Mutations in katG and inhA genes of isoniazid-resistant and -sensitive clinical isolates of Mycobacterium tuberculosis from cases of pulmonary tuberculosis and their association with minimum inhibitory concentration of isoniazid

Phenotypic and genotypic drug susceptibility patterns of Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients in Central and Southern Ethiopia

INTRODUCTION

The persistence of tuberculosis (TB) infection in some patients after treatment has highlighted the importance of drug susceptibility testing (DST). This study aimed to determine the drug susceptibility patterns of Mycobacterium tuberculosis (M. tuberculosis) isolates from pulmonary TB (PTB) patients in Central and Southern Ethiopia.

METHODS

A health institution-based cross-sectional study was conducted between July 2021 and April 2022. Sputum samples were collected from newly diagnosed smear microscopy and/or Xpert MTB/RIF-positive PTB patients. The samples were processed and cultivated in Lowenstein-Jensen (LJ) pyruvate and glycerol medium. M. tuberculosis isolates were identified using polymerase chain reaction (PCR) based region of difference 9 (RD9) deletion typing. Phenotypic DST patterns of the isolates were characterized using the BACTEC MGIT™ 960 instrument with SIRE kit. Isoniazid (INH) and Rifampicin (RIF) resistant M. tuberculosis isolates were identified using the GenoType® MTBDRplus assay.

RESULTS

Sputum samples were collected from 350 PTB patients, 315 (90%) of which were culture-positive, and phenotypic and genotypic DST were determined for 266 and 261 isolates, respectively. Due to invalid results and missing data, 6% (16/266) of the isolates were excluded, while 94% (250/266) were included in the paired analysis. According to the findings, 14.4% (36/250) of the isolates tested positive for resistance to at least one anti-TB drug. Gene mutations were observed only in the rpoB and katG gene loci, indicating RIF and high-level INH resistance. The GenoType® MTBDRplus assay has a sensitivity of 42% and a specificity of 100% in detecting INH-resistant M. tuberculosis isolates, with a kappa value of 0.56 (95%CI: 0.36-0.76) compared to the BACTEC MGIT™ DST. The overall discordance between the two methods was 5.6% (14/250) for INH alone and 0% for RIF resistance and MDR-TB (resistance to both INH and RIF) detection.

CONCLUSION

This study reveals a higher prevalence of phenotypic and genotypic discordant INH-resistant M. tuberculosis isolates in the study area. The use of whole-genome sequencing (WGS) is essential for gaining a comprehensive understanding of these discrepancies within INH-resistant M. tuberculosis strains.

MGIT sensitivity testing and genotyping of drug resistant Mycobacterium tuberculosis isolates from Mizoram, Northeast India

PURPOSE

Tuberculosis, a crucial infectious disease is still a health concern globally. India is among the countries with high MDR-TB burden. Currently, sputum smear microscopy using Ziehl Neelsen stain and GeneXpert are the only diagnostic means in Mizoram. This study was done to characterize local tuberculosis strains circulating in Mizoram.

METHODS

Sputum was cultured using MGIT 960 and DST was performed for Streptomycin, Isoniazid, Rifampicin, Ethambutol and Pyrazinamide. GeneXpert test was done simultaneously. DNA was extracted using Trueprep AUTO v2, molbio diagnostics. Antibiotic Resistance Genes and LSP were amplified and sequenced.

RESULTS

Ser315Thr was the most common mutation in katG among MDR-TB isolates. GeneXpert probes A and D drop out upon sequencing showed L511P, H526Q and H526L mutation. The L511P and H526Q mutations were seen in new and treated cases. Discrepancy between MGIT 960 and GeneXpert were observed. LSP-PCR revealed that Indo-Oceanic, East-African Indian, Euro-American and Beijing lineages were found in Mizoram.

CONCLUSION

This study provides mutation information on the resistant genotypes detected with GeneXpert as well as MGIT 960. It also provides information on the lineages of Mycobacterium tuberculosis circulating in the state. Utilization of sequencing technologies is essential in diagnostic laboratories to rule out discrepant results and as a cautionary measure to prevent wrong diagnosis and treatment.

