Isoniazid resistance profile and associated levofloxacin and pyrazinamide resistance in rifampicin resistant and sensitive isolates/from pulmonary and extrapulmonary tuberculosis patients in Pakistan: A laboratory based surveillance study 2015-19

Clinical presentation and outcome of tuberculosis in chronic kidney disease stage 4 & 5 from a high TB burden country

BACKGROUND

Diagnosis and management of Tuberculosis (TB) in chronic kidney disease (CKD) is challenging. Our aim is to study clinical presentation and outcome in patients with stage 4 & 5 CKD from a high TB burden country.

METHODS

All patients registered in Provincial TB Centre in tertiary care hospital in Pakistan from May 2016 to June 2020 were included. TB cases tested rifampicin resistant (RR) in GeneXpert were excluded from the study. Patients with CKD stage 4 & 5 were studied for demographics, TB history, clinical feature, diagnoses, treatment success and mortality. CKD stage 4 & 5 were compared with other patients registered at the TB treatment center.

RESULTS

Out of 828, 259 (31%) had CKD stage 4 & 5. Out of 259, 156 (60%) had extra-pulmonary TB (EPTB). Microbiological diagnosis done in 118 (45.51%), 25% in EPTB and 72.9% in pulmonary TB (PTB). TB culture was positive in 46 (17.8%), Isoniazid resistance 21.7%. Treatment success was 80.7%. PTB was significantly associated with mortality (p = 0.031). In CKD stage 4 & 5 treatment success was significantly lower with high mortality (p = 0.033).

CONCLUSION

In CKD stage 4 & 5, EPTB is the most common presentation. Microbiological diagnosis could be achieved in one fourth of EPTB. There is high INH resistance. The treatment success is low with high mortality and PTB is a significant risk factor for mortality.

Prevalence and Clinical Implications of Pyrazinamide Resistance in Newly Diagnosed TB Patients in Uganda

Background

Globally, 10.8 million people were diagnosed with tuberculosis during 2023 causing approximately 1.3 million deaths. This study aimed to assess the prevalence and characterization of pyrazinamide resistance by detecting the pncA gene among newly diagnosed Mycobacterium tuberculosis patients attending Bombo General Military Hospital, Central Uganda.

Methods

Cross-sectional study looking at newly diagnosed TB patients in Bombo General Military Hospital. The sputum samples were confirmed TB positive using GeneXpert PCR technology, DNA extraction using the CTAB method, DNA amplification, and finally gel electrophoresis for pncA gene detection.

Results

A total of 166 sputum-positive tuberculosis samples were analyzed. Males were 91/166 (55%), while 115 (70%) of the positive sputum samples were positive HIV status. The majority (96%) of the newly diagnosed Mycobacterium tuberculosis patients showed no detection of rifampicin resistance, while the rest 6/160 (4%) showed indeterminate rifampicin resistance. Of the 52 (31%) patients with positive pncA gene, 29 (56%) had HIV positive status 18 (34%) had unknown HIV status and 5 (10%) had negative HIV status. It was observed that only one patient 1 (2%) showed both rifampicin and pyrazinamide resistance and was a female patient aged 42 years of age with positive HIV status and positive pncA gene status.

Conclusion

This study reveals the important trends regarding drug resistance and its relationship with HIV status. The majority of patients (96%) did not exhibit rifampicin resistance, suggesting that multi-drug-resistant tuberculosis is not widespread among the newly diagnosed cases. The majority (56%) of the patients with the pncA gene mutation, were HIV-positive. This highlights the potential vulnerability of HIV-positive TB patients to multidrug resistance though the overall pyrazinamide resistance rate remains low.

Characterization of isoniazid resistance and genetic mutations in isoniazid-resistant and rifampicin-susceptible Mycobacterium tuberculosis in China

Background

Patients with tuberculosis resistant to isoniazid but susceptible to rifampicin (Hr-Rs TB) remain a neglected demographic, despite a high disease burden and poor outcomes of these patients. The aim of this study was to investigate the characteristics of isoniazid-resistance-related mutations in Mycobacterium tuberculosis and resistance rates to drugs included in WHO-recommended regimens for Hr-Rs patients.

