ZSFG AM Pearls 7/19: GeneXpert, MTB, and cording

Thanks Matt and Leslie for giving follow up for a case we discussed in June of a 71M h/o ADPKD s/p CRT who p/w sub-acute abdominal pain, fever, noted to be significantly hypercalcemic. As part of the original work-up, he was found to have significantly elevated 1,25 Vit D and undetectable PTH. Breaking news now: his bone marrow cultures are growing AFB, and a repair of a groin aneurysm was rumored to “look bacterial” intra-op.

Take a look at our previous discussion of this case and pearls on hypercalcemia and etiologies related to high or low PTH: https://ucsfmed.wordpress.com/2016/06/22/zsfg-morning-report-pearls-hypercalcemia-pth-mgus/

Pearls from Lisa Winston in ID report today:

  • In immunocompetent folks with a negative CXR, the chance of having pulmonary TB is LOW
  • In immunocompromised folks with a negative CXR, need to have a high degree of suspicion as they can and often do have culture positive for TB


  • GeneXpert aka Xpert MTB/RIF:
    • Xpert MTB/RIF assay is a nucleic acid amplification (NAA) test
    • It uses a disposable cartridge with the GeneXpert Instrument which is a system for integrated and automated sample preparation, amplification (by rapid, real-time PCR), and detection
    • The test simultaneously detects Mycobacterium tuberculosis complex (MTBC) and resistance to rifampin (RIF) from unprocessed sputum samples in ~2 hours
    • FDA approved for use in SPUTUM samples only

Review of Mycobacteria:


  • M. kansasii is the most TB-like of the NTM
  • Can distinguish TB on micro with presence of cording (see below)
    • Cording is the tendency of TB to grow end to end, giving them a rope or cord-like appearance in micro lab
    • This serpentine growth pattern is due to cord factor (glycolipid) and contributes to the virulence of the organism
    • Picture below from Micro department at University of Colorado Hospital, more info at http://www.microbeworld.org/component/jlibrary/?view=article&id=13355

cording 1

Evernote link: https://www.evernote.com/shard/s354/sh/12a45932-779c-4561-aeb0-45b060ba7dfc/d6da997a45ab1ab6ab5099decc1f6127


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