Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing

Andre Mu; Jason C Kwong; Nicole S Isles; Anders Goncalves da Silva; Mark B Schultz; Susan A Ballard; Courtney R Lane; Glen P Carter; Deborah A Williamson; Torsten Seemann; Timothy P Stinear; Benjamin P Howden

Journal article

Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing

Andre Mu, Jason C Kwong, Nicole S Isles, Anders Goncalves da Silva, Mark B Schultz, Susan A Ballard, Courtney R Lane, Glen P Carter, Deborah A Williamson, Torsten Seemann, Timothy P Stinear, Benjamin P Howden

MSPHERE | AMER SOC MICROBIOLOGY | Published : 2019

DOI: 10.1128/mSphere.00529-18

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Abstract

Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the pa..

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University of Melbourne Researchers

Torsten Seemann Author Microbiology and Immunology

Ben Howden Author Microbiology and Immunology

Jason Kwong Author Medicine - Austin Health

Anders Goncalves Da Silva Author Microbiology and Immunology

Glen Carter Author Microbiology and Immunology

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Grants

Awarded by CASS Foundation

Awarded by National Health and Medical Research Council of Australia

Funding Acknowledgements

DThis research was supported by grants from the Austin Medical Research Foundation and the CASS Foundation (reference no. 7113). J.C.K. (GNT1142613 and Centre for Research Excellence in Emerging Infectious Diseases GNT1102962), T.P.S. (GNT1008549), and B.P.H. (GNT1105905) are supported by the National Health and Medical Research Council of Australia.