Whole-genome analysis of vancomycin-resistant Enterococcus faecium causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavaria, Germany.

OBJECTIVES: Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the genetic diversity of isolates of VREfm recovered from different nosocomial outbreaks in Bavaria, Germany, by WGS. METHODS: Between January 2018 and April 2019, 99 non-replicate isolates of VREfm originating from nosocomial outbreaks at eight different hospitals in Bavaria were investigated for genetic diversity by WGS. In detail, complex types (CTs) were identified by core-genome MLST. Furthermore, an SNP analysis was performed for all VREfm strains. RESULTS: Most of the isolates of this study (76%) belonged to three major clonal groups, which occurred in at least three hospitals: ST80/CT1065 vanB (n = 45; six hospitals), ST117/CT71 vanB (n = 11; four hospitals) and ST78/CT894like vanA (n = 19; three hospitals). Moreover, isolates of the predominant lineage ST80/CT1065 vanB showed a maximum difference of 36 SNPs as revealed by SNP analysis. CONCLUSIONS: Whole-genome analysis of VREfm causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavarian hospital settings, namely ST80/CT1065 vanB, ST117/CT71 vanB and ST78/CT894like vanA. Further studies are needed for a better understanding of the factors affecting the successful spread of the above-mentioned lineages.

Detection of non-tuberculous mycobacteria in hospital water by culture and molecular methods.

Non-tuberculous mycobacteria (NTM) are emerging pathogens in immunocompromised patients. Therefore, it is important for hospitals to consider tap water as a source for these infections. Aim of the study was to establish highly sensitive and specific techniques to detect and identify NTM in hospital drinking water. A Mycobacterium genus-specific 16S rDNA-based real-time LightCycler PCR assay with internal inhibition control and a M. xenopi-specific PCR were developed. Ninety-three water samples from 53 taps from 4 hospitals were investigated. NTM were cultured from 21 of 49 (43%) cold and 32 of 44 (73%) warm water samples. M. chelonae, M. flavescens, M. frederiksbergense, M. gordonae, M. moriokaense, M. mucogenicum, M. vaccae, and M. xenopi were identified with molecular methods. All 93 water samples were positive in the genus-specific PCR. M. xenopi DNA was detected in 40 of 44 (91%) warm and 33 of 49 (67%) cold water samples including 45 of 65 (69%) M. xenopi culture-negative samples. In conclusion, selective culture followed by molecular identification methods enabled detection of rare species of NTM in hospital drinking water and may be used in further studies investigating the epidemiology of NTM in water samples. The real-time PCR assays have a high sensitivity and allow rapid quantification of mycobacterial DNA in water samples.