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

Sopheak Hem; Veronica M. Jarocki; Dave J. Baker; Ian G. Charles; Barbara Drigo; Sarah Aucote; Erica Donner; Delaney Burnard; Michelle J. Bauer; Patrick N.A. Harris; Ethan R. Wyrsch; Steven P. Djordjevic

Current Research in Microbial Sciences (Jan 2022)

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

Sopheak Hem,
Veronica M. Jarocki,
Dave J. Baker,
Ian G. Charles,
Barbara Drigo,
Sarah Aucote,
Erica Donner,
Delaney Burnard,
Michelle J. Bauer,
Patrick N.A. Harris,
Ethan R. Wyrsch,
Steven P. Djordjevic

Affiliations

Sopheak Hem: iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
Veronica M. Jarocki: iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
Dave J. Baker: Quadram Institute Bioscience, Norwich, United Kingdom
Ian G. Charles: Quadram Institute Bioscience, Norwich, United Kingdom; Norwich Medical School, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
Barbara Drigo: Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
Sarah Aucote: Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
Erica Donner: Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
Delaney Burnard: University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
Michelle J. Bauer: University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
Patrick N.A. Harris: University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
Ethan R. Wyrsch: iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia; Corresponding author at: iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.
Steven P. Djordjevic: iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia; Corresponding author at: iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.

Journal volume & issue: Vol. 3
p. 100083

Abstract

Read online

Elizabethkingia species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents. Elizabethkingia infections are challenging to treat, and case fatality rates are high. Chromosomal blaB, blaGOB and blaCME genes encoding carbapenemases and cephalosporinases are unique to Elizabethkingia spp. and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 Elizabethkingia isolates carrying multiple wide-spectrum metallo-β-lactamase (blaB and blaGOB) and extended-spectrum serine‑β-lactamase (blaCME) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of Elizabethkingia species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental E. anophelis isolates are closely related to E. anophelis from Australian clinical isolates (∼36 SNPs), and a new species, E. umeracha sp. novel, was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.

Published in Current Research in Microbial Sciences

ISSN: 2666-5174 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Microbiology; Science: Biology (General): Genetics
Website: https://www.journals.elsevier.com/current-research-in-microbial-sciences

About the journal