Target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA

Enrique Zozaya-Valdés, Jessica L. Porter, John Coventry, Janet A.M. Fyfe, Glen P. Carter, Anders Gonçalves Da Silva, Mark B Schultz, Torsten Seemann, Paul D.R. Johnson, Andrew J. Stewardson, Ivan Bastian, Sally A. Roberts, Benjamin P. Howden, Deborah A. Williamson, Timothy P. Stinear

Research output: Contribution to journalArticleResearchpeer-review

8 Citations (Scopus)

Abstract

Mycobacterium chimaera is an opportunistic environmental mycobacterium belonging to the Mycobacterium avium-M. intracellulare complex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasive M. chimaera infections following cardiac surgery. Investigations suggest worldwide spread of a specific M. chimaera clone, associated with contaminated hospital heater-cooler units used during the surgery. Given the global dissemination of this clone, its potential to cause invasive disease, and the laboriousness of current culture-based diagnostic methods, there is a pressing need to develop rapid and accurate diagnostic assays specific for M. chimaera. Here, we assessed 354 mycobacterial genome sequences and confirmed that M. chimaera is a phylogenetically coherent group. In silico comparisons indicated six DNA regions present only in M. chimaera. We targeted one of these regions and developed a TaqMan quantitative PCR (qPCR) assay for M. chimaera with a detection limit of 100 CFU/ml in whole blood spiked with bacteria. In vitro screening against DNA extracted from 40 other mycobacterial species and 22 bacterial species from 21 diverse genera confirmed the in silico-predicted specificity for M. chimaera. Screening 33 water samples from heater-cooler units with this assay highlighted the increased sensitivity of PCR compared to culture, with 15 of 23 culture-negative samples positive by M. chimaera qPCR. We have thus developed a robust molecular assay that can be readily and rapidly deployed to screen clinical and environmental specimens for M. chimaera.

Original languageEnglish
Pages (from-to)1847-1856
Number of pages10
JournalJournal of Clinical Microbiology
Volume55
Issue number6
DOIs
Publication statusPublished - 1 Jun 2017
Externally publishedYes

Keywords

  • Diagnostics
  • Genomics
  • Infectious disease
  • Mycobacterium

Cite this

Zozaya-Valdés, E., Porter, J. L., Coventry, J., Fyfe, J. A. M., Carter, G. P., Da Silva, A. G., Schultz, M. B., Seemann, T., Johnson, P. D. R., Stewardson, A. J., Bastian, I., Roberts, S. A., Howden, B. P., Williamson, D. A., & Stinear, T. P. (2017). Target-specific assay for rapid and quantitative detection of Mycobacterium chimaera DNA. Journal of Clinical Microbiology, 55(6), 1847-1856. https://doi.org/10.1128/JCM.00197-17