Virome-associated antibiotic-resistance genes in an experimental aquaculture facility. - Related Documents




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368901.0000Virome-associated antibiotic-resistance genes in an experimental aquaculture facility. We report the comprehensive characterization of viral and microbial communities within an aquaculture wastewater sample, by a shotgun sequencing and 16S rRNA gene profiling metagenomic approach. Caudovirales had the largest representation within the sample, with over 50% of the total taxonomic abundance, whereas approximately 30% of the total open reading frames (ORFs) identified were from eukaryotic viruses (Mimiviridae and Phycodnaviridae). Antibiotic resistance genes (ARGs) within the virome accounted for 0.85% of the total viral ORFs and showed a similar distribution both in virome and in microbiome. Among the ARGs, those encoding proteins involved in the modulation of antibiotic efflux pumps were the most abundant. Interestingly, the taxonomy of the bacterial ORFs identified in the viral metagenome did not reflect the microbial taxonomy as deduced by 16S rRNA gene profiling and shotgun metagenomic analysis. A limited number of ARGs appeared to be mobilized from bacteria to phages or vice versa, together with other bacterial genes encoding products involved in general metabolic functions, even in the absence of any antibiotic treatment within the aquaculture plant. Thus, these results confirm the presence of a complex phage-bacterial network in the aquaculture environment.201626738553
333910.9998Examining the taxonomic distribution of tetracycline resistance in a wastewater plant. Microbial communities serve as reservoirs of antibiotic resistance genes (ARGs) and facilitate the dissemination of these genes to bacteria that infect humans. Relatively little is known about the taxonomic distribution of bacteria harboring ARGs in these reservoirs and the avenues of transmission due to the technical hurdles associated with characterizing the contents of complex microbial populations and the assignment of genes to particular genomes. Focusing on the array of tetracycline resistance (Tc(r)) genes in the primary and secondary phases of wastewater treatment, 17 of the 22 assayed Tc(r) genes were detected in at least one sample. We then applied emulsion, paired isolation, and concatenation PCR (epicPCR) to link tetracycline resistance genes to specific bacterial hosts. Whereas Tc(r) genes tend to vary in their distributions among bacterial taxa according to their modes of action, there were numerous instances in which a particular Tc(r) gene was associated with a host that was distantly related to all other bacteria bearing the same gene, including several hosts not previously identified. Tc(r) genes are far less host-restricted than previously assumed, indicating that complex microbial communities serve as settings where ARGs are spread among divergent bacterial phyla.202438317688
333320.9998A reservoir of 'historical' antibiotic resistance genes in remote pristine Antarctic soils. BACKGROUND: Soil bacteria naturally produce antibiotics as a competitive mechanism, with a concomitant evolution, and exchange by horizontal gene transfer, of a range of antibiotic resistance mechanisms. Surveys of bacterial resistance elements in edaphic systems have originated primarily from human-impacted environments, with relatively little information from remote and pristine environments, where the resistome may comprise the ancestral gene diversity. METHODS: We used shotgun metagenomics to assess antibiotic resistance gene (ARG) distribution in 17 pristine and remote Antarctic surface soils within the undisturbed Mackay Glacier region. We also interrogated the phylogenetic placement of ARGs compared to environmental ARG sequences and tested for the presence of horizontal gene transfer elements flanking ARGs. RESULTS: In total, 177 naturally occurring ARGs were identified, most of which encoded single or multi-drug efflux pumps. Resistance mechanisms for the inactivation of aminoglycosides, chloramphenicol and β-lactam antibiotics were also common. Gram-negative bacteria harboured most ARGs (71%), with fewer genes from Gram-positive Actinobacteria and Bacilli (Firmicutes) (9%), reflecting the taxonomic composition of the soils. Strikingly, the abundance of ARGs per sample had a strong, negative correlation with species richness (r = - 0.49, P < 0.05). This result, coupled with a lack of mobile genetic elements flanking ARGs, suggests that these genes are ancient acquisitions of horizontal transfer events. CONCLUSIONS: ARGs in these remote and uncontaminated soils most likely represent functional efficient historical genes that have since been vertically inherited over generations. The historical ARGs in these pristine environments carry a strong phylogenetic signal and form a monophyletic group relative to ARGs from other similar environments.201829471872
