Pneumonologia i Alergologia Polska 04/2013

Tomasz Jagielski1, Magdalena Grzeszczuk1, Michał Kamiński1, Katarzyna Roeske1, Agnieszka Napiórkowska2, Radosław Stachowiak1, Ewa Augustynowicz-Kopeć2, Zofia Zwolska2, Jacek Bielecki1

1Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw
Head: Prof. J. Bielecki, PhD
2Department of Microbiology, National Tuberculosis and Lung Diseases Research Institute, Warsaw
Head: Prof. E. Augustynowicz-Kopeć, PhD

Identification and analysis of mutations in the katG gene in multidrug-resistant Mycobacterium tuberculosis clinical isolates

Identyfikacja i analiza mutacji w genie katG w szczepach klinicznych Mycobacterium tuberculosis o wielolekooporności typu MDR

This study was financed by the Ministry of Science and Higher Education. “Iuventus Plus” grant. (Project No. IP2011018771)

Address for correspondence: Tomasz Jagielski, PhD, Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw; ul. I. Miecznikowa 1, 02–096 Warszawa. Tel.: +48 22 55 41 312; Fax: +48 22 55 41 402, e-mail: t.jagielski@biol.uw.edu.pl
Praca wpłynęła do Redakcji: 14.09.2012

Abstract

Introduction: A major role in the development of resistance of Mycobacterium tuberculosis to isoniazid (INH) is attributed to mutations in the katG gene coding for the catalase/peroxidase, an enzyme required for obtaining a pharmacologically active form of the drug. Analysis of mutations in the katG gene in M. tuberculosis strains may contribute to the development of reliable and rapid tests for detection of INH resistance.

The aim of the study was to identify and characterize mutations in the katG gene in multidrug-resistant M. tuberculosis clinical isolates.

Material and methods: The study included 46 strains of M. tuberculosis, recovered from MDR-TB patients in Poland in 2004. Mutations in the katG gene were detected by comparing DNA sequences with the corresponding sequence of a wild-type reference laboratory strain (M. tuberculosis H37Rv). The obtained results were interpreted in the context of MIC values of INH and catalase activity of the strains tested.

Results: A total of 43 (93%) strains contained mutations in the katG gene. The most frequently observed were mutations at codon 315, found in 34 (74%) strains. Mutations at other codons were rare: 4 strains contained mutations at codon 463, 2 at codon 131 and another 2 at codon 234. Mutations at codons 68, 91, 101, 126, 128 and 194 were found in single strains only. Two strains, for which no mutations at codon 315 of the katG gene were identified, had a unique translation termination mutation, which would invariably result in polypeptide truncation leading to the generation of dysfunctional catalase polypeptides. Both these strains presented the highest MIC values for INH (80 and 100 µg/mL) and showed a complete loss of catalase activity. For the remaining 41 strains with katG mutations, the MICs of INH were within the range 0.2–10 µg/mL. Thirty-six (88%) of those strains retained their catalase activity.

Conclusions: Mutations at codon 315 within the katG gene, depending on their type might be useful for the prediction of INH resistance. Whereas the missense mutations do not affect the catalase activity or the level of INH resistance, the nonsense mutations result in high-level resistance to INH and a total loss of catalase activity.

Key words: sequence analysis, tuberculosis, katG, mutations, Mycobacterium tuberculosis, multidrug resistance

Pneumonol. Alergol. Pol. 2013; 81: 298–307

Streszczenie

Wstęp: Główną rolę w kształtowaniu oporności prątków gruźlicy (Mycobacterium tuberculosis) na izoniazyd (INH) przypisuje się mutacjom w genie katG kodującym białko katalazy/peroksydazy, enzym niezbędny do otrzymania aktywnej farmakologicznie formy leku. Analiza występowania mutacji w genie katG w szczepach M. tuberculosis może być podstawą dla opracowania wiarygodnych i szybkich testów wykrywania INH-oporności.

Celem pracy jest dentyfikacja i charakterystyka mutacji w genie katG w szczepach klinicznych M. tuberculosis o wielolekooporności typu MDR.