Methods

Mycobacterium tuberculosis isolates (n = 4922) obtained from national tuberculosis drug-resistance surveillance were subjected to whole-genome sequencing to identify Hr-Rs strains. The minimal inhibitory concentrations (MICs) were established for the Hr-Rs strains to determine the isoniazid resistance levels. We also identified drug-resistance-associated mutations for five drugs (fluoroquinolones, ethambutol, pyrazinamide, streptomycin, and amikacin) in the Hr-Rs strains.

Results

Of the 4922 strains, 384 (7.8 %) were Hr-Rs. The subculture of seven strains failed, so 377 (98.2 %) strains underwent phenotypic MIC testing. Among the 384 genotypic Hr-Rs strains, 242 (63.0 %) contained the katG Ser315Thr substitution; 115 (29.9 %) contained the -15C>T in the promoter region of the fabG1 gene; and 16 (4.2 %) contained Ser315Asn in the katG gene. Of the 239 strains with the Ser315Thr substitution, 229 (95.8 %) had MIC ≥ 2 µg/mL, and of the 114 strains with the -15C>T mutation, 103 (90.4 %) had 0.25 µg/mL ≤ MIC ≤ 1 µg/mL. The genotypic resistance rates were 0.8 % (3/384) for pyrazinamide, 2.3 % (9/384) for ethambutol and fluoroquinolones; 39.6 % (152/384) of the strains were resistant to streptomycin, but only 0.5 % (2/384) of the strains were resistant to amikacin.

Conclusion

Ser315Thr in katG was the predominant mutation conferring the Hr-Rs phenotype, followed by the fabG1 -15C>T mutation. The combination of rifampicin, pyrazinamide, ethambutol, and levofloxacin should be effective in the treatment of patients with Hr-Rs tuberculosis because the resistance rates for these drugs in China are low.

Risk assessment and transmission of fluoroquinolone resistance in drug-resistant pulmonary tuberculosis: a retrospective genomic epidemiology study

Fluoroquinolone resistance is a major challenge in treating Multidrug-Resistant Tuberculosis globally. The GenoType MTBDRsl Ver 2.0, endorsed by the WHO, was used to characterize fluoroquinolone resistance. The fluoroquinolone resistance rates in the MDR-TB, Rifampicin-Resistant TB, and non-MDR-TB were 33%, 16.5%, and 5.4%, respectively. The most common mutation found in fluoroquinolone-resistant isolates was D94G (49.5%) in the gyrA gene. Of the 150 MDR-TB isolates, the prevalence of Extensively Drug-Resistant Tuberculosis and pre-XDR-TB was 1.33% and 30%, respectively. Among the 139 RR-TB isolates, pre-XDR-TB prevalence was 15.8%. The fluoroquinolone resistance rates were 5.12% among the 1230 isoniazid-monoresistant isolates. The study found that MDR-TB and RR-TB have higher risk of fluoroquinolone resistance than non-MDR tuberculosis. Rifampicin-resistant isolates with a mutation at codon S450L have a higher risk (RR = 12.96; 95%CI: 8.34-20.13) of developing fluoroquinolone resistance than isolates with mutations at other codons in the rpoB gene. Isoniazid-resistant isolates with a mutation at codon S315T have a higher risk (RR = 2.09; 95%CI: 1.25-3.50) of developing fluoroquinolone resistance. The study concludes that rapid diagnosis of fluoroquinolone resistance before starting treatment is urgently needed to prevent the spread and increase of resistance and to achieve better treatment outcomes in areas where it is higher.

Isoniazid resistance in Rifampicin sensitive pulmonary tuberculosis in children and adolescents

BACKGROUND

Isoniazid (INH) and Rifampicin (RIF) are two crucial drugs used in antitubercular therapy. INH is known for its potent bactericidal effects and has a relatively higher prevalence of resistance compared to RIF. However, RIF resistance has been the subject of more extensive research. On the other hand, Ethambutol (EMB) and Streptomycin (STR) resistance have not been thoroughly studied, particularly in the context of children and adolescents. To address this knowledge gap, a study was designed to investigate the resistance patterns of INH, EMB, and STR in RIF-sensitive pulmonary tuberculosis (PTB) cases among children and adolescents.

METHODS

Seventy-five newly diagnosed RIF sensitive PTB cases up to 18 years of age were enrolled. Retreatment cases were excluded. Sputum/gastric aspirate sample of these patients were sent for culture in Mycobacterium Growth Indicator Tube (MGIT) followed by drug susceptibility testing and Line Probe Assay.

