Exploring the aquatic resistome.

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Recovery of cyanobacterial draft genomes from a metagenome dataset: applications to the detection of antibiotic resistance variants

Publication . Balata, Duarte

Freshwater cyanobacteria are one of the most widely distributed groups of organisms in continental bodies of water worldwide. Cyanobacteria’s evolutionary process granted them a wide variety of shapes and forms of colony organization, making them a very heterogeneous group, both phenotypically and genotypically. Despite being a frequently studied group due to their capacity to form harmful algal blooms and produce bioactive compounds with promising pharmaceutical properties, their known potential as antibiotic resistance genes reservoirs is still understudied, especially in freshwater environments. Antibiotic resistance is a growing concern in terms of human and animal health, but antibiotic resistance mechanisms aren’t restricted to pathogenic bacteria. Environmental microorganisms have also been shown to play a key role in the emergence and propagation of antibiotic resistance genes. In this work, we use high-throughput sequencing technology (Illumina) to taxonomically classify cyanobacteria present in metagenomic samples, sequenced from non-axenic cultures of Portuguese surface freshwater reservoirs and wastewater treatment plants, belonging to Estela Sousa e Silva Algae Culture Collection and Blue Biotechnology and Ecotoxicology Culture Collection. Metagenomic reads from 43 sequenced samples of non-axenic cultures of cyanobacteria were filtered and assembled. Using a metagenome binning approach, we managed to isolate 41 cyanobacterial genomes and perform an analysis for the presence of antibiotic resistance genes, from the Comprehensive Antibiotic Resistance Database, on strains of Anabaena, Aphanizomenon, Microcystis aeruginosa, Planktothrix agardhii and Planktothrix mougeotii. We detected the presence of the fluoroquinolone and tetracycline resistance gene adeF across a multitude of samples from different genera and collection sites. The simultaneous occurrence of mutually potentiating macrolide resistance genes mphG and mefC, as previously described for marine bacteria, was also detected for the first time in cyanobacteria genomes. Copies of similar antibiotic resistance genes found across multiple bins from the same environmental samples suggests that horizontal gene transfer might be playing a role in the fast adaptation of bacteria to antimicrobial products. This work further corroborates the evidence for cyanobacteria’s importance in the freshwater resistome. In order to achieve these results, a GNU Make/ Shell script pipeline (CyanoPipeline) was created in order to increase the reproducibility of the work and facilitate the iterations of a complex workflow.

2020-05-19Master thesis

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