Q_and_A_for_Microbial_Analysis_of_FDA_Foods.docx

Questions and Answers for FDA-18-1195170 (Microbial Analysis of FDA Regulated Foods)

1. Do the goals of this RFP differ in any way from previous contracts related to this ongoing effort?

Our previous contract was sampling different foods. It has ended.

1. Are there technical areas that you would like to improve upon based on previous performance?

We have added some new detection methods. Also in case better method is validated by FDA in the future we want to use, we have the following language in the SOW: The appropriateness of non-BAM or AOAC OMA methods or any other method not listed above, for use with any test, shall be determined in consultation with the Project Officer and no method for the analysis of the samples shall be used without the Project Officer’s consent.

1. Is there a need for additional computational research related to the data collected in the scope of this project?

We are satisfied with previous computational results.

1. The Background section of the RFP ended by discussing the importance of whole genome sequencing for surveying pathogens. Yet the procedures are focused on basic PCR based techniques. Is there interest in using WGS in this project?

Yes. We have done WGS in previous contract. We will do it soon again. I already have an work order ready for WGS work.

1. Is there a need or interest in novel detection platforms for these or other microbes? We have developed methods for extracting DNA from crude samples (water or mud) and are currently using this method to test for trace amounts of invasive species DNA. We believe this method would be incredibly effective if adapted for the goals of this project.

We prefer to use FDA or other standard methods if possible. At this stage of the contract, we are not looking for new methods. However, if thing changes, we can consider other methods.

1. Please verify, Cryptosporidium would be tested via FDA-BAM 19a, would be 19b, the updated protocol?

For isolation of both parasitic contaminants, 19a should be the method. For PCR detection of Cyclospora, should follow the updated 19b.

1. For Water testing, is EPA lab accreditation required?

It would be good. But we do not require it.

1. Pricing:

Not all the tests listed in the text of the RFP are included in the pricing table. Do you only want pricing for those tests listed in the table? If you want pricing for the other tests as well should we assume 5000/year volume?

Can we get an estimated breakdown of number of samples requiring each test? Total estimate specifically for Virus, Shigella, Cyclopsora and Cryptosporidium?

Should we list a separate price for varying sample weights per organism(i.e 25g salmonella vs 3 75g salmonella)?

This is an umbrella contract. We have our focus. That’s the major foodborne pathogens and high risk foods, as outlined in the document. However, in case something thing unexpected happens FDA needs to address, we included those in the proposal, too. Therefore, there are more details on our main targets. Others will be worked out when needed.

Yes. You could present different prices for different sample weights.

1. Virus:

Can we use an adapted kit like bioMerieux's ceeram method (same targets as FDA BAM/ISO method) in place of FDA BAM prescribed method. Or follow FDA BAM method but use a different detection instrument (ie., ABI 7500 or bioMerieux's GeneUP open platform) ?

It is possible if we have more information about other validated methods, which are better than the current method.

1. WGS:

What organisms would be sequenced?

What are the expected capacities?

What form does the sequenced data need to be presented? Do they want reports or just raw files (FASTQ/FASTA)?

As I stated earlier, this is an umbrella contract, the actual research work (pathogens, number of samples, etc.) will depend on budget available in the next few years and FDA needs for policy, enforcement and new regulations, outbreaks, etc. All those are uncertain now. The sequenced data should be in the form ready to be submitted to NCBI.

1. Cosmetics:

On the cosmetic samples do you want USP methods used?

Does the lab need to be registered with the FDA?

Is there an expectation the lab perfroms suitability testing prior to routine testing or has this work already been performed?

The methods listed in this document will be used for this project. If they do not work in some special cases, COR and FDA experts will choose other effective methods.

Lab should verify all methods before officially testing samples.

1. Microbial:

Is there a preferred method/instrumentation (BAX, ELISA, etc)?

For the 375G analytical weight, would a rapid method be acceptable with internal validation data to support the tesing? Specifically, there are few if any AOAC OMA methods with 375g food category data.

For non-O157:H7 would Top 6 Rapid Methods be accepted with internal validation data to support the testing? Specifically, commercial methods look for the Big 6, but do not have AOAC OMA or AOAC RI for 375G produce. However, several kit manufactures of Top 6 methods have completed validations studies for produce.

For cultural isolation of Non-O157 STEC, would the USDA STEC Top 6 Cultural method be acceptable? For Vibrio and Crono, would the cultural method of FDA-BAM be sufficient (no PCR screening)? Where pathogen enumeration is required, is the expecting to run MPN? Direct Plating? Both? For the water tesing, given the limited time between collection and testing (24-31h), how many locations would be required to have this capability and in what geographical area would they need to be located? General: If we are not planning on subcontracting any of the work is a subcontracting plan still required? Please let me know if you need clarification on any of these questions.

In this age, technology is changing and advancing every day. The methods and related instruments presented in this document will be used for this project. If they cannot meet the requirement for unique situations, other methods could be used, with the authorization of COR and related FDA experts, based on new data.

Direct plating could be used for enumeration of pathogens. However, based on our experience, MPN is likely the method to be used. Microbial level in majority of the samples are really low. Direct plating could not do the job.

For Ag water testing, the locations for sample collection will be determined when individual task order is created. It could be domestic or abroad, depending the agency’s need at that time. Budget availability could also affect the plan.

1. Are the methods listed within the RFP methods that must be followed or are other approved methods also considered valid for the RFP?

The contract COR can authorize the use of other methods if needed.