These specimens can contain Pseudomonas aeruginosa, Staphylococcus aureus, and other microbes [8, 17–22]. P. aeruginosa is present
in 50–70% of the clinical CF specimens, which poses a challenge
because it can survive NALC–NaOH decontamination and contaminates 35–70% of subsequent cultures. For more details, see the
reference of Forbes et al. [15].
Since enhanced decontamination protocols may significantly
reduce NTM viability in samples [18], consensus guidelines recommend a two-step approach to sample processing [17, 18, 21]. The
majority of U.S. and European clinical microbiology laboratories
currently use a NALC–NaOH decontamination step prior to mycobacterial culture [17, 21, 23, 24]. This decontamination step
results in the killing of up to one-third of mycobacteria present in
a clinical specimen [25]. The addition of a second decontamination
step using oxalic acid permits the recovery of NTM from persistently contaminated samples, at the expense of further reducing the
sensitivity of the culture for detecting low concentrations of mycobacteria [8, 22]. Alternatively, the use of 1% chlorhexidine as a first
step may improve the recovery of mycobacteria, but at the expense
of higher rates of residual sample contamination [20]. As chlorhexidine needs to be neutralized with lecithin, the use of chlorhexidine
negatively affects the performance of the MGIT-automated liquid
culture system, as lecithin generates random fluorescence reactions
from the MGIT system sensor [20]. More recently, selective RGM
medium for the recovery of NTM has been developed [26], and in
single-center trials has been shown to enhance recovery of
M. abscessus complex from clinical samples, while virtually eliminating contamination by co-pathogens without the need for specimen
decontamination [27]. Others have reported that SGM, which are
found frequently in this population, can be recovered with RGM
medium when incubated for 28 days as a screening culture for all
NTM in CF patients [28]. It is likely that with further modification
and validation, this method will eventually be implemented for
widespread clinical use.
1.10 Biosafety
and Biosecurity
Concerns
for Mycobacterium
tuberculosis Complex
Species within the historically termed “Mycobacterium tuberculosis
complex” [9], which include M. tuberculosis var. tuberculosis,
M. tuberculosis var. bovis including M. bovis BCG, M. tuberculosis
var. africanum, and M. tuberculosis var. microti, can cause tuberculosis in humans. M. bovis BCG is used to treat certain types of
bladder cancer, and as a complication can cause BCG-itis
[29]. More recently identified organisms like M. tuberculosis var.
caprae and M. tuberculosis var. pinnipedii have been isolated from
goats and seals, respectively [30, 31].
When working with mycobacterial organisms, follow all institutional biosafety and biosecurity regulations for handling of cultures and contaminated waste, decontamination procedures, and
requirements for personal protective equipment (PPE). As outlined
10
Elizabeth Wallace et al.
in 50–70% of the clinical CF specimens, which poses a challenge
because it can survive NALC–NaOH decontamination and contaminates 35–70% of subsequent cultures. For more details, see the
reference of Forbes et al. [15].
Since enhanced decontamination protocols may significantly
reduce NTM viability in samples [18], consensus guidelines recommend a two-step approach to sample processing [17, 18, 21]. The
majority of U.S. and European clinical microbiology laboratories
currently use a NALC–NaOH decontamination step prior to mycobacterial culture [17, 21, 23, 24]. This decontamination step
results in the killing of up to one-third of mycobacteria present in
a clinical specimen [25]. The addition of a second decontamination
step using oxalic acid permits the recovery of NTM from persistently contaminated samples, at the expense of further reducing the
sensitivity of the culture for detecting low concentrations of mycobacteria [8, 22]. Alternatively, the use of 1% chlorhexidine as a first
step may improve the recovery of mycobacteria, but at the expense
of higher rates of residual sample contamination [20]. As chlorhexidine needs to be neutralized with lecithin, the use of chlorhexidine
negatively affects the performance of the MGIT-automated liquid
culture system, as lecithin generates random fluorescence reactions
from the MGIT system sensor [20]. More recently, selective RGM
medium for the recovery of NTM has been developed [26], and in
single-center trials has been shown to enhance recovery of
M. abscessus complex from clinical samples, while virtually eliminating contamination by co-pathogens without the need for specimen
decontamination [27]. Others have reported that SGM, which are
found frequently in this population, can be recovered with RGM
medium when incubated for 28 days as a screening culture for all
NTM in CF patients [28]. It is likely that with further modification
and validation, this method will eventually be implemented for
widespread clinical use.
1.10 Biosafety
and Biosecurity
Concerns
for Mycobacterium
tuberculosis Complex
Species within the historically termed “Mycobacterium tuberculosis
complex” [9], which include M. tuberculosis var. tuberculosis,
M. tuberculosis var. bovis including M. bovis BCG, M. tuberculosis
var. africanum, and M. tuberculosis var. microti, can cause tuberculosis in humans. M. bovis BCG is used to treat certain types of
bladder cancer, and as a complication can cause BCG-itis
[29]. More recently identified organisms like M. tuberculosis var.
caprae and M. tuberculosis var. pinnipedii have been isolated from
goats and seals, respectively [30, 31].
When working with mycobacterial organisms, follow all institutional biosafety and biosecurity regulations for handling of cultures and contaminated waste, decontamination procedures, and
requirements for personal protective equipment (PPE). As outlined
10
Elizabeth Wallace et al.