scholarly journals Graph-Based Approaches Significantly Improve the Recovery of Antibiotic Resistance Genes From Complex Metagenomic Datasets

2021 ◽  
Vol 12 ◽  
Author(s):  
Daria Shafranskaya ◽  
Alexander Chori ◽  
Anton Korobeynikov
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Target Genes ◽  
Markov Models ◽  
State Of The Art ◽  
Antibiotic Resistance Genes ◽  
Antimicrobial Substances ◽  
Accuracy And Precision ◽  
Microbial Strains ◽  
Metagenomic Assembly

The lack of control over the usage of antibiotics leads to propagation of the microbial strains that are resistant to many antimicrobial substances. This situation is an emerging threat to public health and therefore the development of approaches to infer the presence of resistant strains is a topic of high importance. The resistome construction of an isolate microbial species could be considered a solved task with many state-of-the-art tools available. However, when it comes to the analysis of the resistome of a microbial community (metagenome), then there exist many challenges that influence the accuracy and precision of the predictions. For example, the prediction sensitivity of the existing tools suffer from the fragmented metagenomic assemblies due to interspecies repeats: usually it is impossible to recover conservative parts of antibiotic resistance genes that belong to different species that occur due to e.g., horizontal gene transfer or residing on a plasmid. The recent advances in development of new graph-based methods open a way to recover gene sequences of interest directly from the assembly graph without relying on cumbersome and incomplete metagenomic assembly. We present GraphAMR—a novel computational pipeline for recovery and identification of antibiotic resistance genes from fragmented metagenomic assemblies. The pipeline involves the alignment of profile hidden Markov models of target genes directly to the assembly graph of a metagenome with further dereplication and annotation of the results using state-of-the art tools. We show significant improvement of the quality of the results obtained (both in terms of accuracy and completeness) as compared to the analysis of an output of ordinary metagenomic assembly as well as different read mapping approaches. The pipeline is freely available from https://github.com/ablab/graphamr.

scholarly journals RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

mSystems ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Taylor K. Dunivin ◽  
Jinlyung Choi ◽  
Adina Howe ◽  
Ashley Shade
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Soil Microorganisms ◽  
Antibiotic Resistance Genes ◽  
Health Concern ◽  
Reference Database ◽  
Chromosome Size ◽  
Microbial Strains ◽  
Plasmid Size ◽  
Host Associations

ABSTRACT Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances. IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.

scholarly journals RefSoil+: A reference for antimicrobial resistance genes on soil plasmids

2018 ◽  
Author(s):  
TK Dunivin ◽  
J Choi ◽  
AC Howe ◽  
A Shade
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Health Concern ◽  
Microbiome Diversity ◽  
Antimicrobial Resistance Genes ◽  
Limited Opportunity ◽  
Microbial Strains ◽  
Plasmid Size ◽  
Host Associations

AbstractPlasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were relatively larger than other described plasmids, which is a trait associated with plasmid mobility. There was no relationship between chromosome size and plasmid size or number, suggesting that these genomic traits are independent in soil. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a baseline for the diversity, composition, and host-associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.ImportanceSoil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate knowledge of soil plasmid characteristics so that the content, host-associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource for investigating clinic-environment dynamics of important plasmid-associated genes, including antibiotic resistance genes.

scholarly journals Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters

2022 ◽  
Vol 8 (1) ◽  
Author(s):  
Wei Yan ◽  
A. Brantley Hall ◽  
Xiaofang Jiang
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Gut Microbiome ◽  
Phase Variation ◽  
Antibiotic Resistance Genes ◽  
Genomic Analysis ◽  
Human Gut ◽  
Bacterial Populations ◽  
Human Gut Microbiome ◽  
Metagenomic Assembly

AbstractAntibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.

Inhibition effect of kaolinite on the development of antibiotic resistance genes in Escherichia coli induced by sublethal ampicillin and its molecular mechanism

2019 ◽  
Vol 16 (5) ◽  
pp. 347 ◽  
Author(s):  
Xiaolin Lai ◽  
Pingxiao Wu ◽  
Bo Ruan ◽  
Juan Liu ◽  
Zehua Liu ◽  
...  
Keyword(s):  
Public Health ◽  
Escherichia Coli ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Natural Environment ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Antibiotic Resistance Genes ◽  
E Coli

Environmental contextAntibiotic resistance by microorganisms in the natural environment poses a threat to ecosystems and public health. We report findings suggesting kaolinite can effectively inhibit the development of antibiotic resistance genes in microorganisms, and present a new understanding of the molecular mechanisms that promote the development of antibiotic resistance. These results are critical to mitigating environmental and public health risks resulting from the abuse of antibiotics. AbstractAntibiotic resistance and antibiotic resistance genes (ARGs) in the natural environment pose a threat to ecosystems and public health; therefore, better strategies are needed to mitigate the emergence of resistance. This study examined the expression of ARGs in Escherichia coli (E. coli) after exposure to sub-MIC (minimum inhibitory concentration) antibiotics for 15 days in the presence and absence of kaolinite. The results of the real-time polymerase chain reaction (PCR) showed that the expression levels of the eight target genes of E. coli adhering to kaolinite were relatively decreased, and the MIC results also indicated that the final resistance was lower than that of the strains without kaolinite. A close relationship between E. coli and kaolinite was also revealed, as well as a unique interfacial interaction. In addition, the differential protein expression was further analysed to detect proteins and genes associated with ARGs mutations, and then the underlying mechanisms of cell growth and metabolism were identified under low dose ampicillin stress to elucidate the role of kaolinite in the process. Molecular mechanisms analysis determined that when cells adhering to kaolinite were stressed, transport of ampicillin to the periplasmic space was reduced, and the redox metabolism of bacteria was promoted to combat the harsh environment. Moreover, cells synthesised related peptides or proteins under the action of ribosomal proteins to prevent toxic damage. Therefore, this work not only provides new insights into the cellular response to antibiotic stress, but also provides a topic for more research on methods to delay the emergence of ARGs.

scholarly journals Using Cy5-dUTP labelling of RPA-amplicons with downstream microarray analysis for the detection of antibiotic resistance genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Christian Warmt ◽  
Carolin Kornelia Fenzel ◽  
Jörg Henkel ◽  
Frank Fabian Bier
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Target Genes ◽  
Point Of Care ◽  
Antibiotic Resistance Genes ◽  
Nucleic Acid Amplification ◽  
Promising Tool ◽  
Point Of Care Diagnostics ◽  
Amplification Process ◽  
First Time

AbstractIn this report we describe Cy5-dUTP labelling of recombinase-polymerase-amplification (RPA) products directly during the amplification process for the first time. Nucleic acid amplification techniques, especially polymerase-chain-reaction as well as various isothermal amplification methods such as RPA, becomes a promising tool in the detection of pathogens and target specific genes. Actually, RPA even provides more advantages. This isothermal method got popular in point of care diagnostics because of its speed and sensitivity but requires pre-labelled primer or probes for a following detection of the amplicons. To overcome this disadvantages, we performed an labelling of RPA-amplicons with Cy5-dUTP without the need of pre-labelled primers. The amplification results of various multiple antibiotic resistance genes indicating great potential as a flexible and promising tool with high specific and sensitive detection capabilities of the target genes. After the determination of an appropriate rate of 1% Cy5-dUTP and 99% unlabelled dTTP we were able to detect the blaCTX-M15 gene in less than 1.6E−03 ng genomic DNA corresponding to approximately 200 cfu of Escherichia coli cells in only 40 min amplification time.

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