Guideline: Management of Drug-Resistant Tuberculosis » Diagnosis Of DR-TB



5.1. Introduction


In the majority of cases, the development of DR-TB is insidious and progresses over weeks and months. As a result, patients often ignore the symptoms or accept them as symptoms related to the daily stresses, lack of sleep and from being overworked, therefore delay seeking health care.

DR-TB may also be associated with other serious disorders, such as HIV infection, alcoholism, renal failure, diabetes mellitus, cancers and drug abuse. The signs and symptoms of these conditions and their complications can easily obscure those of DR-TB and can also result in considerable delays in diagnosis or in misdiagnosis, especially in patients with HIV infection.  It is therefore important that HCWs have a high index of suspicion for DR-TB as early diagnosis and initiation of treatment is critical in the prevention of amplification of resistance and extensive lung damage resulting in complicated forms of disease which are more difficult to treat.


5.2. Signs and Symptoms of DR-TB


The symptoms of DR-TB are the same as for drug-susceptible TB:

  • Cough
  • Chest pain
  • Dyspnoea
  • Haemoptysis
  • Systemic symptoms (i.e.,fever, chills, nights sweats, tiredness, anorexia, weight loss)

In addition to the systemic effects of DR-TB, there may be remote manifestations unrelated to the site of involvement. These include haematologic abnormalities, hyponatraemia and psychological disorders. The most common haematological manifestations include increases in the peripheral blood leukocyte count and anaemia. The increase in leukocyte count is usually slight, but leukemoid reactions and leukopenia may occur. An increase in the peripheral blood monocyte and eosinophil counts may also occur. Anaemia is common in disseminated DR-TB disease.

Extra-pulmonary DR-TB presents more of a diagnostic challenge because it involves relatively inaccessible sites, and depending on the organs involved, fewer bacilli can cause much greater damage.


5.3. Assessing a Patient for DR-TB


An initial evaluation for DR-TB should include:

  • A complete medical history
  • A physical examination
  • Bacteriological investigations to confirm the diagnosis

5.3.1.  Medical History

A proper history of the patient must be recorded. These should include the elements listed below.

  • History of presenting symptoms including cough and duration of the cough, sputum production, fever, night sweats, loss of appetite, unintentional weight loss (determine extent of weight loss and the time period), dyspnoea, chest pains, haemoptysis, abdominal pain, nausea, vomiting, diarrhoea, constipation, headache, peripheral leg pain, hearing loss, depression, anxiety.
  • Medical history should include previous TB episodes, previous treatment regimen, time to smear or culture conversion, treatment outcomes for each episode (if multiple) and participation in clinical trials, chronic medical illness such as other medical conditions such as diabetes mellitus, renal disease, malignancies, chronic malabsorption syndrome, prolonged corticosteroid therapy, immunosuppressive therapy and HIV infection, which may affect clinical management, allergies, pregnancy, last menstrual period, method of contraception, prior psychiatric illness, medication that the patient may be taking other than TB treatment.
  • Surgical history including any surgical procedures the patient has undergone and the reasons.
  • Work history should focus on any experience in the mining industry, stay in either TB hospital or prison and laboratory work.
  • Social history should include substance abuse (alcohol, tobacco and other drugs).
  • Previous confinement in a hospital, prison and duration should be noted.
  • Family history of TB, screening of close contacts, confirmation of disease in and treatment of contacts, history of DR-TB exposure should be noted.

All patients who do not know their HIV status should be offered counselling and voluntary testing.

It is important to determine the baseline clinical parameters on initiation of treatment in order to monitor the patient’s progress whilst on treatment and will enable early detection of any other co- morbid conditions that may require adjustment of the treatment regimen or ancillary treatment.

  • The initial physical examination must include the examination of the skin, head, neck, oropharynx, cardiovascular system, pulmonary system, abdominal organs, extremities, and nervous system. The vital signs (i.e., heart rate, blood pressure, respiratory rate, weight and height) must be recorded.
  • Laboratory and other baseline tests such as chest x-ray, urine pregnancy test (where indicated), urea and electrolytes, creatinine, full blood count, HIV test, liver function tests, audiometry and psychiatric evaluation where indicated.

5.3.2. Physical Examination

A physical examination is an essential part of the evaluation of any patient therefore all vital signs must be obtained. The physical signs cannot be used to confirm or rule out DR-TB, but can provide valuable information about the patient’s overall condition and other factors that may affect patient management.

