Genomic insights from Enterococcus faecium SMAN_Baghdad isolated from the honey bee gut and analysis of its potential antimicrobial activity against multidrug-resistant Pseudomonas aeruginosa

Abstract

Background Bacterial genetics and molecular biology have been investigated rapidly, accurately and revolutionary by high throughput whole genome sequencing. Enterococcus faecium has recently been widely used in fermentation and as a probiotic in food products to promote health, and its products have been used as alternative compounds to conventional antibiotics for bacterial eradication. Genomic analysis provides rapid information about its diversity and evolution, suggesting a significant molecular basis. Objective This study aimed to perform a genome analysis of Enterococcus faecium isolated from the honey bee gut and test the antagonistic activity of its bacteriocin like inhibitor substances against clinically MDR Pseudomonas aeruginosa. Methods The isolated bacterium SMAN_Baghdad was identified as Enterococcus faecium using 16S rRNA gene sequencing. The whole genome of E. faecium SMAN_Baghdad was sequenced and analyzed by bioinformatics tools. Results Our strain genome sequence has 40 contigs, and its genome size is 2,835,588 bp, with a guanine-cytosine(GC) percentage of 38.1%. It comprises 2,667 genes, including 2,599 coding sequences (CDSs) and 68 predicted RNAs (including 60tRNAs and others). Many genes encoding genes involved in the production of probiotics and metabolic properties, such as bacteriocin-like inhibitory substances (e.g., enterolycinA, enterocin SE-K4 and entarocin L50a and b),were detected in BLIS. BLISs exhibit significant antibacterial activity against MDR Pseudomonas aeruginosa Conclusion Analysis of genome supported the ability to consider bacteriocin-like inhibitory substances as bactericidal agents instead of common antibiotics.