Microbiologic Aspects of Processing and Identification of Clinically Relevant NTM [17, 53, 54]
| Assay Technique . | Key Aspect(s) . | Disadvantage . | Advantage . |
|---|---|---|---|
| Decontamination | Critical for all non-sterile sites to reduce contamination and increase yield of mycobacterial recovery | Reduces viability of NTM | |
| N-acetyl-l-cysteine, NaOH, oxalic acid (NALC-NaOH-OxA) | Reduces viability of NTM Optimal recovery when used with the MOD9 liquid media | ||
| Chlorhexidine | Advantageous in cystic fibrosis sputum samples as Pseudomonas is often resistant to (NALC-NaOH-OxA) | ||
| Smear (eg, Kinyon, Ziehl-Neelsen) | Gold standard with culture Indicates presence of Mycobacterial spp. Bleach treatment and concentrating sample may improve sensitivity | Limited sensitivity Does not provide species identification | Rapid detection of Mycobacterium spp. |
| Culture | Gold standard with smear Bodily fluids preferred over swabs Both liquid and solid media should be planted | Long duration of time required for growth and identification | More sensitive than other assays |
| Liquid culture | Typically set up in commercial continuous detection systems | Higher risk of bacterial contamination Can take up to 6 weeks for results | Shorter time to detection compared to solid media |
| Solid culture(egg vs agar-based methods) | Provides pure growth from isolate to facilitate species identification and susceptibility testing | Slower time to detection Takes up to 8 weeks | Provides semi-quantitative measures Selective agar-based media available for rapid-growing NTM |
| Conventional phenotypic identification | Identification based on growth rate, colony morphology, pigment, and biochemical testing | Requires solid media growth Takes weeks of incubation May not distinguish all species of NTM Not reliable and no longer recommended | |
| Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) | Method of rapid identification of NTM Requires pure growth of isolate on solid media | Identifies most, but not all, NTM species Identification may be limited by spectra database Unable to distinguish closely related NTM | Simpler than nucleic acid amplification techniques Low cost Rapid turnover |
| Nucleic Acid Hybridization Probe | Rapid identification of select NTM | Limited NTM isolates identified Discontinued by manufacturers Limited sensitivity as no amplification used | Rapid, cheap Easy to use |
| Nucleic Acid Amplification Techniques (NAAT) | Faster than conventional identification methods | Limited sensitivity Limited spectrum of resistant testing available | May be used for rapid ID and resistance testing |
| Line Probe Assays | Reverse hybridization assay involving amplification of different mycobacterial targets and subsequent identification of specific amplicon | Labor intensive Not FDA approved Limited NTM identified | Can provide rapid identification Can identify resistant markers Labor intensive |
| PCR-DNA based Sequencing | Whole genome sequencing or Sanger sequencing of conserved genes (eg, 16s rRNA, and hsp65) | Dependent on sequence database High cost and complexity (usually reference lab) Limited sensitivity depending on sample type Unable to detect phenotypic resistance Variable performance | Faster than standard culture methods New species can be identified Can detect resistance genotypes (eg, rpoB) |
| Assay Technique . | Key Aspect(s) . | Disadvantage . | Advantage . |
|---|---|---|---|
| Decontamination | Critical for all non-sterile sites to reduce contamination and increase yield of mycobacterial recovery | Reduces viability of NTM | |
| N-acetyl-l-cysteine, NaOH, oxalic acid (NALC-NaOH-OxA) | Reduces viability of NTM Optimal recovery when used with the MOD9 liquid media | ||
| Chlorhexidine | Advantageous in cystic fibrosis sputum samples as Pseudomonas is often resistant to (NALC-NaOH-OxA) | ||
| Smear (eg, Kinyon, Ziehl-Neelsen) | Gold standard with culture Indicates presence of Mycobacterial spp. Bleach treatment and concentrating sample may improve sensitivity | Limited sensitivity Does not provide species identification | Rapid detection of Mycobacterium spp. |
| Culture | Gold standard with smear Bodily fluids preferred over swabs Both liquid and solid media should be planted | Long duration of time required for growth and identification | More sensitive than other assays |
