test showed ARGs distribution was positively correlated with physiochemical properties, integrons and microbial community, among which microbial community primarily contributed to ARGs dissemination (39.74%). Furthermore, redundancy and null model analyses suggested the dominant and potential ARGs host was Fastidiosipila, and homogeneous selection in the determinism factors was the largest factor for driving Fastidiosipila variation, confirming the inhibition of Fastidiosipila was primary reason for mitigating ARGs dissemination by nanoscale ZVI and iron oxides. These results were related to the inhibition of ARGs transfer related functions. This work provides novel evidence for mitigating ARGs dissemination through regulating microbial succession and regulation induced by ZVI and iron oxides.

Distinct Assembly Patterns of Soil Antibiotic Resistome Revealed by Land-Use Changes over 30 Years

Compared with the ever-growing information about the anthropogenic discharge of nutrients, metals, and antibiotics on the disturbance of antibiotic resistance genes (ARGs), less is known about how the potential natural stressors drive the evolutionary processes of antibiotic resistance. This study examined how soil resistomes evolved and differentiated over 30 years in various land use settings with spatiotemporal homogeneity and minimal human impact. We found that the contents of soil organic carbon, nitrogen, soil microbial biomass, and bioavailable heavy metals, as well as related changes in the antibiotic resistome prevalence including diversity and abundance, declined in the order of grassland > cropland > bareland. Sixty-nine remaining ARGs and 14 mobile genetic elements (MGEs) were shared among three land uses. Multiple factors (i.e., soil properties, heavy metals, bacterial community, and MGEs) contributed to the evolutionary changes of the antibiotic resistome, wherein the resistome profile was dominantly driven by MGEs from both direct and indirect pathways, supported by a partial least-squares path model analysis. Our results suggest that pathways to mitigate ARGs in soils can coincide with land degradation processes, posing a challenge to the common goal of managing our environment sustainably.

Composting reduces the risks of resistome in beef cattle manure at the transcriptional level

Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.IMPORTANCEProper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.

Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues

Antibiotic resistance genes (ARGs) are emerging pollutants that enter the farm and surrounding environment via the manure of antibiotic-treated animals. Pretreatment of livestock manure by composting decreases ARGs abundance, but how antibiotic residues affect ARGs removal efficiency remains poorly understood. Here, we explored the fate of the resistome under different doxycycline residue levels during aerobic swine manure composting. Metagenomic sequencing showed that the presence of high levels of doxycycline generally had a higher abundance of tetracycline ARGs, and their dominant host bacteria of Firmicutes, especially Clostridium and Streptococcus, also had limited elimination in composting under high levels of doxycycline stress. Moreover, high levels of doxycycline impaired the removal of the total ARGs number in finished composts, with a removal rate of 51.74 % compared to 63.70 % and 71.52 % for the control and low-level doxycycline manure, respectively. Horizontal gene transfer and strengthened correlations among the bacterial community fostered ARGs preservation at high doxycycline levels during composting. In addition, ARGs carried by both plasmids and chromosomes, such as multidrug ARGs, showed wide host characteristics and rebound during compost maturation. Compared with chromosomes, a greater variety of ARGs on plasmids suggested that the majority of ARGs were characterized by horizontal mobility during composting, and the cross-host characteristics of ARGs during composting deserve further attention. This study provided deep insight into the fate of ARGs under residual antibiotic stress during manure composting and reminded the associated risk for environmental and public health.

Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables

Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.

Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation

Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.

Biofilm-developed biomass residues as novel bulking agents and microbial carriers for synergistically enhanced bioevaporation: Degradation potential and contribution to metabolic heat

Economical and easily prepared bulking agents and microbial carriers are essential in the practical application of bioevaporation process. Biofilm-developed biomass residues not only provide structural support and microbial sources but also may contribute metabolic heat to the bioevaporation process, achieving the enhanced water evaporation and synergistic treatment of biomass residues. In this study, biofilm was cultivated on the rice straw, wheat straw, sawdust, corncob, luffa cylindrica and palm first, then those biofilm-developed biomass residues were successfully used as the bulking agents and microbial carriers in food waste bioevaporation. The degradation potential (volatile solid degradation ratio) of those biomass residues was in the order of corncob (23.96%), wheat straw (21.12%), rice straw (14.57%), luffa cylindrica (11.02%), sawdust (-2.87%) and palm (-9.24%). It's primarily the degradation of the major components, cellulose and hemicellulose, in corncob and wheat straw governed the metabolic heat contribution (91.73 and 79.61%) to the bioevaporation process. While the high lignin content in sawdust (14.57%) and palm (28.62%) caused negligible degradation of cellulose and hemicellulose, hence made them only function as structural supporter and did not contribute any metabolic heat. Moreover, though the metabolic heat contribution of rice straw and luffa cylindrica reached 58.19 and 37.84%, their lowest lignocellulose content (62.99 and 65.95%) and their lower density, as well as the dominated Xanthomonas (bacteria) and Mycothermus (fungi) led to their rapid collapse during the repeated cycles of bioevaporation. The greatest abundance of thermophilic bacteria (22.3-88.0%) and thermophilic fungi (82.0-99.3%) was observed in the corncob pile. Furthermore, considering the Staphylococcus (pathogenic bacteria) and Candida (animal pathogen) was effectively inhibited, the biofilm-developed corncob was the most favorable bulking agents and microbial carrier for the synergistic bioevaporation of highly concentrated organic wastewater and biomass residues.

The key role of denitrification and dissimilatory nitrate reduction in nitrogen pollution along vertical landfill profiles from metagenomic perspective

Landfill are persistent sources of nitrogen (N) pollution even in the decades after closure. However, the biological pathways of N-pollution, particularly N₂O and NH₄⁺, at different landfill depths have received little attention. In this study, metagenomic analysis was conducted on landfill refuse from vertical reservoir profiles in two closed landfills named XT and MT. NH₄⁺ concentrations were found to be higher in deeper layers of MT, while greater potential for N₂O emissions occurred in XT and the shallow layers of MT. Furthermore, the community structure and function of N-metabolizing microbes were more strongly defined by landfill depth than landfill type. Denitrification, involving abundant nirK and norB genes, was identified as the major pathway for N₂O production in both XT and MT-shallow, while dissimilatory nitrate reduction with abundant nirBD genes was identified as the major pathway for NH₄⁺ accumulation. Microbes of norB-type and nirBD-type were positively affected by NO₃^- in XT, whereas negatively affected by contents of organic material and moisture in MT-shallow. The mechanism by which nitrogen fixation, with abundant nifH genes, contributes to NH₄⁺ accumulation in MT-deep should be further elucidated. These findings can provide a theoretical basis for governing scientific N-pollution control strategies throughout the entire landfill process.

