The effects of probiotics/synbiotics are seldom investigated in healthy volunteers; therefore, this study is important, especially considering the safety aspects of multiple probiotics together with prebiotic fiber in consumption by humans. The study explores at the potential of a synbiotic intervention with lactobacilli, bifidobacteria, and inulin in healthy volunteers and tracks the ingested probiotic strain B. animalis subsp. lactis .

Lactobacilli, especially Lactobacillus (L.) rhamnosus, are common and well-documented components of commercial probiotics [1]. Whole genome sequencing (WGS) is often used to compare bacterial genomes and their relatedness. In outbreak situations, it is used to investigate the transmission of pathogenic bacteria. WGS has also been used to determine safety in probiotics, by looking at potential virulence factors and resistance genes. This case report describes a 56-year old multi-traumatised, immunocompetent woman who was given L. rhamnosus GG as a probiotic, and later developed a blood stream infection with L. rhamnosus GG. The patient was fed by a nasogastric tube, and she also had a central venous catheter for parenteral feeding. When the patient developed diarrhoea after long-term hospitalisation, she was given L. rhamnosus GG, as a probiotic, which was standard care on the ward where she was hospitalised. In this case report we describe the use of WGS to demonstrate that a patient fed with L. rhamnosus GG as a probiotic, developed a blood stream infection with the same strain. In this case WGS was applied to show the relatedness of a probiotic and a pathogenic strain of L. rhamnosus GG. This case emphasises the need for caution when administering probiotics to patients with indwelling catheters. The patient was immunocompetent and she cleared the infection without the need for antibiotics.

Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant nosocomial pathogen with a rapidly increasing prevalence. The objectives were to investigate VREfm outbreak duration and study the additional impact that infection control bundle strategies (ICBSs) set up to curb coronavirus disease 2019 (COVID-19) spreading had on VREfm outbreaks. Outbreak data set were collected prospectively from April 2, 2014 to August 13, 2020 at Copenhagen University Hospital Bispebjerg, Denmark. All VREfm samples had polymerase chain reaction performed for vanA / vanB genes before whole genome sequencing using the Illumina MiSeq platform. The relatedness of isolates was studied by core genome multilocus sequence typing (cgMLST) using Ridom SeqSphere. Eighty-one outbreaks had a median outbreak duration of 32.5 days (range 5–204 days) and 1,161 VREfm isolates were sequenced. The same cgMLST cluster types reappeared after outbreaks were terminated. When comparing the first 5 months of the COVID-19 pandemic with the corresponding period in 2019, we found a 10-fold decrease in VREfm outbreak patients and median outbreak duration decreased from 56 to 7 days (88%). Several COVID-19 ICBSs were implemented from March 13 through summer 2020. VREfm outbreaks lasted up to 204 days, but our findings suggest that outbreaks might last longer since the same cgMLST persisted in the same wards for years implying an endemic situation with recurrent outbreaks caused by hospital reservoirs or readmittance of unknown VREfm carriers. The sharp decline in VREfm outbreaks during the COVID-19 pandemic was most likely due to the ICBSs, resulting in a decrease in VREfm transmission.

Background: Since 2012, the incidence of vancomycin-resistant Enterococcus faecium (VREfm) has increased dramatically in Copenhagen and vanA E. faecium has become endemic and polyclonal. Objectives: To examine whether a patient with a positive VRE clinical sample had the same VREfm in a preceding screening sample (within 60days). Methods: We performed a 30month retrospective study. From our laboratory information system (LIS), we identified all patients with an invasive VREfm isolate and a VREfm rectal screening isolate within 60days before infection. VREfm pairs (screening isolate and invasive isolate) were whole-genome sequenced. All isolates were analysed using SeqSphere and core-genome MLST (cgMLST) types were determined. We examined all isolates for the presence of the three most dominant vanA plasmids in the Capital Region of Denmark. Two novel vanA plasmids were closed by Nanopore/Illumina sequencing. Results: We found a total of 19 VREfm pairs. Of these, 13 patients had pairs with matching cgMLST types and vanA plasmids and a median number of 6days from identification of carriage to clinical infection. One patient had a pair with non-matching cgMLST types but matching vanA plasmids and 24days between identification of carriage to clinical infection. Five patients had pairs with non-matching cgMLST types and non-matching vanA plasmids and a median number of 18days from identification of carriage to clinical infection. Conclusions: Of our 19 pairs, 13 were a match regarding cgMLST types (68%) and 1 more (5%) had matching vanA plasmids. Infection was thus preceded by colonization with the same isolates in 13 out of 19 patients. The five mismatches (26%) could be explained by the longer interval between colonization and infection.

Whereas other studies exploring the effect of L. rhamnosus in clearing VREfm from the intestine included children and adults, with a wider age range, our study consisted of a geriatric patient cohort. The natural clearance of VREfm in this study was almost 60% after 4 weeks, thus much higher than described previously.

Since 2012, Denmark has seen a significant rise in vancomycin-resistant Enterococcus faecium (VREfm) cases, mirroring trends in other countries, though exceptions occurred during the coronavirus disease 2019 (COVID-19) lockdown and between 2022 and 2023. This rise has been accompanied by ongoing changes in the endemic VREfm clones, reflecting the species’ high genetic plasticity. VREfm rapidly acquires plasmids and mobile genetic elements, enriching it with putative virulence markers (PVMs), including surface proteins, pili, and factors encoding biofilm production and adhesion. L. Roer, H. Kaya, A.P. Tedim, C. Novias, et al. (Microbiol Spectr 12:e0372423, 2024, https://doi.org/10.1128/spectrum.03724-23 ) released a database of 27 PVMs for Enterococcus faecium and Enterococcus lactis . In this study, we examined 516 VREfm bloodstream isolates from 2015 to 2023, identifying eight new putative virulence genes added to the database, bringing the total to 35 PVMs. Using whole-genome sequencing (WGS) and single linkage clustering, we identified six dominant VREfm clusters: ST80-CT14 vanA , ST117-CT24 vanA , ST203-CT859 vanA , ST1421-CT1134 vanA , ST117-CT36 vanB , and ST80-CT2406 vanB . We observed significant differences in the distribution of PVMs, particularly in pilin, gene clusters (PGC-1, PGC-2, and PGC-4), genes involved in carbohydrate metabolism (e.g., orf1481 , ccpA ), and biofilm production (e.g., hylEfm , capD , lysM3 ). These differences could explain variability in pathogenicity, metabolism, and adaptation to stress, contributing to shifts in endemic clones. IMPORTANCE: The newly developed and now updated database, VirulenceFinder, features 35 potential virulence markers for E. faecium and E. lactis , is highly scalable and provides a valuable tool for the in-depth analysis of closely related species using whole-genome sequencing (WGS) data. It holds considerable promise for a range of public health applications, such as hospital outbreak investigations, surveillance, and assessment of pathogenicity of bacterial species.