Dear Colleague Letters

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Rapid Testing for Fluoroquinolone (FQ) Resistance

May 22, 2023

Dear Colleagues:

In response to reported drug shortages and to support programmatic implementation of the alternate 4-month rifapentine-moxifloxacin (RPT-MOX) regimen, CDC’s Division of Tuberculosis Elimination/ Laboratory Branch will implement rapid testing for fluoroquinolone (FQ) resistance beginning Wednesday, May 24, 2023.

  • Acceptable samples include nucleic-acid amplification test-positive sediments and Mycobacterium tuberculosis isolates with a strong preference for submission of isolates given that sediments with low bacterial burden are less likely to be successfully tested.
  • Samples received for rapid FQ testing will only be assessed by CLIA-compliant molecular methods. The sequencing panel used will also include examination of genetic loci associated with resistance to rifampin, isoniazid, and pyrazinamide.
  • Given unknowns regarding the potential volume of requests for rapid FQ testing and the need to assure sufficient resources to meet testing needs, phenotypic drug susceptibility testing (DST) will not generally be performed.
    • Samples with detected reportable mutations in genetic loci associated with rifampin and FQ resistance will be reflexed for the full Molecular Detection of Drug Resistance (MDDR) testing panel, along with concurrent growth-based DST.
    • To ensure compliance with the laboratory’s CLIA acceptance criteria, submissions will be subject to the same preapproval process as MDDR.
      • To request rapid FQ testing, please indicate “rapid FQ testing needed” in Section 3: Submission Criteria under “Other” in the MDDR Request Form and indicate if the request is due to drug shortages or use of the alternate 4-month RPT-MOX regimen. Providing this information is critical to ensure appropriate laboratory workflow.
      • Submitting laboratories should use test order number 10191 (MycobacteriumTB Complex – Special Study) on the CDC Test Requisition Form (50.34).

Routine MDDR testing using our full panel of genetic loci remains available for cases where drug resistance is suspected or known.

If you have any questions regarding CDC’s services, please feel free to reach out to or Please refer to the MDDR User Guide for additional submission requirements. Depending on capacity and resources, laboratories are encouraged to explore implementation of in-house testing for FQs.

Public health laboratories submitting samples to the DST Reference Center at the California Microbial Diseases Laboratory (MDL) should continue to use that mechanism. For questions related to testing at the DST Reference Center at MDL, please reach out to

Kind regards,

Angela Starks
Chief, Laboratory Branch
Division of Tuberculosis Elimination
Centers for Disease Control and Prevention