Composition, structure, and functional shifts of prokaryotic communities in response to co-composting of various nitrogenous green feedstocks

BACKGROUND

Thermophilic composting is a promising method of sanitizing pathogens in manure and a source of agriculturally important thermostable enzymes and microorganisms from organic wastes. Despite the extensive studies on compost prokaryotes, shifts in microbial profiles under the influence of various green materials and composting days are still not well understood, considering the complexity of the green material sources. Here, the effect of regimens of green composting material on the diversity, abundance, and metabolic capacity of prokaryotic communities in a thermophilic compost environment was examined.

METHODS

Total community 16S rRNA was recovered from triplicate compost samples of Lantana-based, Tithonia-based, Grass-based, and mixed (Lantana + Tithonia + Grass)- based at 21, 42, 63, and 84 days of composting. The 16S rRNA was sequenced using the Illumina Miseq platform. Bioinformatics analysis was done using Divisive Amplicon Denoising Algorithm version 2 (DADA2) R version 4.1 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States version 2 (PICRUSt2) pipelines for community structure and metabolic profiles, respectively. In DADA2, prokaryotic classification was done using the Refseq-ribosomal database project (RDP) and SILVA version 138 databases.

RESULTS

Our results showed apparent differences in prokaryotic community structure for total diversity and abundance within the four compost regimens and composting days. The study showed that the most prevalent phyla during composting included Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Proteobacteria. Additionally, there were differences in the overall diversity of metabolic pathways but no significant differences among the various compost treatments on major metabolic pathways like carbohydrate biosynthesis, carbohydrate degradation, and nitrogen biosynthesis.

CONCLUSION

Various sources of green material affect the succession of compost nutrients and prokaryotic communities. The similarity of amounts of nutrients, such as total Nitrogen, at the end of the composting process, despite differences in feedstock material, indicates a significant influence of composting days on the stability of nutrients during composting.

Enhancing control of multidrug-resistant plasmid and its host community with a prolonged thermophilic phase during composting

The plasmid-mediated horizontal transfer of antibiotic resistance genes (ARGs) among bacteria facilitates the evolution and dissemination of antibiotic resistance. Broad-host-range plasmids can be transferred to different bacterial hosts in soil, plant rhizospheres, and wastewater treatment plants. Although composting is an effective way to convert organic waste into fertilizer and reduce some ARGs, few studies have focused on its effects on the spread of ARG-carrying plasmids and their bacterial host communities during composting. In this study, a fluorescently labeled Pseudomonas putida (P. putida) harboring a broad-host-range plasmid RP4 carrying three ARGs was inoculated into a raw material microcosm and composted with different durations of the thermophilic phase. The fate of the donor and RP4 in composting was investigated. The prolonged thermophilic composting removed 95.1% of dsRed and 98.0% of gfp, and it inhibited the rebound of P. putida and RP4 during the maturation phase. The spread potential of RP4 decreased from 10⁻⁴ to 10⁻⁶ transconjugants per recipient after composting. In addition, we sorted and analyzed the composition of RP4 recipient bacteria using fluorescence-activated cell sorting combined with 16S rRNA gene amplicon sequencing. The recipient bacteria of RP4 belonged to eight phyla, and Firmicutes, accounting for 75.3%–90.1%, was the dominant phylum in the transconjugants. The diversity and richness of the RP4 recipient community were significantly reduced by prolonged thermophilic periods. Overall, these findings provide new insights for assessing the contribution of composting in mitigating the dissemination of plasmid-mediated ARGs, and the prolonged thermophilic phase of composting can limit the transfer of multidrug-resistant plasmids.

Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost

BACKGROUND

Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS

In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS

Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.

Profiles of Microbial Community and Antibiotic Resistome in Wild Tick Species

Infections caused by antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, the environment and wildlife as major sources and reservoirs of antibiotic resistance genes (ARGs) are being increasingly investigated. There have been many reports on bacterial community in ticks, but little is known about ARGs they carry, and the correlation between bacterial and ARGs in wild ticks also remains unknown. Here, the profiles of microbial community and antibiotic resistome in wild tick species were investigated using high-throughput 16S rRNA sequencing and smart chip-based high-throughput quantitative PCR approach (HT-qPCR), respectively. We found that bacterial composition in wild tick species is variable; the sequenced reads from all samples were assigned to 37 different phyla at the phylum level. The dominant phylum was Proteobacteria, which accounted for 75.60 ± 10.34%, followed by Bacteroidetes accounting for 13.78 ± 11.68% of the total bacterial community. In total, 100 different ARGs across 12 antibiotic classes and 20 mobile genetic elements (MGEs) were identified by HT-qPCR, and among them aminoglycosides, multidrug, macrolide-clinolamide-streptogramin B, and tetracycline resistance genes were the dominant ARG types. Co-occurrence patterns revealed by network analysis showed that eight bacterial genera may serve as the potential hosts for different ARGs. For the first time, this study provides comprehensive overview of the diversity and abundance of ARGs in wild ticks and highlights the possible role of wild ticks as ARG disseminators into the environment and vertebrate hosts, with implications for human and animal health.

IMPORTANCE The emergence of antibiotic-resistant bacteria poses serious threat to the public health around the world. Ticks are obligate hematophagous ectoparasites, surviving via feeding on the blood of various animal hosts. Although some previous studies have confirmed wild ticks carried various bacterial community, the role of wild ticks in the antibiotic resistance remains unknown. Here, identification of microbial community and antibiotic resistome in wild tick species revealed that wild ticks are the reservoir, postulated potential spreaders of antibiotic resistance. Our findings highlight the contribution of wild ticks to the maintenance and dissemination of ARGs, and the associated health risks.

