Increase of vancomycin-resistant Enterococcus faecium strain type ST117 CT71 at Charité - Universitätsmedizin Berlin, 2008 to 2018

Abstract

Background: In addition to an overall rise in vancomycin-resistant Enterococcus faecium (VREfm), an increase in certain strain types marked by sequence type (ST) and cluster type (CT) has been reported in Germany over the past few years. Outbreak analyses at Charité - Universitätsmedizin Berlin revealed the frequent occurrence of VREfm ST117 CT71 isolates in 2017 and 2018. To investigate whether ST117 CT71 have emerged in recent years or whether these strains have been circulating for a longer time, we retrospectively analyzed non-outbreak strains that occurred between 2008 and 2018 to identify frequent STs and CTs.Methods: In total, 120 VREfm isolates obtained from clinical and surveillance cultures from the years 2008, 2013, 2015, and 2018 were analyzed. Thirty isolates per year comprising the first 7 - 8 non-outbreak isolates of each quarter of the respective year were sequenced using whole genome sequencing. MLST and cgMLST were determined as well as resistance genes and virulence factors. Risk factors for VREfm ST117 were analyzed in a multivariable analysis with patient characteristics as possible confounders. Results: The percentage of VREfm of type ST117 increased from 17% in 2008 to 57% in 2018 (p=0.012). In 2008, vanA genotype accounted for 80% of all ST117 isolates compared to 6% in 2018. VanB CT71 first appeared in 2018 and predominated over all other ST117 at 43% (p<0.0001). The set of resistance genes (msrC, efmA, ermB, dfrG, aac(6')-Ii, gyrA, parC and pbp5) and virulence factors (acm, esp, hylEfm, ecbA and sgrA) in CT71 was also found in other ST117 non-CT71 strains, mainly in CT36. The study population did not differ among the different calendar years analyzed in terms of age, gender, length of stay, or ward type (each p>0.2).Conclusion: This study revealed an increase in ST117 strains from 2008 to 2018, accompanied by a shift toward CT71 strains with the vanB genotype in 2018. We did not detect resistance or virulence traits in CT71 that could confer survival advantage compared to other CTs among ST117 strains. To date, it is not clear why ST117 and in particular strain type ST117 CT71 predominates over other strains.

Genomic surveillance of vancomycin-resistantEnterococcus faeciumreveals spread of a linear plasmid conferring a nutrient utilization advantage

“…This strain type has been reported to predominate over other clones in Germany in the last few years 29,[50][51][52] . The finding that the isolates from cluster 3 were very closely related with one of the isolates of these studies highlights the power of genomics for global surveillance of nosocomial pathogens and the advantage of genomic data sharing at an international level.…”

Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany

“…The most frequent strains in German university hospitals on patient admission were ST117, ST80, ST203, and ST78, in that order [4]. At our hospital, Charité -Universitätsmedizin Berlin, we observed an increase of VREfm prevalence on admission from 1.10 to 2.59 per 100 admissions, and an increase of VREfm strain type ST117 complex type (CT)71 between 2008 and 2018 [5].…”

“…Certain complex types such as ST117 CT71 have been identified in epidemiologically unrelated settings all over Germany [3][4][5]. Some of the complex types identified in Berlin were also found during outbreak investigations in Bavaria and the Rhine-Main area [26,27].…”