Live Genomics for Pathogen Monitoring in Public Health
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Live Genomics for Pathogen Monitoring in Public Health

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Live Genomics for Pathogen Monitoring in Public Health

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dc.contributor.author D’Auria, Giuseppe es_ES
dc.contributor.author Schneider, Maria Victoria es_ES
dc.contributor.author Moya, Andrés es_ES
dc.date.accessioned 2015-06-05T12:39:08Z
dc.date.available 2015-06-05T12:39:08Z
dc.date.issued 2014
dc.identifier.uri http://hdl.handle.net/10550/44189
dc.description.abstract Whole 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 a short lapse 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 include 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. es_ES
dc.source Pathogens Vol. 3 Issue 1: pp. 93-108 es_ES
dc.subject pathogens outbreaks es_ES
dc.subject pan-genome es_ES
dc.subject comparative genomics es_ES
dc.subject bioinformatics es_ES
dc.subject resistance es_ES
dc.subject public health es_ES
dc.title Live Genomics for Pathogen Monitoring in Public Health es_ES
dc.type info:eu-repo/semantics/article
dc.identifier.doi 10.3390/pathogens3010093 es_ES
dc.identifier.idgrec 094634 es_ES

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