The Association of Public Health Laboratories (APHL), in cooperation with the US Centers for Disease Control and Prevention (CDC) Division of Tuberculosis Elimination (DTBE), is seeking to identify up to 10 state or local public health laboratories to participate in an evaluation of performing whole genome sequencing (WGS) from primary (i.e., diagnostic) BD BACTEC MGIT cultures positive for Mycobacterium tuberculosis complex (MTBC). Laboratories will obtain the samples for WGS (minimum of 32) through one of the following approaches.

  • Option 1. Utilize samples from a defined jurisdiction (e.g., city, county, region, or state)
  • Option 2. Collaborate with another jurisdiction to obtain a sufficient number of samples.

Eligibility

APHL is looking for up to 10 eligible laboratories including all member public health laboratories with the following capabilities, resources and facilities in place.

  • Minimum of 32 MTBC positive primary MGIT cultures/year (can partner with other jurisdictions to meet this requirement) from at least 10 unique patients
  • Capacity for isolating chromosomal DNA from MTBC suitable for WGS
  • Established and demonstrated performance of WGS for bacterial pathogen(s)
  • Sufficient equipment, laboratory space and workforce for the project     

Anticipated RFP Schedule

June 27, 2019              –             RFP Issued

July 11, 2019                –             Informational Teleconference (Q&A)      

July 15, 2019                            Letter of Intent Due to APHL (see below)

August 8, 2019                        RFP Responses Due

August 9-16                 –             Proposal review completed

August 19-20 2019     –             If needed, follow-up interviews and updated proposals due

August 21, 2019          –             Final review completed and awardees selected

August 30, 2019          –             Draft contracts submitted to APHL Legal Dept. for final internal review

APHL will communicate any modification to this anticipated schedule on APHL's procurement website (www.aphl.org/rfp) and via an email blast to the public health laboratories (PHLs).

Response Submittal

Confirmation of Intent to Respond

APHL requests that prospective applicants submit a brief email statement indicating an intent to submit a proposal. APHL must receive this email by no later than 5:00pm EST on July 15, 2019

Final Response

APHL must receive complete responses by 5:00 pm EST on August 8, 2019. Please see Proposal-Required Submissions section for items that must be included in the completed proposal.  Applicants may send proposals via email to Anne.Gaynor@aphl.org.

APHL will send an email acknowledging the receipt of your application; if you do not receive an acknowledgement within 48 hours, please email the RFP points of contact above to confirm receipt.

Proposal – Required Submissions

In order to be considered for selection, submit the completed response table (Appendix C) (font size > 11pt, 1 inch margins, response table must not exceed 6 pages) and attach a letter of support from any collaborating laboratories.

Include a completed response table/Appendix C.

Include a completed and signed copy of Appendix B as an attachment.

If Applicable: Include a letter of support from any collaborating laboratories.

Additional Information and Deadlines for Application Submission

Applicants must direct all questions to Anne Gaynor at anne.gaynor@aphl.org. APHL will post questions received from interested PHLs, together with the answers provided by APHL or CDC staff to APHL's procurement website (www.aphl.org/rfp).

Applicants must submit applications to Anne Gaynor at APHL (anne.gaynor@aphl.org; 8515 Georgia Ave Suite 700, Silver Spring, MD, 20910; telephone: 240-485-2739; fax: 240-485-2700).

APHL will hold an optional teleconference on Thursday July 11, 2019 at 3:00pm ET. The purpose of this call will be to provide a brief overview of the project and to allow potential applicants to ask CDC and APHL questions. Please come with questions prepared.

Teleconference Call-in Information is below, or please contact anne.gaynor@aphl.org or infectious.diseases@aphl.org no later than 12:00pm ET on Thursday July 11, 2019 to be sent the calendar invitation.

Join Zoom Meeting
https://aphl.zoom.us/j/187003737

Call-in Information
+1-646-876-9923US OR
+1-669-900-6833US

Meeting ID 187 003 737

APHL must receive applications, attention Anne Gaynor by close of business (5:00pm ET) August 8, 2019. Either electronic or physical submission is acceptable. APHL will send an email acknowledging the receipt of each application; if you do not receive an acknowledgement within 48 hours, call 240-485-2739 to confirm receipt.

Materials

The Official RFP Document will provide detailed information in regards to this request, please read it on its entirety. Additionally, make sure to download Appendix C and include it on your application packet.

Feel free to contact Anne Gaynor at anne.gaynor@aphl.org with any questions.

Questions and Answers

General Questions

Has the study protocol been approved by CDC IRB?

We serve as a reference laboratory for all TB testing in our state. Do we need a letter of support from our TB Control Program?

Is there any issue with us un-linking sample identifiers from the LIMS system?

Samples

Would we need to have 32 positive MTBC cultures that were received by our jurisdiction(s) within the project period?

Would we be able to use cultures that were collected before the start of this contract? If so, how far back can we go in terms of original collection dates?

Should isolates that have been sent for genotyping not be included in the study?

What is the maximum number of samples we should include in our project proposal?

Can we include isolates that were received on other media types (e.g. Lowenstein-Jensen slant, BacT/Alert MP bottles, Versa-Trek Myco bottles) and then using some of that specimen to inoculate new MGIT tubes?

Can we spike MGIT broths with growth from LJ?

Can primary diagnostic VersaTREK positive MTBC cultures be used in lieu of MGIT?

Should we try to include primary diagnostic cultures from suspected or known drug resistance specimens?

Are you only looking for respiratory specimens?

Can we use samples that are known to contain human cells?

Is there a preference for identification method for MTBC?

DNA Extraction and Sequencing

Are multiple extractions from the same primary diagnostic culture required?

Can samples be batched for extraction? If they are batched should the same process be used throughout the project?

Can you confirm that we are sequencing everything in the primary diagnostic culture without targeted amplification?

Has CDC performed testing to assure that DNA prepared using their DNA extraction protocol is noninfectious?

Is there a preference for which library preparation kit to use?

Is there a sequencing protocol available? Are there any specific modifications from the PulseNET protocol?

Are dedicated runs/flowcells required for this project?

What are the requirements for sequence quality? Is there an optimal depth of coverage?

Compensation

The RFP indicates participants will receive an initial award of at least $4000 plus $250 per specimen. Are these additive? If a laboratory tests and reports 32 valid results, would they expect a total of $12000?

Are sites only compensated for samples that meet the minimum read requirements (500,000 reads/sample)?

Bioinformatics and Reporting

What reports will come back to the submitting labs after CDC has performed analysis of the submitted sequences?

Is CDC planning to share the bioinformatics pipelines with the sites so they can perform their own analysis?

If the specimen was PZA monoresistance will the site get any results back on resistance?