Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures

Abstract

The shortage of wild fishery resources and the rising demand for human nutrition has driven a great expansion in aquaculture during the last decades in terms of production and economic value. As such, sustainable aquaculture production is one of the main priorities of the European Union’s 2030 agenda. However, the intensification of seafood farming has resulted in higher risks of disease outbreaks and in the increased use of antimicrobials to control them. The selective pressure exerted by these drugs provides the ideal conditions for the emergence of antimicrobial resistance hotspots in aquaculture facilities. Omics technology is an umbrella term for modern technologies such as genomics, metagenomics, transcriptomics, proteomics, culturomics, and metabolomics. These techniques have received increasing recognition because of their potential to unravel novel mechanisms in biological science. Metagenomics allows the study of genomes in microbial communities contained within a certain environment. The potential uses of metagenomics in aquaculture environments include the study of microbial diversity, microbial functions, and antibiotic resistance genes. A snapshot of these high throughput technologies applied to microbial diversity and antimicrobial resistance studies in aquacultures will be presented in this review.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

“…Currently, antibiotics are commonly used to protect or treat against pathogens. Nevertheless, this practice is controversial because of the emergence of antimicrobial resistance genes and the promotion of horizontal gene transfer, in addition to mutagenesis in aquatic bacteria [105]. Furthermore, because of epidemiological connections between humans, animals, and the environment, the increase of antimicrobial resistance genes poses one of the greatest human health and sustainability challenges of the 21 st century, according to the World Health Organization [106].…”

Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome

“…Quinolones and tetracyclines (such as oxytetracycline) have been extensively used in aquaculture settings as prophylaxis, being administered mostly in food [ 8 , 34 ]. Furthermore, this group of genes, which are here called “high” ( Figure 3 and Figure S1 ), confer resistance to antibiotics for animal and human use, revealing the critical and especially key role of aquatic environments as a reservoir of resistance genes linking animal and human health [ 35 ].…”

“…Furthermore, spillover between and within marine and terrestrial food production sectors occurred, along with the flow of microorganisms, antibiotics, antibiotic residues, and AR genes [ 6 ], and the same resistance patterns have been seen in land animal husbandry and aquaculture [ 7 ]. Therefore, antimicrobial resistance can develop in aquatic bacteria due to antibiotic therapy or to contamination of the aquatic environment with human or animal waste [ 8 ]. Antibiotic and antibiotic-resistant bacteria in aquaculture systems are likely to last for a long time and be transferred to humans through the contamination of products for human consumption [ 9 ].…”

Bacterial and Fungal Biocontrol Agents for Plant Disease Protection: Journey from Lab to Field, Current Status, Challenges, and Global Perspectives

“…Integrating advanced omics and metagenomic techniques could provide a deeper understanding of the interactions between beneficial microbes and pathogens. Studying the genomic, transcriptomic, and proteomic profiles of microbes, pathogens, and plants during biocontrol interactions could reveal key mechanisms and factors influencing disease suppression [ 123 , 124 ]. It is expected that by using biotechnological approaches, researchers will be able to develop potential BCAs for efficient control of multiple crop diseases [ 43 ].…”