Succession and change of potential pathogens in the co-composting of rural sewage sludge and food waste

Composting is an effective way to prevent and control the spread of pathogenic microorganisms which could put potential risk to humans and environment, from rural solid waste, especially sewage sludge and food waste. In the study, we aim to analyze the changes of pathogenic bacteria during the co-composting of rural sewage sludge and food waste. The results showed that only 27 pathogenic bacteria were detected after composting, compared to 50 pathogenic bacteria in the raw mixed pile. About 74% of pathogen concentrations dropped below 1000 copies/g after composting. Lactobacillus, Bacillus, Paenibacillus and Comamonas were the core pathogenic bacteria in the compost, of which concentrations were all significantly lower than that in the raw mixed pile at the end of composting. The concentration of Lactobacillus decreased to 3.03 × 10³ copies/g compared to 0 d with 1.25 × 10⁹ copies/g by the end of the composting, while that of Bacillus, Paenibacillus and Comamonas decreased to 2.77 × 10⁴ copies/g, 2.13 × 10⁴ copies/g and 3.38 × 10² copies/g, respectively, with 1.26 × 10⁷ copies/g, 4.71 × 10⁶ copies/g, 1.69 × 10⁸ copies/g on 0 d. Redundancy analysis (RDA) indicated that physicochemical factors and substances could affect the changes of pathogenic bacteria during composting, while temperature was the key influencing factor. In addition, certain potential pathogenic bacteria, such as Bacteroides-Bifidobacterium, show statistically strong and significant co-occurrence during composting, which may increase the risk of multiple infections and also influence their distribution. These findings provide a theoretical reference for biosafety prevention and control in the treatment and disposal of rural solid waste.

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

The emergence of resistance against common antibiotics in the gut microbiota is a major issue for both human and livestock health. This highlights the need for understanding the impact of such application on the reservoir of antibiotic resistance genes in poultry gut and devising means to circumvent the potential resistome expansion. Phytogenic feed additives (PFAs) are potential natural alternative to antibiotic to improve animal health and performance, supposedly via positively affecting the gut microbial ecosystem, but there is little systematic information available. In this time-course study, we applied a shotgun meta-transcriptomics approach to investigate the impact of a PFA product as well as the commonly used antibiotic, zinc bacitracin either at AGP concentration or therapeutic concentration on the gut microbiome and resistome of broiler chickens raised for 35 days. Over the course of the trial, PFA treatments increased the abundance of Firmicutes such as Lactobacillus and resulted in a lower abundance of Escherichia, while the latter group increased significantly in the feces of chickens that received either AGP or AB doses of bacitracin. Tetracycline resistance and aminoglycoside resistance were the predominant antibiotic resistance gene (ARG) classes found, regardless of the treatment. PFA application resulted in a decrease in abundance of ARGs compared to those in the control group and other antibiotic treatment groups. In summary, the findings from this study demonstrate the potential of phytogenic feed additives could be an alternative to antibiotics in poultry farming, with the added benefit of counteracting antimicrobial resistance development.

Prevalent and highly mobile antibiotic resistance genes in commercial organic fertilizers

Compost-based organic fertilizers made from animal manures may contain high levels of antibiotic resistance genes (ARGs). However, the factors affecting the abundance and profile of ARGs in organic fertilizers remain unclear. We conducted a national-wide survey in China to investigate the effect of material type and composting process on ARG abundance in commercial organic fertilizers and quantified the contributions of bacterial composition and mobile genetic elements (MGEs) to the structuring of ARGs, using quantitative PCR and Illumina sequencing of 16S rRNA gene amplicons. The tetracycline, sulfonamide, aminoglycoside and macrolide resistance genes were present at high levels in all organic fertilizers. Seven ARGs that confer resistance to clinically important antibiotics, including three β-lactam resistance genes, three quinolone resistance genes and the colistin resistance gene mcr-1, were detected in 8 - 50% the compost samples, whereas the vancomycin resistance gene vanC was not detected. Raw material type had a significant (p < 0.001) effect on the ARG abundance, with composts made from animal feces except some cattle feces generally having higher loads of ARGs than those from non-animal raw materials. Composting process type showed no significant (p > 0.05) effect on ARG abundance in the organic fertilizers. MGEs exerted a greater influence on ARG composition than bacterial community, suggesting a strong mobility of ARGs in the organic fertilizers. Our study highlights the need to manage the risk of ARG dissemination from agricultural wastes.

Industrial Composting of Sewage Sludge: Study of the Bacteriome, Sanitation, and Antibiotic-Resistant Strains

Wastewater treatment generates a huge amount of sewage sludge, which is a source of environmental pollution. Among the alternatives for the management of this waste, industrial composting stands out as one of the most relevant. The objective of this study was to analyze the bacterial population linked to this process and to determine its effectiveness for the reduction, and even elimination, of microorganisms and pathogens present in these organic wastes. For this purpose, the bacteriome and the fecal bacteria contamination of samples from different sewage sludge industrial composting facilities were evaluated. In addition, fecal bacteria indicators and pathogens, such as Salmonella, were isolated from samples collected at key stages of the process and characterized for antibiotic resistance to macrolide, β-lactam, quinolone, and aminoglycoside families. 16S rRNA phylogeny data revealed that the process clearly evolved toward a prevalence of Firmicutes and Actinobacteria phyla, removing the fecal load. Moreover, antibiotic-resistant microorganisms present in the raw materials were reduced, since these were isolated only in the bio-oxidative phase. Therefore, industrial composting of sewage sludge results in a bio-safe final product suitable for use in a variety of applications.

Multiple driving factors contribute to the variations of typical antibiotic resistance genes in different parts of soil-lettuce system

The application of manure compost may cause the transmission of antibiotic resistance genes (ARGs) in agroecological environment, which poses a global threat to public health. However, the driving factors for the transmission of ARGs from animal manure to agroecological systems remains poorly understood. Here, we explored the spatiotemporal variation in ARG abundance and bacterial community composition as well as relative driving factors in a soil-lettuce system amended with swine manure compost. The results showed that ARGs abundance had different variation trends in soil, lettuce phylloplane and endophyere after the application of swine manure compost. The temporal variations of total ARGs abundance had no significant different in soil and lettuce phylloplane, while lettuce endosphere enriched half of ARGs to the highest level at harvest. There was a significant linear correlation between ARGs and integrase genes (IGs). In contrast to the ARGs variation trend, the alpha diversity of soil and phylloplane bacteria showed increasing trends over planting time, and endosphere bacteria remained stable. Correlation analysis showed no identical ARG-related genera in the three parts, but the shared Proteobacteria, Pseudomonas, Halomonas and Chelativorans, from manure compost dominated ARG profile in the soil-lettuce system. Moreover, redundancy analysis and structural equation modelling showed the variations of ARGs may have resulted from the combination of multiple driving factors in soil-lettuce system. ARGs in soil were more affected by the IGs, antibiotic and heavy metals, and bacterial community structure and IGs were the major influencing factors of ARG profiles in the lettuce. The study provided insight into the multiple driving factors contribute to the variations of typical ARGs in different parts of soil-lettuce system, which was conducive to the risk assessment of ARGs in agroecosystem and the development of effective prevention and control measures for ARGs spread in the environment.

