Diagnosis of drug-resistant TB’

Clinical description

The diagnosis of Drug Resistant TB (DR-TB) is done by Xpert MTB/RIF, Line Probe Assay (first and second line LPA), culture and phenotypic Drug Susceptibility Test (DST).Xpert MTB/RIF has been recommended as the primary diagnostic test in all adults and children with signs and symptoms of TB where available (See Algorithm 10.3.1 & 10.3.2 ).

All health care workers involved in the diagnosis and treatment of TB should actively participate in the identification, prioritization, and confirmation of drug-resistant TB among presumptive patients using nationally recommended diagnostic algorithms. The initial screening tool for drug-resistant TB at health facility level is Xpert MTB/RIF. Collection and transportation of samples to testing sites must follow the Malawi standard operating procedure for specimen transportation.

In facilities where Xpert MTB/RIF is not yet available, samples from priority patients should be referred to the nearest facility where the test is available. Priority patients includes: PLHIV, Children, And EPTB, patients with risk of DR-TB: DR-TB contacts, previously treated TB patients, smear positive at ≥2 months, health care workers, miners and prisoners.

Case finding strategies for Pre XDR/XDR-TB All strains of confirmed RR/MDR TB patients should routinely undergo second-line DST to determine susceptibility for the newly constructed TB regimen. The following group of patients shall be prioritized for second-line DST.

• All RR patients before starting RR-MDR TB treatment
• Symptomatic contact of known Pre XDR/XDR-TB patients
• Lack of culture conversion by end of the fourth months of the standardized regimen
• Bacteriological reversion in the continuation phase after conversion to negative among

RR/MDR-TB patients on second-line treatment

• Evidence of MDR-TB treatment failure
• MDR-TB patients who return after being lost to follow up.

Identif ication and referral of presumptive drug-resistant TB patients All health care workers involved in the diagnosis and treatment of TB should actively participate in the identification, prioritisation, and confirmation of drug-resistant TB among presumptive cases using nationally recommended diagnostic algorithms. The initial screening tool for drug-resistant TB at health facility level is Xpert MTB/RIF. Collection and transportation of samples to testing sites must follow the Malawi standard operating procedure for specimen transportation.

Investigations

• For all patients with rifampicin resistance detected on Xpert MTB/RIF, samples should

be sent for FL and SL LPA, culture and phenotypic DST; for those eligible, the shorter DR-TB treatment regimen should be started while awaiting results.

• The turnaround time (specimen collection until receipt of results) for LPA and culture/

DST results varies on when the test becomes positive and the type of media used (e.g.

liquid or solid media for culture):

70 National Tuberculosis Control Programme  Line probe assay results should take between 3-14 days (turnaround time of LPA within the processing lab should be 48 hours);

 Liquid culture (MGIT): positive results at 4-14 days, negative result by 42 days;

 Solid culture (LJ): positive results at 28-56 days, negative result by 60 days;

 Phenotypic DST results (from the date culture was positive): MGIT 14 days, LJ 30 days;

• Phenotypic DST(pDST) is reliable and reproducible for RIF, INH, Km, Am, Ofx, Lfx.
• EMB, Sm, Cm, Eto/Pto, Cs, PZA, PAS: pDST is not reliable;
• The critical concentrations for pDST of Mfx, new and repurposed drugs Bdq,

Dlm, Cfz, Lzd have been reviewed and updated (WHO guidelines)and the p DST for this drugs is not widely available outside of research settings.

Drug-resistant TB diagnostic algorithm NTP has developed algorithms to diagnose drug-resistant TB for health centres, hospitals and reference laboratories. The primary test is Xpert MTB RIF.

Figure 10.3-1: TB and drug-resistant TB diagnosis at health facility level National Tuberculosis Control Programme 71 Interpretation of DST results Results of Xpert MTB/RIF Assay  When Xpert MTB/RIF does not detect MTB: re-evaluate the patient clinically and use clinical judgment for treatment decision (especially in PLHIV, children and EPTB that can be difficult to confirm bacteriologically) When Xpert MTB/RIF detects MTB without rifampicin resistance: start or continue patient on first line anti-TB regimen.

For patients at high risk of DR-TB, a sample should be sent for LPA and culture/pDST  When Xpert MTB/RIF detects MTB with rifampicin resistance: immediately repeat the Xpert MTB/RIF test on fresh specimen.

 If result shows RR-TB again treat with second-line drugs.

 If result is MTB detected, Rif resistance not detected treat with first-line drugs and perform culture and phenotypic DST. If Rif is sensitive in the second test, patient should be carefully re -evaluated. A clinical judgement need to be taken into account.

