Epidemiology of carbapenem-resistant Enterobacteriaceae: Persistent dominance of Klebsiella pneumoniae ST258.
Carbapenem-resistant Enterobacteriaceae (CRE) are multidrug resistant agents of nosocomial infections with limited therapy options, claiming tens of thousands of lives each year. The pathogenic success and global expansion of CRE was largely attributed to a single prevailing strain of Kelbsiella pneumoniae. ST258, which has an incredibly high correlation with the carbapanemase enzyme KPC, conferring resistance to all β-lactam antibiotics. After clinically emerging in year 2000, ST258 has remained relatively unchanged. To better understand present day epidemiology of CRE in the United States, we completed whole genome sequencing of twenty-four carbapenem resistant K. pneumoniae samples from across the nation and made comparisons with past data to identify if new strains have emerged or if significant mutations have occurred within the ST258 strain. Our data set included a total of 97 ST258 samples collected from 2003 and 2016. We then used bioinformatics, phylogenetics, and genomic epidemiology to try and understand the spread of various ST258 lineages within the U.S. Our analyses confirmed that the KPC producing strain type ST258 is still the dominating CRE seen nationwide; 17 of our 24 randomly selected samples from 2014-2016 were ST258. Phylogenetic analysis showed that with the exception of a distinct Southwestern clade, no distinct lineages have appeared to emerge. We see little geographical clustering eliminating the idea that any one strain is isolated to a single geographical region, and evidencing transmission of ST258 among distant healthcare facilities. Recently collected isolates of ST258 can be seen interspersed throughout the phylogeny mixing new and old strains homogenously. The findings of this study show that the fitness of ST258 continues to evolve and underscores the need for continued epidemiological mapping of this pathogen and further solidifies the emergent public health threat that it presents.