Disentangling the Effects of Physicochemical, Genetic, and Microbial Properties on Phase-Driven Resistome Dynamics during Multiple Manure Composting Processes

Composting alters manure-derived antibiotic resistance genes (ARGs) to a certain extent, which is largely dependent upon the composting phase, manure type, microbial phylogeny, and physicochemical properties. However, little is known about how these determinants influence the fate and dynamics of ARGs as well as the mechanisms underlying the ecological process of ARGs during composting. Here, we investigated the temporal patterns of ARGs and their correlations with a series of physicochemical, genetic, and microbial properties during pilot-scale composting of chicken, maggot, bovine, and swine manure. We detected 237 ARGs, 71 of which were co-occurring across all four composting processes and accounted for >80% of the sum of resistome abundance. In support of this ARG co-occurrence, variance partition analyses demonstrated that the manure type explained less resistome variations (5.6%) than the composting phase (21.6%). During the phase-driven resistome dynamics, ARGs showed divergent variations in abundance, and certain beta-lactams and multidrug ARGs were consistently enriched across multiple manure composting processes. Correlation analyses all led to the conclusion that the divergent ARG variations during composting were attributable to the unequal effects of physicochemical properties, mobile elements, and succession of indigenous microbiota, whereas antibiotic residues' effects were marginal. Ultimately, this study determines the relative importance of various key determinants in the phase-driven divergence of ARGs during multiple manure composting processes and demonstrates a clear need to evaluate risks posed by enriched ARGs toward their receiving environments.

Co-composting materials can further affect the attenuation of antibiotic resistome in soil application

This study investigated the effects of representative co-substrate (corncob particles) and additive (brick granules) alone on antibiotic resistome of swine manure during composting and subsequent compost application. For relative abundances, four antibiotic resistance gene (ARG) types encoding resistance to aminoglycoside, multidrug, florfenicol-chloramphenicol-amphenicol-fluoroquinolone-quinolone, and sulfonamide increased remarkably during composting, whereas all the ARG types decreased after compost application. Interestingly, much more ARG subtypes (50.1% in total) were reduced in corncob addition treatment. Meanwhile, the addition of corncob particles lowered the relative abundance and diversity of ARGs more significantly. Microbial community exhibited conspicuous changes across the manure, compost, and soil samples where the dominant genera were completely different. Procrustes test proved the co-occurrence and driving effect of microbial community on resistome variation, especially in corncob addition treatment during composting. Network analysis demonstrated that the dissipation of the dominant genera such as Ruminofilibacter, Luteimonas, and Pseudidiomarina in the composts after application contributed greatly to the reduction in ARG relative abundance. Besides, the low abundance of mobile genetic elements (MGEs) in soil also accounted for the attenuation of ARGs to some extent. Our findings clearly proved that co-composting materials can further affect the attenuation of antibiotic resistome in soil application, which can help in understanding the spread and control of ARGs during agricultural process.

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

Occurrence of antibiotic resistance genes (ARGs) in animal manure impedes the reutilization of manure resources. Aerobic composting is potentially effective method for resource disposal of animal manure, but the fate of ARGs during composting is complicated due to the various material sources and different operating conditions. This review concentrates on the biotic and abiotic factors influencing the variation of ARGs in composting and their potential mechanisms. The dynamic variations of biotic factors, including bacterial community, mobile genetic elements (MGEs) and existence forms of ARGs, are the direct driving factors of the fate of ARGs during composting. However, most key abiotic indicators, including pH, moisture content, antibiotics and heavy metals, interfere with the richness of ARGs indirectly by influencing the succession of bacterial community and abundance of MGEs. The effect of temperature on ARGs depends on whether the ARGs are intracellular or extracellular, which should be paid more attention. The emergence of various controlling strategies renders the composting products safer. Four potential removal mechanisms of ARGs in different controlling strategies have been concluded, encompassing the attenuation of selective/co-selective pressure on ARGs, killing the potential host bacteria of ARGs, reshaping the structure of bacterial community and reducing the cell-to-cell contact of bacteria. With the effective control of ARGs, aerobic composting is suggested to be a sustainable and promising approach to treat animal manure.

Stockpiling versus Composting: Effectiveness in Reducing Antibiotic-Resistant Bacteria and Resistance Genes in Beef Cattle Manure

Manure storage methods can affect the concentration and prevalence of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in cattle manure prior to land application. The objective of this study was to compare stockpiling and composting with respect to their effectiveness in reducing ARB and ARGs in beef cattle manure in a field-scale study. Field experiments were conducted in different seasons with different bulking agents for composting. For both the winter-spring cycle and the summer-fall cycle, ARB concentrations declined below the limit of quantification rapidly in both composting piles and stockpiles; however, ARB prevalence was significantly greater in the composting piles than in the stockpiles. This was likely due to the introduction of ARB from bulking agents. There was no significant change in ARG concentrations between initial and final concentrations for either manure storage treatment during the winter-spring cycle, but a significant reduction of the ARGs erm(B), tet(O), and tet(Q) over time was observed for both the composting pile and stockpile during the summer-fall cycle. Results from this study suggest that (i) bulking agent may be an important source of ARB and ARGs for composting; (ii) during cold months, the heterogeneity of the temperature profile in composting piles could result in poor ARG reduction; and (iii) during warm months, both stockpiling and composting can be effective in reducing ARG abundance. IMPORTANCE Proper treatment of manure is essential to reduce the spread of antibiotic resistance and protect human health. Stockpiling and composting are two manure storage methods which can reduce antibiotic-resistant bacteria and resistance genes, although few field-scale studies have examined the relative efficiency of each method. This study examined the ability of both methods in both winter-spring and summer-fall cycles, while also accounting for heterogeneity within field-scale manure piles. This study determined that bulking agents used in composting could contribute antibiotic-resistant bacteria and resistance genes. Additionally, seasonal variation could hinder the efficacy of composting in colder months due to heterogeneity in temperature within the pile; however, in warmer months, either method of manure storage could be effective in reducing the spread of antibiotic resistance.