Materiał i metody: Badanie objęło 46 szczepów wyizolowanych od chorych na gruźlicę MDR w Polsce w 2004 roku. Mutacje wykrywano, analizując sekwencje genu katG (2 223 pz) w porównaniu z sekwencją genu katG w szczepie M. tuberculosis H37Rv. Wyniki sekwencjonowania interpretowano w kontekście miana oporności na INH oraz aktywności katalazowej badanych szczepów.

Wyniki: Mutacje w genie katG wykryto w 43 (93%) szczepach. Najczęściej obserwowaną była mutacja w kodonie 315, którą stwierdzono w 34 (74%) szczepach. Mutacje w innych kodonach występowały znacznie rzadziej; w 4 szczepach wykryto zmianę w kodonie 463, w 2 — w kodonie 131, a w innych 2 — w kodonie 234. Mutacje w kodonach 68, 91, 101, 126, 128 i 194 dotyczyły pojedynczych szczepów.

W 2 szczepach wykryto pojedyncze mutacje typu nonsens, które, wprowadzając przedwczesne kodony terminacji translacji, powodowały powstanie skróconego, niefunkcjonalnego białka katalazy. Szczepy te charakteryzowały się najwyższym mianem oporności na INH (MIC = 80 i 100 µg/ml) oraz całkowitą utratą aktywności katalazy. Dla pozostałych 41 szczepów niosących mutacje w genie katG, wartości MIC INH mieściły się w zakresie 0.2–10 µg/ml. Trzydzieści sześć (88%) spośród tych szczepów miało dodatni odczyn katalazy.

Wnioski: Rodzaj mutacji w kodonie 315 genu katG może służyć jako czynnik predykcyjny oporności na INH. Mutacje typu missens nie wpływają na aktywność katalazy oraz miano oporności na INH. Mutacje typu nonsens skutkują wysokim mianem INH-oporności oraz utratą aktywności katalazy.

Słowa kluczowe: analiza sekwencyjna, gruźlica, katG, mutacje, Mycobacterium tuberculosis, oporność typu MDR

Pneumonol. Alergol. Pol. 2013; 81: 298 – 307

Introduction

Tuberculosis (TB) is still one of the greatest threats to human health in the contemporary world. It is estimated that 1/3 of the human population (more than 2 billion people) is infected with Mycobacterium tuberculosis. About 9 million new TB cases and 2 million deaths from the disease are noted each year [1]. The biggest challenge for a control and treatment system of TB is multidrug resistance of Mycobacterium tuberculosis. The multidrug resistance (MDR), i.e. resistance of mycobacteria to at least isoniazid (INH) and rifampicin (RMP), which are key drugs used in anti-TB therapy, is of crucial importance. It is estimated that MDR-TB constitutes about 5% of all TB cases in the world. In Poland multidrug resistance concerns almost exclusively previously treated patients. The proportion of MDR-TB cases in this group of patients is about 8% [2].

A significant parameter, which describes the phenotype of drug-resistant strains of M. tuberculosis, including MDR strains, is the enzymatic activity of the catalase-peroxidase system. In the middle of the previous century it was shown that many INH-resistant strains are characterized by a partial or complete loss of catalase and peroxidase activity [3,4,5]. This phenomenon has been used for diagnostic purposes. The examination of catalase activity has become an easy and rapid test that allows the susceptibility of clinical isolates to INH to be asessed.

Genetic research conducted in the early 1990s has been of vital importance in explaining the relation between catalase activity of mycobacteria and their resistance to INH. Zhang et al. proved that transformation of the INH-resistant strains of Mycobacterium smegmatis and M. tuberculosis, made with the help of the functional katG gene coding for catalase-peroxidase protein (KatG), restored these strains’ sensitivity to INH [6,7]. Hence it has been proved that KatG plays a major role in the biological activity of INH and the conditions the susceptibility of mycobacteria to this drug. However, the molecular mechanisms behind the INH activity are still unknown. Generally, it is assumed that INH is a prodrug, which after penetrating into the pathogen’s cell is oxidized — in the reaction catalysed by KatG — to pharmacologically active derivatives. Then they form adducts with molecules of the NAD+ or NADP+ coenzyme. These adducts operate as inhibitors of the enzyme participating in the biosynthesis of nucleic acids and mycolic acids, the latter being constituents of the mycobacterial cell wall [8].