Novel mutations detected from drug resistant Mycobacterium tuberculosis isolated from North East of Thailand

The emergence of drug-resistant tuberculosis is a major global public health threat. Thailand is one of the top 14 countries with high tuberculosis and multi-drug resistant tuberculosis rates. Immediate detection of drug-resistant tuberculosis is necessary to reduce mortality and morbidity by effectively providing treatment to ameliorate the formation of resistant strains. Limited data exist of mutation profiles in Northeastern Thailand. Here, 65 drug-resistant Mycobacterium tuberculosis isolates were used to detect mutations by polymerase chain reaction (PCR) and DNA sequencing. In the katG gene, mutations were occurred in 47 (79.7%) among 59 isoniazid resistant samples. For rpoB gene, 31 (96.9%) were observed as mutations in 32 rifampicin resistant isolates. Of 47 katG mutation samples, 45 (95.7%) had mutations in katG315 codon and 2 (4.3%) showed novel mutations at katG365 with amino acid substitution of CCG-CGG (Pro-Arg). Moreover, out of 31 rpoB mutation isolates, the codon positions rpoB516, rpoB526, rpoB531 and rpoB533 were 3 (9.7%), 8 (25.8%), 11 (35.5%) and 1 (3.2%), respectively. Seven isolates of double point mutation were found [rpoB516, 526; 1 (3.2%) and rpoB516, 531; 6 (19.4%)]. In addition, 1 (3.2%) sample had triple point mutation at codon positions rpoB516, 526 and 531. Common and novel mutation codons of the rpoB and katG genes were generated. Although DNA sequencing showed high accuracy, conventional PCR could be applied as an initial marker for screening drug-resistant Mycobacterium tuberculosis isolates in limit resources region. Mutations reported here should be considered when developing new molecular diagnostic methods for implementation in Northeastern Thailand.

Identifying isoniazid resistance markers to guide inclusion of high-dose isoniazid in tuberculosis treatment regimens

OBJECTIVES

Effective use of antibiotics is critical to control the global tuberculosis pandemic. High-dose isoniazid (INH) can be effective in the presence of low-level resistance. We performed a systematic literature review to improve our understanding of the differential impact of genomic Mycobacterium tuberculosis (Mtb) variants on the level of INH resistance. The following online databases were searched: PubMed, Web of Science and Embase. Articles reporting on clinical Mtb isolates with linked genotypic and phenotypic data and reporting INH resistance levels were eligible for inclusion.

METHODS

All genomic regions reported in the eligible studies were included in the analysis, including: katG, inhA, ahpC, oxyR-ahpC, furA, fabG1, kasA, rv1592c, iniA, iniB, iniC, rv0340, rv2242 and nat. The level of INH resistance was determined by MIC: low-level resistance was defined as 0.1-0.4 μg/mL on liquid and 0.2-1.0 μg/mL on solid media, high-level resistance as >0.4μg/mL on liquid and >1.0 μg/mL on solid media.

RESULTS

A total of 1212 records were retrieved of which 46 were included. These 46 studies reported 1697 isolates of which 21% (n = 362) were INH susceptible, 17% (n = 287) had low-level, and 62% (n = 1048) high-level INH resistance. Overall, 24% (n = 402) of isolates were reported as wild type and 76% (n = 1295) had ≥1 relevant genetic variant. Among 1295 isolates with ≥1 variant, 78% (n = 1011) had a mutation in the katG gene. Of the 867 isolates with a katG mutation in codon 315, 93% (n = 810) had high-level INH resistance. In contrast, only 50% (n = 72) of the 144 isolates with a katG variant not in the 315-position had high-level resistance. Of the 284 isolates with ≥1 relevant genetic variant and wild type katG gene, 40% (n = 114) had high-level INH resistance.

CONCLUSIONS

Presence of a variant in the katG gene is a good marker of high-level INH resistance only if located in codon 315.

Genetic and phenotypic characterizations of drug-resistant Mycobacterium tuberculosis isolates in Cheonan, Korea

BACKGROUND

Mycobacterium tuberculosis (MTB) causes tuberculosis (TB), which is a fatal disease. Cases of drug-resistant MTB have increased in recent years. In this study, we analyzed 7 sites of MTB DNA sequences, including the rpoB and inhA gene, to investigate the relationship between gene mutations and drug resistance in MTB.

METHODS

Mycobacterium tuberculosis liquid culture samples (197 specimens from 74 cases) were collected between June 2015 and May 2016 and sequenced. The results were compared with those obtained from antibiotic susceptibility tests.

RESULTS

In 65 (87.8%) cases, the antibiotic-resistant phenotype was consistent with genotyping results, whereas in 9 (12.2%) cases, there was no match. Eight mutations were detected in the rpoB gene, which showed the highest mutation rate. Sequencing results indicated that these mutations were present in 12 cases.

CONCLUSION

Previously published data on antibiotic resistance genes are insufficient for effective prevention of multidrug- or extensive drug-resistant TB. Additional studies are needed to characterize the complement of antibiotic resistance genes in MTB.