Identification of a novel genomic island specific for Enterococcus faecium CC17 by using the deltarho-Web model
Abstract number: P923
Heikens E., Leavis H.L., van Schaik W., Bonten M.J.M., Willems R.J.L.
Objectives: Most hospital outbreak and invasive Enterococcus faecium belong to a single clonal lineage, complex 17 (CC17). We hypothesise that acquisition of genes, involved in antibiotic resistance, metabolic pathways, and virulence, contributes to the ecological success of CC17. So far, antibiotic resistance genes and the enterococcal surface protein gene, esp, which is contained on a putative pathogenicity island and plays an important role in biofilm formation, are documented CC17-specific determinants. To identify more genes, which contribute to the success of CC17, we used the deltarho-Web model (http://deltarho.amc.uva.nl). This model analyses the dinucleotide composition of a complete genome, which allows the identification of horizontally transferred genes, recognised by their anomalous dinucleotide frequency (DF).
Methods: A complete genome sequence was designed from the only sequenced strain, E. faecium DO, a CC17 isolate. Because this strain is sequenced partially and the order of the contigs is not known, we created a so-called complete genome sequence by randomly concatenating all contigs larger than 2022 bp, which was submitted to the model. PCR and dot blot hybridisation (DBH) were performed to determine presence and absence of genes located in regions with anomalous DF in 41 CC17 isolates and 95 non-CC17 isolates. Expression of CC17 specific genes at mRNA level was determined by RT-PCR.
Results: The model identified 5 regions with anomalous DF. PCR and DBH showed that 1 of these regions is CC17 specific and consist of a genomic island (GI) of 8 genes. Forty of the 41 CC17 isolates (97.56%) harbour this GI and only 5 of the 95 non-CC17 isolates (5.26%). The GI genes putatively encode 2 sugar transporters, 2 glycosyl hydrolases, an extracellular sugar binding protein, 2 proteins with unknown function, and a transcriptional regulator. At both sides of the GI inverted and direct repeats were found and one end is flanked by an integrase gene, indicating horizontal transfer. RT-PCR showed expression of all 8 genes.
Conclusion: By using the deltarho-Web model, a GI specific for CC17 was found. This illustrates that detection of anomalous DF using this model is a good approach for identifying acquired genes in E. faecium. We hypothesise that ST-17, the presumed founder of CC17, acquired this GI, tentatively encoding a novel metabolic pathway, as an adaptive mechanism providing CC17 a selective advantage in hospitalised patients.
|Session name:||18th European Congress of Clinical Microbiology and Infectious Diseases|
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