Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.

Sebastien Breurec,Olaya Rendueles,Valérie Caro,Virginie Passet,Eduardo P C Rocha,Mathias Vandenbogaert,Laure Diancourt,Sylvain Brisse,Marie Touchon,Alexis Criscuolo

doi:10.1038/srep30379

Abstract

Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.

Highlights

As an emerging opportunistic pathogen, and its clinical significance was underlined recently, with a majority of Elizabethkingia isolates being identified as E. anophelis, rather than E. meningoseptica[13]
The aims of this study were to determine the phylogenetic origin and genomic features of the two African neonatal meningitis E. anophelis isolates; to compare them with Elizabethkingia isolates from other world regions and sources; to take advantage of the high resolution of whole genome sequencing to distinguish Elizabethkingia species unambiguously, and to develop a publicly-accessible genotyping system enabling a common language on strain types in order to ease future collaborations on biodiversity studies and epidemiological investigations of Elizabethkingia clinical and environmental isolates
Our comparative phylogenetic analyses led us to refine the identification of Elizabethkingia strains and to demonstrate firmly the phylogenetic distinctness of the three established species of the genus

Summary

Introduction

As an emerging opportunistic pathogen, and its clinical significance was underlined recently, with a majority of Elizabethkingia isolates being identified as E. anophelis, rather than E. meningoseptica[13]. The clinical significance and biological distribution of E. anophelis is restricted, as this novel species is not well distinguished from other Elizabethkingia species in routine microbiological identification procedures, and as reference identification of E. anophelis relies mostly on the low-resolution 16S rRNA gene. The aims of this study were to determine the phylogenetic origin and genomic features of the two African neonatal meningitis E. anophelis isolates; to compare them with Elizabethkingia isolates from other world regions and sources; to take advantage of the high resolution of whole genome sequencing to distinguish Elizabethkingia species unambiguously, and to develop a publicly-accessible genotyping system enabling a common language on strain types in order to ease future collaborations on biodiversity studies and epidemiological investigations of Elizabethkingia clinical and environmental isolates

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Conclusion