368830.9998Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China. Soil has been regarded as a rich source of antibiotic resistance genes (ARGs) due to the complex microbial community and diverse antibiotic-producing microbes in soil, however, little is known about the ARGs in unculturable bacteria. To investigate the diversity and distribution of ARGs in soil and assess the impact of agricultural practice on the ARGs, we screened soil metagenomic library constructed using DNA from four different agricultural soil for ARGs. We identified 45 clones conferring resistance to minocycline, tetracycline, streptomycin, gentamicin, kanamycin, amikacin, chloramphenicol and rifampicin. The similarity of identified ARGs with the closest protein in GenBank ranged from 26% to 92%, with more than 60% of identified ARGs had low similarity less than 60% at amino acid level. The identified ARGs include aminoglycoside acetyltransferase, aminoglycoside 6-adenyltransferase, ADP-ribosyl transferase, ribosome protection protein, transporters and other antibiotic resistant determinants. The identified ARGs from the soil with manure application account for approximately 70% of the total ARGs in this study, implying that manure amendment may increase the diversity of antibiotic resistance genes in soil bacteria. These results suggest that antibiotic resistance in soil remains unexplored and functional metagenomic approach is powerful in discovering novel ARGs and resistant mechanisms.201424412260
323240.9998Metagenome-Based Analysis of the Microbial Community Structure and Drug-Resistance Characteristics of Livestock Feces in Anhui Province, China. We analyzed metagenome data of feces from sows at different physiological periods reared on large-scale farms in Anhui Province, China, to provide a better understanding of the microbial diversity of the sow intestinal microbiome and the structure of antibiotic-resistance genes (ARGs) and virulence genes it carries. Species annotation of the metagenome showed that in the porcine intestinal microbiome, bacteria were dominant, representing >97% of the microorganisms at each physiological period. Firmicutes and Proteobacteria dominated the bacterial community. In the porcine gut microbiome, the viral component accounted for an average of 0.65%, and the species annotation results indicated that most viruses were phages. In addition, we analyzed the microbiome for ARGs and virulence genes. Multidrug-like, MLS-like, and tetracycline-like ARGs were most abundant in all samples. Evaluation of the resistance mechanisms indicated that antibiotic inactivation was the main mechanism of action in the samples. It is noteworthy that there was a significant positive correlation between ARGs and the total microbiome. Moreover, comparative analysis with the Virulence Factor Database showed that adhesion virulence factors were most abundant.202438393105
346050.9998Bioprospecting for β-lactam resistance genes using a metagenomics-guided strategy. Emergence of new antibiotic resistance bacteria poses a serious threat to human health, which is largely attributed to the evolution and spread of antibiotic resistance genes (ARGs). In this work, a metagenomics-guided strategy consisting of metagenomic analysis and function validation was proposed for rapidly identifying novel ARGs from hot spots of ARG dissemination, such as wastewater treatment plants (WWTPs) and animal feces. We used an antibiotic resistance gene database to annotate 76 putative β-lactam resistance genes from the metagenomes of sludge and chicken feces. Among these 76 candidate genes, 25 target genes that shared 40~70% amino acid identity to known β-lactamases were cloned by PCR from the metagenomes. Their resistances to four β-lactam antibiotics were further demonstrated. Furthermore, the validated ARGs were used as the reference sequences to identify novel ARGs in eight environmental samples, suggesting the necessity of re-examining the profiles of ARGs in environmental samples using the validated novel ARG sequences. This metagenomics-guided pipeline does not rely on the activity of ARGs during the initial screening process and may specifically select novel ARG sequences for function validation, which make it suitable for the high-throughput screening of novel ARGs from environmental metagenomes.201728584911
334360.9998Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. There is increasing evidence for an environmental origin of many antibiotic resistance genes. Consequently, it is important to identify environments of particular risk for selecting and maintaining such resistance factors. In this study, we described the diversity of antibiotic resistance genes in an Indian lake subjected to industrial pollution with fluoroquinolone antibiotics. We also assessed the genetic context of the identified resistance genes, to try to predict their genetic transferability. The lake harbored a wide range of resistance genes (81 identified gene types) against essentially every major class of antibiotics, as well as genes responsible for mobilization of genetic material. Resistance genes were estimated to be 7000 times more abundant than in a Swedish lake included for comparison, where only eight resistance genes were found. The sul2 and qnrD genes were the most common resistance genes in the Indian lake. Twenty-six known and 21 putative novel plasmids were recovered in the Indian lake metagenome, which, together with the genes found, indicate a large potential for horizontal gene transfer through conjugation. Interestingly, the microbial community of the lake still included a wide range of taxa, suggesting that, across most phyla, bacteria has adapted relatively well to this highly polluted environment. Based on the wide range and high abundance of known resistance factors we have detected, it is plausible that yet unrecognized resistance genes are also present in the lake. Thus, we conclude that environments polluted with waste from antibiotic manufacturing could be important reservoirs for mobile antibiotic resistance genes.201425520706
