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dc.contributor.authorMu, A
dc.contributor.authorKwong, JC
dc.contributor.authorIsles, NS
dc.contributor.authorda Silva, AG
dc.contributor.authorSchultz, MB
dc.contributor.authorBallard, SA
dc.contributor.authorLane, CR
dc.contributor.authorCarter, GP
dc.contributor.authorWilliamson, DA
dc.contributor.authorSeemann, T
dc.contributor.authorStinear, TP
dc.contributor.authorHowden, BP
dc.date.accessioned2020-12-10T00:36:34Z
dc.date.available2020-12-10T00:36:34Z
dc.date.issued2019-01-01
dc.identifierpii: 4/1/e00529-18
dc.identifier.citationMu, A., Kwong, J. C., Isles, N. S., da Silva, A. G., Schultz, M. B., Ballard, S. A., Lane, C. R., Carter, G. P., Williamson, D. A., Seemann, T., Stinear, T. P. & Howden, B. P. (2019). Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing. MSPHERE, 4 (1), https://doi.org/10.1128/mSphere.00529-18.
dc.identifier.issn2379-5042
dc.identifier.urihttp://hdl.handle.net/11343/253526
dc.description.abstractCulture-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 patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium.IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.
dc.languageEnglish
dc.publisherAMER SOC MICROBIOLOGY
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleReconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
dc.typeJournal Article
dc.identifier.doi10.1128/mSphere.00529-18
melbourne.affiliation.departmentMicrobiology and Immunology
melbourne.source.titlemSphere
melbourne.source.volume4
melbourne.source.issue1
melbourne.identifier.nhmrc1008549
melbourne.identifier.nhmrc1105905
melbourne.identifier.nhmrc1142613
dc.rights.licenseCC BY
melbourne.elementsid1367795
melbourne.contributor.authorSeemann, Torsten
melbourne.contributor.authorHowden, Benjamin
melbourne.contributor.authorSchultz, Mark
melbourne.contributor.authorLane, Courtney
melbourne.contributor.authorKwong, Jason
melbourne.contributor.authorGoncalves Da Silva, Anders
melbourne.contributor.authorStinear, Timothy
melbourne.contributor.authorMu, Andre
melbourne.contributor.authorCarter, Glen
melbourne.contributor.authorBatt, Susan
melbourne.contributor.authorWilliamson, Deborah
melbourne.contributor.authorIsles, Nicole
dc.identifier.eissn2379-5042
melbourne.identifier.fundernameidNHMRC, 1008549
melbourne.identifier.fundernameidNHMRC, 1105905
melbourne.identifier.fundernameidNHMRC, 1142613
melbourne.accessrightsOpen Access


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