Treatment Guideline Chart
Tuberculosis (TB) suspect is any one who has signs or symptoms suggestive of TB (eg >2 weeks productive cough).
Definite TB is considered in patients with culture or molecular line probe assay positive for Mycobacterium tuberculosis, or in patients with at least 1 sputum smear positive for acid-fast bacilli.
TB cases are also classified based on the disease anatomical site, bacteriological results (including drug resistance), previous treatment history and patient's HIV status.
Pulmonary TB is a case of TB that involves the lung parenchyma.
Miliary TB is considered as PTB since lung lesions are also seen.
TB in the pleural effusion, mediastinal and/or hilar lymph nodes with no evidence of abnormalities in the chest x-ray are considered extrapulmonary TB.
Patients presenting with both PTB and extrapulmonary TB are classified as a case of PTB.

Tuberculosis%20-%20pulmonary Diagnosis


  • Most common symptom of pulmonary tuberculosis (PTB) is cough ≥2 weeks that is productive and may be accompanied by both/either:
    • Respiratory symptoms: Shortness of breath, chest pains, hemoptysis
    • Constitutional symptoms: Loss of appetite, unexplained weight loss, fever, night sweats, fatigue
  • Important to ask about history of previous treatment with anti-TB drugs
    • Has higher risk for drug resistance, including multidrug-resistant tuberculosis (MDR-TB)


  • Basis of the management in each patient
New Patient
  • Patients who never had tuberculosis (TB) treatment or have taken anti-TB regimen for <1 month
  • Assumed to be drug susceptible unless the patient is from an area with high prevalence of Isoniazid resistance or if the patient had active TB after contact with a documented multi-drug resistant TB (MDR-TB) patient
  • Patients who will have MDR-TB at any time during the therapy will be considered as a treatment failure
Previously Treated Patient
  • Has history of taking anti-TB drugs for ≥1 month and currently smear or culture positive again
  • Further subclassified based on the outcome of their most recent treatment course
    • Relapse: Patient has been cured or most recent prior treatment was completed
    • Failure: Most recent prior treatment has failed
    • Default: Treatment was interrupted for ≥2 consecutive months
  • Strongly determines resistance of drugs
    • Timely detection of multi-drug resistance (MDR) and start of MDR regimen with 2nd-line drugs gives a better likelihood of cure and prevents development and transmission of further resistance
    • Incidence of MDR is higher in previously treated patients than in new patients
      • Patients returning after defaulting or relapsing has lesser MDR rates than patients who had treatment failure
    • Patients with prior treatment failure should be given an empirical MDR regimen while waiting for the results if conventional drug susceptibility testing (DST) was used
      • Prevents clinical deterioration of the patient and decreases risk of transmission to contacts
    • National TB Control Program (NTP) should use country-specific drug resistance data of patient groups on failure, relapse and default to know the level of MDR
    • High MDR levels are noted in patients:
      • Treated in poorly operating NTP
      • Living with human immunodeficiency virus (HIV)
      • With type 2 diabetes mellitus
      • With history of using poor or unknown quality of anti-TB drugs
      • Exposed in institutions with high-prevalence rate or outbreak of MDR
      • With conditions associated with malabsorption or rapid-transit diarrhea
      • Whose prior regimen included Rifampicin throughout the course
      • Who still has positive sputum smear at months 2 or 3 of treatment
    • The World Health Organization (WHO) classifies cases of drug-resistant TB into 5 categories:
      • Isoniazid-resistant TB
      • Rifampicin-resistant TB (RR-TB)
      • MDR-TB
        • Defined as resistance to Isoniazid and Rifampicin
      • Pre-extensively drug-resistant TB (pre-XDR-TB)
        • Defined as resistance to Rifampicin and any fluoroquinolone
      • Extensively drug-resistant TB (XDR-TB)
        • Defined as resistance to Rifampicin, plus any fluoroquinolone, plus at least 1 of the drugs Bedaquiline and Linezolid

