scholarly journals Global ocean resistome revealed: exploring Antibiotic Resistance Genes (ARGs) abundance and distribution on TARA oceans samples through machine learning tools

2019 ◽  
Author(s):  
Rafael R. C. Cuadrat ◽  
Maria Sorokina ◽  
Bruno G. Andrade ◽  
Tobias Goris ◽  
Alberto M. R. Dávila
Keyword(s):  
Machine Learning ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Opportunistic Pathogen ◽  
Global Ocean ◽  
Natural Environments ◽  
Learning Tools ◽  
Global Public Health ◽  
Ocean Environment

AbstractThe rise of antibiotic resistance (AR) in clinical settings is one of the biggest modern global public health concerns. Therefore, the understanding of AR mechanisms, evolution and global distribution is a priority due to its impact on the treatment course and patient survivability. Besides all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental uncultivable microorganisms. In this study, 293 metagenomic from the TARA Oceans project were used to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. After extensive manual curation, we show the global ocean ARG abundance, distribution, taxonomy, phylogeny and their potential to be horizontally transferred by plasmids or viruses and their correlation with environmental and geographical parameters. A total of 99,205 environmental ORFs were identified as potential ARGs. These ORFs belong to 560 ARG families that confer resistance to 26 antibiotic classes. 24,567 ORFs were found in contigs classified as plasmidial sequences, suggesting the importance of mobile genetic elements in the dynamics of ARGs transmission. Moreover, 4,804 contigs with more than 2 ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. This also raises the possibility of horizontal gene transfer (HGT) between clinical and natural environments. The abundance of ARGs showed different patterns of distribution, with some classes being significantly more abundant in coastal biomes. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs from the recently discovered MCR-1 family with high abundance on Polar Biomes. Of these, 5 were assigned to the genus Psychrobacter, an opportunistic pathogen that can cause fatal infections in humans. Our results are available on Zenodo in MySQL database dump format and all the code used for the analyses, including a Jupyter notebook can be accessed on GitHub (https://github.com/rcuadrat/ocean_resistome).

scholarly journals Global ocean resistome revealed: Exploring antibiotic resistance gene abundance and distribution in TARA Oceans samples

GigaScience ◽  
2020 ◽  
Vol 9 (5) ◽  
Author(s):  
Rafael R C Cuadrat ◽  
Maria Sorokina ◽  
Bruno G Andrade ◽  
Tobias Goris ◽  
Alberto M R Dávila
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Web Application ◽  
Antibiotic Resistance Gene ◽  
Antibiotic Resistance Genes ◽  
Open Reading Frames ◽  
Global Ocean ◽  
Learning Tools ◽  
Human Pathogens ◽  
Abundance And Distribution

Abstract Background The rise of antibiotic resistance (AR) in clinical settings is of great concern. Therefore, the understanding of AR mechanisms, evolution, and global distribution is a priority for patient survival. Despite all efforts in the elucidation of AR mechanisms in clinical strains, little is known about its prevalence and evolution in environmental microorganisms. We used 293 metagenomic samples from the TARA Oceans project to detect and quantify environmental antibiotic resistance genes (ARGs) using machine learning tools. Results After manual curation of ARGs, their abundance and distribution in the global ocean are presented. Additionally, the potential of horizontal ARG transfer by plasmids and their correlation with environmental and geographical parameters is shown. A total of 99,205 environmental open reading frames (ORFs) were classified as 1 of 560 different ARGs conferring resistance to 26 antibiotic classes. We found 24,567 ORFs in putative plasmid sequences, suggesting the importance of mobile genetic elements in the dynamics of environmental ARG transmission. Moreover, 4,804 contigs with >=2 putative ARGs were found, including 2 plasmid-like contigs with 5 different ARGs, highlighting the potential presence of multi-resistant microorganisms in the natural ocean environment. Finally, we identified ARGs conferring resistance to some of the most relevant clinical antibiotics, revealing the presence of 15 ARGs similar to mobilized colistin resistance genes (mcr) with high abundance on polar biomes. Of these, 5 are assigned to Psychrobacter, a genus including opportunistic human pathogens. Conclusions This study uncovers the diversity and abundance of ARGs in the global ocean metagenome. Our results are available on Zenodo in MySQL database dump format, and all the code used for the analyses, including a Jupyter notebook js avaliable on Github. We also developed a dashboard web application (http://www.resistomedb.com) for data visualization.