The katG gene deletion observed in some INH-resistant strains has proven to be the main mechanism of resistance to INH. This hypothesis has not been confirmed by numerous subsequent studies. They have shown that a complete katG gene deletion occurs rarely and usually concerns strains with a high level of INH resistance (MIC > 5 μg/mL) [9,10,11,12]. Currently it is considered that the main role in developing INH resistance is played by spontaneous mutations in the katG gene. They are usually single point mutations (missense mutations) or small (from 1 to 3 nucleotides) insertions or deletions. It is important that single mutations occur at different frequencies and influence, in various ways, the activity of the KatG protein. The phenotypic effect of mutations, i.e. changed enzymatic activity of KatG, is evaluated in the in vitro tests.

The purpose of this study was to investigate the occurrence of mutations in the katG gene of multidrug-resistant M. tuberculosis clinical isolates recovered from MDR-TB patients in Poland in 2004.

Material and methods

Bacterial strains

The study included 46 strains of M. tuberculosis, which are part of the collection of the Department of Microbiology of the National Tuberculosis and Lung Diseases Research Institute in Warsaw. The strains were isolated from 46 Polish patients, diagnosed with TB in 20 medical facilities located in 11 provinces, and from whom MDR M. tuberculosis were cultured during the 12 months from January 1st to December 31st, 2004.

The culture of mycobacterial strains was done using a conventional method on Löwenstein-Jensen (L.-J.) medium [13].

Species identification was performed with the help of the niacin test, NAP test (the Bactec 460-Tb system), genetic probe AccuProbe (Gen-Probe), ProbeTec (Becton-Dickinson) and the analysis of mycolic acids by high pressure liquid chromatography (Varian).

Drug susceptibility testing

Drug susceptibility of M. tuberculosis strains was determined in subculture on L.-J. medium, in accordance with the methodology applied in all mycobacteria laboratories in Poland. Briefly, the following drug concentrations were used: 0.2 µg/mL for INH, 40 µg/mL for RMP, 4 µg/mL for streptomycin (SM) and 2 µg/mL for ethambutol (EMB). The strains whose growth was at least 1% of that on drug-free medium, and with resistance ratio (RR) at least four times higher in relation to the reference strain H37Rv (RR ≥ 4), were recognized as resistant [13].

To determine the minimal inhibitory concentration (MIC) of INH for the studied strains, a series of 10 different concentrations, i.e. 0.2, 0.5, 1, 2.5, 5, 10, 20, 40, 80 and 100 µg/mL was used.

Catalase activity

The catalase activity of M. tuberculosis strains was determined semi-quantitatively using the Kubica method [14]. The catalase activity was expressed as the height of the foam column (h), measured in millimetres. The following scale was used: h ≤ 5, negative reaction; h > 5, positive reaction; h > 45, strongly positive reaction.

DNA isolation

Isolation of chromosomal DNA of mycobacteria was conducted from the culture on L.-J. medium, according to the method using cetyltrimethylammonium bromide (CTAB) [15].

Detection of mutations in the katG gene

Mutations in the katG gene were detected by sequencing the entire gene, obtained as a result of amplification performed by PCR method, as described by Cardoso et al. [16].

Amplification of the katG gene (2,223 pz) was performed in 4 PCR assays (A-D), with the primers, using the following scheme: 1. KatG-1-KatG-5 (A); 2. KatG-4-KatG-9 (B); 3. KatG-8-KatG-13 (C); 4. KatG-12-KatG-14 (D) (Tab. 1).

Reaction mixtures were prepared by using a TopTaq MasterMix (Qiagen). The mixture of a final volume of 50 μL contained: 25 μL 2x TopTaq MasterMix (final concentration 1x), 0.5 μL of each primer (final concentration 0.2 μM), 22 μL of water and 2 μL of template genomic DNA (earlier diluted with water in a ratio of 1:50). The following PCR conditions were used: 95°C for 5 min (initial denaturation), followed by 35 cycles of: 95°C for 30 s, 68°C or 62°C (only in amplification with primers KatG-12-KatG-14) for 30 s and 72°C for 1 min. The final elongation step was performed at a temperature of 72°C for 7 min.