Laboratory Tests

Sputum Smear Microscopy
  • Recommended for all individuals highly suspected of pulmonary tuberculosis (PTB) 
  • 2 sputum specimens are submitted for evaluation, amounting to at least 3 mL (ideal volume: 5-10 mL)
    • Patient must submit at least 1 early-morning sputum sample which usually has the highest yield
    • 2 sputum samples submitted on the same day are comparable to 2 consecutive days-sputum specimens
      • With similar sensitivity and specificity rates
  • Recommended also for patients with chest radiograph suggestive of TB
  • PTB cases without results of sputum smear are classified as “smear not done”
  • Also used in monitoring treatment response of patients
  • Fluorescence microscopy preferred over conventional microscopy because of its higher sensitivity and better time efficiency
  • Individuals suspected to have PTB, who are either negative for AFB smear or unable to provide appropriate sputum samples are recommended to still submit proper sputum specimens via induction, than having to obtain them through flexible bronchoscopy, which is recommended for individuals suspected to have PTB who are incapable of providing induced sputum specimens
  • Individuals suspected to have PTB who are incapable of providing induced sputum specimens are recommended to undergo flexible bronchoscopy technique to yield samples
  • If there is a need for an immediate diagnosis, transbronchial biopsy (TBB) may be done
  • Sputum samples of post-bronchoscopy PTB-suspected patients should be sent for culture and AFB smear
  • Patients under miliary TB consideration, with negative AFB smear, with no other available specimens to submit for laboratory diagnosis and unable to provide induced sputum, are recommended to have specimens obtained by means of flexible bronchoscopy
  • Samples should include TBB and/or bronchial brushings
  • AFB smear is indicated on specimens from sites that are being considered for extrapulmonary TB
Smear-Positive Pulmonary Tuberculosis (PTB)
  • Considered smear-positive if ≥1 sputum smear specimens at the start of treatment in countries with well functioning external quality assurance (EQA) system are positive for acid-fast bacilli (AFB) 
  • In countries with no functional EQA, a smear-positive PTB is considered when:
    • ≥2 initial sputum smear exams are positive for AFB, or
    • 1 sputum smear exam is positive for AFB with abnormalities consistent with active PTB in chest X-ray, or
    • 1 sputum smear positive for AFB with culture positive for M tuberculosis
Smear-Negative Pulmonary Tuberculosis (PTB)
  • Considered in patients with negative sputum smear but with positive culture for M tuberculosis or when at least 2 sputum samples at the start of treatment in countries with a functional EQA system are negative for AFB
    • To confirm the diagnosis of TB, sputum culture for M tuberculosis is advised in patients who live in areas with human immunodeficiency virus (HIV) prevalence of >1% in pregnant women or ≥5% in TB patients that have smear-negative sputum
  • Also regarded in patients who are being treated by a clinician with a full course of anti-TB regimen with abnormalities in chest X-ray consistent with active PTB, and patient is either positive for HIV or if with negative or unknown HIV status that lives in area of low HIV prevalence, has no improvement in response to a course of broad-spectrum antibiotics (excluding anti-TB drugs and fluoroquinolones and aminoglycosides)
Rapid Molecular Tests
  • Nucleic acid amplification tests (NAATs) are recommended for better detection of M tuberculosis
  • An initial pulmonary sample should undergo NAAT
    • In patients who are AFB smear-positive and with negative NAAT, TB disease is improbable
    • In patients who are AFB smear-negative and with moderate to high index of having TB disease, a positive NAAT enables the assumption of TB disease, however, a negative NAAT does not disregard TB disease
    • In patients who are unlikely to have TB disease, NAAT is not recommended since the yield of results that are false-positive are very common
    • Acceptable NAAT are Hologic amplified M tuberculosis direct (MTD) test and Xpert MTB/RIF test
  • NAAT is also performed on specimens from patients in whom extrapulmonary TB is a consideration
    • A negative result should not rule out the possibility of extrapulmonary TB
  • Older NAATs have low sensitivity and with negative predictive value for smear-negative and extrapulmonary TB
  • A highly sensitive and specific cartridge-based fully automated NAATs for the detection of M tuberculosis and Rifampicin resistance
    • 68% sensitive, 99% specific when compared to sputum culture; 88% sensitive and 98% specific when compared with smear microscopy
    • 94% pooled sensitivity, 98% pooled specificity for Rifampicin resistance
    • 84.9% sensitive for extrapulmonary TB (eg lymph nodes, lung aspirates)
    • 79.5% sensitive for CSF analysis for TB meningitis
