ena-STUDY-University Medical Center Groningen-05-01-2021-09:56:54:479-308
The role of mobile genetic elements in the typing of nosocomial VREfm outbreak isolates of a successful MLST: ST117 cluster type 24
Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The rapid emergence of specific VREfm lineages makes it challenging to distinguish outbreak isolates solely based on their core genome. Here, we explored if characterisation of mobile genetic elements could be useful for molecular epidemiology and typing of VREfm isolates belonging to the same genetic background. Materials/methods: The genomes of 39 VREfm isolates from patients and environmental samples from 2011 to 2017 were sequenced using short-read sequencing. Two representative isolates were also sequenced using long-read sequencing,  to close the genome sequences. Molecular typing by core genome MLST (cgMLST) and pangenome analysis were performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins and prophages. Results: All of the investigated isolates belonged to ST117 and cluster type (CT) 24. cgMLST analysis showed that the isolates could be divided into two distinct genetic clades. The vanB-carrying transposon Tn1549 was present in all isolates. However, its genomic position differed between strains depending on the outbreak event. The pangenome analysis revealed differences in the accessory genes mainly related to prophages and bacteriocins content, while a similar profile was observed for known predicted virulence and resistance genes.Conclusions: In case of closely related isolates sharing a similar genetic background, a detailed analysis of mobile genetic elements and the integration point of the vanB-carrying transposon allows to achieve a higher discriminatory power compared to cgMLST alone. Thus, enabling identification of epidemiological links among hospitalised patients.
Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The rapid emergence of specific VREfm lineages makes it challenging to distinguish outbreak isolates solely based on their core genome. Here, we explored if characterisation of mobile genetic elements could be useful for molecular epidemiology and typing of VREfm isolates belonging to the same genetic background. Materials/methods: The genomes of 39 VREfm isolates from patients and environmental samples from 2011 to 2017 were sequenced using short-read sequencing. Two representative isolates were also sequenced using long-read sequencing,  to close the genome sequences. Molecular typing by core genome MLST (cgMLST) and pangenome analysis were performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins and prophages. Results: All of the investigated isolates belonged to ST117 and cluster type (CT) 24. cgMLST analysis showed that the isolates could be divided into two distinct genetic clades. The vanB-carrying transposon Tn1549 was present in all isolates. However, its genomic position differed between strains depending on the outbreak event. The pangenome analysis revealed differences in the accessory genes mainly related to prophages and bacteriocins content, while a similar profile was observed for known predicted virulence and resistance genes.Conclusions: In case of closely related isolates sharing a similar genetic background, a detailed analysis of mobile genetic elements and the integration point of the vanB-carrying transposon allows to achieve a higher discriminatory power compared to cgMLST alone. Thus, enabling identification of epidemiological links among hospitalised patients.