Airborne and indigenous microbiomes co-drive the rebound of antibiotic resistome during compost storage

Composting is widely used to reduce the abundance of antibiotic resistance genes (ARGs) in solid waste. While ARG dynamics have been extensively investigated during composting, the fate and abundance of residual ARGs during the storage remain unexplored. Here, we tested experimentally how ARG and mobile genetic element (MGE) abundances change during compost storage using metagenomics, quantitative PCR and direct culturing. We found that 43.8% of ARGs and 39.9% of MGEs quickly recovered already during the first week of storage. This rebound effect was mainly driven by the regrowth of indigenous, antibiotic-resistant bacteria that survived the composting. Bacterial transmission from the surrounding air had a much smaller effect, being most evident as MGE rebound during the later stages of storage. While hyperthermophilic composting was more efficient at reducing the relative abundance of ARGs and MGEs, relatively greater ARG rebound was observed during the storage of hyperthermophilic compost, exceeding the initial levels of untreated sewage sludge. Our study reveals that residual ARGs and MGEs left in the treated compost can quickly rebound during the storage via airborne introduction and regrowth of surviving bacteria, highlighting the need to develop better storage strategies to prevent the rebound of ARGs and MGEs after composting.

Fitness reduction of antibiotic resistome by an extra carbon source during swine manure composting

This study employed high-throughput quantitative polymerase chain reaction to evaluate the effects of specific co-substrate and additive on the fitness of antibiotic resistome during swine manure composting. The results showed that corncob particle as a co-substrate significantly reduced the relative abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) simultaneously. The diversity of ARGs was also reduced more effectively by corncob addition. Brick granule as an additive reduced the concentrations of bioavailable Cu and Zn. However, the relative abundances of ARGs and MGEs were not reduced by the addition of brick granule subsequently. Redundancy analysis indicated a negative effect of the C content and positive effects of class I integrase gene (intI) and bioavailable metals on the variation of the relative abundance of ARGs (p < 0.01). The Procrustes test showed a higher goodness-of-fit between the relative abundance of ARGs and 16S rRNA genes (r = 0.8166; p < 0.0001). Our results suggests that the effect of corncob particle on the relative abundance of ARGs was achieved by driving the changes in physicochemical properties and microbial communities. This study confirmed the hypothesis of fitness cost and demonstrated the contribution of extra C source to ARG attenuation during composting.

Using the heat generated from electrically conductive concrete slabs to reduce antibiotic resistance in beef cattle manure

Proper treatment is necessary to reduce antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in livestock manure before land application. Conventional stockpiling suffers unreliable removal efficiency, while composting can be complicated and expensive. The objective of this study was to test the feasibility of a novel heat-based technology, i.e., stockpiling manure on conductive concrete slabs, to inactivate ARB and ARGs in beef cattle manure. In this study, two independent bench-scale trials were conducted. In both trials, samples were taken from manure piles on conductive concrete slabs and regular slabs (i.e., heated and unheated piles). In the heated pile of the first trial, 25.9% and 83.5% of the pile volume met the EPA Class A and Class B biosolids standards, respectively. For the heated pile of the second trial, the two values were 43.9% and 74.2%. In both trials, nearly all forms of the total and resistant Escherichia coli and enterococci were significantly lower in the heated piles than in the unheated piles. Besides, significant reduction of ARGs in heated piles was observed in the first trial. Through this proof-of-concept study, the new technology based on conductive concrete slabs offers an alternative manure storage method to conventional stockpiling and composting with respect to reduce ARB and ARGs in manure.

A comparison of antibiotics, antibiotic resistance genes, and bacterial community in broiler and layer manure following composting

Animal manure is an important source of antibiotics and antibiotic resistance genes (ARGs) in the environment. However, the difference of antibiotic residues and ARG profiles in layer and broiler manure as well as their compost remains unexplored. In this study, we investigated the profiles of twelve antibiotics, seventeen ARGs, and class 1 integrase gene (intI1) in layer and broiler manure, and the corresponding compost at large-scale. Compared with layer manure, broiler manure exhibited approximately six times more residual tetracyclines, especially chlortetracycline. The relative abundances of qnrS and ermA genes in broiler manure were significantly higher than those in layer manure. The concentration of tetracyclines not only had a significantly positive correlation with tetracycline resistance genes (tetA and tetC) but was also positively correlated with quinolone resistance (qepA, qnrB, and qnrS) and macrolide resistance (ermA and ermT). Most ARGs in manure were reduced after composting. However, the relative abundance of sulfonamide resistance gene sul1 increased up to 2.41% after composting, which was significantly higher than that of broiler (0.41%) and layer (0.62%) manure. The associated bacterial community was characterized by high-throughput 16S rRNA gene sequencing. The relative abundances of thermophilic bacteria had significant positive correlations with the abundance of sul1 in compost. The composting has a significant impact on the ARG-associated gut microbes in poultry manure. Variation partitioning analysis indicated that the change of bacterial community compositions and antibiotics contributed partially to the shift in ARG profiles. The results indicate that at industry-scale production broiler manure had more antibiotics and ARGs than layer manure did, and composting decreased most ARG abundances in poultry manure except for sulfonamide resistance genes.

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

BACKGROUND

Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures.

RESULTS

Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types.

CONCLUSIONS

Antimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.

Eleutheroside K isolated from Acanthopanax henryi (Oliv.) Harms suppresses methicillin resistance of Staphylococcus aureus

Acanthopanax (A.) henryi (Oliv.) Harms contain many bioactive compounds commonly used in traditional Chinese medicine. The objective of the present study was to investigate the antibacterial activity of the single constituent, Eleutheroside K (ETSK) isolated from the leaves of A. henryi (Oliv.) Harms, against methicillin-resistant Staphylococcus (S.) aureus (MRSA). Broth microdilution assay was used to measure the minimal inhibitory concentration (MIC) and the MIC values of ETSK against eight clinical S. aureus strains were all 50 µg ml^-1 . At sub-inhibitory concentrations, a synergistic effect between oxacillin (OXA) and ETSK was confirmed using checkerboard dilution assay and time-kill curve analysis. The bacteriostatic effect became more pronounced when ETSK was used in combination with detergent (Triton X-100) or ATPase inhibitor (N, N'-dicyclohexylcarbodiimide). According to western blot analysis, the down-regulated expression of Penicillin-binding protein 2a (PBP2a) further validated that the bacterial activity was inhibited when treated with ETSK in a dose-dependent manner. Results based on our study verified that ETSK significantly suppressed MRSA infections and emphasized the potential application of ETSK as a novel anti-MRSA natural drug.

Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis

Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the diversity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host sampled. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable diversity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.

Adding a complex microbial agent twice to the composting of laying-hen manure promoted doxycycline degradation with a low risk on spreading tetracycline resistance genes

Poultry manure is a reservoir for antibiotics and antibiotic resistance genes and composting is an effective biological treatment for manure. This study explored the effect of using two methods of adding a complex microbial agent to the composting of laying-hen manure on doxycycline degradation and tetracycline resistance genes elimination. The results showed that incorporating a complex microbial agent at 0.8% (w/w) on the 0^th and 11th day (group MT2) effectively degraded doxycycline with a final degradation rate of 46.83 ± 0.55%. The half-life of doxycycline in this group was 21.90 ± 0.00 days and was significantly lower than that of group MT1 (1.6% (w/w) complex microbial agent added on the 0^th day) and group DT (compost without complex microbial agent). But there was no significant difference in the final degradation rate of doxycycline between group DT and group MT1. The addictive with the complex microbial agent changed the microbial community structure. Bacteroidetes, Firmicutes and Proteobacteria were the dominant phyla during composting. Aerococcus, Desemzia, Facklamia, Lactobacillus, Streptococcus, and Trichococcus were the bacteria related to the degradation of doxycycline. Moreover, the incorporation of a complex microbial agent could decrease the risk on spreading tetracycline resistance genes. The single addition promoted the elimination of tetM, whose possible hosts were Enterococcus, Lactobacillus, Staphylococcus, and Trichococcus. Adding the complex microbial agent twice promoted the elimination of tetX, which was related to the low abundance of Chryseobacterium, Flavobacterium and Neptunomonas in group MT2. Redundancy analysis showed that the bacterial community, residual doxycycline and physiochemical properties have a potential effect on the variation in tetracycline resistance genes levels. Overall, adding the complex microbial agent twice is an effective measure to degrade doxycycline.

Changes in microbial community structure during pig manure composting and its relationship to the fate of antibiotics and antibiotic resistance genes

Animal manure containing veterinary antibiotics is a significant source of microbial antibiotic resistance genes (ARGs). Composting of animal manure with wheat straw and sawdust was explored as a means to reduce ARGs load in the final material. The effects of ciprofloxacin, oxytetracycline, sulfamerazine on the bacterial community composition, and how this then affected the removal of seven tetracycline resistance genes (TARGs), four sulfonamide resistance genes (SARGs), and two fluoroquinolone resistance genes (QARGs) were investigated. Treatments receiving either ciprofloxacin or the three mixed antibiotics had reduced bacterial alpha-diversity and displayed shifts in the abundance of Proteobacteria and Firmicutes. This demonstrated that different antibiotics played an important role in bacterial community composition. Furthermore, variation in the physicochemical properties of compost, particularly pH and temperature, was also strongly linked to shifts in bacterial composition over time. Based on network analysis, the reduction of TARGs were associated with loss of Pseudomonas, Pseudoxanthomonas, Pusillimonas, Aquamicrobium, Ureibacillus, Lysinibacillus, Bacillus and Brachybacterium during the thermophilic stage. However, QARGs and SARGs were more strongly affected by the presence of multiple antibiotics. Our results have important implications for reducing the spread of certain ARGs by controlling the composting temperature, pH or the antibiotics species used in husbandry.

Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes

Gut microbiota is a reservoir of antibiotic resistance genes (ARGs). Yet, limited information is available regarding the presence (metagenomic DNA level) and expression profiles (metatranscriptomic RNA level) of ARGs in gut microbiota. Here, we used both metagenomic and metatranscriptomic approaches to comprehensively reveal the abundance, diversity, and expression of ARGs in human, chicken, and pig gut microbiomes in China. Based on deep sequencing data and ARG databases, a total of 330 ARGs associated with 21 antibiotic classes were identified in 18 human, chicken, and pig fecal samples. Metatranscriptomic analysis revealed that 49.4, 66.5, and 56.6% of ARGs identified in human, chicken, and pig gut microbiota, respectively, were expressed, indicating that a large proportion of ARGs were not transcriptionally active. Further analysis demonstrated that transcript abundance of tetracycline, aminoglycoside, and beta-lactam resistance genes was mainly contributed by acquired ARGs. We also found that various biocide, chemical, and metal resistance genes were actively transcribed in human and animal guts. The combination of metagenomic and metatranscriptomic analysis in this study allowed us to specifically link ARGs to their transcripts, providing a comprehensive view of the prevalence and expression of ARGs in gut microbiota. Taken together, these data deepen our understanding of the distribution, evolution, and dissemination of ARGs and metal resistance genes in human, chicken, and pig gut microbiota.

The fate of antibiotic resistance genes during co-composting of swine manure with cauliflower and corn straw

Composting is not completely effective in reducing antibiotic resistance genes (ARGs) in animal manure. This work studied the effects of different treatment conditions on the fate of ARGs in composting swine manure with cauliflower and corn straw as bulking agents. The results showed that the addition of microbial agents or the ratio of corn stalks to cauliflower (1:12) could significantly decrease the absolute abundances of most ARGs (an average of 480 times) compared with the control treatment. Principal component analysis indicated that bacterial communities were significantly correlated with ARG abundance, suggesting that microbial communities have an impact on ARG variation during co-composting. Redundancy and Network analysis confirmed the changing patterns of individual ARGs (qnrS, bla_AmpC, bla_TEM-1) were influenced by the selectivity of host bacteria (Pseudomonas, Klebsiella, and Halocella) and environmental variables (TN, NH₃-N, TOC, and pH). These findings helped to optimize composting conditions, thereby reducing the risk of ARGs spread.