  • A single automated PCR test (molecular test) using the GeneXpert platform which can detect M tuberculosis bacteria and Rifampicin resistance within 2 hours of starting the test
  • Recommended as an initial diagnostic tool for for TB and Rifampicin resistance detection in adults and children with PTB signs and symptoms:
    • In children sputum, gastric aspirate, nasopharyngeal aspirate and stool may be used
  • Recommended for CSF examination of patients suspected to have TB meningitis rather than smear microscopy or culture
  • Recommended for detection of Rifampicin resistance in adults and children with signs and symptoms of EPTB rather than culture or DST
  • Recommended for repeat testing of children with signs and symptoms of PTB in high prevalence settings using sputum, gastric fluid, nasopharyngeal aspirate and stool specimens 
  • Recommended as a confirmatory test for suspected TB patients with negative sputum smear microscopy results
  • May also be used as an initial diagnostic tool for:
    • Non-sputum specimens (lymph node aspirate/biopsy, pleural fluid, peritoneal fluid, pericardial fluid, synovial fluid or urine) from adult and pediatric patients with signs and symptoms of EPTB rather than smear microscopy or culture
    • Disseminated TB in HIV-positive adults and children using blood as specimen
    • In patients with chest radiograph findings pertinent to PTB
Xpert MTB/RIF Ultra (Xpert Ultra)
  • Uses a similar platform as the Xpert MTB/RIF and was developed to overcome the limitations in sensitivity for TB diagnosis of Xpert MTB/RIF
    • More sensitive compared to Xpert MTB/RIF in detecting M tuberculosis in smear-negative culture-positive specimens, extrapulmonary specimens, specimens from HIV-infected persons and pediatric specimens
  • Recommended as an initial diagnostic tool for TB and Rifampicin resistance in adults and children with PTB signs and symptoms
    • In children, nasopharyngeal aspirate may be used
  • Recommended for CSF examination of patients suspected to have TB meningitis
  • Recommended for detection of Rifampicin resistance in adults and children with signs and symptoms of EPTB
  • May be used in the following:
    • Initial diagnostic test in adults and children for the corresponding form of EPTB using lymph node aspirate or biopsy
    • Repeat testing of children with signs and symptoms of PTB in both low or high prevalence settings using sputum and nasopharyngeal aspirate specimens
    • As a replacement for culture as the initial test in patients with signs and symptoms of PTB or chest radiograph with lung abnormalities or both
  • Not recommended to perform repeated testing with Xpert Ultra in adults with signs and symptoms of PTB who initially have Xpert Ultra trace results
    • Trace results will require follow-up which includes reassessing clinical symptoms and information on prior history of TB
Hologic Amplified Mycobacterium Tuberculosis Direct (MTD) Test
  • A nucleic acid probe test for the identification of M tuberculosis complex rRNA from sputum, bronchial or tracheal specimens
  • A negative result does not mean that M tuberculosis complex is not present since the procedure may be influenced by different factors (eg handling of samples, laboratory errors)
Interferon-Gamma Release Assay (IGRA)
  • A diagnostic blood test used to identify a patient’s immune reactivity to M tuberculosis
  • May be considered for the initial diagnosis of children suspected to have TB; not recommended for the initial diagnosis in adults
  • Tuberculin testing still preferred over IGRA for patients belonging to low-middle class families
  • In determining the presence of latent TB infection (LTBI)
    • IGRA is preferred over tuberculin skin test (TST) in patients ≥5 years old who are likely infected with M tuberculosis, those with low-intermediate risk of disease progression, patients highly suspected of LTBI and previously vaccinated with BCG or may not follow-up for TST reading
      • Note: TST may be performed instead if IGRA is unavailable or not preferred by the patient
    • May perform IGRA instead of TST in patients ≥5 years of age at high risk for M tuberculosis, those at low to intermediate risk for disease progression, and if LTBI test is warranted
    • For patients at high risk of disease progression, IGRA may be performed if initial TST is negative
      • May consider 2nd test result as confirmatory of M tuberculosis infection if positive
    • There is no need for M tuberculosis examination for individuals with low risk of having the disease, except in certain instances (eg as instituted by law), wherein patients ≥5 years old should undergo IGRA preferebly (or TST as an alternative), with those whose results revealed infection should undergo another test (TST or IGRA, whichever is not used initially) for confirmation
    • Active TB infection should be ruled out prior to LTBI treatment, since IGRA and TST only indicate M tuberculosis infection, without differentiating between active and latent

