Case of the Month

October 2013

Helena Rabie, Rabeen Lutchman and Mark Cotton Tygerberg Hospital

A 6-year-old HIV infected boy who previously defaulted antiretroviral therapy, presented with a chronic cough that worsened in the prior 4 weeks. He also complained of increasing shortness of breath and fever for the past 3 weeks.

He had presented to his local clinic in the 3 months prior to admission, and been diagnosed with pulmonary tuberculosis based on symptoms and a suggestive chest radiograph. Sputum smear was negative and culture not requested. At this time his HIV viral load was log 4.64 copies/ml and the CD4 count 2 cells/mm3.

Therapy with rifampicin, isoniazid, pyrazinamide, abacavir, lamivudine, and efavirenz was started at the local clinic.

His mother regularly attended tuberculosis and antiretroviral clinic and on interview, a good understanding of medication routine was noted.

Examination revealed a chronically ill-looking boy with acute, severe respiratory distress requiring supplemental oxygen

His HIV viral load on admission had suppressed and his CD4 count had increased to 210 cells/mm3. Sputum smear was positive for acid fast bacilli.

Question 1: What is the differential diagnosis?

Answer to Q1

The differential diagnosis this child should include the following:

  • Drug resistant tuberculosis
  • Late presentation with immune reconstitution inflammatory syndrome
  • Non-adherence to anti-tuberculosis therapy
  • Other organisms that would be ZN positive including other bacteria from the mycobacterial family as well as nocardia

Question 2: Which test/s would you request next?

Answer to Q2

Line probe assay or Xpert® MTB/RIF should be requested to try and rapidly asses for drug resistant tuberculosis

Sputum for Xpert® MTB/RIF was requested twice and was found to be negative on both occasions.

Question 3: How does this result influence you thinking?

Answer to Q3

This suggests that the patient does not have tuberculosis. In the case of this child Mycobacterium avium-intracellulare infection was confirmed on numerous sputum cultures. In our case we did not confirm dissemination as the blood culture was negative and bone marrow aspiration and culture was not done. The abdominal ultrasound was normal.

Non-tuberculous mycobacterial pulmonary infection in children

Non-tuberculous mycobacteria (NTM) are widespread in the environment including water, soil, food products and domestic and wild animals. More than 130 species, not all human pathogens, have been identified. The organisms cause a variety of infections and presentation will depend on the species and the host. Table 1 represents a classification of NTM according to growth pattern.

Table 1: Classification of nontuberculous mycobacteria*

Rapidly growing nontuberculous mycobacteria
M. fortuitum complex
  M. fortuitum
  M. peregrinum
  M. porcinum
M. chelonae
M. abscessus
  M. abscessus
  M. bolletii (previously M. massiliense)
M. smegmatis
M. mucogenicum
Slowly growing nontuberculous mycobacteria
M. kansasii
M. marinum
M. gordonae
M. scrofulaceum
M. avium complex
M. avium
M. intracellulare
M. terrae complex
M. ulcerans
M. xenopi
M. simiae
M. malmoense
M. szulgai
M. asiaticum
M. haemophilum

Rogall T, Wolters J, Flohr T, Böttger EC (October 1990). "Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium". International journal of systematic bacteriology 40 (4): 323–30.
Runyon EH (January 1959). "Anonymous mycobacteria in pulmonary disease". The Medical clinics of North America 43 (1): 273–90.
Brown-Elliott BA, Wallace RJ (October 2002). "Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria". Clin. Microbiol. Rev. 15 (4): 716–46.

There are well-described clinical syndromes of NTB in children (table 2).. In addition some organisms are specific to geographic areas.

Table 2: Clinical syndromes of non-tuberculosis mycobacteria in children
Pulmonary NTM infections

There is increasing recognition of pulmonary NTM infection in children in the context of underlying lung disease. In addition geographic factors may influence risk

The risk factors for pulmonary disease are:
  • Cystic fibrosis and polymorphisms in the cystic fibrosis transmembrane conductance regulatory genes without classic cystic fibrosis is the most common risk factor for pulmonary NTM
  • Hematopoietic stem cell transplantation
  • Genetic susceptibility due to macrophage protein 1 (NRAMP1) gene abnormalities
  • Disseminated disease

Clinical features of pulmonary disease:
In the literature clinically significant NTM pulmonary disease is most often described in children with preexisting lung disease (eg, cystic fibrosis).The features depend, to some extent, upon the underlying medical condition. Symptoms and signs include:

