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.

The Interplay Between Nutrition and the Dynamics of the Midgut Microbiome of the MosquitoAedes aegyptiReveals Putative Symbionts

“…The presence of E. anophelis in the post-digestion microbiomes of adult females is noteworthy, mainly because this gram-negative flavobacterium has been identified as the causative agent of multiple outbreaks in humans worldwide. The species has also been isolated from Anopheles gambiae, raising concerns about the possibility of its vectorial transmission (Chew et al, 2018; McTaggart et al, 2019; Perrin et al, 2017; Reed et al, 2020). Its pathogenesis is characterized by nosocomial bacteremia leading to sepsis in humans and has been associated with neonatal meningitis (Lau et al, 2016).…”

Elizabethkingia anophelis MSU001 Isolated from Anopheles stephensi: Molecular Characterization and Comparative Genome Analysis

“…These limitations highlight the need for updating standard MALDI-ToF databases, as well as for thorough, enhanced identification methodologies that utilize a combination of widely adopted bacterial identification methods like 16s rDNA sequencing in conjunction with biochemical testing [ 41 , 46 , 48 ]. Moreover, whole genomic sequence analysis and average nucleotide identity as a complementary method may be used to correctly identify E. anophelis [ 46 , 49 ].…”

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission

“…The fact that E. anophelis was misidentified here and elsewhere ( Chen et al., 2019 ; Han et al., 2017 ; McTaggart et al., 2019 ; Snesrud et al., 2019 ) as E. meningosepticum by conventional clinical methods has led to speculation that E. anophelis is not only underrepresented but may actually be the primary species to cause disease in humans. This hypothesis is strengthened by recent reports of life-threatening E. anophelis infections in Asia, Australia, and the USA ( Burnard et al., 2020 ; Lin et al., 2019a ).…”