Homogeneity of PCR products was assessed electrophoretically. Electrophoresis was conducted in 1.5% agarose gels in TBE buffer. The gels were stained with ethidium bromide (0.5 µg/mL), and the DNA was visualized under UV light. The gel images were captured and analysed using ImageMaster® VDS (Video Documentation System) software (Amersham Pharmacia Biotech.).

The obtained PCR products were purified by using a PCR “Clean Up” kit (A&A, Biotechnology), according to the manufacturer’s instructions.

The purified PCR products of at least 10 ng/µL concentration were sequenced by using the ABI PRISM 310 analyser (Applied Biosystems, CA, USA). Sequencing was performed in both forward and reverse directions (i.e. 5’→3’ and 3’→5’). Sequencing was done with the help of the same primers used for thePCR amplification of the katG gene (Tab. 1).

 

Table 1. Primers used for PCR amplification and sequencing of thekatG gene ofM. tuberculosis and their basic characteristics

Primer designation Sequence(5’ → 3’) Location (bp)b TaC)c PCR product size(bp)
X68081a KatG–1 GCCCGATAACACCAACTCCTG 1947–2606 68 680
KatG–5 CAGATCCCGCTACCGCTGTA
KatG–4 CCTGGCTCGGCGATGA 2586–3213 68 648
KatG–9 CTCGGTGGATCAGCTTGTACC
KatG–8 GAGGAATTGGCCGACGAGTT 3182–3828 68 667
KatG–13 TCTCAGGGGCACTGAGCGTAA
KatG–12 GCCGAGTACATGCTGCTCGAC 3794–4229 62 452
KatG–14 CGGCGGGTTGTGGTTGA

 

aGenBank accession number for the M. tuberculosis H37Rv katG gene
bPositioning of the primers; Numbers refer to the nucleotide position within the referenced GenBank sequence (X68081)
cAnnealing temperature of the primers

Analysis of the obtained nucleotide sequences was conducted using Chromas 1.45 software and programs from the EMBOSS package (Matcher, Revseq, Transeq). Sequences were analysed by comparing with the wild-type katG gene sequence originating from the M. tuberculosis H37Rv reference strain available in GenBank (GenBank accession number: X68081).

Results

The occurrence of mutations in the katG gene in 46 MDR-resistant M. tuberculosis strains with different resistance levels to INH and different catalase activity was investigated.

Electrophoretic separation of 4 products of the katG gene amplification revealed, for each of the studied strains, the presence of a single DNA band of an expected size of 680, 648, 667 and 452 bp, for the katG gene fragments amplified by using primers KatG-1-KatG-5 (A), KatG-4-KatG-9 (B), KatG-8-KatG-13 (C) and KatG-12-KatG-14 (D), respectively (Fig. 1).

Among the 46 examined M. tuberculosis strains, mutations in the katG gene were found in 43 strains (93%). Three strains did not show any mutation in the katG gene sequence (Tab. 2). Among strains with an altered katG gene sequence, 34 (74%) had mutations at nucleotide position 944; in 32 strains (69%) it was transition G→C, in 1 strain (no. 4832) it was transversion G→T, and in one strain (no. 1377) it was transversion G→A. Mutations other than those at position 944 were rare. Mutation at position 1388 (G→T) was found in 4 strains (nos. K131, 3430, 3020 and 1334). Mutation at position 392 was found in 2 strains; in one case it was transition C→G (strain no. 101), in another - transversion C→A (535). In two strains (nos. 11420 and 12489) mutation at position 945, being a transversion C→T was found. In another two strains (nos. 590 and 5895) mutation at position 701 (C→G) was discovered. Furthermore, substitutions were found in single strains at the following positions: 203 (T→G) (strain no. 590), 271 (T→C) (4991), 302 (T→C) (2497), 378 (G→A) (103), 383 (G→A) (4619), 580 (G→T) (101) and 1360 (G→T) (590).

All discovered mutations were point mutations and relied on substitution of individual nucleotides. Only one strain (no. 5895) had a mutation which was an insertion of thymine at position 135 (insT135).

As for the number of mutations per individual strains, 35 strains (76%) had single mutations in the katG gene, whereas 8 (17%) had one or two additional mutations. More precisely, 3 strains had, apart from a mutation at position 944, a change at position 1388 (strains nos. K131, 3430, 1334), 2 strains had mutations at positions 944 and at position 945 (11420, 12489), one strain had mutations at positions 392 and 580 (no. 101), and another strain (5895) — at positions 135 and 701. Only one strain (no. 590) had 3 mutations, i.e. at positions 203, 701 and 1360.

