title: A platform for leveraging next generation sequencing for routine microbiology and public health use.
abstract: Even with the advent of next-generation sequencing (NGS) technologies which have revolutionised the field of bacterial genomics in recent years, a major barrier still exists to the implementation of NGS for routine microbiological use (in public health and clinical microbiology laboratories). Such routine use would make a big difference to investigations of pathogen transmission and prevention/control of (sometimes lethal) infections. The inherent complexity and high frequency of data analyses on very large sets of bacterial DNA sequence data, the ability to ensure data provenance and automatically track and log all analyses for audit purposes, the need for quick and accurate results, together with an essential user-friendly interface for regular non-technical laboratory staff, are all critical requirements for routine use in a public health setting. There are currently no systems to answer positively to all these requirements, in an integrated manner. In this paper, we describe a system for sequence analysis and interpretation that is highly automated and tackles the issues raised earlier, and that is designed for use in diagnostic laboratories by healthcare workers with no specialist bioinformatics knowledge.
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Laura I
authors: LI
authors: Rusu
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Kelly L
authors: KL
authors: Wyres
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Matthias
authors: M
authors: Reumann
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Carlos
authors: C
authors: Queiroz
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Alexe
authors: A
authors: Bojovschi
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Tom
authors: T
authors: Conway
authors: IBM Research, Australia, 204 Lygon Street, Carlton, Victoria 3053, Australia.
authors: Saurabh
authors: S
authors: Garg
authors: Department of Biochemistry and Molecular Biology and Bio21 MolecularScience and Biotechnology Institute, The University of Melbourne, Parkville VIC 3010, Victoria, Australia.
authors: David J
authors: DJ
authors: Edwards
authors: Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, Parkville Victoria 3010, Australia.
authors: Geoff
authors: G
authors: Hogg
authors: Department of Biochemistry and Molecular Biology and Bio21 MolecularScience and Biotechnology Institute, The University of Melbourne, Parkville VIC 3010, Victoria, Australia.
authors: Kathryn E
authors: KE
authors: Holt