Loop-mediated Isothermal Amplification (TB-LAMP)

  • Based on loop-mediated isothermal amplification (LAMP) reaction which requires less than 1 hour to perform and can be read with the naked eye under ultraviolet (UV) light
  • May be used as:
    • Replacement test for sputum-smear microscopy for the diagnosis of PTB in adults with signs and symptoms
    • Follow-up test to sputum-smear negative results in adults with signs and symptoms consistent with PTB
Tuberculin Skin Testing (TST, Mantoux Method)
  • Recommended for the initial diagnosis of children suspected to have TB, but with no history of contact with persons with active TB disease
  • Not recommended as an initial diagnostic tool for adults
  • May be used to screen for LTBI
  • Also used as a screening examination for pediatric patients in contact with persons with active PTB
  • Is considered positive in the following instances:
    • ≥5 mm induration in immunocompromised patients, with diagnostic evaluation indicating current or previous TB, individuals who are in close contact with people with PTB, those who are receiving immunosuppressive agents
    • ≥10 mm induration for those at increased risk for LTBI and those with medical conditions that predispose them to progress from LTBI to TB disease
    • ≥15 mm induration for all other individuals
  • A positive skin test is not conclusive of an active TB disease; other confirmatory tests should be performed
  • Used for definitive diagnosis of TB in patients with negative sputum smear, especially in areas with high HIV prevalence
  • Also advised in patients in whom drug resistance is likely considered
  • Specimen should undergo culture for M tuberculosis in both liquid and solid media
    • Liquid system detects mycobacteria more and increases the case yield by 10%, and provides DST result within 10 days as compared to solid media
  • Also performed on specimens from patients in whom extrapulmonary TB is suspected
    • Positive results can be used for documentation of extrapulmonary TB and assist in patient evaluation, but a negative result should not rule out the possibility of extrapulmonary TB
  • A culture isolate indicative of mycobacterial growth should be sent to a regional laboratory for genotyping
Lateral Flow Urine Lipoarabinomannan Assay (LF-LAM)
  • Involves detection of lipoarabinomannan (LAM) antigen in urine
  • Have shown improved sensitivity for the diagnosis of TB in persons coinfected with HIV
  • Strongly recommended by the World Health Organization (WHO) to support the diagnosis of active TB in HIV-positive individuals in inpatient settings with the following:
    • Signs and symptoms consistent with pulmonary and/or extrapulmonary TB
    • Seriously ill (respiratory rate >30/minute, temperature >39˚C, heart rate >120/minute and unable to walk unaided) or advanced HIV disease (CD4 cell count <200 cells/mm3 or WHO clinical stage 3 or 4)
    • CD4 cell count <200 cells/mm3 irrespective of signs and symptoms of TB
  • May be used in outpatient settings to support the diagnosis of active TB in HIV-positive individuals with:
    • Signs and symptoms of pulmonary and/or extrapulmonary TB or seriously ill
    • CD4 cell count <100 cells/mm3 irrespective of signs and symptoms of TB
  • Not recommended for use in outpatient settings to support the diagnosis of active TB in HIV-positive individuals in the following conditions:
    • Without assessment for symptoms of TB
    • Without symptoms of TB and unknown CD4 cell count or without symptoms of TB and CD4 cell count ≥200 cells/mm3
    • Without symptoms of TB and with CD4 cell count of 100-200 cells/mm3
Drug Susceptibility Testing (DST)
  • Ideally done to all patients at the start of the treatment to identify and provide the most appropriate therapy
  • Should be done at or prior to the start of treatment in:
    • New patients who had active TB after contact with a documented multidrug-resistant tuberculosis (MDR-TB) patient
    • All previously treated patients, especially in patients with sputum smear-positive after 3 months therapy, treatment failure, patients lost to follow-up, and those with disease relapse after treatment
    • Patients living with HIV
    • HIV-infected TB patients with CD4 counts <200 cells/mm3
    • All new patients in countries with >3% MDR-TB level in new patients
  • Should be performed for at least Isoniazid and Rifampicin
  • Susceptibility testing for fluoroquinolones is recommended by the WHO before the initiation of shorter all-oral Bedaquiline-containing MDR-TB regimen
  • In patients who are either positive for AFB smear or hologic amplified MTD, a rapid molecular DST for Rifampin, with or without the inclusion of Isoniazid is recommended, if any is present:
    • History of TB treatment
    • Birthplace or place of residency for 1 year is in a country wherein the average prevalence of TB is ≥20/100,000 or that of MDR-TB is ≥2%
    • Exposed to MDR-TB patients
    • With HIV disease
    • Culture-based DST is the gold standard in the detection of drug resistance amd the rapid molecular DST is only for a selected few such as those enumerated above
  • Rapid molecular DST is recommended by WHO as the initial test to detect drug resistance prior to initiation of appropriate treatment for all patients including new patients and patients with previous history of therapy for TB 
  • Conventional DST provides result within a week for liquid media or month for solid media; therefore, patients should be given empirical regimen while awaiting the results
    • Shorter waiting time for DST results may stop continued spread of multidrug-resistant (MDR), prevent increase of resistance, and avoid increased risk of patient defaulting from treatment due to adverse effects of unnecessary empiric drugs
Xpert MTB/RIF (please see above)