Among the 16 different changes at the nucleotide sequence level, 14 resulted in amino acid substitution in the polypeptide chain of KatG (Fig. 2). It concerned mainly codon 315 (34 tested strains (74%)) resulting in 94% of the strains (32 strains), in substitution Ser→Thr. At the nucleotide sequence level it concerned AGC→ACC substitution for 30 strains (88% of strains with mutation at this codon) or AGC→ACT substitution for 2 strains. Two other mutations at codon 315 were changes Ser→Asn (AGC→AAC) and Ser→Ile (AGC→ATC), both found in single strains. The Arg→Leu (CGG→CTG) substitution within the KatG codon 463 was observed in 4 strains (9%). In two cases there was a change in codon 131: in the first case it was Pro→Gln (CCG→CAG) and in the second — Pro→Arg (CCG→CGG). The substitution Ala→Gly (GCG→GGG) within the KatG codon 234 was noted in the next two strains. In the remaining cases only single mutations were present: Val68Gly (GTG→GGG), Trp91Arg (TGG→CGG), Leu101Pro (CTG→CCG), Met126Ile (ATG→ATA), Arg128Gln (CGG→CAG) and Asp194Tyr (GAT→TAT).

Figure 1. Products of the amplification of the entire katG gene in 4 PCR assays (A–D) generated for two selected M. tuberculosis strains (nos. 590 and 5895); MW, molecular weight marker (PerfectTM 100 bp DNA Ladder, EURx)

Among the 43 strains in which mutations in the katG gene sequence occurred, in 41 (95%) strains the mutations led to amino acid substitutions in the KatG peptide chain (the missense mutations). In 2 strains single nonsense mutations were demonstrated. By introducing unique translation termination codons (STOP), these mutations resulted in polypeptide truncation. While transversion G→T at position 1360 generated codon STOP (TAG) at position 454 of the amino acid sequence, an insertion of thymine at position 135 (insT135) generated a frameshift mutation and produced termination codon (TAA) at protein position 46. As a result of the described mutations, catalase polypeptide was shortened by 287 and 695 amino acid residues, accordingly, as compared to the wild-type protein (740 amino acids).

Thirty-seven (80%) strains had single substitutions in the amino acid sequence of the KatG. Six (13%) strains had additional changes: in 3 cases next to the change Ser315Thr, substitution Arg463Leu (strains nos. K131, 3430, 1334) was found; a change being a substitution Ala234Gly and another introducing codon STOP (5895) were discovered in one strain, whereas changes Pro131Arg and Asp194Tyr (101) were found in another strain. One strain (no. 590) had 3 different changes: Val68Gly, Ala234Gly and Glu454STOP.

Among the 43 strains with mutations within the katG gene, thirty-six (84%) retained catalase activity (Tab. 2). In the group of strains without mutations, catalase reaction was positive in 2 strains (nos. 6679 and 11844), whereas in the case of one strain (73) the reaction was negative. Thirty-two (94%) out of 34 strains with mutations associated with codon 315 showed catalase activity: in 20 strains the catalase reaction was positive, and in 12 strains it was strongly positive. Two strains (nos. 1114 and 647) showed no catalase activity.

The MIC values for INH in strains with mutations in the katG gene were within the range of the following concentrations: 0.1 µg/mL ≤ MIC ≤ 100 µg/mL. The MICs for INH of strains with a wild--type version of of the katG gene were 1 µg/mL for 2 strains (nos. 6679 and 11844) and 10 µg/mL for one strain (no. 73). The MICs for strains with mutations at codon 315 ranged as follows: 1 ≤ MIC ≤ 10 µg/mL. For the majority of these strains (26 strains, 76%) the MIC value of INH was 2.5 µg/mL (Tab. 2).