Results of line probe assay for f irst-line drugs

• When LPA detects resistance to both rifampicin and isoniazid: Treat with second line

TB regimen When LPA detects rifampicin resistance but susceptibility to isoniazid:

Treat with second-line TB regimen plus INH. When LPA detect Inh resistance but rifampicin susceptible: perform Xpert MTB/Rif and culture/pDST. Discuss the patient with NTP/DR-TB committee for treatment regimen. When LPA detects susceptibility to both rifampicin and isoniazid: Treat with first-line TB regimen.

• When LPA result is invalid: Repeat test with new sample and refer sample for culture

and pDST.

Whenever possible consider baseline second-line genotypic and phenotypic DST for early detection of resistance to FQ and /or SLI and adjust the regimen accordingly.

Communication of results from culture and DST laboratory All efforts must be made to deliver the culture and pDST results to referring health facilities as soon as available. The laboratory unit and TB officer should arrange reliable and fast mechanisms to return results to the providers. All confirmed drug-resistant TB patients should be linked to the designated treatment centre without delay once the DST results are received from the diagnostic centre. Patients should be provided with the following key information:

• Interpretation of the laboratory results and next action
• Need for clinical evaluation of household and close contacts of the confirmed patient
• Infection control measures at home and community
• Basic information on the nature of the disease
• Treatment modality and duration of treatment
• Treatment sites and mechanism of follow up of treatment
• Expected follow-up visits including necessary laboratory monitoring examinations.

72 National Tuberculosis Control Programme Approach to discordant drug susceptibility testing (DST) results Discordance in DST results may happen, usually when comparing culture-based results (phenotypic DST) with molecular results (genotypic DST). Each individual case of discordant results will need to be investigated in collaboration with laboratory personnel, and treatment regimen decisions should be discussed with the clinical expert committee (CEC). As a general rule, the patient should be treated according to the positive result and highest resistance pattern. DNA sequencing of the TB genome can solve the dilemma when it potentially becomes available in the future.

Different possibilities for potential discordant results are as follows [GLI guidelines}:

1. Xpert MTB/RIF MTB detected, culture negative: treat the patient according to the Xpert MTB/RIF detected result (submit another sample for culture).

Possible reasons for negative cultures in persons with pulmonary TB:

• Patient is being treated for TB;
• Transport or processing problems that inactivates the tubercle bacilli;
• Inadequate testing volume;
• Laboratory or clerical error.

2. Xpert MTB/RIF MTB not detected, culture positive: treat the patient based on the positive culture result.

• The positive culture result should be considered as bacteriological confirmation

of TB (compared with culture, Xpert MTB/RIF can detect the presence of M.

tuberculosis bacteria weeks before culture for 72-98% - higher for smear positives - of patients suspected to have pulmonary TB whose TB is ultimately confirmed by culture [8]);

• Xpert MTB/RIF sensitivity is lower in PLHIV, children, and other specimen types

such as CSF;

• False positive culture results are very rare due to laboratory errors such as cross

contamination and sample labelling problems.

3. Xpert MTB/RIF MTB detected, rifampicin resistance detected; rifampicin susceptible by phenotypic DST: treat the patient according to the Xpert MTB/RIF resistant result and repeat culture and phenotypic DST using solid media.

• Certain mutations are known to generate this discordant result, particularly in the

BACTECTM MGITTM system (e.g. a false-susceptible phenotypic result).

• In some low DR-TB prevalence settings, silent mutations have been observed that

generate a false resistant MTB/RIF result, but these tend to be very rare.

4. Xpert MTB/RIF MTB detected, rifampicin resistance not detected (susceptible);

rifampicin resistance by phenotypic DST: treatment decisions should be based on the culture phenotypic DST rifampicin resistant result.

National Tuberculosis Control Programme 73

• False rifampicin-susceptible Xpert MTB/RIF results are rare but have been

observed in 1–5% of TB cases tested in various epidemiologic settings.

• Mutations in the region of the rpoB gene sampled by the Xpert MTB/RIF tests

have been shown to account for 95–99% of rifampicin resistance. The remainder of rifampicin resistance arises from mutations outside the sampled region, which produce an Xpert MTB/RIF result of rifampicin resistance not detected.

5. Xpert MTB/RIF MTB detected Rifampicin not detected (susceptible); FL LPA rifampicin detected (resistant): treat the patient based on FL LPA (rifampicin resistant).

• This discordance is rare, due to hetero-resistant strains. Different populations of

bacteria are co-existing with varying susceptibility to TB drugs (some are resistant and some sensitive).

• Depending on the treatment and “fitness” of the bacteria, different DST results

from different samples may occur (especially if an interval has elapsed).

• Rifampicin hetero-resistance can be detected in FL LPA (detect absence of wild

type and mutations) but not always in Xpert MTB/RIF (detects resistance by absence of wild type and single copy target of rpoB).

• Culture results can vary too, according to the prevalent population.