Characteristics of submicron aerosols produced during aeration in wastewater treatment

Submicron aerosols (SAs) emitted during wastewater treatment may harm the human circulation system, respiratory cells, and deep lungs. Despite this threat, SAs remain poorly understood. In this study, a laboratory simulation aerosol generator was manufactured, and the particle number size distributions, aerosol liquid water content (ALWC), and chemical and microbial composition of SAs from aeration were analyzed. Under stable aeration conditions, the unimodal SA size distribution ranged from 68 to 350 nm. The ALWC of peak size (170 nm) was 11-21 μg/m³. Na was the dominant major element in SAs with the concentration of 5.61 μg/m³. Total organic carbon accounted for 97% of the total carbon in the SAs. Arcobacter, Methanobrevibacter, and Fusarium were the dominant SA bacteria, archaea, and fungi, respectively, and a number of viruses were also detected. Thirty-two antibiotic resistant genes, and virulence factors of which 23% were offensive virulence factors, were detected in the SAs. The results predicted that 2% of the genes in SAs were directly related to human health. Thus, SAs may pose disproportionately high risks to human health.

Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.

Metagenomic assembly provides a deep insight into the antibiotic resistome alteration induced by drinking water chlorination and its correlations with bacterial host changes

Chlorination can contribute to the enrichment of specific antibiotic resistance genes (ARGs) in drinking water, but the underlying molecular ecological mechanisms remain unknown, which may hinder the assessment and control of the resulting health risks. In this study, metagenomic assembly and Resfams annotation were used to profile the co-occurrence patterns of ARGs, mobile genetic elements (MGEs) and their bacterial hosts, as well as the correlations of potential pathogens with the antibiotic resistome, in a full-scale drinking water treatment and transportation system. Seven ARG types involved in different resistance mechanisms occurred in drinking water and chlorination enhanced the total abundance of the ARGs (p <  0.05). The ARGs encoding resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux pumps predominated in all the samples and were primarily responsible for the ARG accumulation. After chlorination, the ARGs were primarily carried by predominant Sphingomonas, Polaromonas, Hyphomicrobium, Acidovorax, Pseudomonas and Fluviicola. Further, enrichment of the bacterial hosts and MGEs greatly contributed to alteration of the antibiotic resistome. Pseudomonas alcaligenes, carrying multiple ARGs, was identified as a potential pathogen in the chlorinated drinking water. These findings provide novel insights into the host-ARG relationship and the mechanism underlying the resistome alteration during drinking water chlorination.

Inorganic and organic fertilizers application enhanced antibiotic resistome in greenhouse soils growing vegetables

Antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in fertilizers pose risks to human health and their variation in soil after fertilization has been reported. However, some important questions, such as the origin of ARG and ARB observed in soil following fertilization, which are present in soil regardless of fertilizer type (i.e., core (shared) ARGs and ARB), and the contribution of various ARG subtypes to the soil antibiotic resistome, need to be addressed. In this study, the effects of a long-term (9-year) application of organic (manure) and inorganic (chemistry) fertilizers on ARGs in greenhouse soils growing vegetables were investigated using metagenomic sequencing. The results showed that both organic and inorganic fertilizers application increased the diversity and abundance of soil ARGs. The dominant ARG types in organic fertilizer (OF) were different from that in organic fertilizer treated soil (SO), inorganic fertilizer treated soil (SI) and no fertilizer control plots (SC). The difference of core ARGs abundance reflected the variation of ARG profiles among SC, SI and SO. The OF is likely a source of the elevated ARG subtypes in soil and almost all the soil core ARG subtypes can be detected in organic fertilizer. Fifteen ARG types were enriched in the soil with OF, and some ARG subtypes such as sul1, sul2, tetX and tetL might derived from OF while others including as vanR, tcmA, rosB, and mexF might be from indigenous microbes in soil. The nutrition factors were found to influence the ARG profiles in fertilized soil. In summary, this study revealed the possible reason for the soil total ARG numbers and their relative abundance increase after fertilization, which will facilitate the control of ARGs and ARB dissemination.

The role of substrate types and substrate microbial community on the fate of antibiotic resistance genes during anaerobic digestion

Anaerobic digestion (AD) is regarded as a promising technology in energy recovery and the spread mitigation of antibiotic resistance. However, the performance of AD is dependent on various factors, and substrate type is one of the most important. In this study, the fate of antibiotic resistance genes (ARGs) response to the substrate types was investigated, and three typical environmental reservoirs of ARGs (pig manure, chicken manure and sewage sludge) were selected. The role of substrate microbial community on the fate of ARGs was clarified through the comparison between the AD of the substrates with and without a prior autoclave-disinfected step. Results showed that substrate types significantly influenced the fate of ARGs, while the influence from the substrate microbial community was limited. The concentration of antibiotics, the horizontal gene transfer reflected by intI1 and co-selection from heavy metals reflected by metal resistance genes (MRGs) were all reduced effectively. Microbial community varied from substrate types and dominated the ARGs fate concerning the standardized total effects through the mantel test and SEM analysis. The fate of tetX, ermF, tetM and ermB was mainly determined by the physicochemical parameters and the phyla of Firmicutes and Bacteroides. The phyla of Actinobacteria, pcoA and czcA contributed most to the reduction of bla_TEM and mcr-1, and the phyla of Proteobacteria, Chloroflexi, Synergistetes, Euryarchaeote, intI1 and merA correlated significantly with the fate of bla_CTX-M, ereA, tetG and sulI. This study highlighted the importance of substrate types when considering the fate of ARGs during AD.

Decoupling the Dynamics of Bacterial Taxonomy and Antibiotic Resistance Function in a Subtropical Urban Reservoir as Revealed by High-Frequency Sampling

Aquatic environments serve as important reservoirs of antibiotic resistance genes (ARGs), but the information on the high-resolution temporal pattern of ARGs in waterbodies is extremely limited. In this study, the weekly dynamics of ARGs and their relationships with microbial taxonomic communities and environmental variables were analyzed in a subtropical urban reservoir over the period of 1 year using high-throughput approaches. In total, 197 ARGs and 10 mobile genetic elements (MGEs) were detected. The results showed that the bacterial community had a seasonal pattern, while ARGs composition did not exhibit seasonality, thereby indicating the asynchrony or decoupling of temporal patterns of microbial taxonomy and function. More importantly, bacterial abundance and community diversity were more strongly correlated with 17 measured environmental variables than ARGs (36 significant correlations for OTUs, 11 for ARGs). However, stochastic processes appeared to have a minor role in the structuring of the ARG profiles, but a more important role in the structuring of bacterial taxonomic communities. Furthermore, we found that precipitation and turbidity were significantly correlated with the richness and diversity of ARGs, suggesting that multiple environmental factors influence the composition and dynamics of ARGs in complex ways. MGEs were abundant and showed significant positive correlations with ARGs, indicating a plausible influence of MGEs on the variation of ARGs. This is the first study which provides an overview of high-resolution dynamics of ARGs in a subtropical waterbody. Our results improve the understanding of microbial processes and mechanisms of ARGs at fine temporal scale, and offer empirical data of use in the monitoring, assessment and management of the urban water environments.

Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: advances and applications

Our inability to cultivate most microorganisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and nonliving environments. As a result, reservoirs, sources and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes.

Effect of cation type in mixed Ca-Na systems on transport of sulfonamide antibiotics in saturated limestone porous media

Retention and transport of sulfonamides (SAs) in subsurface can strongly affect groundwater quality. In this work, a range of laboratory batch sorption and column transport experiments were conducted to determine the effect of cation type in mixed Ca-Na systems on the retention and transport of two typical SAs, sulfadimethoxine (SDM) and sulfacetamide (SCA), in saturated limestone porous media. Column experimental data showed divalent cation Ca²⁺ played a more important role than monovalent cation Na⁺ in decreasing the transport of only SDM in co-cation systems in the saturated limestone media. Further, in the single-cation (i.e., including either Ca²⁺ or Na⁺) system, increasing ionic strength (IS) of either NaCl or CaCl₂ had little effect on SCA transport; however, increasing of IS of CaCl₂ promoted the retention of SDM in the saturated limestone porous media. This is mainly due to the cation bridging effect of Ca²⁺ on SDM and limestone. Overall, SDM showed much higher retention in the limestone columns than SCA, which can be attributed to the two SAs' different physicochemical properties. Moreover, limestone showed stronger ability to retain the two SAs than quartz sand. Findings in this study suggest that cation type and the concentration of certain electrolyte (e.g., CaCl₂) as well as medium type play an important role in controlling the environmental fate and transport of antibiotics.

Antibiotic Resistome Alteration by Different Disinfection Strategies in a Full-Scale Drinking Water Treatment Plant Deciphered by Metagenomic Assembly

Disinfection regimes are considered the most solid strategy to reduce microbial risks in drinking water, but their roles in shaping the antibiotic resistome are poorly understood. This study revealed the alteration of antibiotic resistance genes (ARGs) profiles, their co-occurrence with mobile genetic elements (MGEs), and potential hosts during drinking water disinfection based on metagenomic assembly. We found the ozone/chlorine (O₃/Cl₂) coupled disinfection significantly increased the relative abundance of ARGs and MGE-carrying antibiotic resistance contigs (ARCs) through the enrichment of ARGs within the resistance-nodulation-cell division and ATP-binding cassette antibiotic efflux families that are primarily carried by Pseudomonas, Acinetobacter, Mycobacterium, and Methylocystis, whereas the antimicrobial resin/chlorine coupled disinfection posed unremarkable changes to the ARG and MGE abundances. Moreover, the co-occurrence patterns of antibiotic efflux and beta-lactam ARGs and MGEs were widely identified, and ARCs carrying the recR and mexH genes were detected in all the samples, with the highest abundance of 2.25 × 10^-2 copies per cell after O₃/Cl₂ disinfection. Sequence-independent binning analysis successfully retrieved two draft ARG-carrying genomes of Acidovorax sp. MR-S7 and Hydrogenophaga sp. IBVHS2, further revealing the host-ARG relationship during O₃/Cl₂ disinfection. Overall, this study provides novel insights into the antibiotic resistome alteration during drinking water disinfection.

Turning pig manure into biochar can effectively mitigate antibiotic resistance genes as organic fertilizer

The composting of fresh manure is an effective way to inactivate pathogens and reduce the levels of antibiotics and some antibiotic resistance genes (ARGs) prior to its application on agricultural land as organic fertilizer. However, some ARGs could still exist and even be enriched after composting. This study investigated whether converting composted pig manure into biochar could reduce the dissemination of ARGs into the soil in comparison with a compost amendment. We performed a pot experiment using pakchoi (Brassica chinensis), with two pig manure-based composts and the biochar derived from composted pig manure, as organic fertilizers. The distributions of the antibiotic resistome, mobile genetic elements (MGEs) and bacterial community composition in soils during cultivation were evaluated by high-throughput qPCR and Illumina sequencing. The total ARGs and MGEs abundance in the biochar-treated soils were significantly lower than those in the compost-amended soils during cultivation. The total ARGs abundance in the biochar-amended soils was similar to that in the control soils during cultivation. Thus, the dissemination of ARGs from animal waste to the environment can be effectively mitigated by converting manure into biochar.

Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils

Composting has been suggested as a potential strategy to eliminate antibiotic residues and pathogens in livestock manure before its application as an organic fertilizer in agro-ecosystems. However, the impacts of composting on antibiotic resistance genes (ARGs) in livestock manure and their temporal succession following the application of compost to land are not well understood. We examined how aerobic composting affected the resistome profiles of cattle manure, and by constructing laboratory microcosms we compared the effects of manure and compost application to agricultural soils on the temporal succession of a wide spectrum of ARGs. The high-throughput quantitative PCR array detected a total of 144 ARGs across all the soil, manure and compost samples, with Macrolide-Lincosamide-Streptogramin B, aminoglycoside, multidrug, tetracycline, and β-lactam resistance as the most dominant types. Composting significantly reduced the diversity and relative abundance of ARGs and mobile genetic elements (MGEs) in the cattle manure. In the 120-day microcosm incubation, the diversity and abundance of ARGs in manure-treated soils were significantly higher than those in compost-treated soils at the beginning of the experiment. The level of antibiotic resistance rapidly declined over time in all manure- and compost-treated soils, coupled with similar temporal patterns of manure- and compost-derived bacterial communities as revealed by SourceTracker analysis. The network analysis revealed more intensive interactions/associations among ARGs and MGEs in manure-treated soils than in compost-treated soils, suggesting that mobility potential of ARGs was lower in soils amended with compost. Our results provide evidence that aerobic composting of cattle manure may be an effective approach to mitigate the risk of antibiotic resistance propagation associated with land application of organic wastes.