Mycobacterium Chelonae Workup

Updated: Jun 07, 2022
  • Author: Mary B Ford, MD; Chief Editor: Michael Stuart Bronze, MD  more...
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Laboratory Studies


Initial laboratory work-up for M chelonae requires sending a sample for acid-fast bacillus (AFB) stain and culture. M chelonae and other NTM cannot be distinguished from one another or MTB on AFB smear, but rapid nucleic acid amplification tests are available to identify MTB from an AFB positive smear. [41]  Mycobacterial organisms are grown on both solid and liquid media. As a RGM, M chelonae growth typically will appear on culture media within 3 to 5 days; it ideally grows at 28C, but between 28C and 35C, which is lower than most other NTM. [5, 15]  


Historically, identification of RGM including M chelonae was based on phenotypic factors including growth rate, pigmentation, and colony morphology. [5]  Phenotypically, the colonies appear smooth, and transparent to cream-colored. [15]  There are a variety of biochemical tests such as iron uptake, nitrate reductase activity, and arylsulfatase reaction that also are used to distinguish RGM – for example, M chelonae exhibits strong arylsulfatase activity at 3 days. [5]  However, given the time consuming nature and often poor reducibility of these tests, identification of RGM via biochemical methods alone no longer is done. [42]  High-performance liquid chromatography (HPLC) of mycobacterial cell wall mycolic acids is a technique used for identification of mycobacterial groups; however, given the inability of HPLC to correctly separate species within RGM groups, it typically is not relied upon as the sole method of identification. [5]

Molecular techniques including DNA probe systems and genetic sequencing are the techniques most commonly used for species level identification of NTM. [42]  With rare exception, identification of mycobacterial species can be accomplished with sequencing of the 16S rRNA gene. However, M chelonae and M abscessus differ by only 4 base pairs in 16S rDNA sequencing, and typically cannot be distinguished using 16S gene sequencing alone unless complete 16S rRNA sequence analysis is performed. [5]  There are additional rRNA genes that often are sequenced in an effort to identify Mycobacterium species, including rpoB and hsp65, the latter of which can be sequenced to differentiate between M abscessus and M chelonae. [6]

Susceptibility testing

Given the difficulty of performing antimicrobial susceptibility testing (AST) on NTM, it generally is accepted that NTM AST should be performed only for clinically significant isolates. [9]  For pulmonary isolates, the accepted criteria for determining a clinically significant isolate were defined by the American Thoracic Society (ATS) and Infectious Disease Society of American (IDSA) joint NTM guidelines. Among NTM species, there is significant variability in antimicrobial susceptibility, and as such if an isolate is felt to be clinically significant, performing AST is critical. M chelonae in particular is one of the most resistant pathogenic RGM. [5]

Susceptibility testing for NTM species is typically performed by broth microdilution, as Agar based tests (including the E-test) have shown inconsistent results. [9, 8]  The Clinical and Laboratory Standards Institute (CLSI) recommends for RGM such as M chelonae that a standard panel for AST should include amikacin, cefoxitin, ciprofloxacin, clarithromycin, doxycycline (or minocycline), imipenem, linezolid, moxifloxacin, and trimethoprim-sulfamethoxazole. For the M chelonae/M immunogenum complex only, the addition of tobramycin susceptibility is recommended. [43]  There are additional antimicrobials that may be tested for, but in the setting of insufficient data to establish MIC breakpoints, these agents are not routinely tested. [43]  Gene sequencing also is routinely performed for RGM species to determine the presence or absence of the erm gene, which confers inducible resistance to macrolides. This gene is notably absent in M chelonae, and these organisms are considered 100% susceptible to macrolides, [44]  although rapid development of macrolide resistance may occur with macrolide monotherapy. [9]  In vitro data suggest that tobramycin is the most active aminoglycoside for M chelonae isolates, and this typically will be the only aminoglycoside reported. [8]  M chelonae isolates are considered 100% susceptible to tobramycin. Other general antimicrobial susceptibilities reported for M chelonae include linezolid (54-90% susceptible), imipenem (40-60% susceptible, the most active of the carbapenems), amikacin (50-70% susceptible), doxycycline (25% susceptible), and ciprofloxacin (20% susceptible). [6, 8]  Of note, susceptibility testing often is done by a reference laboratory only.


Imaging Studies

Imaging studies as appropriate for the site of clinical concern should be performed when evaluating a patient with a suspected or confirmed NTM infection. Diagnosis of NTM pulmonary disease requires radiographic findings that are identified as “nodular or cavitary opacities on chest radiograph or a high-resolution computed tomography (CT) scan that shows bronchiectasis and multiple small nodules.” [2]  Chest radiographs or CT scans also may be performed to monitor response to therapy, although radiographic response may not always correlate with clinical response. [2]  A CT scan or MRI of areas of concern for localized skin and soft tissue or bone infections may be performed to characterize the degree of infection. If there is concern for disseminated infection, a CT of the abdomen and pelvis also may be warranted.


Other Tests

AFB culture, identification, and susceptibility testing are by far the most important tests for diagnosis and treatment of M chelonae infection. In general, clinicians may use laboratory values such as white blood cell count, erythrocyte sedimentation rate (ESR) and c-reactive protein (CRP), to help establish the inflammatory state of a patient felt to have a NTM infection. However, these tests are all non-specific and are not required in the evaluation of M chelonae. Skin testing with NTM specific antigens is neither routinely performed nor recommended.



In general, procedures performed for M chelonae fall into 1 of 2 categories – diagnostic or treatment. Diagnostic procedures may include bronchoscopy with bronchial alveolar lavage (BAL) and biopsy of concerning skin lesions. Surgical procedures fall on a spectrum from incision and drainage of cutaneous lesions to surgical lung resection for patients with localized pulmonary disease, which is rare with M chelonae. [9]  When pulmonary disease does occur secondary to M chelonae, 20% of patients  ultimately will have adjunctive partial pulmonary resection. [39]


Histologic Findings

Histologic examination of tissue often will show granulomatous inflammation and or acid-fast bacilli (AFB). [2]  Hematoxylin and eosin (H&E) staining of biopsy specimens from cutaneous lesions can demonstrate both caseating and non-caseating granulomas and perifollicuitis. Fite stain can be performed to specifically identify AFB. [12]



In general, disease secondary to M chelonae can be considered localized or disseminated. There are no formal staging systems for NTM disease.