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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). 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). It is clear that anthropogenic forces impact in different ways the b-lactamase content across the analyzed environments, since the abundance can be high in very impacted environments such as wastewater, but also can be high in less impacted environments such glaciers.

Similarly to blaOXA, the other selected genes show the same trend, a very low percent of similarity to sequences in the EX-B database. This is particularly right in the case of soils, glaciers, fresh water and wastewater environments, but some differences can be observed in the distribution of the those genes across the different environments. for example a higher similarity to sequences in the EX-B database is observed in the case of blaCTX-M gene, with many hits classified in the range of 60 to 79 % of similarity, and more hits classified with 90 to 100% of similarity in the case of blaTEM (glaciers, fresh water and wastewater environmnets). In some cases few hits were obtained (less than 10) and the results need to be consider in accordance; thus one hit of blaCTX-M was obtained in among the rumen cow metagenomes, with a similarity classified in the range on 70 to 79%. In the opposite side, blaTEM exhibit 1335 hits among the human gut metagenomes; however, 1196 of them were obtained from a specific metagenome (human gut 8) and 113 of them show a 100% of similarity to blaTEM variants in the EX-B database. Certainly the two described examples are outliers, but in the case of the human gut metagenome, probably we are facing a sick person case, although more information about this metagenome is required to validate this hypothesis. 



This hypothesis. 

In addition, the comparison of the four selected b-lactamase genes show that the abundance of those genes is different in the analyzed environments, and blaOXA gene is the most abundant in each environment with the exception of ocean environments, where blaTEM is the most abundant b-lactamase gene.



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,