RESULTS

INH, EMB and STR resistance among RIF sensitive PTB cases was found to be 5.7%, 0% and 0.7% respectively. RIF resistance detected by CBNAAT was found to be 8.4%.

CONCLUSION

Detection of INH resistance is as important as detecting RIF resistance as prevalence of INH resistance in RIF sensitive PTB among children and adolescents up to 18 years is around 6%.

TB drug susceptibility testing in high fluoroquinolone resistance settings

BACKGROUND

The insurgence of resistance to key drugs of the BPaLM (bedaquiline + pretomanid + moxifloxacin) regimen is a major concern. In settings with widespread resistance to fluoroquinolones (FQs), like Pakistan, new technologies, such as Xpert® MTB/XDR, may ensure drug resistance upfront screening. This study aims to assess MTB/XDR's performance in detecting FQs and isoniazid resistance, proposing a renewed diagnostic algorithm for drug-resistant TB (DR-TB).

METHODS

This cross-sectional prospective study, approved by the local ethical committee, collected samples from people newly and previously diagnosed with TB over 6 months. Xpert® MTB/RIF Ultra, MTB/XDR, Genotype® MTBDRplus, Genotype® MTBDRsl, culture, and phenotypic drug susceptibility testing (pDST) for relevant drugs (including bedaquiline and levofloxacin) were performed. Next-generation sequencing (NGS) resolved discordances between MTB/XDR and pDST results.

RESULTS

The analysis showed that MTB/XDR has 91.5% and 88.2% sensitivity and 99.5% and 97.7% specificity in detecting respectively isoniazid (INH) and resistance to FQs, demonstrating that MTB/XDR meets the WHO targets for INH resistance detection at the peripheral level. NGS effectively resolved discordances between MTB/XDR and pDST results.

CONCLUSIONS

The obtained results allowed designing the proposed diagnostic algorithm for rapid identification of DR-TB, ensuring rapid and equitable access to drug susceptibility testing for TB, ultimately improving TB care and control.

Establishment and evaluation of an overlap extension polymerase chain reaction technique for rapid and efficient detection of drug-resistance in Mycobacterium tuberculosis

BACKGROUND

Rapid and accurate detection of drug resistance in Mycobacterium tuberculosis is critical for effective control of tuberculosis (TB). Herein, we established a novel, low cost strategy having high accuracy and speed for the detection of M. tuberculosis drug resistance, using gene splicing by overlap extension PCR (SOE PCR).

METHODS

The SOE PCR assay and Sanger sequencing are designed and constructed to detect mutations of rpoB, embB, katG, and inhA promoter, which have been considered as the major contributors to rifampicin (RFP), isoniazid (INH), and ethambutol (EMB) resistance in M. tuberculosis. One hundred and eight M. tuberculosis isolates came from mycobacterial cultures of TB cases at Chongqing Public Health Medical Center in China from December 2018 to April 2019, of which 56 isolates were tested with the GeneXpert MTB/RIF assay. Performance evaluation of the SOE PCR technique was compared with traditional mycobacterial culture and drug susceptibility testing (DST) or GeneXpert MTB/RIF among these isolates. Kappa identity test was used to analyze the consistency of the different diagnostic methods.

RESULTS

We found that the mutations of S531L, S315T and M306V were most prevalent for RFP, INH and EMB resistance, respectively, in the 108 M. tuberculosis isolates. Compared with phenotypic DST, the sensitivity and specificity of the SOE PCR assay for resistance detection were 100.00% and 88.00% for RFP, 94.64% and 94.23% for INH, and 68.97% and 79.75% for EMB, respectively. Compared with the GeneXpert MTB/RIF, the SOE PCR method was completely consistent with results of the GeneXpert MTB/RIF, with a concordance of 100% for resistance to RFP.

CONCLUSIONS

In present study, a novel SOE PCR diagnostic method was successfully developed for the accurate detection of M. tuberculosis drug resistance. Our results using this method have a high consistency with that of traditional phenotypic DST or GeneXpert MTB/RIF, and SOE PCR testing in clinical isolates can also be conducted rapidly and simultaneously for detection of drug resistance to RFP, EMB, and INH.