| Liquid culture | Typically set up in commercial continuous detection systems | Higher risk of bacterial contamination Can take up to 6 weeks for results | Shorter time to detection compared to solid media |
| Solid culture(egg vs agar-based methods) | Provides pure growth from isolate to facilitate species identification and susceptibility testing | Slower time to detection Takes up to 8 weeks | Provides semi-quantitative measures Selective agar-based media available for rapid-growing NTM |
| Conventional phenotypic identification | Identification based on growth rate, colony morphology, pigment, and biochemical testing | Requires solid media growth Takes weeks of incubation May not distinguish all species of NTM Not reliable and no longer recommended | |
| Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) | Method of rapid identification of NTM Requires pure growth of isolate on solid media | Identifies most, but not all, NTM species Identification may be limited by spectra database Unable to distinguish closely related NTM | Simpler than nucleic acid amplification techniques Low cost Rapid turnover |
| Nucleic Acid Hybridization Probe | Rapid identification of select NTM | Limited NTM isolates identified Discontinued by manufacturers Limited sensitivity as no amplification used | Rapid, cheap Easy to use |
| Nucleic Acid Amplification Techniques (NAAT) | Faster than conventional identification methods | Limited sensitivity Limited spectrum of resistant testing available | May be used for rapid ID and resistance testing |
| Line Probe Assays | Reverse hybridization assay involving amplification of different mycobacterial targets and subsequent identification of specific amplicon | Labor intensive Not FDA approved Limited NTM identified | Can provide rapid identification Can identify resistant markers Labor intensive |
| PCR-DNA based Sequencing | Whole genome sequencing or Sanger sequencing of conserved genes (eg, 16s rRNA, and hsp65) | Dependent on sequence database High cost and complexity (usually reference lab) Limited sensitivity depending on sample type Unable to detect phenotypic resistance Variable performance | Faster than standard culture methods New species can be identified Can detect resistance genotypes (eg, rpoB) |
Microbiologic Aspects of Processing and Identification of Clinically Relevant NTM [17, 53, 54]
| Assay Technique . | Key Aspect(s) . | Disadvantage . | Advantage . |
|---|---|---|---|
| Decontamination | Critical for all non-sterile sites to reduce contamination and increase yield of mycobacterial recovery | Reduces viability of NTM | |
| N-acetyl-l-cysteine, NaOH, oxalic acid (NALC-NaOH-OxA) | Reduces viability of NTM Optimal recovery when used with the MOD9 liquid media | ||
| Chlorhexidine | Advantageous in cystic fibrosis sputum samples as Pseudomonas is often resistant to (NALC-NaOH-OxA) | ||
| Smear (eg, Kinyon, Ziehl-Neelsen) | Gold standard with culture Indicates presence of Mycobacterial spp. Bleach treatment and concentrating sample may improve sensitivity | Limited sensitivity Does not provide species identification | Rapid detection of Mycobacterium spp. |
| Culture | Gold standard with smear Bodily fluids preferred over swabs Both liquid and solid media should be planted | Long duration of time required for growth and identification | More sensitive than other assays |
| Liquid culture | Typically set up in commercial continuous detection systems | Higher risk of bacterial contamination Can take up to 6 weeks for results | Shorter time to detection compared to solid media |
| Solid culture(egg vs agar-based methods) | Provides pure growth from isolate to facilitate species identification and susceptibility testing | Slower time to detection Takes up to 8 weeks | Provides semi-quantitative measures Selective agar-based media available for rapid-growing NTM |
| Conventional phenotypic identification | Identification based on growth rate, colony morphology, pigment, and biochemical testing | Requires solid media growth Takes weeks of incubation May not distinguish all species of NTM Not reliable and no longer recommended | |
| Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) | Method of rapid identification of NTM Requires pure growth of isolate on solid media | Identifies most, but not all, NTM species Identification may be limited by spectra database Unable to distinguish closely related NTM | Simpler than nucleic acid amplification techniques Low cost Rapid turnover |