Call of the wild: antibiotic resistance genes in natural environments

2010 ◽  
Vol 8 (4) ◽  
pp. 251-259 ◽  
Author(s):  
Heather K. Allen ◽  
Justin Donato ◽  
Helena Huimi Wang ◽  
Karen A. Cloud-Hansen ◽  
Julian Davies ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Natural Environments

scholarly journals Modified U-Tube for Ruling out Naked DNA Transfer during Conjugation and Application in Antibiotic Resistance Genes Transfer Research

Water ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 1313
Author(s):  
Ning Zhang ◽  
Xiang Liu ◽  
Bing Li ◽  
Limei Han ◽  
Xuejiao Ma ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Public Health Issue ◽  
Primary Concern ◽  
Conjugative Transfer ◽  
Donor Strain ◽  
Global Public Health ◽  
Pseudomonas Putida Kt2440 ◽  
Naked Dna

Antibiotic resistance is currently a major global public health issue. In particular, the emergence and transfer of antibiotic resistance genes (ARGs) is a matter of primary concern. This study presented a method for ruling out the transfer of naked DNA (plasmid RP4 lysed from donor cells) during the cell-to-cell conjugation, using a modified “U-tube”. A series of gene transfer assays was conducted in both flask and modified U-tube, using Pseudomonas putida KT2440 (P. putida (RP4)) harboring the RP4 plasmid as the donor strain, Escherichia coli (E. coli, ATCC 25922) in pure culture as sole recipient, and bacteria from reclaimed water microcosms as multi-recipients. The verification experiments showed that the U-tube device could prevent direct contact of bacteria without affecting the exchange of free plasmid. In the experiments involving a sole recipient, the transconjugants were obtained in flask samples, but not in modified U-tube. Furthermore, in experiments involving multi-recipients, transfer of naked DNA in the modified U-tube accounted for 5.18% in the transfer frequency of the flask transfer experiment. The modified U-tube proved to be useful for monitoring the interference of naked DNA in the research of conjugative transfer and calculating the exact conjugative transfer rate. This device is identified as a promising candidate for distinguishing different gene transfers in practical application because of its convenient use and easy and simple manufacture.

scholarly journals The resistome of common human pathogens

2017 ◽  
Author(s):  
Christian Munck ◽  
Mostafa M. Hashim Ellabaan ◽  
Michael Schantz Klausen ◽  
Morten O.A. Sommer
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Pathogens ◽  
Antibiotic Resistance Genes ◽  
Gene Clusters ◽  
Species Level ◽  
Natural Environments ◽  
Human Pathogens ◽  
Bacterial Genomes ◽  
Risk Ranking

AbstractGenes capable of conferring resistance to clinically used antibiotics have been found in many different natural environments. However, a concise overview of the resistance genes found in common human bacterial pathogens is lacking, which complicates risk ranking of environmental reservoirs. Here, we present an analysis of potential antibiotic resistance genes in the 17 most common bacterial pathogens isolated from humans. We analyzed more than 20,000 bacterial genomes and defined a clinical resistome as the set of resistance genes found across these genomes. Using this database, we uncovered the co-occurrence frequencies of the resistance gene clusters within each species enabling identification of co-dissemination and co-selection patterns. The resistance genes identified in this study represent the subset of the environmental resistome that is clinically relevant and the dataset and approach provides a baseline for further investigations into the abundance of clinically relevant resistance genes across different environments. To facilitate an easy overview the data is presented at the species level at www.resistome.biosustain.dtu.dk.

scholarly journals The Evolution of Class 1 Integrons and the Rise of Antibiotic Resistance

2008 ◽  
Vol 190 (14) ◽  
pp. 5095-5100 ◽  
Author(s):  
Michael Gillings ◽  
Yan Boucher ◽  
Maurizio Labbate ◽  
Andrew Holmes ◽  
Samyuktha Krishnan ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Lateral Transfer ◽  
Natural Environments ◽  
Class 1 Integrons ◽  
Wide Range ◽  
Human Food Chain ◽  
Class 1 ◽  
Phylogenetic Signature

