Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole

Delaney Burnard; Letitia Gore; Andrew Henderson; Ama Ranasinghe; Haakon Bergh; Kyra Cottrell; Derek S Sarovich; Erin P Price; David L Paterson; Patrick N. A Harris

doi:10.1101/2020.03.12.20032722

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Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole

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Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole

Delaney Burnard, Letitia Gore, Andrew Henderson, Ama Ranasinghe, Haakon Bergh, Kyra Cottrell, Derek S Sarovich, Erin P Price, David L Paterson and Patrick N. A Harris

medRxiv

Cold Spring Harbor Laboratory Press

2020

DOI: https://doi.org/10.1101/2020.03.12.20032722

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Abstract

Elizabethkingia

MDR

multidrug resistance

nosocomial

MIC

minimum

The Elizabethkingia genus has gained global attention in recent years as a nosocomial pathogen. Elizabethkingia spp. are intrinsically multidrug resistant, primarily infect immunocompromised individuals, and are associated with high mortality (~20-40%). Although Elizabethkingia infections appear sporadically worldwide, gaps remain in our understanding of transmission, global strain relatedness and patterns of antimicrobial resistance. To address these knowledge gaps, 22 clinical isolates collected in Queensland, Australia, over a 16-year period along with six hospital environmental isolates were examined using MALDI-TOF MS (VITEK MS) and whole-genome sequencing to compare with a global strain dataset. Phylogenomic reconstruction against all publicly available genomes (n=100) robustly identified 22 E. anophelis, three E. miricola, two E. meningoseptica and one E. bruuniana from our isolates, most with previously undescribed diversity. Global relationships show Australian E. anophelis isolates are genetically related to those from the USA, England and Asia, suggesting shared ancestry. Genomic examination of clinical and environmental strains identified evidence of nosocomial transmission in patients admitted several months apart, indicating probable infection from a hospital reservoir. Furthermore, broth microdilution of the 22 clinical Elizabethkingia spp. isolates against 39 antimicrobials revealed almost ubiquitous resistance to aminoglycosides, carbapenems, cephalosporins and penicillins, but susceptibility to minocycline, levofloxacin and trimethoprim/sulfamethoxazole. Our study demonstrates important new insights into the genetic diversity, environmental persistence and transmission of Australian Elizabethkingia species. Furthermore, we show that Australian isolates are highly likely to be susceptible to minocycline, levofloxacin and trimethoprim/sulfamethoxazole, suggesting that these antimicrobials may provide effective therapy for Elizabethkingia infections.

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Title: Comparative genomics and antimicrobial resistance profiling of Elizabethkingia isolates reveals nosocomial transmission and in vitro susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole
Authors: Delaney Burnard (Author) - University of the Sunshine Coast, Queensland, School of Science and Engineering - Legacy
Letitia Gore (Author) - Queensland Health
Andrew Henderson (Author) - The University of Queensland
Ama Ranasinghe (Author) - The University of Queensland
Haakon Bergh (Author) - Queensland Health
Kyra Cottrell (Author) - The University of Queensland
Derek S Sarovich (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
Erin P Price (Author) - University of the Sunshine Coast, Queensland, GeneCology Research Centre - Legacy
David L Paterson (Author) - The University of Queensland
Patrick N. A Harris (Author) - The University of Queensland
Publication details: medRxiv
Publisher: Cold Spring Harbor Laboratory Press
Date published: 2020
DOI: 10.1101/2020.03.12.20032722
Copyright note: The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Organisation Unit: School of Science and Engineering - Legacy; Information Technology; University of the Sunshine Coast, Queensland; Centre for Bioinnovation; Sustainability Research Cluster
Language: English
Record Identifier: 99500808802621
Output Type: Preprint

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