The clinical presentation of patients with DR-TB is similar to those of patients with drug-susceptible TB, and patients often present with cavitary lung lesions.

5.3.3. Laboratory Diagnosis of MDR- and XDR -TB

MDR-TB is often suspected clinically when a patient has a persistently positive smear microscopy or culture result, or when a patient fails to respond to treatment despite documented good adherence. MDR- or XDR -TB can also be suspected when a person has had exposure to a confirmed or suspected MDR- or XDR -TB patient. Demonstrating in vitro resistance in the M. tuberculosis isolate from the patient is the only definitive diagnosis of MDR- or XDR-TB.

The quality of DST is of paramount importance and impacts directly on treatment. All laboratories performing TB culture and drug susceptibility testing must be part of a recognised external quality assurance programme including TB microscopy, TB culture and DST. The use of line probe assay is recommended. However, it must be noted that the line probe assay will only be done on TB smear positive patients or culture positive patients. Therefore the line probe assay does not replace conventional DST. Patients diagnosed on line probe assay will be started on treatment immediately. Conventional DST confirmation is not required. Microscopy

Although direct microscopy is the cornerstone of diagnosis of pulmonary TB, it cannot distinguish between drug-susceptible and drug-resistant M. tuberculosis, or between different species of mycobacterium. The use of microscopy in DR-TB is limited to:

  • Evaluating the infectiousness of patients.
  • Triaging specimens for culture and DST.
  • Confirming that bacterial growth on culture are acid-fast bacilli and not contaminants.

The sensitivity of smear microscopy is in the region of 30% to 60% when compared to culture, as at least 5 000 to 10 000 organisms per ml of sputum need to be present to allow visualisation, as only a small amount of the sputum is actually viewed.  Nevertheless, the infectiousness of DR-TB patients correlates crudely with the number of AFB in the sputum smear as measured by conventional semi-quantitative methods, other factors being equal. Smear microscopy, however, cannot distinguish viable from nonviable bacilli, so its use in monitoring of progress on treatment is limited.  For example, even with adequate treatment, DR-TB patients may become culture negative but remain smear positive suggesting that the bacilli are non-viable.

The turnaround time for microscopy results should be less than 48 hours, depending on the work load and the transport time to the laboratory. Results must be reported as ‘positive/ negative for acid fast bacilli’ and quantified, as quantification may serve as an indication of disease severity. Culture

Mycobacteria are slow growing organisms with a mean generation time of 12 to 18 hours, so culture results for TB may take several weeks. Mycobacteria also require special culture media. A variety of suitable culture media and differential tests for species identification are available. A commercial automated system using liquid media (BACTEC Mycobacterial Growth Indicator Tube (MGIT) 960; Becton Dickinson) is used as the culture medium of choice in the National Health Laboratory Service (NHLS). This system uses a fluorescence quenching-based oxygen sensor to detect mycobacterial growth.

Timeous transport of specimens to the laboratory is critical, as any delays will result in a decrease in the viability of the mycobacteria as well as contamination due to overgrowth of common respiratory bacteria. Specimens should therefore be kept cool during transportation or refrigerated at 4°C if

delays are anticipated. Inadequate decontamination process in the laboratory compromises the growth and isolation of mycobacteria. It can also adversely affect the culture yield.

Culture results are reported as positive or negative in the MGIT automated system, together with an indication of the time to positivity, which may be a reflection of the severity of disease. The results should always be correlated with the patient’s clinical condition, and investigations repeated if necessary.

False negative cultures may result from inadequate specimens, poor laboratory technique, and delayed transport of the specimens to the laboratory. Cross contamination of specimens may lead to false positive results. Identification of M. tuberculosis

The overwhelming majority of mycobacterial isolates will be M. tuberculosis in HIV negative patients. However, the prevalence of non-tuberculous mycobacteria (NTM) can be higher in HIV positive patients.  Unless the species is confirmed as M. tuberculosis, mycobacterial isolates appearing phenotypically resistant to anti-TB drugs may not be DR-TB, but due to infection with NTM. Treatment of NTM is entirely different from DR-TB; therefore M. tuberculosis should always be confirmed following culture. Drug Susceptibility Testing

Drug susceptibility testing (DST) is required to make a definite diagnosis of MDR-TB. DST can be done by several methods. The MGIT methodology distinguishes susceptibility from resistance by comparing growth in plain (control) medium to growth in medium to which specified concentrations of drugs have been added.

