Identifying genetic markers associated with mobile genetic elements in Enterococcus faecium

Chenai P Kheswa

Enterococcus faecium (E. faecium) is a commensal inhabiting the gut of humans and animals. Due to high genome plasticity, E. faecium is emerging as a leading cause of nosocomial infections with increased antimicrobial resistance and an ability to acquire other resistance genes from other pathogenic bacterial species residing in the gut. Whole genome sequencing data (WGS) of 2,450 E. faecium strains from Australia, Denmark and Germany were analysed to identify the antimicrobial resistance encoding genes and virulent factors located on the mobile genetic elements (MGEs). Using bioinformatics tools, we will determine the correlation between genes to MGEs and identify genes that can be useful as markers to infer MGEs carrying antimicrobial resistance. Out of the 2,450 strains analysed, the bioinformatic analysis showed 2,375 in Scoary results of the E. faecium strains with various insertion sequence (IS) elements as the MGE trafficking resistance genes. The Roary bioinformatics tool identified seventy-five isolates with poor sequencing errors. Scoary results showed fifty-four insertion sequence elements, but only twenty-eight IS elements repeatedly appear in at least ten strains. Utilizing a genome-wide association study approach, results showed the top eight IS elements harbouring potential resistance genetic traits; msr(C), aacA-ENT1, dfrG, eat(A), vanH-A, vanA, vanR-A, aph(3')-IIIa, ant(6)-Ia, vanX-A, and vanS-A. The common MGEs linked to resistance traits are IS16, represented in 91.9% of the dataset, IS1678 (62.7%), and ISEfa17 (54.7%) of the data, while IS1251, ISEfa7, ISEfa4, ISEfa18, and IS1216E appear in less than 50% of the 2,450 sequenced strains. The genome plasticity of E. faecium continues to show a wide range of resistance gene acquisitions in some of the genetic markers within the study’s dataset. Identifying the relevant genetic markers associated with MGEs that carry antimicrobial genes or virulence factors in E. faecium bacteria is vital in combating growing antibiotic drug therapy. The genetic markers can be used to track a pattern of infections and develop Polymerase Chain Reaction (PCR) primers designed explicitly from these MGEs of interest. Insertion sequences have become clinically essential disseminators of resistance genes and seem to endorse gene acquisition amongst bacteria due to their ability to move between genomes.

Identifying genetic markers associated with mobile genetic elements in Enterococcus faecium

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