Development and evaluation of a core genome multi-locus sequence typing scheme for the Enterobacter cloacae complex

The Enterobacter cloacae species complex (ECC) comprises a group of closely related, opportunistic Gram negative bacteria of major public health concern due to their frequent involvement in healthcare-associated infections and their capacity to acquire and disseminate multidrug resistance, including carbapenemases. Because members of this complex are often difficult to distinguish phenotypically and their taxonomic status is subject to debate, there is a need for a standardized, species-complex wide typing scheme based on whole genome sequencing (WGS) that can be applied to any species within the complex. In this study we have developed and evaluated a core genome multi-locus sequence typing (cgMLST) scheme suitable for species within the ECC. Using 3442 publicly available genomes from 27 ECC species or subspecies we developed a scheme with 1812 loci, comprising loci present in 99% of all genomes. Among the 3442 isolates in our study, 99.9% had 95% or more of the cgMLST targets, indicating that the schema is well-defined and representative for the breadth of ECC species in our study. On two independent evaluation datasets, the scheme reliably resolved epidemiologically linked isolates with 0-3 allelic differences and returned the same outbreak clusters defined previously by higher resolution core genome SNP (cgSNP) analysis. Hierarchical clustering analysis at different levels of resolution showed that the cgMLST profiles could potentially be used to differentiate between species and sub-lineages in the complex. The cgMLST schema will improve the ability of public health laboratories to perform WGS-based surveillance of ECC species.