ABSTRACT Class 1 integrons are central players in the worldwide problem of antibiotic resistance, because they can capture and express diverse resistance genes. In addition, they are often embedded in promiscuous plasmids and transposons, facilitating their lateral transfer into a wide range of pathogens. Understanding the origin of these elements is important for the practical control of antibiotic resistance and for exploring how lateral gene transfer can seriously impact on, and be impacted by, human activities. We now show that class 1 integrons can be found on the chromosomes of nonpathogenic soil and freshwater Betaproteobacteria. Here they exhibit structural and sequence diversity, an absence of antibiotic resistance genes, and a phylogenetic signature of lateral transfer. Some examples are almost identical to the core of the class 1 integrons now found in pathogens, leading us to conclude that environmental Betaproteobacteria were the original source of these genetic elements. Because these elements appear to be readily mobilized, their lateral transfer into human commensals and pathogens was inevitable, especially given that Betaproteobacteria carrying class 1 integrons are common in natural environments that intersect with the human food chain. The strong selection pressure imposed by the human use of antimicrobial compounds then ensured their fixation and global spread into new species.

scholarly journals Novel Aminoglycoside Resistance Transposons and Transposon-Derived Circular Forms Detected in Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates

2016 ◽  
Vol 60 (3) ◽  
pp. 1801-1818 ◽  
Author(s):  
Nabil Karah ◽  
Chinmay Kumar Dwibedi ◽  
Karin Sjöström ◽  
Petra Edquist ◽  
Anders Johansson ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Acinetobacter Baumannii ◽  
Resistance Genes ◽  
Point Mutations ◽  
Antibiotic Resistance Genes ◽  
Opportunistic Pathogen ◽  
Clinical Isolates ◽  
Aminoglycoside Resistance ◽  
Content Type ◽  
Carbapenem Resistant

Acinetobacter baumanniihas emerged as an important opportunistic pathogen equipped with a growing number of antibiotic resistance genes. Our study investigated the molecular epidemiology and antibiotic resistance features of 28 consecutive carbapenem-resistant clinical isolates ofA. baumanniicollected throughout Sweden in 2012 and 2013. The isolates mainly belonged to clonal complexes (CCs) with an extensive international distribution, such as CC2 (n= 16) and CC25 (n= 7). Resistance to carbapenems was related toblaOXA-23(20 isolates),blaOXA-24/40-like(6 isolates),blaOXA-467(1 isolate), and ISAba1-blaOXA-69(1 isolate). Ceftazidime resistance was associated withblaPER-7in the CC25 isolates. Two classical point mutations were responsible for resistance to quinolones in all the isolates. Isolates with high levels of resistance to aminoglycosides carried the 16S rRNA methylasearmAgene. The isolates also carried a variety of genes encoding aminoglycoside-modifying enzymes. Several novel structures involved in aminoglycoside resistance were identified, including Tn6279, ΔTn6279, Ab-ST3-aadB, and different assemblies of Tn6020and TnaphA6. Importantly, a number of circular forms related to the IS26or ISAba125composite transposons were detected. The frequent occurrence of these circular forms in the populations of several isolates indicates a potential role of these circular forms in the dissemination of antibiotic resistance genes.

scholarly journals Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome

mSystems ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Sumayah F. Rahman ◽  
Matthew R. Olm ◽  
Michael J. Morowitz ◽  
Jillian F. Banfield
Keyword(s):  
Machine Learning ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Sequence Data ◽  
Antibiotic Resistance Genes ◽  
Machine Learning Model ◽  
Infant Gut Microbiome ◽  
Microbial Systems ◽  
Gut Microbial Community ◽  
Insight Into

The process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical applications.

scholarly journals Antimicrobial-resistance genes in the human gut prior the antibiotic-therapy era

2019 ◽  
Author(s):  
Tasha Santiago-Rodriguez
Keyword(s):  
Antibiotic Resistance ◽  
Antimicrobial Resistance ◽  
Antibiotic Therapy ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Natural Environments ◽  
Beta Lactams ◽  
Human Gut ◽  
Antimicrobial Resistance Genes

Antibiotic-resistance has long been associated with the use and abuse of antibiotics. However, increasing evidence is suggesting that antibiotic-resistance is in fact a phenomenon that has been occurring in natural environments for thousands and possibly millions of years. With the expansion of the microbiome field, it is now possible to characterize antibiotic-resistance genes altogether in different samples, including the human gut. This has also enabled the characterization of ancient human gut microbiomes, which also include antibiotic-resistance genes. Mummified gut remains represent a unique opportunity to characterize the microbiome and antibiotic-resistance genes prior the antibiotic-therapy era. Surprisingly, mummies from the Inca and Italian nobility cultures showed to possess antibiotic-resistance-like genes similar to modern-day antibiotic-resistance genes conferring resistance to beta-lactams, sulfa, quinolones and vancomycin, just to mention a few examples. This is intriguing as it further supports that antibiotic-resistance began in the environment and was transferred to the human gut by means that remain to be investigated and are a matter of ongoing speculation.

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