772470.9998Taxonomic and functional analyses reveal existence of virulence and antibiotic resistance genes in beach sand bacterial populations. Coastal sands are important natural recreational facilities that have become hotspots for tourism and economic development. However, these sands harbour diverse microbial assemblages that play a critical role in the balance between public health and ecology. In this study, targeted high-throughput sequencing analysis was used to identify sand-borne bacterial populations at four public beaches in Durban. The effect of heavy metal in shaping the distribution of bacterial metacommunities was determined using canonical correspondence analysis (CCA), while the functional gene profiles were predicted using PICRUSt2 analysis. Sequences matching those of the bacterial phylum Proteobacteria were the most abundant in all samples, followed by those of the phyla Firmicutes, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. Genus-level taxonomic analysis showed the presence of 1163 bacterial genera in all samples combined. The distribution of bacterial communities was shaped by heavy metal concentrations, with the distribution of Flavobacteria, Bacteroidia, and Deltaproteobacteria influenced by Pb and Zn, while B and Cr influenced the distribution of Clostridia and Gammaproteobacteria, respectively. Identified antibiotic resistance genes included the peptidoglycan biosynthesis gene II, III, IV, and V, as well as the polymyxin resistance gene, while the virulence genes included the sitA, fimB, aerobactin synthase, and pilL gene. Our findings demonstrate that beach sand-borne bacteria are reservoirs of virulence and antibiotic resistance genes. Contamination of beach sands with heavy metals selects for both heavy metal resistance and antibiotic resistance in beach sand bacterial communities. Children and immunocompromised people engaging in recreational activities on beaches may be exposed to higher risk of infection.202133474608
325580.9998Early life dynamics of ARG and MGE associated with intestinal virome in neonatal piglets. The pre- and post-weaning stages for piglets are critical periods for the maturation of intestinal functions and contamination with antibiotic resistant bacterial pathogens will threaten their intestinal health. The presence of bacteriophage can also alter bacterial populations in the intestine but whether transmission of antibiotic resistance genes (ARG) is affected by phage during maturation of the neonatal piglet intestine is not known. We therefore identified the intestinal virome along with ARGs and mobile genetic elements (MGE) from piglet fecal samples collected from 3 to 28 days representing the different growth stages. We found wide fluctuations for the intestinal virome of weaning piglets and most virus - related antibiotic resistance was derived from temperate phage suggesting a reservoir of multidrug resistance was present in the neonatal porcine gut. Our results provide a comprehensive understanding of ARGs associated with the intestinal virome that therefore represents a potential risk for horizontal ARG transfer to pathogenic bacteria.202236191572
740590.9998Microbial Diversity and Antimicrobial Resistance Profile in Microbiota From Soils of Conventional and Organic Farming Systems. Soil is one of the biggest reservoirs of microbial diversity, yet the processes that define the community dynamics are not fully understood. Apart from soil management being vital for agricultural purposes, it is also considered a favorable environment for the evolution and development of antimicrobial resistance, which is due to its high complexity and ongoing competition between the microorganisms. Different approaches to agricultural production might have specific outcomes for soil microbial community composition and antibiotic resistance phenotype. Therefore in this study we aimed to compare the soil microbiota and its resistome in conventional and organic farming systems that are continually influenced by the different treatment (inorganic fertilizers and pesticides vs. organic manure and no chemical pest management). The comparison of the soil microbial communities revealed no major differences among the main phyla of bacteria between the two farming styles with similar soil structure and pH. Only small differences between the lower taxa could be observed indicating that the soil community is stable, with minor shifts in composition