Application of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada

Abstract

Bioinformatic analysis of whole genome sequence (WGS) data is emerging as a tool to provide powerful insights for clinical microbiology. We used WGS data to investigate the genetic diversity of clinical isolates of the bacterial pathogen Elizabethkingia anophelis to query the existence of a single-strain outbreak in Ontario, Canada. The Public Health Ontario Laboratory (PHOL) provides reference identification of clinical isolates of bacteria for Ontario and prior to 2016 had not identified E. anophelis . In the wake of the Wisconsin outbreak of 2015-2016 for which a source was never elucidated, the identification of E. anophelis from clinical specimens from five Ontario patients gave reason to question the presence of an outbreak. Genomic comparisons based on core genome multi-locus sequence typing conclusively refuted the existence of an outbreak, since the 5 Ontario isolates were genetically dissimilar, representing at least 3 distinct sub-lineages scattered among a set of 39 previously characterized isolates. Further interrogation of the genomic data revealed multiple antimicrobial resistance genes. Retrospective reidentification via rpoB sequence analysis of 22 clinical isolates of Elizabethkingia spp. collected by PHOL from 2010 to 2018 demonstrated that E. anophelis was isolated from clinical specimens as early as 2010. The uptick in E. anophelis in Ontario was not due to an outbreak or increased incidence of the pathogen, but rather enhanced laboratory identification techniques and improved sequence databases. This study demonstrates the usefulness of WGS analysis as a public health tool to quickly rule out the existence of clonally related case clusters of bacterial pathogens indicative of single-strain outbreaks.

Keywords: Elizabethkingia anophelis; antimicrobial resistance; core genome MLST; outbreak; whole genome sequence.

Fig. 1.

Genomic comparison using the UPGMA algorithm based on cgMLST profiles (1546 genes) of E. anophelis strains. The position of the 5 Ontario isolates (black arrows) is shown among a collection of 2 Wisconsin outbreak (grey arrows) isolates and 37 other strains representing the known diversity of the sublineages [6]. The scale bar corresponds to 10 % allelic mismatches (out of 1546 gene loci). Nodes with >80 % bootstrap support (n=1000 replicates) are indicated.