High Complexity Reverse Hybridization-based NAATs for detection of Pyrazinamide Resistance

  • May be used on M tuberculosis isolates for the detection of Pyrazinamide resistance rather than culture-based phenotypic DST
    • Pyrazinamide resistance is strongly associated with MDR/RR-TB
Line-Probe Assay
  • A rapid molecular-based DST that provides result for Isoniazid or Rifampicin within 1-2 days which can be used in deciding the treatment appropriate for the patient
  • Confirmatory diagnostic tool for sputum smear positive patients and culture-positive TB isolates
  • Not to be used as an initial test for TB detection; should be used together with culture and drug susceptibility testing
  • GenoType M tuberculosis drug-resistant second-line assay (MTBDRsl) or GenoType MTBDRsl line probe assay may be used to detect resistance to fluoroquinolones and 2nd-line injectable medications in patients diagnosed with MDR-TB or Rifampicin-resistant TB (RR-TB)

Low Complexity Automated NAATs (Xpert MTB/XDR)

  • New class of diagnostics intended for use as a reflex test in specimens determined to be M tuberculosis-positive
    • Can be used to complement existing DSTs that only test for Rifampicin
  • Can rapidly detect resistance (under 90 minutes) to Isoniazid, fluoroquinolones, Ethionamide and Amikacin
Phenotypic Drug Susceptibility Testing for Anti-TB Drugs
  • Testing for all fluoroquinolones and injectable aminoglycosides are recommended for Rif-resistant and MDR-TB patients
Tests for Extrapulmonary Tuberculosis
  • Cell counts and chemistries are performed on samples from extrapulmonary TB-infected regions (eg abdominal, pleural, joint fluids, etc)
  • Measurement of adenosine deaminase (ADA) may be considered for patients suspected to have TB meningitis, pleural, peritoneal or pericardial TB
  • Measurement of interferon-γ (IFN-γ) may be used for patients suspected of pleural or peritoneal TB
  • Histologic examination may also be considered, together with AFB smear microscopy, mycobacterial cultures and NAAT


Chest X-ray
  • Sensitive but nonspecific test to detect tuberculosis (TB) [98% sensitive, 75% specific for any abnormality suggestive of TB]
  • Cannot establish the diagnosis of TB alone
  • Used to evaluate patients with negative sputum smears and/or negative Xpert MTB/RIF, and identify other possible diagnosis
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