being able to handle the different styles of treatment and fertilization. It is still unclear what level of intensity can change microbial composition but current conventional farming in Central Europe demonstrates acceptable level of intensity for soil bacterial communities. When the resistome of the soils was assessed by screening the total soil DNA for clinically relevant and soil-derived antibiotic resistance genes, a low variety of resistance determinants was detected (resistance to β-lactams, aminoglycosides, tetracycline, erythromycin, and rifampicin) with no clear preference for the soil farming type. The same soil samples were also used to isolate antibiotic resistant cultivable bacteria, which were predominated by highly resistant isolates of Pseudomonas, Stenotrophomonas, Sphingobacterium and Chryseobacterium genera. The resistance of these isolates was largely dependent on the efflux mechanisms, the soil Pseudomonas spp. relying mostly on RND, while Stenotrophomonas spp. and Chryseobacterium spp. on RND and ABC transporters.201931105678
7718100.9998Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome. Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.201930604012
3687110.9998Genome Sequence of a Novel Multiple-Antibiotic-Resistant Member of the Erysipelotrichaceae Family Isolated from a Swine Manure Storage Pit. The swine gastrointestinal tract and stored swine manure may serve as reservoirs of antibiotic resistance genes, as well as sources of novel bacteria. Here, we report the draft genome sequence of a novel taxon in the Erysipelotrichaceae family, isolated from a swine manure storage pit that is resistant to multiple antibiotics.201627660777
7714120.9998Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach. The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.202438183799
7692130.999716S rRNA gene sequencing data of the human skin microbiome before and after swimming in the ocean. These data represent the abundance, diversity and predicted function gene profiles of the microbial communities present on human skin before and after swimming in the ocean. The skin microbiome has been shown to provide protection against infection from pathogenic bacteria. It is well-known that exposure to ocean water can cause skin infection, but little is known about how exposure can alter the bacterial communities on the skin. Skin microbiome samples were collected from human participants before and after swimming in the ocean. These data were used to analyze the changes in abundance and diversity of microbial communities on the skin and the changes in the functional profiles of the bacteria, specifically focusing on genes involved in antibiotic resistance and bacterial virulence.202134189199
3874140.9997Culture-enriched human gut microbiomes reveal core and accessory resistance genes. BACKGROUND: Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer. RESULTS: Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements. CONCLUSION: Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance. Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.201930953542
3680150.9997Metagenomic Insights Into the Contribution of Phages to Antibiotic Resistance in Water Samples Related to Swine Feedlot Wastewater Treatment. In this study, we examined the types of antibiotic resistance genes (ARGs) possessed by bacteria and bacteriophages in swine feedlot wastewater before and after treatment using a metagenomics approach. We found that the relative abundance of ARGs in bacterial DNA in all water samples was significantly higher than that in phages DNA (>10.6-fold), and wastewater treatment did not significantly change the relative abundance of bacterial- or phage-associated ARGs. We further detected the distribution and diversity of the different types of ARGs according to the class of antibiotics to which they confer resistance, the tetracycline resistance genes were the most abundant resistance genes and phages were more likely to harbor ATP-binding cassette transporter family and ribosomal protection genes. Moreover, the colistin resistance gene mcr-1 was also detected in the phage population. When assessing the contribution of phages in spreading different groups of ARGs, β-lactamase resistance genes had a relatively high spreading ability even though the abundance was low. These findings possibly indicated that phages not only could serve as important reservoir of ARG but also carry particular ARGs in swine feedlot wastewater, and this phenomenon is independent of the environment.201830459724
