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author = {Jos{\'{e}} L. Mart{\'{\i}}nez},
title = {Bottlenecks in the Transferability of Antibiotic Resistance from Natural Ecosystems to Human Bacterial Pathogens},
journal = {Front. Microbio.}
}" data-bib-key="Mart_nez_2012" contenteditable="false">
Mart' 2012, Forsberg 2014, Udikovic-Kolic 2014).
In the same way that in our study, Fondi et al (2016) found that geography does not influence the microbial gene pool distributions, indicating that the dispersal potential of microorganisms is affected by environmental factors more than by geographical distances.
In order to analyze the grade of similarity between the b-lactamases detected in this study and the b-lactamases of clinical origin, present in the EX-B database, we choose four clinical important b-lactamases such blaTEM, blaCTX-M, blaGES (class A b-lactamases) and blaOXA (class D),
This D). Our results show that the distributions of those genes is different in the analyzed environments; thus, blaOXA was the most abundant gene, with a thousand of hits in soils, glaciers, fresh water, wastewater and human gut metagenomes. In the whole, blaOXA similarity was low, with 43.7 to 69.9% of hits showing a similarity between 50 to 59% to blaOXA sequences harbored in EX-B database; however, particularly interesting is the the human gut metagenome show a 24.3% of hits with high similarty (90 to 100% of similarity) to the blaOXA genes of the EX-B database. In addition; some differences were observed between the abundance of blaOXA gene in soil metagenomes; thus, non-agricultural metagenomes show a higher abundance (6480 hits) than the abundance observed in agricultural soils (3147 hits).
This study is an attempt to screen the presence of b-lactamases on non-clinical environments based on public shotgun metagenome studies. The methodology here presented, try to reduce the differences produced by the comparison of several sequencing studies; however, in the whole, our results shed light for first time on the wide distribution and content of b-lactamases on different environments, including non-clinical and non anthropogenically impacted environments. Despite the wide b-lactamase distribution, b-lactamases exhibit certain environmental fingerprint; in addition, some b-lactamase genes exhibit a higher presence in some specific environments, which strengthening this environmental b-lactamase fingerprint. Finally, our network analysis suggest that b-lactamases can move from a given environment to other, but this type of events are rare in the time.
Materials and methods
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/). 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 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,