Figure 2. Schematic representation of the katG gene mutations identified among 46 multidrug-resistant M. tuberculosis strains, evaluated in this study. Nucleotide alleles and corresponding amino acid alleles at which mutations occurred are indicated by their codon positions in light grey boxes at the top and bottom of the figure, respectively. Number and percentage of strains bearing the specific mutation are given in brackets

Discussion

According to different studies, mutations in the katG gene occur in 50-95% of INH-resistant strains [11,12,16,17,18,19]. The most commonly observed mutations in locus katG are substitutions at codon 315. The most frequent is transition G→C (AGC→ACC), resulting in the replacement of serine with threonine (Ser→Thr) in the amino acid chain. Much more unusual are other nucleotide substitutions generating codons: ACA (Thr), ATC (Ile), AGA (Arg), AGG (Arg), CGC (Arg), AAC (Asn) and GGC (Gly) [11,12,16,18,19,20,21,22,23,24,25,26,27,28,29,30,31]. The frequency at which mutations at codon 315 of the katG gene occur differs between geographical regions. Such mutations have been discovered in 97% of INH-resistant strains isolated in South Africa [32], 86–94% of strains isolated in Russia, Lithuania and Latvia [24,33,34], 60-87% in Brazil [16,35], about 65% in Australia, China and Kuwait [12,22,27], 53% in the Netherlands [36], 46% in Spain [37] and 38% in Italy [38]. A relatively small proportion of mutations at codon 315 have been noted in INH-resistant strains obtained from patients from Japan (28%) [21], even lower from patients from Finland (7%) [32], and the lowest from South Korea and the United States (4%) [39]. Pretorius et al. described 39 INH-resistant strains isolated from patients from South Africa, the United States and Switzerland, all of which had an unchanged (wild-type) version of the katG gene [40].

Thus far there have been only two studies on genetic determination of INH resistance in M. tuberculosis strains from Poland. Molecular analysis conducted by Sajduda et al. has shown that 55 (66%) out of 83 INH-resistant strains had mutations at codon 315 within the katG gene. Fifty (90%) strains had the most frequent mutation AGC→ACC [41]. In another study, Wojtyczka et al., while investigating the occurrence of mutation Ser315Thr among 23 INH-resistant strains (including 6 MDR strains) isolated from patients from Silesia, found it only in 2 strains (9%) (including 1 MDR strain) [42].

 

Table 2. Mutations in the katG gene, identified among 46 multidrug-resistant M. tuberculosis strains and their selected phenotypic characteristics