  • Chronic or recurrent cough
  • Increased sputum production,
  • Dyspnea,
  • Hemoptysis,
  • Chest pain
  • Auscultatory findings including rhonchi, crackles, wheezing, and stridor.
  • Constitutional findings such as fever, fatigue, malaise, and weight loss are more prevalent in immune deficient children, children with advanced disease and se with dissemination.
Radiographic features:
Features depend on the underlying disease

  • Nodular or cavitary opacities on chest radiograph
  • Multifocal bronchiectasis with multiple small nodules on high-resolution computed tomography (HRCT)
  • Hilar lymphadenopathy and a tree-in-bud appearance associated with endobronchial spread is the most common finding in otherwise healthy children
  • Pleural effusions are uncommon, and cavitary lesions in young children are rare.

The species may influence the findings

  • M. avium complex (MAC) – Apical fibrocavitary disease or nodular and interstitial nodular infiltrates often involving the right middle lobe or lingula
  • M. kansasii – Cavitary infiltrates in the upper lobes
  • M. abscessus – Multilobar, patchy, reticulonodular or mixed interstitial alveolar opacities with an upper lobe predominance; cavitation may occur
Laboratory diagnosis

If NTM is suspected it is advisable to contact the laboratory personnel at the time specimens are taken to ensure that optimal growth.

Sputum smear positivity is variable. Traditionally organisms take 2-4 weeks to grow on solid media and 1-2 weeks in liquid methods.

Commercial DNA probes and 16S rRNA gene sequencing can facilitate more rapid diagnosis and speciation. The GeneXpert system permits rapid detection of M. tuberculosis complex and rifampin resistance, but has not been developed for NTM.

Susceptibility or resistance does not always correlate well with clinical efficacy. The exception is of clarithromycin resistance for treatment of disseminated or pulmonary MAC, clarithromycin resistance for M. chelonae and M. abscessus infections, and rifampin resistance for pulmonary M. kansasii.

Diagnostic criteria for pulmonary disease.
The diagnostic criteria for pulmonary disease as per the American Thoracic Society are noted below, however there is no validation in children.

  • Pulmonary symptoms, nodular or cavitary opacities on chest radiograph, or a high-resolution computed tomography scan that shows multifocal bronchiectasis with multiple small nodules. Other diagnosis must be excluded appropriately.
  • Positive culture results from at least 2 separate expectorated sputum samples
  • Positive culture result from at least one bronchial wash or lavage
  • Transbronchial or other lung biopsy with mycobacterial histopathologic features (granulomatous inflammation or AFB) and positive culture for NTM or biopsy showing mycobacterial histopathologic features (granulomatous inflammation or AFB) and one or more sputum or bronchial washings that are culture positive for NTM

The isolation of NTM from respiratory specimens does not necessarily suggest that therapy is needed. The clinical relevance should be determined and therapy only instituted if it is thought to be relevant.

The choice of antimicrobial should be reviewed according to the specific species and with susceptibility testing. Much of the guidance on therapy is based on studies in adults.

M. avium complex (MAC)
Therapy of HIV uninfected children should take into consideration the extent of disease:

Nodular or non-cavitating bronchiectatic MAC lung disease should be treated with a regimen that includes

  • A macrolide (clarithromycin or azithromycin), plus
  • Ethambutol, plus
  • A rifamycin (rifampin or rifabutin)

Extensive bronchiectasis or fibrocavitary MAC lung disease is treated with

  • A macrolide (clarithromycin or azithromycin), plus
  • Ethambutol, plus
  • A rifamycin (rifampin or rifabutin), plus
  • An aminoglycoside (amikacin or streptomycin)

The macrolide, ethambutol, rifamycin and aminoglycoside should be administered daily in children but in older adolecents the aminoglycoside can be given 3 times per week. The aminoglycoside should be discontinued after eight weeks;

HIV-positive children who meet the diagnostic criteria for pulmonary disease should be treated in the same manner as those with disseminated infection.

  • A macrolide (clarithromycin or azithromycin) plus
  • Ethambutol plus
  • A rifamycin (rifampin or rifabutin) plus
  • With aminoglycoside or fluoroquinolone

Children should be treated until the sputum is negative for 12 months.
The aminoglocoside can be discontinued after 2 months of improvement is shown.

