Functional and comparative genomics of Enterococcus faecium isolated from animals

Shami, Ashwag Functional and comparative genomics of Enterococcus faecium isolated from animals. PhD thesis, University of Liverpool.

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Abstract

Enterococci are Gram-positive bacteria that inhabit the gastrointestinal tract of humans and animals as commensal flora. In recent years two species, Enterococcus faecalis and Enterococcus faecium, have become an increasing medical concern by virtue of their ability to gain and spread antibiotic resistance. In this study, genomes of vancomycin-resistant isolates of E. faecium from pig, chicken and calf were sequenced using 454 and PacBio platforms. The assembled genomes were annotated and compared with human E. faecium isolates to identify their repertoire of genes potentially associated with colonising each host. Phylogenomics of E. faecium was used to investigate the relationship between animal and human strains. The genomes of the chicken, pig and calf isolates differed in size (2.5 Mb to 3.3 Mb) with the size difference due to horizontally-acquired elements (mostly phage, transposons and insertion sequences); the chicken isolate genome contained five prophages. A mega-plasmid present in each of the sequenced E. faecium was revealed to be integrated into the genome of the chicken isolate. Comparison of the three genomes identified putative niche adaptation genes with a variety of proposed functions, particularly carbohydrate utilisation. Possible factors that explain E. faecium sub-populations, including clinical, commensal and animal isolate clades were examined. Use of the PhenoLink relationship tool to examine the E. faecium sub-populations identified that putative niche specific genes include carbohydrate utilisation genes and mobile genetic elements. Temperate bacteriophages are known to be important drivers of genome plasticity in E. faecium species. The diversity of prophages and their relationship between was investigated after locating 56 prophage elements containing integrase and lysin genes encoded in the 139 publicly available E. faecium genomes. Comparative analysis of these prophages identified eight sequence types, which differed in size and gene content. The prophage genomes comprised between 17 to 72 ORFs and their size ranged from 13.9 to 55.1 kb with 35% to 37.9% average G+C content. Based on alignment analyses of the major functional proteins encoded in the prophage genomes (integrase, terminase large subunit, tail protein and holin) each was assigned a sequence type. All of the prophage integrases were identified to be tyrosine (XerC) recombinases and many of their respective attP/attR sequences were identified. The mosaic nature of E. faecium prophage genome sequence types supports previous hypotheses that extensive genetic recombination drives chimeric phage types.

Item Type:	Thesis (PhD)
Additional Information:	Date: 2014-12-18 (completed)
Subjects:	?? QR ??
Depositing User:	Symplectic Admin
Date Deposited:	27 Aug 2015 09:54
Last Modified:	17 Dec 2022 00:50
DOI:	10.17638/02009300
URI:	https://livrepository.liverpool.ac.uk/id/eprint/2009300