No. Strain no. Drug resistance profile a MIC INH [μgx ml–1] Catalase activity b Changes identified at c:
Nucleotide level Amino acid level
1. 101 INH+RMP 1 > 45 C → G (392)
G → T (580)
Pro → Arg (131)
Asp → Tyr (194)
2 124 SM+INH+RMP+EMB 2.5 34 G → C (944) Ser → Thr (315)
3. 4991 INH+RMP+EMB 1 3 T → C (271) Trp → Arg (91)
4. 1334 SM+INH+RMP 2.5 > 45 G → C (944)
G → T (1388)
Ser → Thr (315)
Arg → Leu (463)
5. 9310 SM+INH+RMP 1 7 G → C (944) Ser → Thr (315)
6. 2497 SM+INH+RMP 0.1 > 45 T → C (302) Leu → Pro (101)
7. 4619 SM+INH+RMP+EMB 0.5 > 45 G → A (383) Arg → Gln (128)
8. 4202 SM+INH+RMP 2.5 11 G → C (944) Ser → Thr (315)
9. 4365 SM+INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
10. 3312 SM+INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
11. 1885 SM+INH+RMP 2.5 26 G → C (944) Ser → Thr (315)
12. 5325 SM+INH+RMP+EMB 2.5 > 45 G → C (944) Ser → Thr (315)
13. 794 SM+INH+RMP 2.5 34 G → C (944) Ser → Thr (315)
14. 692 SM+INH+RMP 2.5 8 G → C (944) Ser → Thr (315)
15. 6679 SM+INH+RMP+EMB 1 6
16. 535 INH+RMP 1 4 C → A (392) Pro → Gln (131)
17. 874 SM+INH+RMP 2.5 11 G → C (944) Ser → Thr (315)
18. 434 SM+INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
19. 469 INH+RMP 10 10 G → C (944) Ser → Thr (315)
20. 3832 SM+INH+RMP+EMB 2.5 > 45 G → C (944) Ser → Thr (315)
21. 524 SM+INH+RMP 2.5 27 G → C (944) Ser → Thr (315)
22. 590 SM+INH+RMP 100 0 T → G (203)
C → G (701)
G → T (1360)
Val → Gly (68)
Ala → Gly (234)
STOP (454)
23. 12489 SM+INH+RMP 1 27 G → C (944)
C → T (945)
Ser → Thr (315)
24. 11420 INH+RMP 1 32 G → C (944)
C → T (945)
Ser → Thr (315)
25. 2575 INH+RMP 2.5 8 G → C (944) Ser → Thr (315)
26. 456 INH+RMP 2.5 22 G → C (944) Ser → Thr (315)
27. 1114 INH+RMP 2.5 3 G → C (944) Ser → Thr (315)
28. 1377 SM+INH+RMP 2.5 > 45 G → A (944) Ser → Asn (315)
29. 17170 INH+RMP 2.5 10 G → C (944) Ser → Thr (315)
30. 2688 INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
31. 947 INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
32. 3298 SM+INH+RMP 1 19 G → C (944) Ser → Thr (315)
33. 11844 SM+INH+RMP 1 16
34. 2233 SM+INH+RMP+EMB 2.5 16 G → C (944) Ser → Thr (315)
35. 3020 SM+INH+RMP+EMB 2.5 43 G → T (1388) Arg → Leu (463)
36. 3430 SM+INH+RMP 2.5 10 G → C (944)
G → T (1388)
Ser → Thr (315)
Arg → Leu (463)
37. K131 SM+INH+RMP 10 37 G → C (944)
G → T (1388)
Ser → Thr (315)
Arg → Leu (463)
38. 1233 INH+RMP 2.5 >45 G → C (944) Ser → Thr (315)
39. 5895 INH+RMP 80 0 insT (135)
C → G (701)
STOP (46)
Ala → Gly (234)
40. 446 SM+INH+RMP 2.5 17 G → C (944) Ser → Thr (315)
41. 2086 SM+INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
42. 103 SM+INH+RMP 2.5 4 G → A (378) Met → Ile (126)
43. 1612 SM+INH+RMP 2.5 > 45 G → C (944) Ser → Thr (315)
44. 4832 SM+INH+RMP 10 18 G → T (944) Ser → Ile (315)
45. 73 INH+RMP+EMB 10 2
46. 647 INH+RMP 5 3 G → C (944) Ser → Thr (315)

 

a INH, isoniazid; RMP, rifampicin; SM, streptomycin; EMB, ethambutol
b Catalase activity according to Kubica test, measured (in millimetres) as the height of the foam column
c Nucleotide or amino acid positions are given in brackets

In this study, the presence of mutation at codon 315 was found in 34 (74%) out of 46 MDR-TB strains (for 32 strains it was mutation Ser315Thr, which in case of 30 strains was a AGC→ACC substitution).

All but 2 strains (32; 94%) with mutation at codon 315 were catalase-positive, which indicates that this type of mutation does not adversely influence the enzymatic activity of the KatG protein. Similarly, studies by other authors have proved that the majority of INH-resistant strains with mutations at codon 315 retained their catalase activity [11,17,18,20] (differences in the level of the enzymatic activity that occur between these strains may be a result, for example, of the presence of additional mutations in the katG gene). In order to find the physiological role of the mutation at codon 315, Wengenack et al. compared the enzymatic activity of the wild-type protein KatG with the KatG protein bearing a single Ser315Thr mutation [43]. They showed that the mutated protein retained significant catalase activity while showing a lowered ability to activate INH. The loss of the ability to metabolize INH is due to the fact that mutation Ser315Thr changes the stereochemical structure of the protein that decreases its affinity to the drug [44]. Furthermore, as it has been proven on a mouse model that the virulence of the katG Ser315Thr mutants is similar to that observed in wild-type strains [45]. Analysis of the phenotype of M. tuberculosis strains with the katG Ser315Thr mutation shows explicitly that it is physiologically profitable. The high prevalence of this mutation among INH-resistant strains may be attributed to the positive selective pressure.

