Methods to predict antibiotic resistance: From genes to metagenomes

Resumen

As many antibiotics exist as many mechanisms of resistance will rise. Antibiotic resistance is a worldwide problem and deserves all sort of attention and dedication to identify the critical points which might promote or facilitate the emergence of novel resistance genes in one community, as well the propagation of the already known genes. The increasing of antimicrobial resistant organisms, mediated by the transference of genes vertically or horizontally and by spontaneous mutations represent a risk for human health. Frequently, bacteria suffer injuries from antibiotics, biocides and heavy‐metals, in clinical and environmental environments, which exert a selective pressure over these organisms interfering at the abundance and composition of environmental communities. This pressure of antimicrobials compounds leads to evolutionary and ecological consequences that are not fully understood and are highlighted in this work. For this purpose, we performed a comprehensive study of the effects leaded by antibiotics and biocides from the smallest genetic elements, as genes, passing through the organized arrangement of the genome and finishing in the complex group forming the metagenome. To this, wet‐lab techniques and bioinformatics approaches were applied to elucidate the main questions of this Thesis: (1) Does the presence of plasmids containing quinolone resistance genes affect the fitness of the cell? (2) Low‐level resistance qnr genes can evolve towards high‐level resistance?; (3) Infective and environmental strains of Stenotrophomonas maltophilia constitute two different phylogenetic branches?; (4) May the biocide triclosan exerts influence at the selection of antibiotic resistance genes and genetic mobile elements involved in the antimicrobial resistance in sludge from Waste Water Treatment (WWTP); (5) How does the presence of triclosan affects the taxonomic composition of an environmental microbiota? The answers for our questions were: (1) In the absence of quinolone selective pressure, the plasmids containing qnr resistance genes are expulsed from the cell to minimize the costs of maintaining useless elements inside; (2) Cells with the capability of generating their own mechanisms of resistance and adaptation to antibiotics do not make use of foreign helper genes and mutate their genomes; (3) Independently on the origin, clinical and environmental strains of S. maltophilia present similar genomic composition; there is not an "infective" S. maltophilia lineage; (4) Triclosan alters the number of antibiotic resistance genes present in a microbiota in a concentration‐dependent way; (5) Triclosan affects the composition of the microbiota collected from a WWTP. Altogether, these results serve to understand the multi‐level procedure that operates for selecting antibiotic resistance and propose different complimentary approaches to study this problem.