title: Target-Specific Assay for Rapid and Quantitative Detection of Mycobacterium chimaera DNA.
abstract: Mycobacterium chimaerais an opportunistic environmental mycobacterium belonging to theMycobacterium avium-M. intracellularecomplex. Although most commonly associated with pulmonary disease, there has been growing awareness of invasiveM. chimaerainfections following cardiac surgery. Investigations suggest worldwide spread of a specificM. chimaeraclone, 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 forM. chimaeraHere, we assessed 354 mycobacterial genome sequences and confirmed thatM. chimaerais a phylogenetically coherent group.In silicocomparisons indicated six DNA regions present only inM. chimaeraWe targeted one of these regions and developed a TaqMan quantitative PCR (qPCR) assay forM. chimaerawith a detection limit of 100 CFU/ml in whole blood spiked with bacteria.In vitroscreening against DNA extracted from 40 other mycobacterial species and 22 bacterial species from 21 diverse genera confirmed thein silico-predicted specificity forM. chimaeraScreening 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 byM. chimaeraqPCR. We have thus developed a robust molecular assay that can be readily and rapidly deployed to screen clinical and environmental specimens forM. chimaera.
authors.affiliation: Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Enrique
authors.initials: E
authors.lastname: Zozaya-Valdés
authors.affiliation: Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Jessica L
authors.initials: JL
authors.lastname: Porter
authors.affiliation: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: John
authors.initials: J
authors.lastname: Coventry
authors.affiliation: Victorian Infectious Diseases Laboratory, The Doherty Institute for Infection and Immunity, Victoria, Australia.
authors.forename: Janet A M
authors.initials: JAM
authors.lastname: Fyfe
authors.affiliation: Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Glen P
authors.initials: GP
authors.lastname: Carter
authors.affiliation: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Anders
authors.initials: A
authors.lastname: Gonçalves da Silva
authors.affiliation: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Mark B
authors.initials: MB
authors.lastname: Schultz
authors.affiliation: Victorian Life Sciences Computational Initiative, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Torsten
authors.initials: T
authors.lastname: Seemann
authors.affiliation: Austin Health, Heidelberg, Victoria, Australia.
authors.forename: Paul D R
authors.initials: PDR
authors.lastname: Johnson
authors.affiliation: Austin Health, Heidelberg, Victoria, Australia.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Stewardson
authors.affiliation: SA Pathology, Adelaide, South Australia, Australia.
authors.forename: Ivan
authors.initials: I
authors.lastname: Bastian
authors.affiliation: Mycobacterial Laboratory, LabPlus, Auckland, New Zealand.
authors.forename: Sally A
authors.initials: SA
authors.lastname: Roberts
authors.affiliation: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.|Doherty Applied Microbial Genomics, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia.
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Howden
authors.affiliation: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.
authors.forename: Deborah A
authors.initials: DA
authors.lastname: Williamson
authors.affiliation: Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia tstinear@unimelb.edu.au.|Doherty Applied Microbial Genomics, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria, Australia.
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Stinear
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics* / Q000302:isolation & purification*; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009161:Mycobacterium / Q000235:genetics* / Q000302:isolation & purification*; D009164:Mycobacterium Infections / Q000175:diagnosis* / Q000382:microbiology; D016133:Polymerase Chain Reaction / Q000379:methods*; D012680:Sensitivity and Specificity
chemical_list: D004269:DNA, Bacterial
keywords: diagnostics; genomics; infectious disease; mycobacterium