SOLICITATION NOTICE
66 -- MiSeq - SOL1198985
- Notice Date
- 7/5/2018
- Notice Type
- Combined Synopsis/Solicitation
- NAICS
- 334516
— Analytical Laboratory Instrument Manufacturing
- Contracting Office
- Department of Health and Human Services, Food and Drug Administration, Office of Acquisitions and Grants Services - Rockville, 5630 Fishers Lane, Room 2129, Rockville, Maryland, 20857-0001, United States
- ZIP Code
- 20857-0001
- Solicitation Number
- SOL1198985
- Point of Contact
- Telisha Wilson, Phone: 2404027572
- E-Mail Address
-
telisha.wilson@fda.hhs.gov
(telisha.wilson@fda.hhs.gov)
- Small Business Set-Aside
- N/A
- Description
- MiSeq=4 Option Years BACKGROUND Recent disease outbreaks have reinforced the notion that infectious diseases remain a global challenge. Fifteen million (>25%) of 57 million annual deaths worldwide are the direct result of infectious disease. An estimated 76 million disease cases linked to food-borne pathogens yield 325,000 hospitalizations, and 5,200 deaths per year in the United States (51) causing an economic burden estimated at $152 billion dollars annually, $39 billion of which is attributed solely to fresh, canned and processed produce (Produce Safety Project 2010). Salmonella enterica is responsible for an estimated 1.4 million infections in the United States annually. Infection can occur after eating undercooked meat, poultry and eggs or from eating raw produce that has been contaminated with the bacterium. In recent years several outbreaks have occurred in the United States that were associated with Salmonella contamination of produce, one of the most devastating being an S. enterica Saintpaul outbreak associated with tomatoes, jalapeno and Serrano peppers that sickened over 1500 individuals including 2 deaths and over 300 hospitalizations (http://www.cdc.gov). Approximately 400 people are killed in the U.S. annually by Salmonella infections (CDC, 2010), with 31% of all food related deaths in 2005 being attributed to Salmonella infections (CDC, 2005). The accurate subtyping and subsequent clustering of isolates of a bacterium associated with a foodborne outbreak event is essential for successful investigation and eventual traceback to a specific food or environmental source. In this regard, PFGE continues to deliver the "gold standard" by facilitating public health investigations for nearly two decades. In certain cases, however, highly clonal strains, particularly common within the salmonellae, stymie epidemiological investigations because PFGE and other conventional molecular typing tools provide limited genetic differentiation of these strains. That is, conventional approaches often lack the resolution for differentiating tightly linked bacterial isolates. In response to such events, federal public health and food safety laboratories have adopted next-generation sequencing (NGS) to define complex outbreak scenarios. NGS refers to highly parallel robotic genomic sequencers, like MiSeq illumina technology, that are being used to accomplish the whole genome sequencing (WGS) of a bacterial pathogen. Whole-genome sequencing technology is contributing long anticipated solutions to what were once viewed as insurmountable challenges, in the genetic analysis of bacterial pathogens. Complete genome sequences from multiple bacterial strains can now be collected and analyzed in just a few days, underscoring the potential of this technology as a molecular epidemiological tool to assist in foodborne outbreak investigations. Recent examples in the literature illustrate the ability of NGS to discern the high-resolution genetic relatedness of otherwise indistinguishable isolates based on the micro-evolutionary genetic change that define clinical isolates, outbreak isolates found in foods, and their environmental counterparts. These novel applications of whole-genome sequencing are buttressed by a massive influx of new genomic data, producing new discoveries about the critical genes that define particular pathogens, and important genomic changes associated with pathogenicity, antibiotic resistance, and unique carbon source usages. Ultimately, these data will provide new ways for identifying outbreak isolates. However, this technology, like most typing tools, will be limited to the strength of its own databases. That is, while outbreak strains continue to amass in the national database at NCBI-NIH, a great void remains concerning numbers of background pathogen isolates and their subsequent genomes. Isolates from the field, farms, processing houses with rich and diverse geographic and ecologic origins will be critical to success of the WGS-based disease cluster identification and source tracking efforts. Our national and state field laboratories represent outlets where numerous and diverse enteric pathogens are detected, isolated, and processed. Such a bank of biomaterials would be ideal for the development of databases and for proof-of-concept that WGS data can be rapidly uploaded to a national database and blended with other remaining WGS data for effective analyses of source and traceback. The purpose of this contract is to continue to provide FDA with proof of concept that this emerging technology can be implemented in national and state field laboratories and to provide FDA with data that is crucial to source tracking Salmonella that may be involved in future produce related outbreaks. The vendor for this contract will provide numerous national and state field laboratories with the necessary resources to establish and continue the GenomeTrakr network, a WGS-based laboratory program for the generation of high quality whole-genome sequences originating from the laboratory historical enteric pathogen collections and from enteric bacterial isolates collected from various produce sources and from disparate parts of the country during the term of this contract. Equipment, service