Multi-drug resistant Klebsiella pneumoniae strains circulating in hospital setting: wholegenome sequencing and Bayesian phylogenetic analysis for outbreak investigations

Carbapenems resistant Enterobacteriaceae infections are increasing worldwide representing an emerging public health problem. The application of phylogenetic and phylodynamic analyses to bacterial whole genome sequencing (WGS) data have become essential in the epidemiological surveillance of multi-drug resistant nosocomial pathogens. In this study, K. pneumoniae KPC strains circulating within different wards of the University Hospital Campus Bio-Medico were collected and WGS applied. These applications could help in the epidemiological surveillance of MDR pathogens to discern outbreak from non-outbreak strains in both community and hospital settings. The aim was to infer the origin and the spread of K. pneumoniae nosocomial strains and to clarify the epidemiological transmission as so as the eventual reservoir in the hospital setting supporting the epidemiological surveillance and infections control strategies. Among patients undergoing endoscopic retrograde cholangiopancreatography (ERCP), patients have investigated infections by KPC K. pneumoniae and endoscope were sampled to check the correct duedonoscope reprocessing. A microbiological surveillance on duedonoscope was performed. Between January 2012 and February 2013, twenty-one multi-drug resistant K. pneumoniae strains, were collected from patients hospitalized among different wards of the University Hospital Campus Bio-Medico. Epidemiological contact tracing of patients and Bayesian phylogenetic analysis of bacterial WGS data were used to investigate the evolution and spatial dispersion of K. pneumoniae in support of hospital infection control. The epidemic curve of incident K. pneumoniae cases showed a bimodal distribution of cases with two peaks separated by 46 days between November 2012 and January 2013. The time-scaled phylogeny suggested that K. pneumoniae strains isolated during the study period may have been introduced into the hospital setting as early as 2007. Moreover, the phylogeny showed two different epidemic introductions in 2008 and 2009. The results of the sampling performed highlighted a first multi-microbial contamination supported by MDR organism (K. pneumoniae, P. aeruginosa and A. baumanii) eliminated from the introduction of the new reprocessing protocols. Due to the complex design of duodenoscopes, it is difficult an adequate disinfection of the channels. Duodenoscopes can be difficult to dry and a potential risk of cross contamination is higher using this type of endoscope. New duodenoscope designs should facilitate more efficient disinfection, FDA has identified design features that facilitate cleaning, disinfection and sterilization and reduce the likelihood of retaining debris. Bayesian genomic epidemiology is a powerful tool that promises to improve the surveillance and control of multi-drug resistant pathogens in an effort to develop effective infection prevention in healthcare settings or constant strains reintroduction.