Whole genome multilocus sequence typing of extended-spectrum beta-lactamase-producing Enterobacteriaceae

Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labour intensive, are difficult to standardize or have limited resolution. Whole genome multilocus sequence typing (wgMLST) has emerged as a whole genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations, and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic complex- and species-specific wgMLST schemes were developed for Citrobacter spp., Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca and Klebsiella pneumoniae, and used to type a national collection of 1,798 ESBL-E isolates obtained from patients in Dutch hospitals. Genus-, genetic complex- and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates, were defined for Citrobacter spp., E. cloacae complex, E. coli and K. pneumoniae. wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice, and may contribute to further elucidation of the complex epidemiology of antimicrobial resistant Enterobacteriaceae. wgMLST opens up possibilities for the creation of a web-accessible database for the global surveillance of ESBL-producing bacterial clones.