The Association of Public Health Laboratories, Inc. (APHL), in cooperation with the US Centers for Disease Control and Prevention’s (CDC) Division of Bacterial Diseases (DBD), is seeking to identify approximately six state or local public health laboratories that will (a) perform next generation sequencing for various
Legionella spp., including L. pneumophila (“Option 1”) and/or (b) conduct shotgun metagenomic sequencing of DNA extracted from lower respiratory tract specimens (“Option 2”).
Eligibility
APHL is looking for eligible PHLs with the following capabilities and facilities in place. APHL and/or CDC will provide technical assistance and troubleshooting by regular teleconference. Each applicant must certify in their application that they meet the minimum requirements set forth below for the option(s) they are applying for.
Applicants may apply for Option 1, Option 2, or both.
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Option 1: Development and Evaluation of wgMLST
- Applicant must have a repository of at least 50 archived Legionella spp isolates with associated metadata. Eligible repositories may include clinical L. pneumophila isolates and/or non-pneumophila Legionella isolates from any source;
- Applicant must have an established capability to perform culture of Legionella spp;
- Applicant must have established and demonstrated capability to perform Next Generation Sequencing (NGS) using Illumina MiSeq (previous Legionella NGS experience not a requirement);
- Applicant must have sufficient equipment, laboratory space, and workforce capacity for the proposed workload;
- Applicant must have local instance of Bionumerics (version 7.5 or 7.6); and
- Applicant must have the ability to upload genome sequence data to the Office of Advanced Molecular Detection (OAMD) portal data transfer tool using SAMS authentication (current access not required)
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Option 2: Development and Evaluation of Culture-Independent Subtyping Methods
- Applicant must have established capability to perform culture of Legionella spp.;
- Applicant must have established and demonstrated capability to perform NGS using Illumina MiSeq (previous Legionella NGS experience not a requirement);
- Applicant must have sufficient equipment, laboratory space and workforce capacity for the proposed workload;
- Applicant must have the ability to upload metagenomic sequence data to OAMD Portal data transfer tool using SAMS authentication (current access not required) – note that specimens must be sequenced at the participating laboratory, but recovered isolates can be either sequenced by the participating laboratory or sent to CDC;
- Applicant must have ability to perform or implement a Legionella real time PCR assay directly on clinical specimens; and
- Applicant must have access Legionella positive clinical specimens such as sputa, bronchoalveolar lavage, or any lower respiratory tract aspirates
Anticipated RFP Schedule
October 15, 2018 – RFP Issued
October 19, 2018 – Informational Teleconference (Q&A)
October 23, 2018 - Letter of Intent Due to APHL
November 16, 2018 - RFP Responses Due
December 4, 2018 – Proposal review completed
December 13-18, 2018 – If needed, follow-up interviews and updated proposals due
December 18, 2018 – Final review completed and awardees selected
January 14, 2019 – Anticipated project start date
Please send the Letter of Intent (Due 10/23/18) and completed application (Due 11/16/18) to Anna Tate,
anna.tate@aphl.org
Any modification to this anticipated schedule will be communicated on APHL’s procurement website (www.aphl.org/rfp) and via an email blast to the PHLs.
Request for Proposal Materials
The
Legionella RFP provides details on how to complete this RFP. The RFP contains a copy of the scoring criteria that will be used for evaluation of proposals in Appendix C.
Questions and Answers
What is the timeline for submission of deliverables? Does sequencing need to be completed by a certain date?
A: In order to keep sequencing and deliverable submission on track, we will have two time periods by which sequencing should be conducted -- i.e., half of sequencing should be completed by the mid-way point of the project and the other half by the end of the project term, June 30, 2019.
For DNA isolation, is it possible to batch Legionella specimens with PulseNet organisms and to use PulseNet protocols to sequence Legionella specimens/isolates?
A: Yes, it is possible to follow the PulseNet protocol (using Nextera XT library kits) with potentially very minor changes with respect to DNA isolation. In CDC's experience working with several other laboratories, sequencing of Legionella has been relatively simple to bring on for laboratories that are familiar implementing PulseNet protocols.
Will all of the data ultimately be submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA)?
A: It depends on which RFP option you are referring to:
For Option 1, sites must agree to submit (or work with CDC to submit) raw sequencing data directly to the NCBI Sequence Read Archive (SRA) by the end of the project period. APHL and CDC can work with your laboratory on IRB issues as needed.
For Option 2, sites must agree to submit (or work with CDC to submit) processed sequencing data (e.g., metagenomic assemblies) to publicly accessible databases by the end of the project period. CDC will help ensure that human DNA is removed from any raw data that are submitted.
Will the funds for this work need to be obligated by the end of June 30, 2019 (the end of the project term), or do all deliverables need to be completed by June 30, 2019? Is June 30 a hard deadline?
A: Yes, pending any unforeseen delays with the project, please consider June 30, 2019 as a hard deadline for deliverable completion and submission.
Are there any expectations or preferences regarding whether participating laboratories use version 2 vs. version 3 reagent kits with the MiSeq instrument for sequencing purposes?
A: No, CDC does not have a preference. Laboratories should follow their existing methodology and use what they are most comfortable with.
For Option 2 (metagenomic shotgun sequencing), will CDC be providing a protocol for DNA extraction of specimens?
A: Yes, CDC can provide an extraction protocol for respiratory samples upon request. However, note that laboratories would not necessarily be bound to that particular method if they are already currently using methods that are adequate (and measured as such by sharing, for instance, previous PCR results to ensure adequate concentrations of DNA in Legionella positive specimens).
What kind of freezing conditions are required/preferred for samples for metagenomic shotgun sequencing?
A: Storage at-70 to -80◦C conditions are preferred. CDC has not formally evaluated the effects of long-term storage at -20◦C , but storage for more than about a week at refrigerated (non-frozen) temperatures tends to result in poor isolate recovery statistics, as well as issues with PCR detection.
For Option 2 (metagenomic shotgun sequencing), can you confirm that sequencing is NOT restricted to Legionella pneumophilia positive samples?
A: Correct. Any Legionella spp. positive sample would be considered adequate for sequencing.
In considering Option 2, our laboratory would need to identify a hospital/clinic/laboratory willing to send us specimens, or we would need to tap into our only other source of sputum specimens (from our routine TB testing). The goal would be for us to process those specimens, identify five that are PCR positive over the course of the performance period, and then do shotgun sequencing. Can you confirm that it would be up to us (the laboratory) to ensure we tap into an adequate stream of specimens in order to ensure we have five specimens?
A: Yes, that is correct. Part of the reason CDC is interested in partnering with laboratories is that they have closer relationships with clinics and hospitals and may be able to tap into existing resources, and to potentially tap in to surveillance testing occurring in hospitals or laboratories where there may be reflex testing (e.g., collection of lower respiratory system specimens from Legionella urinary antigen test positive individuals). Identifying ways to tap into those types of reflexive samples would certainly increase the likelihood that you will find Legionella positive samples. Ultimately, it is up to the laboratory to identify specimens using an appropriate Legionella PCR assay.