| Nucleic Acid Hybridization Probe | Rapid identification of select NTM | Limited NTM isolates identified Discontinued by manufacturers Limited sensitivity as no amplification used | Rapid, cheap Easy to use |
| Nucleic Acid Amplification Techniques (NAAT) | Faster than conventional identification methods | Limited sensitivity Limited spectrum of resistant testing available | May be used for rapid ID and resistance testing |
| Line Probe Assays | Reverse hybridization assay involving amplification of different mycobacterial targets and subsequent identification of specific amplicon | Labor intensive Not FDA approved Limited NTM identified | Can provide rapid identification Can identify resistant markers Labor intensive |
| PCR-DNA based Sequencing | Whole genome sequencing or Sanger sequencing of conserved genes (eg, 16s rRNA, and hsp65) | Dependent on sequence database High cost and complexity (usually reference lab) Limited sensitivity depending on sample type Unable to detect phenotypic resistance Variable performance | Faster than standard culture methods New species can be identified Can detect resistance genotypes (eg, rpoB) |
| Assay Technique . | Key Aspect(s) . | Disadvantage . | Advantage . |
|---|---|---|---|
| Decontamination | Critical for all non-sterile sites to reduce contamination and increase yield of mycobacterial recovery | Reduces viability of NTM | |
| N-acetyl-l-cysteine, NaOH, oxalic acid (NALC-NaOH-OxA) | Reduces viability of NTM Optimal recovery when used with the MOD9 liquid media | ||
| Chlorhexidine | Advantageous in cystic fibrosis sputum samples as Pseudomonas is often resistant to (NALC-NaOH-OxA) | ||
| Smear (eg, Kinyon, Ziehl-Neelsen) | Gold standard with culture Indicates presence of Mycobacterial spp. Bleach treatment and concentrating sample may improve sensitivity | Limited sensitivity Does not provide species identification | Rapid detection of Mycobacterium spp. |
| Culture | Gold standard with smear Bodily fluids preferred over swabs Both liquid and solid media should be planted | Long duration of time required for growth and identification | More sensitive than other assays |
| Liquid culture | Typically set up in commercial continuous detection systems | Higher risk of bacterial contamination Can take up to 6 weeks for results | Shorter time to detection compared to solid media |
| Solid culture(egg vs agar-based methods) | Provides pure growth from isolate to facilitate species identification and susceptibility testing | Slower time to detection Takes up to 8 weeks | Provides semi-quantitative measures Selective agar-based media available for rapid-growing NTM |
| Conventional phenotypic identification | Identification based on growth rate, colony morphology, pigment, and biochemical testing | Requires solid media growth Takes weeks of incubation May not distinguish all species of NTM Not reliable and no longer recommended | |
| Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) | Method of rapid identification of NTM Requires pure growth of isolate on solid media | Identifies most, but not all, NTM species Identification may be limited by spectra database Unable to distinguish closely related NTM | Simpler than nucleic acid amplification techniques Low cost Rapid turnover |
| Nucleic Acid Hybridization Probe | Rapid identification of select NTM | Limited NTM isolates identified Discontinued by manufacturers Limited sensitivity as no amplification used | Rapid, cheap Easy to use |
| Nucleic Acid Amplification Techniques (NAAT) | Faster than conventional identification methods | Limited sensitivity Limited spectrum of resistant testing available | May be used for rapid ID and resistance testing |
| Line Probe Assays | Reverse hybridization assay involving amplification of different mycobacterial targets and subsequent identification of specific amplicon | Labor intensive Not FDA approved Limited NTM identified | Can provide rapid identification Can identify resistant markers Labor intensive |
| PCR-DNA based Sequencing | Whole genome sequencing or Sanger sequencing of conserved genes (eg, 16s rRNA, and hsp65) | Dependent on sequence database High cost and complexity (usually reference lab) Limited sensitivity depending on sample type Unable to detect phenotypic resistance Variable performance | Faster than standard culture methods New species can be identified Can detect resistance genotypes (eg, rpoB) |
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