antibiotic resistance is usually studied in clinical environments

metagenomes environments

The target of antibiotic resistance genes in natural environments should be considered, specially if we consider that these genes have a long evolutionary history in natural environments, where originated more than two billions years ago (Aminov 2009).

metageno mes  offer the opportunity to assess antibiotic resistance in non clinical environments

The presence and diversity of b-lacatamases in different environments could shed light about both b-lactamase gene transfer between environments and the anthropogenic impact in natural environments.

Data set

Shotgun metagenomic sequences obtained by Illumina sequencing process were used in this study and downloaded from two repositories, MG-RAST (http://metagenomics.anl.gov/) and EBI METAGENOMICS (https://www.ebi.ac.uk/metagenomics/;jsessionid=5B7CC5F7C4C8CD7C9FB5F7E8A4D1C621). A total of 232 metagenomes related to X different projects (Table S1) embedding 4.7 billion sequences, were retrieved after quality control steps performed by each repositorie. Each metagenome was associated with different sampling habitats including soil (undisturbed and agricultural), agricultural soils),  fresh water, ocean, glaciers, human gut, animal gut (rumen and feces), and effluents from wastewater treatment plants.

Construction of a comprehensive β-lactamases database 

Characterization of metagenome sequences associated to β-lactamase genes was preceded by construction of an  extensive β-lactamase database (EX-B) that integrated four clinically-important  publically-available databases: The Lahey β-lactamase database,