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J Clin Pathol. 2018 Feb;71(2):148-153. doi: 10.1136/jclinpath-2016-204128. Epub 2017 Jul 22.

Acid-fast bacterium detection and identification from paraffin-embedded tissues using a PCR-pyrosequencing method.

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Department of Microbiology, Quest Diagnostics Nichols Institute Chantilly, Chantilly, Virginia, USA.



Acid-fast bacterium (AFB) identification from formalin-fixed paraffin-embedded (FFPE) tissues is challenging and may not be readily available to the clinical laboratory. A method to detect and identify AFB from FFPE tissues using PCR and pyrosequencing (PCR-Seq) was developed and evaluated.


The method was validated using spiked cell-clotted paraffin blocks before use with patients' specimens. DNA was extracted from tissue sections, and a 16S rRNA gene fragment was amplified and a signature sequence was produced on a PyroMark ID system. Sequences were aligned to established databases for AFB identification. Additional tissue sections were stained and examined for AFB.


Both sensitivity and specificity were 100% on spiked cell-clotted blocks without cross-reactivity with non-AFB. Of 302 FFPE tissues from patients, 116 (38%) were AFB-stain positive; 83 (72%) of these had AFB identified. The 21 AFB identified included Mycobacterium tuberculosis complex (14 cases), Mycobacterium leprae (3), Mycobacterium genavense (2), Mycobacterium marinum-ulcerans group (3) and 17 other AFB (61). Thirteen cases were AFB-stain indeterminate and 4 were positive by the PCR-Seq method. Of the AFB stain-negative cases, 167 were negative and 6 were positive by PCR-Seq.


The PCR-Seq method provided specific identification of various AFB species or complexes from FFPE tissues.


PCR-sequencing; acid-fast bacterial identification; paraffin-embedded tissue

[Indexed for MEDLINE]

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