The impact of combined gene mutations in inhA and ahpC genes on high levels of isoniazid resistance amongst katG non-315 in multidrug-resistant tuberculosis isolates from China

Abstract

Whole-genome sequencing was used to analyze the profiles of isoniazid (INH) resistance-related mutations among 188 multidrug-resistant strains of Mycobacterium tuberculosis (MDR-TB) and mono-INH-resistant isolates collected in a recent Chinese national survey. Mutations were detected in 18 structural genes and two promoter regions in 96.8% of 188 resistant isolates. There were high mutation frequencies in katG, the inhA promoter, and ahpC-oxyR regulator regions in INH-resistant isolates with frequencies of 86.2%, 19.6%, and 18.6%, respectively. Moreover, a high diversity of mutations was identified as 102 mutants contained various types of single or combined gene mutations in the INH-resistant group of isolates. The cumulative frequencies of katG 315 or inhA-P/inhA mutations was 68.1% (128/188) for the INH-resistant isolates. Of these isolates, 46 isolates (24.5% of 188) exhibited a high level of resistance. A high level of resistance was also observed in 21 isolates (11.2% of 188) with single ahpC-oxyR mutations or a combination of ahpC-oxyR and katG non-315 mutations. The remaining 17 mutations occurred sporadically and emerged in isolates with combined katG mutations. Such development of INH resistance is likely due to an accumulation of mutations under the pressure of drug selection. Thus, these findings provided insights on the levels of INH resistance and its correlation with the combinatorial mutation effect resulting from less frequent genes (inhA and/or ahpC). Such knowledge of other genes (apart from katG) in high-level resistance will aid in developing better strategies for the diagnosis and management of TB.

Genomic Analysis Identifies Mutations Concerning Drug-Resistance and Beijing Genotype in Multidrug-Resistant Mycobacterium tuberculosis Isolated From China

“…In the present study, There were 90.5% INH-resistant isolates that carried mutations in katG, which was higher than the 86.2% reported by Liu et al (2018) and the 74.5% reported by Luo et al (2019). Liu et al (2018) reported that 47.1% (16/34) INHresistant isolates had inhA promoter mutations combined with a mutation in katG, which was far lower than the 89.3% (25/28) found in our study. One explanation may be that they only sequenced 518 bp of katG while we analyzed the whole sequence of katG.…”

“…Mutations in the katG gene are the major contributors for INH resistance, followed by inhA , ahpC , kasA , ndh , iniABC , efpA , fadE , furA , Rv1592c , and Rv1772 ( Unissa et al, 2016 ). In the present study, There were 90.5% INH-resistant isolates that carried mutations in katG , which was higher than the 86.2% reported by Liu et al (2018) and the 74.5% reported by Luo et al (2019) . Liu et al (2018) reported that 47.1% (16/34) INH-resistant isolates had inhA promoter mutations combined with a mutation in katG , which was far lower than the 89.3% (25/28) found in our study.…”

“…Acquired antibiotic resistance in M. tuberculosis mostly arises from the serial acquisition of point mutations in genes encoding drug targets or drug-activating enzymes. Many known mutations have been identified, e.g., katG 315 and inhA (-15) for isoniazid (INH) resistance ( Liu et al, 2018 ; Luo et al, 2019 ; Unissa et al, 2016 ), 81-bp of rifampicin (RMP) resistant determined region (RRDR) for RMP resistance ( Li et al, 2010 ; Maningi et al, 2018 ; Luo et al, 2019 ), embB 306 for ethambutol (EMB) resistance ( Mokrousov et al, 2002 ; Campbell et al, 2011 ; Moure et al, 2014 ; Zhao et al, 2015a ), and rpsL 44 and rpsL 88 for streptomycin (STR) resistance ( Li et al, 2010 ; Maningi et al, 2018 ). Current molecular diagnostics amplify and detect known drug resistance–associated mutations, and their performance depends on the inclusion of a comprehensive catalog of these mutations.…”

Accuracy of a reverse dot blot hybridization assay for simultaneous detection of the resistance of four anti-tuberculosis drugs in Mycobacterium tuberculosis isolated from China

“…The sensitivity of this study was comparable to that reported from Pakistan (90.6%) [27] but much higher than that from China (80.25%) [28] which both used GenoType MTBDRplus. We speculated that the difference between this study and another study from China [28] may be attributed to that the mutation prevalence of oxyR-ahpC intergenic region were showed in 5-20% INH resistant M. tuberculosis in China [5,29,30], however, GenoType MTBDRplus did not include probes targeted in oxyR-ahpC intergenic region. Previous studies showed that mutations in oxyR-ahpC intergenic region could compensate for loss of KatG/CP activity caused by mutations in katG [31] or were directly associated with low level INH resistance [32].…”

Higher genome mutation rates of Beijing lineage of Mycobacterium tuberculosis during human infection

“…katG encodes catalase peroxidase, an enzyme that converts isoniazid (INH) to its biologically active form 18 . INH resistance commonly occurs due to mutations in the katG gene 19 . In this case, this large deletion in the katG gene region accounts for INH resistance in Isolate D. Large deletions with more than 1 kb were explored in all strains.…”