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Joao Gatica Arias edited AbstractImportanceIntroductionHistorically_b_lactam_antibiotics_are__.html
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author = {Kevin J. Forsberg and Sanket Patel and Molly K. Gibson and Christian L. Lauber and Rob Knight and Noah Fierer and Gautam Dantas},
title = {Bacterial phylogeny structures soil resistomes across habitats},
journal = {Nature}
}" data-bib-key="Forsberg_2014" contenteditable="false">
Forsberg 2014), due to we chose a identity percent equal o higher than 50%. Reads matching b-lactamases were used to construct distance matrices and b-lactamase gene networks, which were used for all the downstream analysis.
Abundance and diversity of b-lactamases in the environment
The metagenomic analysis show that b-lactamases were present in each metagenome analyzed, ranged from 0.0003% (percent of total b-lactamases in the total number of reads obtained after quality control) in a ocean metagenome (accession number SRS582462) to 0.0335% in a human gut metagenome (accession number SRS056259). The abundance of b-lactamases per environment is in average a 0,01% in soils (n=80 metagenomes, including agricultural and non-agricultural soils), 0.0068% in glacier (n=11), 0.0046% in fresh water (n=11), 0.002% in ocean metagenomes (n=22), 0.0121 in human gut (n=63), 0.0049% in cow gut (n=27 metagenomes, including feces and rumen samples) and 0.0092% in wastewater treatment plant environment (n=19). Parameters of abundance and diversity of b-lactamases in the environment can be observed in Fig.1; thus, soil and glacier environments show the higher abundance of b-lactamases genes, followed by fresh water and wastewater environments (Fig. 1a). Is important indicate that some b-lactamase genes can present different variants, i.e. blaOXA gen present 257 different variants in the EX-B database, but all the variants hits obtained in a given sample/environment are assigned to blaOXA gene, which explains the differences between the number of b-lactamases in the EX-B database and the number of b-lactamase genes in the richness graph. Diversity indexes show that the XXX, YYYY and ZZZ are the most b-lactamase diverse environments (Fig 1, B and C).
The C).
The presence of b-lactamases, grouped according molecular classes, show differences according environment (Fig. 2); thus, class A b-lactamases are dominant in non-agricultural soils, cow (including feces and rumen metagenomes) and human gut environments (more than 70% in each case), class B b-lactamases are dominant in agricultural soils, fresh water, oceans and wastewater treatment plant environments (between 40 to 60% in each environment), class C b-lactamases are more represented in agricultural soils and fresh water environments (20% approx. in each environment) and class D b-lactamases being more abundant in fresh water, wastewater treatment plant and glacier environments (from 15% to 30% approx.). A more detailed picture of b-lactamases in the environment is presented in table 1; where b-lactamase genes were analyzed according their occurrence in a particular environment throughout a indicator species analysis (
...
author = {Marc Dufrene and Pierre Legendre},
title = {Species Assemblages and Indicator Species: The Need for a Flexible Asymmetrical Approach},
journal = {Ecological Monographs}
}" data-bib-key="Dufrene_1997" contenteditable="false">Dufrene 1997). According these results, non-agricultural soils, agricultural soils and wastewater treatment plant are the environments with a high level of faithfulness of occurrence of b-lactamase genes (16, 16 and 14 genes respectively) according the environments previously defined. Only four b-lactamases (blaEBR, CfxA, HGI and mecA) were found to be statistically present in the human gut environment (p<0.005) instead of other analyzed environments. Interestingly, when the environments are grouped according level of anthropogenic impact (anthropogenic impact level 1= wastewater treatment plant; level 2= human gut; level 3= agricultural soils, fresh water, oceans and cow gut; level 4= non-agricultural soils and glaciers), the less impacted environments show a high level of faithfulness of occurrence of b-lactamase genes (50 genes for anthropogenic impact level 3 and 4) than the observed in the more anthropogenic impacted environments, where only 13 b-lactamase genes show faithfulness of
occurrence.
b-lactamase hits obtained in the BLAST process were used to construct metagenome distance matrices and the matrices were used to construct b-lactamase gene networks. When all the b-lactamase hits were used to construct the gene network (Fig. 3), different cluster are clearly observable. The network analysis indicate that each clusters harbor metagenomes almost exclusively related to a given environment; thus, the clusters represent human gut , cow gut and wastewater treatment plant environments. Other two identified clusters include metagenomes related to different environments; one of those cluster include mainly metagenomes of
agricultural soils, glaciers and fresh water, and the other cluster include non-agricultural soil metagenomes thogheter with some glacier and fresh water metagenomes
The target of antibiotic resistance genes in natural environments should be considered, specially if we consider the evidence that these genes have a long evolutionary history in natural environments (
