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Objectives: Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark., Methods: We performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature., Results: The most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study., Conclusions: WGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations., Competing Interests: The authors have declared that no competing interests exist.

The number of children in daycare centers (DCCs) is rising. This increases exposure to microorganisms and infectious diseases. Little is known about which bacteria and viruses are present in the DCC environment and where they are located. In the study described in this article, the authors set out to determine the prevalence of pathogenic bacteria and viruses and to find the most contaminated fomites in DCCs. Fifteen locations in each DCC were sampled for bacteria, respiratory viruses, and gastrointestinal viruses. The locations were in the toilet, kitchen, and playroom areas and included nursery pillows, toys, and tables, among other things. Coliform bacteria were primarily found in the toilet and kitchen areas whereas nasopharyngeal bacteria were found mostly on toys and fabric surfaces in the playroom. Respiratory viruses were omnipresent in the DCC environment, especially on the toys.

Background: The rising number of children in daycare nurseries increases opportunities for the transmission of infectious diseases. Pathogens may be transmitted directly from child to child via sneezing, coughing and touching, or indirectly via the environment. Toys are among the fomites with the highest pathogen load, but their role in disease transmission is unknown., Aim: To determine if washing and disinfection of toys can reduce sickness absence and microbial pathogen load in the nursery environment., Methods: Twelve nurseries (caring for 587 children) were randomized to intervention and control groups. The intervention consisted of washing and disinfection of toys and linen every two weeks for three months by a commercial cleaning company. The extent and causes of sickness absence among the children were recorded in both groups before and after introduction of the intervention. Ten sampling points in each nursery were examined for bacteria and respiratory viruses., Results: The presence of respiratory virus DNA/RNA was widespread, but very few pathogenic bacteria were found in the environment. The intervention reduced the presence of adenovirus [odds ratio (OR) 2.4, 95% confidence interval (CI) 1.1-5.0], rhinovirus (OR 5.3, 95% CI 2.3-12.4) and respiratory syncytial virus (OR 4.1, 95% CI 1.5-11.2) compared with the control group, but the intervention had no effect on sickness absence or disease patterns in the nurseries., Conclusion: Although cleaning and disinfection of toys every two weeks can decrease the microbial load in nurseries, it does not appear to reduce sickness absence among nursery children., (Copyright © 2014 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.)

Environmental sampling in hospitals is becoming increasingly important because of the rise in nosocomial infections. In order to monitor and track these infections and optimize cleaning and disinfection, we need to be able to locate the fomites with the highest amount of microorganisms, but the optimal method for this is not clear. The aim of this study was to evaluate which of four different dipslides or a standard TSA contact plate were best at recovering human bacteria from the environment. We tested four different dipslides with selective and non-selective agars versus a standard TSA contact plate in order to find the best sampling media. Two hundred sites in a children's medical ward in Copenhagen University hospital were sampled in autumn 2012. There was no difference in total bacteria count between the TSA contact plate and the dipslides. Faecal indicator bacteria recovery was the same for the dipslides and the TSA contact plate. Dipslides may be equally well suited for environmental sampling and hygiene assessment as TSA contact plates. Dipslides have some advantages, such as better sample security, easier sampling in confined spaces and longer shelf life that may speak in favour of choosing these for bacteria environmental sampling in hospitals, depending on the task.