Supply of a Vega HiFi Long-Read Sequencing System, Associated Reagents, Consumables and Maintenance for Galway Reference Laboratory Services

HSE Procurement intends to enter into a six-year arrangement with Pacific Biosciences of California, Inc. (PacBio) for the supply of one Vega HiFi long-read sequencing system, together with associated sequencing consumables, library preparation reagents, indexing reagents, maintenance and delivery, for use by Galway Reference Laboratory Services (GRLS). GRLS provides national reference laboratory services supporting human clinical laboratories in Ireland in relation to Salmonella, Shigella, Listeria monocytogenes and Carbapenemase Producing Enterobacterales (CPE), as well as supporting the investigation of other Carbapenemase Producing Organisms and antimicrobial-resistant organisms associated with suspected outbreaks. The requirement is to provide highly accurate native long-read sequencing capability to enhance the detection, characterisation and tracking of mobile genetic elements, including plasmids carrying antimicrobial resistance genes. Existing short-read sequencing is limited in its ability to generate complete sequences of these mobile genetic elements and to determine transmission where resistance genes move between different bacterial strains and species. To fulfil this operational requirement, the sequencing system must provide long sequencing reads while maintaining the high sequence accuracy required for national reference and outbreak investigation functions. In particular, GRLS requires greater than 90% of bases to achieve a quality score of Q30 or greater. The sequencing output must also integrate with the laboratory's existing bioinformatics analysis workflow and facilitate plasmid characterisation and clustering. Alternative long-read sequencing technology was considered. Oxford Nanopore technology was assessed but does not currently satisfy the laboratory's required raw-read accuracy, reporting raw-read accuracy of Q26 compared with the GRLS requirement for greater than 90% of bases at Q30 or greater. PacBio HiFi sequencing provides long reads with typical read accuracy of 99.9% and therefore satisfies the required combination of long-read capability and sequence accuracy. The Vega system also provides primary analysis on-instrument, including base calling, HiFi read generation, methylation calling, barcode demultiplexing and BAM file generation. Pacific Biosciences is the sole provider of its proprietary Single Molecule Real-Time (SMRT®) sequencing technology and the sole manufacturer of the Vega sequencing system. The associated sequencing consumables, library preparation reagents and indexing reagents required for the proposed sequencing workflow are proprietary to PacBio. Having considered alternative long-read sequencing technology, HSE Procurement considers that no reasonable alternative or substitute currently meets the identified technical requirements and that competition is therefore absent for technical reasons. HSE Procurement intends to award the contract to Pacific Biosciences of California, Inc. in accordance with Article 32(2)(b)(ii) of Directive 2014/24/EU. HSE Procurement undertakes that no contract shall be awarded to Pacific Biosciences of California, Inc. for the supply of these items until a period of fourteen days has elapsed, commencing on the day after the date of publication of this notice at European level.