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 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 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.

Functional Metagenomics as a Tool for Identification of New Antibiotic Resistance Genes from Natural Environments

2016 ◽  
Vol 73 (2) ◽  
pp. 479-491 ◽  
Author(s):  
Débora Farage Knupp dos Santos ◽  
Paula Istvan ◽  
Betania Ferraz Quirino ◽  
Ricardo Henrique Kruger
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antibiotic Resistance Genes ◽  
Natural Environments ◽  
Functional Metagenomics

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).

Quintuplex PCR to Detect Antibiotic Resistance Genes in Streptococcus pneumoniae

2016 ◽  
Vol 1 (2) ◽  
pp. 22 ◽  
Author(s):  
Navindra Kumari Palanisamy ◽  
Parasakthi Navaratnam ◽  
Shamala Devi Sekaran
Keyword(s):  
Antibiotic Resistance ◽  
Streptococcus Pneumoniae ◽  
Resistance Genes ◽  
Bacterial Pathogen ◽  
Antibiotic Resistance Genes ◽  
Pcr Amplification ◽  
Penicillin Resistance ◽  
Penicillin Binding Proteins ◽  
Efflux Mechanism ◽  
Mic Value

Introduction: Streptococcus pneumoniae is an important bacterial pathogen, causing respiratory infection. Penicillin resistance in S. pneumoniae is associated with alterations in the penicillin binding proteins, while resistance to macrolides is conferred either by the modification of the ribosomal target site or efflux mechanism. This study aimed to characterize S. pneumoniae and its antibiotic resistance genes using 2 sets of multiplex PCRs. Methods: A quintuplex and triplex PCR was used to characterize the pbp1A, ermB, gyrA, ply, and the mefE genes. Fifty-eight penicillin sensitive strains (PSSP), 36 penicillin intermediate strains (PISP) and 26 penicillin resistance strains (PRSP) were used. Results: Alteration in pbp1A was only observed in PISP and PRSP strains, while PCR amplification of the ermB or mefE was observed only in strains with reduced susceptibility to erythromycin. The assay was found to be sensitive as simulated blood cultures showed the lowest level of detection to be 10cfu. Conclusions: As predicted, the assay was able to differentiate penicillin susceptible from the non-susceptible strains based on the detection of the pbp1A gene, which correlated with the MIC value of the strains.

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