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.

  • 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)
  • 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?

For DNA isolation, is it possible to batch Legionella specimens with PulseNet organisms and to use PulseNet protocols to sequence Legionella specimens/isolates?

Will all of the data ultimately be submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA)?

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?

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?

For Option 2 (metagenomic shotgun sequencing), will CDC be providing a protocol for DNA extraction of specimens?

What kind of freezing conditions are required/preferred for samples for metagenomic shotgun sequencing?

For Option 2 (metagenomic shotgun sequencing), can you confirm that sequencing is NOT restricted to Legionella pneumophilia positive samples?

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?