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.
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 12-23 – Proposal review completed
August 26-27 – If needed, follow-up interviews and updated proposals due
August 30, 2019 – Final review completed and awardees selected
September 16, 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).
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
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
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 firstname.lastname@example.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 (email@example.com; 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
no later than 12:00pm ET on Thursday July 11, 2019 to be sent the calendar invitation.
Join Zoom Meeting
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.
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 firstname.lastname@example.org with any questions.
Questions and Answers
Has the study protocol been approved by CDC IRB?
A: CDC submitted the protocol for review and it was deemed a non-human research. APHL can provide the documentation upon request.
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?
A: A letter is not required for this RFP from TB Control. However, we do encourage you to discuss with TB Control Program so they are aware of the activities being undertaken in the laboratory.
Is there any issue with us un-linking sample identifiers from the LIMS system?
A: We don’t anticipate that this will be an issue. We would want to ensure that the primary positive MGIT culture can be linked to the DST control tube (from the same patient). It is not needed to link back to any other patient information or to the genotyping number.
Would we need to have 32 positive MTBC cultures that were received by our jurisdiction(s) within the project period?
A: Yes. Up to 3 primary cultures from a single patient may be used so samples must come from a minimum of 10 unique patients and a minimum of 32 MTBC positive primary diagnostic cultures.
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?
A: No. Primary diagnostic cultures (MGIT or VersaTREK) that are positive for MTBC should be used starting at the beginning of the project period, ideally testing in near real-time when the sample becomes positive.
Should isolates that have been sent for genotyping not be included in the study?
A: There is no need to exclude primary diagnostic cultures that are sent for genotyping. Samples collected after the start of the contract period are allowed and isolates should still be sent to MI for genotyping.
What is the maximum number of samples we should include in our project proposal?
A: The maximum number of samples that could be awarded for any given site is 100 which could be a combination of primary diagnostic culture and the paired no drug growth control. We know not every primary diagnostic culture will have an appropriately suitable no drug growth control so there could be more primary diagnostic cultures than no drug growth control. The exact award amounts will be determined after evaluation of the applications, dependent on the number of sites selected and the total amount of funding available. So, it is possible that even if you propose 100 you may not be awarded that full amount.
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?
A: No, primary diagnostic cultures positive for MTBC should be used. However, primary diagnostic cultures from VersaTREK, BacT/Alert MP are allowed as well as MGIT.
Can we spike MGIT broths with growth from LJ?
A: No, we are requesting primary diagnostic cultures that are MTBC positive for this project.
Can primary diagnostic VersaTREK positive MTBC cultures be used in lieu of MGIT?
A: Yes, either MGIT or VersaTREK can be used.
Should we try to include primary diagnostic cultures from suspected or known drug resistance specimens?
A: It is not necessary to include any cultures with any particular drug susceptibility/resistance profiles.
Are you only looking for respiratory specimens?
A: We will accept any source type. We will add a place on the data collection sheet to notate whether it is pulmonary or extra-pulmonary.
Can we use samples that are known to contain human cells?
A: Yes, as long as it is a primary diagnostic culture (MGIT or VersaTREK) and MTBC positive it is acceptable. We anticipate that samples will contain human cells/DNA.
Is there a preference for identification method for MTBC?
A: No. The data collection sheet will capture this information.
DNA Extraction and Sequencing
Are multiple extractions from the same primary diagnostic culture required?
A: No. At CDC they are able to extract sufficient quantity and quality of DNA using about 1mL of the liquid MGIT and using Nextera XT library prep to meet the data quality metrics.
Can samples be batched for extraction? If they are batched should the same process be used throughout the project?
A: We prefer to have samples extracted in real-time as it improves DNA quality. However, applicants may do whatever works for their workflow, including batching. The data collection sheet will capture how many days after the culture was positive that the DNA was extracted. Batching or not does not need to be consistent as long as it is documented.
Can you confirm that we are sequencing everything in the primary diagnostic culture without targeted amplification?
A: Correct. No targeted amplification occurs—the primary diagnostic culture should be extracted and whole genome sequencing performed.
Has CDC performed testing to assure that DNA prepared using their DNA extraction protocol is noninfectious?
A: Yes, the CDC has validated that the protocol depletes viable organisms. However, any laboratory using this protocol or any other extraction protocol must do their own validation. CDC also performs continual validation with each new kit that is opened.
Is there a preference for which library preparation kit to use?
A: Any can be used. There is a slight preference for the NextTerra XT or Nextera FLEX kits.
Is there a sequencing protocol available? Are there any specific modifications from the PulseNET protocol?
A: At this time no specific sequencing protocol being provided. It is expected that laboratories have experience with whole genome sequencing. There are recommendations in Appendix A of the RFP for required metrics. CDC uses a modified PulseNET process which works well.
Are dedicated runs/flowcells required for this project?
A: No, dedicated runs are not required.
What are the requirements for sequence quality? Is there an optimal depth of coverage?
A: The full details are in Appendix A of the RFP—Paired end sequencing with read lengths of at least 150bp and 500,000 reads per specimen are required. There is not an optimal depth of coverage because it depends on the composition of the specimen.
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?
A: All applicants will receive the minimum compensation. The maximum compensation has not been determined at this time as it depends on a number of factors including the number of accepted applications, the total number of samples that will be sequenced and the total amount of funding available.
Are sites only compensated for samples that meet the minimum read requirements (500,000 reads/sample)?
A: Yes. We know that this project comes with some risk so we have included a minimum compensation amount that is not dependent on meeting the minimum read requirements.
Bioinformatics and Reporting
What reports will come back to the submitting labs after CDC has performed analysis of the submitted sequences?
A: There is no plan to provide any reports back to the submitting laboratories in real-time. CDC plans to share aggregate data on the evaluation at the end of the project via a presentation.
Is CDC planning to share the bioinformatics pipelines with the sites so they can perform their own analysis?
A: The pipelines will not be shared at this time.
If the specimen was PZA monoresistance will the site get any results back on resistance?
A: No, CDC will not provide this level of detail. This testing is not being performed in a CLIA-waived setting. If this type of information is required for clinical management the sample should be sent for MDDR. If it’s an academic discussion it can be discussed but is not the goal or intent of the project.