Show simple item record

dc.contributor.authorD'Auria, G
dc.contributor.authorSchneider, MV
dc.contributor.authorMoya, A
dc.date.accessioned2021-02-04T01:13:09Z
dc.date.available2021-02-04T01:13:09Z
dc.date.issued2014-01-21
dc.identifierpii: pathogens3010093
dc.identifier.citationD'Auria, G., Schneider, M. V. & Moya, A. (2014). Live genomics for pathogen monitoring in public health.. Pathogens, 3 (1), pp.93-108. https://doi.org/10.3390/pathogens3010093.
dc.identifier.issn2076-0817
dc.identifier.urihttp://hdl.handle.net/11343/259296
dc.description.abstractWhole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the "local" level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a "streaming approach" (pipeline). Such pipeline would NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted "comprehensible" results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences.
dc.languageeng
dc.publisherMDPI AG
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleLive genomics for pathogen monitoring in public health.
dc.typeJournal Article
dc.identifier.doi10.3390/pathogens3010093
melbourne.affiliation.departmentMedicine Dentistry & Health Sciences
melbourne.affiliation.facultyMedicine, Dentistry & Health Sciences
melbourne.source.titlePathogens
melbourne.source.volume3
melbourne.source.issue1
melbourne.source.pages93-108
dc.rights.licenseCC BY
melbourne.elementsid1061172
melbourne.openaccess.pmchttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235738
melbourne.contributor.authorSchneider, Maria Victoria
dc.identifier.eissn2076-0817
melbourne.accessrightsOpen Access


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record