CAPITAL PURCHASE OF Next Generation Sequencer (NGS)

HSE are looking to procure a Next Generation Sequencing (NGS) system for routine bacterial and fungal identification purposes that will require the partial sequencing of targeted genes, rather than the whole genome work.

The system must be capable of identifying microorganisms to species level either from purified colonies (culture) or from mixed populations of microorganisms without the need for culture; the latter based on direct DNA extraction and target gene amplification from mainly environmental samples (e.g. soil, water, air).

Based on current and expected future identification requirements, HSE expect that most if not all bacterial work will focus on the 16S rRNA gene (16S rDNA sequencing).

Any fungal work would likely focus on the internal transcribed Spacer regions (ITS) or 18S rRNA gene sequencing.

HSE is not a diagnostic laboratory and we do not envisage very high output requirements and are therefore interested in accuracy and cost effectiveness over throughput.

HSE require a machine that can provide species level identification for fungi and bacteria, including those derived from environmental isolates.

Based on the above requirement, HSE expect that the NGS system will be able to offer between a 500bp to 600bp read (i.e. between a 2 x 250 bp to 2 x 300 bp read capability) from its standard application; this would, for example, enable the reliable routine sequencing of relevant hyper variable regions of the 16S gene (e.g. V3, V4).

HSE Science Division's laboratory space is limited, so the machine needs to be compact and user-friendly; a bench space of 1m2 would be a reasonable guide as to what space it needs to fit in to.

The system must have dedicated on-board software as part of the package to enable sequence alignment/identification; this needs to be user friendly, with a good user interface and not just designed for the specialist user. This is because our trained operators will not be using the system all of the time - sequencing will be one of several tasks they regularly undertake.

At the very least, the sequencing output software needs to link to open access gene sequence databases, such as NCBI to enable instant access to integrated sequence identification, which will be performed at the end of the sequencing process. We do not want to be constrained by access that is restricted to licensed sequence datasets only, although we appreciate that this may be an option The system needs to have design considerations whereby the machine and its accessories do not require high maintenance or high levels of operator hands-on input i.e. a high degree of process automation is required for most of the sequencing process.

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