6891160.9997Feedstock-dependent antibiotic resistance gene patterns and expression profiles in industrial scale biogas plants revealed by meta-omics technology. This study investigated antimicrobial resistance in the anaerobic digesters of two industrial-scale biogas plants processing agricultural biomass and municipal wastewater sludge. A combination of deep sequencing and genome-centric workflow was implemented for metagenomic and metatranscriptomics data analysis to comprehensively examine potential antimicrobial resistance in microbial communities. Anaerobic microbes were found to harbour numerous antibiotic resistance genes (ARGs), with 58.85% of the metagenome-assembled genomes (MAGs) harbouring antibiotic resistance. A moderately positive correlation was observed between the abundance and expression of ARGs. ARGs were located primarily on bacterial chromosomes. A higher expression of resistance genes was observed on plasmids than on chromosomes. Risk index assessment suggests that most ARGs identified posed a significant risk to human health. However, potentially pathogenic bacteria showed lower ARG expression than non-pathogenic ones, indicating that anaerobic treatment is effective against pathogenic microbes. Resistomes at the gene category level were associated with various antibiotic resistance categories, including multidrug resistance, beta-lactams, glycopeptides, peptides, and macrolide-lincosamide-streptogramin (MLS). Differential expression analysis revealed specific genes associated with potential pathogenicity, emphasizing the importance of active gene expression in assessing the risks associated with ARGs.202539461216
3853170.9997Co-selection of antibiotic-resistant bacteria in a paddy soil exposed to As(III) contamination with an emphasis on potential pathogens. The increased acquisition of antibiotic resistance by pathogens is a global health concern. The environmental selection of antibiotic resistance can be caused by either antibiotic residues or co-selecting agents such as toxic metal(loid)s. This study explored the potential role of As(III) as a co-selecting driver in the spread of antibiotic resistance in paddy soils. By applying high-throughput sequencing, we found that the diversity and composition of soil microbial communities was significantly altered by As(III) exposure, resulting in an increased proportion of potential pathogens (9.9%) compared to the control soil (0.1%). Meanwhile, a total of 46 As(III)-resistant isolates were obtained from As(III)-exposure soil, among which potential pathogens accounted for 54.3%. These As(III)-resistant bacteria showed a high incidence of resistance to sulfanilamide (100%) and streptomycin (88-93%). The association between antibiotic and As(III) resistances was further investigated in a potentially pathogenic isolate by whole-genome sequencing and a transcription assay. The results showed that As(III) and antibiotic resistance genes might co-occur in a mobile genomic island and be co-regulated by As(III), implying that antibiotic resistance could be co-selected by As(III) via co-resistance and co-regulation mechanisms. Overall, these results suggest that As(III) exposure provides a strong selective pressure for the expansion of soil bacterial resistome.202032302839
3244180.9997Metagenomic analysis of virulence-associated and antibiotic resistance genes of microbes in rumen of Indian buffalo (Bubalus bubalis). A major research goal in rumen microbial ecology is to understand the relationship between community composition and its function, particularly involved in fermentation process is of a potential interest. The buffalo rumen microbiota impacts human food safety as well as animal health. Although the bacteria of bovine rumen have been well characterized, techniques have been lacking to correlate total community structure with gene function. We applied 454 next generations sequencing technology to characterize general microbial diversity present in buffalo rumen metagenome and also identified the repertoire of microbial genes present, including genes associated with antibiotic resistance and bacterial virulence. Results suggest that over six percent (6.44%) of the sequences from our buffalo rumen pool sample could be categorized as virulence genes and genes associated with resistance to antibiotic and toxic compounds (RATC), which is a higher proportion of virulence genes reported from metagenome samples of chicken cecum (5.39%), cow rumen (4.43%) and Sargasso sea (2.95%). However, it was lower than the proportion found in cow milk (11.33%) cattle faeces (8.4%), Antarctic marine derived lake (8.45%), human fecal (7.7%) and farm soil (7.79%). The dynamic nature of metagenomic data, together with the large number of RATC classes observed in samples from widely different ecologies indicates that metagenomic data can be used to track potential targets and relative amounts of antibiotic resistance genes in individual animals. In addition, these data can be also used to generate antibiotic resistance gene profiles to facilitate an understanding of the ecology of the microbial communities in each habitat as well as the epidemiology of antibiotic resistant gene transport between and among habitats.201222850272
9653190.9997Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics. Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes. We applied Inverse PCR on sediment samples and identified 79 different MGE clusters associated with the studied resistance genes, including novel mobile genetic elements, co-selected resistance genes and a new putative antibiotic resistance gene. The results show that the method can be used in antibiotic resistance early warning systems. In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances.201627767072