Emergence of vanA Enterococcus faecium in Denmark, 2005–15

Hammerum, Anette M.; Baig, Sharmin; Kamel, Yasmin; Roer, Louise; Pinholt, Mette; Gumpert, Heidi; Holzknecht, Barbara Juliane; Røder, Bent; Justesen, Ulrik Stenz; Samulioniené, Jurgita; Kjærsgaard, Mona; Østergaard, Claus; Holm, Anette; Dzajic, Esad; Søndergaard, Turid Snekloth; Gaïni, Shahin; Edquist, Petra; Alm, Erik; Lilje, Berit; Westh, Henrik; Stegger, Marc; Hasman, Henrik

doi:10.1093/jac/dkx138

Cited by 55 publications

(32 citation statements)

References 12 publications

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“…Such approaches provide results in high resolution for investigating closely related individuals, as in outbreaks mostly restricted to a local setting (e.g., one ward, one hospital, or one country) (52). In contrast, phylogenetic investigations on a “global” scale or long-term studies often lack a reference suitable for the entire set of strains to be analyzed (53). Although programs such as refRank will select for the best reference for a given data set, it is always a trade-off with respect to the genomic variety of the strain collection (39).…”

Section: Discussionmentioning

confidence: 99%

A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis

et al. 2019

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Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146 E. faecalis strains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+ software. To test the E. faecalis cgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.

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Section: Discussionmentioning

confidence: 99%

A Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis

et al. 2019

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“…Most of the VRE isolates belonged to prominent German hospital-associated E. faecium lineages such as ST117, ST80, ST192, or ST203; almost all of them exhibited vanB-type vancomycin resistance, which recently emerged in German clinics [11]. Also as demonstrated by Hammerum et al, Danish VRE analyzed from 2005 to 2015 revealed genotypes such as ST80 (CT14), ST117 (CT24), and ST203 (CT859) [58]. Our study proved genotype ST117/CT469 as the predominant clone that was occasionally detected also in other countries such as Luxembourg and the Netherlands (www.cgMLST.org) and is known to be distributed across Germany [59].…”

Section: Molecular Analyses and Bioinformaticsmentioning

confidence: 91%

Comprehensive integrated NGS-based surveillance and contact-network modeling unravels transmission dynamics of vancomycin-resistant enterococci in a high-risk population within a tertiary care hospital

et al. 2020

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Vancomycin-resistant E. faecium (VRE) are an important cause of nosocomial infections, which are rapidly transmitted in hospitals. To identify possible transmission routes, we applied combined genomics and contact-network modeling to retrospectively evaluate routine VRE screening data generated by the infection control program of a hemato-oncology unit. Over 1 year, a total of 111 VRE isolates from 111 patients were collected by anal swabs in a tertiary care hospital in Southern Germany. All isolated VRE were whole-genome sequenced, followed by different in-depth bioinformatics analyses including genotyping and determination of phylogenetic relations, aiming to evaluate a standardized workflow. Patient movement data were used to overlay sequencing data to infer transmission events and strain dynamics over time. A predominant clone harboring vanB and exhibiting genotype ST117/CT469 (n = 67) was identified. Our comprehensive combined analyses suggested intra-hospital spread, especially of clone ST117/CT469, despite of extensive screening, single room placement, and contact isolation. A new interactive tool to visualize these complex data was designed. Furthermore, a patient-contact network-modeling approach was developed, which indicates both the periodic import of the clone into the hospital and its spread within the hospital due to patient movements. The analyzed spread of VRE was most likely due to placement of patients in the same room prior to positivity of screening. We successfully demonstrated the added value for this combined strategy to extract well-founded knowledge from interdisciplinary data sources. The combination of patient-contact modeling and high-resolution typing unraveled the transmission dynamics within the hospital department and, additionally, a constant VRE influx over time.

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“…In Denmark, vanA Enterococcus faecium is most prevalent among clinical vancomycin-resistant Enterococcus (VRE) isolates ( 1 ).…”

Section: Announcementmentioning

confidence: 99%

“… E. faecium VRE1589 was the earliest vanA E. faecium isolate belonging to sequence type 203 and complex type 859 (ST203-CT859) identified among the VRE isolates submitted to Statens Serum Institut as part of the Danish national surveillance program. Comparison to the cgMLST.org database ( https://cgmlst.org/ncs ), previous Danish studies, and personal communications with neighboring countries with whole-genome sequencing (WGS) data available suggests that the novel complex type (CT859) emerged in October 2014 in Copenhagen and spread to the rest of Denmark, the south of Sweden, and the Faroe Islands during 2015 ( 1 ). In 2016, 64% of the clinical vanA E. faecium isolates detected in Denmark belonged to ST203 and CT859 ( 2 ).…”

Section: Announcementmentioning

confidence: 99%