and chemical reagents will be provided to generate data that the field labs will uploaded in real-time into the NCBI-curated national database for enteric pathogen genomes and will greatly enhance the database for source-tracking queries using whole genome sequence data. At the same time, these data will continue to serve as an early proof-of-concept for the rapid networking of various resources using a WGS-based approach to pathogen detection, identification, and traceback. This project will support FDA's mission of protecting the public health by generating data to identifying contaminated produce which will be removed from the nation's food supply. SCOPE OF WORK The contractor shall provide the equipment necessary to perform WGS data collection and analysis on produce and produce-related environmental Salmonella, Listeria, Campylobacter and shigatoxigenic E. coli (STEC; both O157:H7 and non-O157:H7) isolates. 1. The contractor shall provide all of the necessary NGS sequencing equipment and reagents so that field laboratory staff can produce draft genomes on related bacterial isolates (see 2 below) and report 40 sequences per month (480 sequences per year) at a minimum quality of 30x coverage. Equipment and reagents will be based on the equivalent of the Illumina, MiSeq (see below) Sequencer and related equipment and reagents need to deliver the throughput as listed above. Minimum delivery of equivalent equipment and reagents for a field sites in first year. 2. The contractor shall provide all of the necessary equipment and reagents to establish an independent field laboratory NGS field sites, with the ability to sequence roughly 500 draft genomes per year. 3. Contract will include all costs associated with delivery and installation of equipment, training for each of a field laboratory site, service for the instruments for full year and reagents to support the sequencing at the above listed quantity and quality. CONTRACTOR'S TECHNICAL WORKPLAN The final delivery and timing for installation of equipment and reagents will be designed and approved working with the FDA Project Officer and other technical advisors. Processing and Analysis All equipment, reagents and approved training and protocols will be those designed or equivalent to Illumina for use with the MiSeq Sequencer or equivalent. Any modifications of these protocols must be reported to the Project Officer and must be acceptable to FDA before they are implemented. All genomes must be completed at a minimum quality of 30x coverage. The contractor shall provide the equipment necessary to perform WGS data collection and analysis on produce and produce-related environmental Salmonella, Listeria, Campylobacter and shigatoxigenic E. coli (STEC; both O157:H7 and non-O157:H7) isolates. The contractor shall provide the necessary NGS sequencing equipment and reagents so that field laboratory staff can produce draft genomes on related bacterial isolates and report 40 genomic sequences per month (480 genomic sequences per year) at a minimum quality of 30x coverage. Equipment and reagents shallbe based on the equivalent of the Illumina, MiSeq Sequencer and related equipment and reagents need to deliver the throughput as listed above. Provide minimum delivery of equivalent equipment and reagents for a field sites in first year. The contractor shall provide the necessary equipment and reagents to establish an independent field laboratory and NGS field sites, with the ability to sequence roughly 500 draft genomes per year. Contract shallinclude all costs associated with delivery and installation of equipment, training for each of a field laboratory site, service for the instruments for full year and reagents to support the sequencing at the above listed quantity and quality. Contractors shallprovide estimated cost to produce one bacterial genome at 30k coverage including all costs to produce this data at the capacity listed. DELIVERABLES The contractor shall: 1. The contractor shall provide all of the necessary NGS sequencing equipment and reagents so that field laboratory staff can produce draft genomes on related bacterial isolates (see 2 below) and report 40 sequences per month (480 sequences per year) at a minimum quality of 30x coverage. 2. The contractor shall provide all of the necessary equipment and reagents to establish an independent field laboratory NGS field sites, each with the ability to sequence roughly 500 draft genomes per year. 3. Contract will include all costs associated with delivery and installation of equipment, training for a field laboratory sites, service for the instruments for full year and reagents to support the sequencing at the above listed quantity and quality. Provide the Project Officer with all information necessary to confirm that the tasks contained within this contract are being executed in a manner that is acceptable to FDA. 1st Option year 1. Service contracts for all new and previous purchased instruments. Delivery of an additional NGS sequencers, with installation, training, service as specified in the base year. 2nd Option year 1. Service contracts for all new and previous purchased instruments. Delivery of an additional NGS sequencers, with installation, training, service as specified in the base year. 3rd Option year 1. Service contracts for all new and previous purchased instruments. Delivery of an additional NGS sequencers, with installation, training, service as specified in the base year. 4th Option year Service contracts for all new and previous purchased instruments. Delivery of an additional NGS sequencers, with installation, training, service as specified in the base year
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/FDA/DCASC/SOL1198985/listing.html)
- Record
- SN04980630-W 20180707/180705230623-3e32c076a3006b1f686d89b23edac2fb (fbodaily.com)
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