Members of the genus Elizabethkingia are environmental bacteria that can cause opportunistic hospital-acquired infections with the potential for life-threatening complications. Although clinical outbreaks have been documented in the United States, Taiwan, Mauritius and Hong Kong over the last 10 years, very little is known about the species diversity or evolutionary relationships between strains and species. Further, epidemiological factors such as transmission routes and pathogenesis potential of many Elizabethkingia species remain undefined.
To resolve the relationships among Elizabethkingia species, 22 clinical isolates collected from throughout Queensland, Australia, over a 16-year period were subjected to speciation using both the VITEK MS system and whole-genome sequencing. These 22 genomes were combined with 100 publicly available Elizabethkingia genomes. Using the comparative genome pipeline SPANDx, 127,130 core-genome biallelic single-nucleotide polymorphisms (SNPs) were identified among these genomes. Phylogenomic reconstruction using these SNPs robustly identified 14 E. anophelis, 3 E. miricola, 2 E. meningoseptica and 1 E. brunniana strains in the Queensland isolates. In addition, two pairs of E. anophelis Queensland strains were near identical, suggesting patient to patient transmission.
Consistent with previous studies, E. anophelis was the dominant pathogenic species. Phylogenomic analysis resolved eight VITEK MS speciation errors within the E. miricola, E. brunniana and E. meningoseptica clades. Furthermore, 60% of Australian clinical isolates resided on novel branches within the global phylogeny, with no overlap found between Australian cases and those of international origin. Representing almost 15% of available public data, these Australian genomes add valuable reference diversity to the Elizabethkingia genus from a previously unsampled geographic region. Taken together, these findings highlight the need for phylogenomic-based approaches for correct assignment of Elizabethkingia species; and reveal untapped diversity present in this genus.