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Metagenomic analysis of veterinary probiotics in broiler chickens
Román István László - year 4
University of Veterinary Medicine Budapest, Department of Pharmacology and Toxicology
Supervisor: Dr. Ádám Kerek

Abstract:

Antimicrobial resistance is one of the greatest challenges facing humanity. The products of our farm animals can pose a risk of contamination by mycobacteria and with them the spread of antimicrobial resistance genes, i.e. the potential for horizontal gene transfer. There are several alternatives to reduce antibiotic use, such as the use of probiotics, which are beneficial micro-organisms that, when properly administered, have a beneficial effect on the living organism. A little studied area is the antimicrobial resistance gene (ARG) expression and its effect on the gut microbiome, in particular on changes in the gut resistome.

Our study investigated the ARG carriage of probiotics approved for poultry using next-generation sequencing, with a focus on their encoding as plasmid, phage or mobile genetic elements. In addition, we investigated the changes in the intestinal resistome and gut microbiome during the whole rearing period of broiler chickens in response to feeding different probiotic preparations and looked for a correlation between the phenotypic expression of resistance after determination of the minimum inhibitory concentration (MIC) values for each identified ARG and the ARGs.

We identified genes responsible for the development of antibiotic resistance mechanism critical in each formulation as fluoroquinolone efflux pump encoding genes, peptide antibiotic target mutation and efflux pump encoding genes. In addition, genes encoding enzymatic inactivation of aminoglycosides of public health relevance, aadK and AAC(6')-Ii, were identified. Several genes coding for multidrug resistance were also identified (vmlR, ykkC, ykkD, msrC, clbA, eatAv). However, no mobile genetic element or plasmid-encoded gene was found; only one phage-encoded gene was detected (DfrA43). MIC values were determined in the phenotypic analysis and in several cases the gene responsible for the development of resistance was found in the strains. In the metagenomic analysis of faecal samples, no significant differences were found between the paired samples at genus level, time and feeding as a function of time and feeding using Shannon diversity distribution and Mann-Withney test.

Probiotics may also carry ARGs of public health significance. In the future, more research on probiotics using molecular genetic methods is worthwhile, and transcriptomic studies are needed to investigate the expression of individual genes.



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