Alternatively, significant efforts have been invested in the
development of molecular biology-based assays to identify and
enumerate mycobacteria in environmental samples, including
the detection of mycobacteria with antibodies [16–18], fluorescence
in situ hybridization (FISH) targeting 16S ribosomal
ribonucleic acid (16S rRNA) [16,19–22], and fatty acid methyl
ester (FAME) analysis [23]. These methods show promise for
identifying mycobacteria because they are sensitive, specific,
and rapid. However, molecular biology-based techniques often
lack the ability to distinguish between living and dead organisms,
do not generate cultures that may be assayed subsequently
for additional phenotypic traits (e.g., including antibiotic sensitivity),
and are yet to be integrated into a user-friendly format.
These drawbacks have caused cultivation to remain the primary
means of screening for mycobacteria in clinical and environmental
samples.