Atypical Mycobacterial Diseases Workup

Updated: Nov 12, 2019
  • Author: Erisa Alia, MD; Chief Editor: Dirk M Elston, MD  more...
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Approach Considerations

Diagnosis of infections due to atypical mycobacteria differs depending on the site of infection. Patients with nontuberculous mycobacteria (NTM) infections usually present with an indolent or subacute course. Fever is the most common symptom reported. The isolation of NTM remains a challenge for clinicians.

Diagnostic criteria for pulmonary NTM infection are established in the guidelines published by American Thoracic Society and involve clinical, radiographic, and microbiologic criteria. The three components are equally important and all must be met to establish the diagnosis. The minimum evaluation of a patient suspected of NTM lung disease should include (1) a chest radiograph or, in the absence of cavitation, chest high-resolution CT scan; (2) three or more sputum specimens for acid-fast bacilli analysis; and (3) exclusion of other disorders, such as tuberculosis. [4]

If lymphadenitis due to NTM is suspected acid-fast stain and culture of surgically excised tissue must be ordered in order to rule out other organisms or typical mycobacteria as causative agents.

Skin and soft-tissue infection (SSTI) presumptive diagnosis is made based on signs and symptoms, clinical presentation, and history of exposure and geographic location. It requires a low threshold of clinical suspicion given the broad spectrum of potential clinical presentations. Definitive diagnosis is confirmed by tissue culture of biopsy material and real-time polymerase chain reaction detection, which enables a more rapid diagnosis.

Disseminated disease diagnosis relies on isolation of the offending organism from normally sterile sites such as blood, bone marrow, or affected lymph nodes.


Laboratory Studies

Diagnosis of infection due to nontuberculous mycobacteria (NTB) is not easy, as it must be distinguished from colonization or contamination by other NTB. Acid-fast bacilli staining and culture for mycobacteria remain the core diagnostic processes.


The optimal way to diagnose atypical mycobacteria is by performing a culture of a tissue specimen (skin, lymph node, blood). This should be performed at multiple temperatures (28°C [82.4°F], 30°C [86°F], 31°C [87.8°F], 35°C [95°F], 37°C [98.6°F], and 42°C [107.6°F]) to ensure that the cultures grow out all possible pathogens. Specimens should be cultured on both liquid and solid media.

Smear microscopy

Since the culture needs to be incubated for a long time, sometimes weeks, smear microscopy remains an important technique for preliminary results.

The recommended staining method for clinical specimens for acid-fast bacilli is the fluorochrome technique, although the Ziehl-Neelsen staining method remains still an acceptable option. It is important to note that acid-fast bacilli staining cannot differentiate between M tuberculosis and NTMs.

High-performance liquid chromatography for NTM identification

This method analyzes an organism’s mycolic acids (fatty acids found in the cell walls of mycobacteria) and is highly species specific. [80]


Imaging Studies

In 1999, Erasmus et al [81] noted that the radiologic manifestations of pulmonary atypical mycobacteria infection are protean and include consolidation, cavitation, fibrosis, nodules, bronchiectasis, and adenopathy. Pulmonary atypical mycobacteria infection has five distinct clinicoradiologic manifestations: (1) classic infection, (2) nonclassic infection, (3) nodules in patients who are asymptomatic, (4) infection in patients with achalasia, and (5) infection in patients who are immunocompromised. Although classic atypical mycobacteria infection may be indistinguishable from active tuberculosis, it is usually more indolent. The characteristic radiologic features of nonclassic atypical mycobacteria infection include bronchiectasis and centrilobular nodules isolated to or most severe in the lingula and the middle lobe. In patients with acquired immunodeficiency syndrome, mediastinal or hilar adenopathy is the most common radiographic finding.


Other Tests

Molecular techniques

Molecular identification of species by using polymerase chain reaction (PCR) restriction fragment length polymorphism analysis, real-time PCR, line probe hybridization, DNA sequencing, and matrix-assisted laser desorption ionization–time of flight spectrometry aid in detecting the diagnosis earlier. [82] Sequencing of the 16S rRNA gene, hsp65, and rpoB allows discrimination at the species and subspecies level. [83]

Purified protein derivative

The purified protein derivative test result is usually negative in infections with atypical mycobacteria.



Biopsy of the skin, involved lymph nodes, and lung can be used to diagnose atypical mycobacteria. The tissue obtained can be used for cultures of the tissue and for histopathologic examination.


Histologic Findings

Histopathologic examination of tissue based on the causative species can reveal tuberculoid, palisading, and sarcoidlike granulomas; a diffuse infiltrate of histiocytic foamy cells; acute and chronic panniculitis; nonspecific chronic inflammation; cutaneous abscesses; suppurative granulomas; and necrotizing folliculitis. Suppurative granulomas are the most characteristic feature in skin biopsy specimens from cutaneous atypical mycobacteria infections. The evolution of the disease and the immunologic status of the host may explain this spectrum of morphologic changes. In Buruli ulcer, mature lesions can show extensive necrosis with destruction. of nerves, appendages, and blood vessels. [10]

Some authorities note severe inflammatory lesions involved with the dermis and the hypodermis; these can have three main histopathologic patterns: (1) granulomatous nodular or diffuse inflammation with mixed granulomas, (2) prevailing abscesses with mild granulomatous reaction, and (3) deep dermal and subcutaneous granulomatous inflammation with no neutrophil component.