M. abscessus
M. abscessus has a predilection for infecting diseased lungs and is difficult to eradicate; cure is possible only with surgical resection when lung disease is limited The goal of M. abscessus therapy is not eradication but rather symptomatic and radiographic improvements. Therapy should include three drugs to which there is documented susceptibility; after four to eight weeks of intensification therapy, two drugs may be used to complete therapy (usually 6-12 months). The regimen often includes:

  • Clarithromycin, plus
  • Amikacin, plus
  • Cefoxitin or a carbapenem (eg, meropenem)
M. kansasii

There have been no randomized trials of treatment for M. kansasii

  • Isoniazid, plus
  • Rifampin, plus
  • Ethambutol, plus
  • A macrolide (clarithromycin or azithromycin)

Treatment should continue until sputum cultures have been negative for at least one year.

Rifampin-resistant isolates should be treated with three drugs based upon in vitro susceptibilities. Potential agents include macrolides, fluoroquinolones, aminoglycosides, and trimethoprim-sulfamethoxazole.

  1. American Academy of Pediatrics. Diseases caused by nontuberculous mycobacteria: (atypical mycobacteria, mycobacteria other than Mycobacterium tuberculosis. In: Red Book: 2012 Report of the Committee on Infectious Diseases, 29th, Pickering LK. (Ed), American Academy of Pediatrics, Elk Grove Village, IL 2012. p.759
  2. Brown-Elliott BA, Wallace RJ (October 2002). "Clinical and taxonomic status of pathogenic nonpigmented or late-pigmenting rapidly growing mycobacteria". Clin. Microbiol. Rev. 15 (4): 716–46.
  3. Chesney PJ. Nontuberculous mycobacteria. Pediatr Rev 2002; 23:300.
  4. Cruz AT, Ong LT, Starke JR. Mycobacterial infections in Texas children: a 5-year case series. Pediatr Infect Dis J 2010; 29:772.
  5. Esther CR Jr, Henry MM, Molina PL, Leigh MW. Nontuberculous mycobacterial infection in young children with cystic fibrosis. Pediatr Pulmonol 2005; 40:39.
  6. Levy I, Grisaru-Soen G, Lerner-Geva L, et al. Multicenter cross-sectional study of nontuberculous mycobacterial infections among cystic fibrosis patients, Israel. Emerg Infect Dis 2008; 14:378.
  7. Olivier KN, Weber DJ, Wallace RJ Jr, et al. Nontuberculous mycobacteria. I: multicenter prevalence study in cystic fibrosis. Am J Respir Crit Care Med 2003; 167:828.
  8. Pierre-Audigier C, Ferroni A, Sermet-Gaudelus I, et al. Age-related prevalence and distribution of nontuberculous mycobacterial species among patients with cystic fibrosis. J Clin Microbiol 2005; 43:3467.
  9. Long: Principles and Practice of Pediatric Infectious Diseases, 4th ed. 2012 Saunders. Chapter 135 786-78
  10. Mandell: Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 7th ed. 2009 Churchill Livingstone. Chapter/s 129, 252, 253
  11. Rogall T, Wolters J, Flohr T, Böttger EC (October 1990). "Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium". International journal of systematic bacteriology 40 (4): 323–30.
  12. Roux AL, Catherinot E, Ripoll F, et al. Multicenter study of prevalence of nontuberculous mycobacteria in patients with cystic fibrosis in france. J Clin Microbiol 2009; 47:4124.
  13. Runyon EH (January 1959). "Anonymous mycobacteria in pulmonary disease". The Medical clinics of North America 43 (1): 273–90
Lessons Learned

This case illustrates a number of important points with regards mycobacterial diagnosis

  • Although M. tuberculosis remains the most important mycobacterium to consider, in the correct setting we need to keep other potential mycobacteria in mind.
  • We must remember that M. tuberculosis is not the only ZN positive organism.
  • The value of requesting sputum specimens cannot be under rated in children with complicated disease. This child was able to expectorate sputum very easily with out induction.
  • Although the patient was referred to the infectious diseases service as a drug resistant tuberculosis case, the clue here is in the discrepancy between the sputum smear and the Xpert® MTB/RIF test. All data suggests that Xpert® MTB/RIF should detect nearly all cases of smear positive tuberculosis. This information immediately prompted us to consider norcardia and NTM as a possible diagnosis. We where then able to collaborate with the laboratory in order to facilitate handling of further specimens in addition we expanded antimicrobial cover with this in mind. We elected to do this as the child had significant respiratory failure. Understanding the properties of tests such as sensitivity, specificity and positive and negative predictive values is an absolutely essential component of decision making in medicine.

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