Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks

Abstract

Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis.Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content.Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes.Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.

Occult Vancomycin-Resistant Enterococcus faecium ST117 Displaying a Highly Mutated vanB2 Operon

“…Our results highlighted that vanB 2 -VREfm and nearly half of VSEfm analyzed were from the hospital-associated (HA) ST117/CC17 or CladeA1 [ 22 ]. These STs are frequently associated with nosocomial outbreaks in Europe [ 23 , 24 , 25 ] and have also been reported in Italian hospitals [ 26 ], along with the other HA-STs that were detected here (ST78, ST916, ST80, and ST780).…”

Vancomycin-resistant enterococci (VRE) in hospital settings across European borders: a scoping review comparing the epidemiology in the Netherlands and Germany

“…All outbreaks in both countries were caused by VREfm. In three of eight outbreaks observed in Dutch hospitals and in four of six outbreaks observed in German hospitals, VREfm infections were reported alongside patients colonized with VREfm [ 34 , 37 , 40 , 42 , 45 – 47 ]. One common factor observed in these reports was that colonization played a pivotal role in the occurrence of outbreaks in both countries.…”

Zoonotic Transmission of Vaccine-Derived Bordetella bronchiseptica

“…The patient suggested the potential zoonotic transmission of B. bronchiseptica following vaccination of her dog. Comparison of core genome multilocus sequence typing, based on short-read sequencing as described previously [ 4 ], using an ad hoc scheme including 4121 target genes ( Supplementary Tables 1 and 2 ) showed only 3 allelic differences between the sputum sample isolate UMCGBbp2 and the B. bronchiseptica vaccine (batch A135E01) strain UMCGBbv1, thus confirming the vaccine as the source of the infection. The patient was treated with trimethoprim/sulfamethoxazole 960 mg bid for 14 days, after which her symptoms gradually improved.…”