Limitations of DST

  • With conventional methodologies, growth detection, identification of M. tuberculosis and DST may take weeks or even months.
  • Different anti-TB drugs have different ‘critical concentrations’ (the breakpoint between calling a strain resistant or susceptible), which also depend on the culture medium used for DST.
  • DST for first-line anti-TB drugs has  been thoroughly studied and consensus reached on appropriate methodologies, critical drug concentrations, and reliability and reproducibility of testing. The intrinsic accuracy of DST varies with the drug tested: for first-line drugs DST is most accurate for rifampicin and isoniazid and less so for streptomycin and ethambutol.
  • DST for second-line anti-TB drugs (SLDs) is much more problematic and has not been standardised internationally, due to technical difficulties related to in vitro drug instability leading to drug loss.  Laboratory technique also influences DST results. In addition, the drug concentration defining resistance (critical concentration) is often very close to the minimal inhibitory concentration (MIC) required to achieve anti-mycobacterial activity, increasing the probability for misclassification of susceptibility or resistance and leading to poorer reproducibility of second-line DST results.
  • SLDs that are more stable in different test environments and have shown relatively good reproducibility are aminoglycosides, polypeptides, and fluoroquinolones. The reproducibility and reliability of DST for PAS, cycloserine, terizidone and thioamides are much more limited while the correlation of DST results with clinical response to treatment has not yet been established. In addition, the relevance of in vitro cross-resistance between drugs in the same group is difficult to interpret clinically.

HCWs treating patients with DR-TB must be aware of the limitations of DST and interpret the results with the constraints in mind.  TB organisms that test susceptible to specific drugs have a higher probability of responding effectively on treatment with those drug(s) than organisms that test drug-resistant.  Discrepant results must be interpreted with care. The Use of GeneXpert in the Diagnosis of MDR-TB

GeneXpert MTB/RIF (GXP) is a relatively new diagnostic tool for TB diagnosis in South Africa. This test has an advantage over the existing TB smear microscopy because it has higher sensitivity, specificity and identifies many patients that would not have been diagnosed using TB microscopy. The Xpert MTB/RIF test reports MTB detected or not detected and also provides data on the state of susceptibility or resistance to rifampicin.


All patients with GXP MTB positive results (rifampicin susceptible or inconclusive) will be started on TB treatment at the point of diagnosis.

All patients with GXP MTB positive results with resistance to rifampicin will be referred to MDR-TB facilities to commence MDR-TB treatment. The following steps will be followed at the MDR-TB facility regarding GXP MTB positive patients with resistance to rifampicin:

  1. Open patient’s file.
  2. Examine patient prior to starting treatment.
  3. Take a sputum sample for TB culture and DST for MDR-TB confirmation.
  4. Start MDR-TB treatment. Isoniazid (INH) may be included.
  5. Register these patients under the category MDR-TB ‘not confirmed’.
  6. Review MDR-TB treatment after receiving laboratory confirmation, meaning that MDR-TB treatment will be continued if diagnosis is confirmed; MDR-TB treatment maybe stopped if MDR-TB is not confirmed. However, as already outlined conventional culture and DST is an imperfect gold standard and therefore results should be interpreted in the clinical context and the possibility of falsely negative phenotypic DST should also be borne in mind. An experienced physician should be consulted if appropriate. A new and updated Xpert cartridge will become available late 2011 and this recommendation may be revised in the light on performance characteristics of the new cartridge.
  7. Review patient’s category in the register: change from MDR-TB not confirmed to MDR-TB confirmed upon laboratory TB culture and DST or Line Probe Assay (LPA); on the contrary the MDR-TB not confirmed will be de-registered or deleted from DR-TB register and recorded as drug-susceptible TB on

Note: When a sample is taken from GXP MTB positive rifampicin-resistant patients, the following will take place:

  1. The sample will be subjected to smear microscopy test
  2. All smear positive tests will be subjected to Line Probe Assay leading to a quick confirmation
  3. All smear negative samples will go through TB culture (MGIT) and later be subjected to LPA if the sample becomes culture positive and TB bacilli identified. This will take longer.
  4. If an organism is shown to be resistant to rifampicin and/or isoniazid, DST for second-line drugs (fluoroquinolone and aminoglycoside) will also be performed.