A number of studies have shown that the presence of a mutation at codon 315 in the katG gene is often associated with a high level of INH resistance (MIC ≥ 4 μg/mL) [12,16,17,25,35,36]. This correlation was confirmed only partially by the results of the present study. All strains with mutations at codon 315 had their MIC values for INH within the range of 1–10 μg/mL. For the majority of these strains (26, 76%) the MIC value was 2.5 μg/mL.

Among the strains in which mutations at codon 315 were absent, 2 strains had the highest level of INH resistance (MIC = 80 and 100 μg/ml). These strains were also the only ones for which the catalase reaction was entirely negative (h = 0).
In the katG sequence of these two strains the presence of single nonsense mutations (Lys46STOP, Glu454STOP) was reported. These mutations led to catalase polypeptide truncation and thus abolished its enzymatic activity. It is plausible that the lack of functional KatG also conditioned a particularly high resistance to INH in those strains, as can be seen in the case of katG gene deletion [9,10,11,12].

Many authors emphasize the usefulness of the analysis of mutation at codon 315 (mainly Ser315Thr) in the katG gene for detecting resistance to INH in M. tuberculosis. The diagnostic value of such analysis is particularly important in countries with high TB prevalence and high TB transmission rate of drug-resistant M. tuberculosis strains. Here, mutations at codon 315 occur in more than 90% of INH-resistant strains [32,33,34,46]. However, in countries where the frequency of mutations at codon 315 is significantly lower, the usefulness of finding such mutations such mutations for the detection of INH resistance is rather limited. Although mutations at codon 315 within the katG gene occur only in some MDR M. tuberculosis strains, which was confirmed by the present study (such mutations were absent in a quarter of the studied MDR-resistant strains), examination of their occur­rence may serve as a rapid screening test for drug resistance. Such an approach is justified by the fact that the above mensioned mutations are 100% specific for INH-resistant strains, and their identification takes significantly less time than determination of drug resistance using a conventional method. Amplification techniques used for detecting mutations associated with drug resistance do not require the growth of mycobacteria and may be applied directly to clinical specimens [47].

A fast screening test for mutations at codon 315 may be of great significance for detection of MDR resistance. According to many authors, mutations at codon 315 in the katG gene occur more frequently in MDR strains than in the INH-monoresistant strains [24,26,36,48]. Additionally, 78–94% of MDR tubercle bacilli harbour these mutations [24,31,34,46]. One of the hypotheses explaining this phenomenon assumes that mutations within katG codon 315 increase the fitness of mycobacteria, thus strengthening their ability to survive in the human host, be transmitted, and develop complex drug resistance patterns [26]. This hypothesis has recently been supported by the studies of van Doorn et al. from the Netherlands [49] and Gagneux et al. from San Francisco [50], who demonstrated that INH-resistant M. tuberculosis strains with mutations at codon 315 (especially Ser315Thr mutation) are more frequently involved in recent TB transmission than other INH-resistant strains without this mutation.

Conclusions

Mutations in the katG gene were found in 43 (93%) of the MDR M. tuberculosis strains tested. The most frequent mutation was substitution at codon 315, which was demonstrated in 34 (74%) strains. The presence of mutations at this codon may serve as a predictive factor for INH resistance.

Among the 16 different mutations discovered at the level of the katG nucleotide sequence, 14 (87.5%) resulted in the amino acid change in the KatG polypeptide chain (the missense mutations). In the case of 2 strains, single nonsense mutations were disclosed. By introducing unique translation termination codons, they led to polypeptide truncation.

While the missense mutations did not influence catalase activity or the level of INH resistance, the nonsense mutations resulted in a high level of INH resistance and a complete loss of catalase activity.

Conflict of interest

The authors declare no conflict of interest.

References:

  1. Jagielski T., Augustynowicz-Kopeć E., Zwolska Z. Epidemiologia gruźlicy w perspektywie świata, Europy i Polski. Wiad. Lek. 2010; 63: 230–246.
  2. Jagielski T., Augustynowicz-Kopeć E., Zwolska Z. Epidemiologia gruźlicy lekoopornej: świat–Europa–Polska. Wiad. Lek. 2010; 63: 345–357.
  3. Hedgecock L.W., Faucher I.O. Relation of pyrogallol-peroxidative activity to isoniazid resistance in Mycobacterium tuberculosis. Am. Rev. Tuberc. 1957; 75: 670–674.
  4. Middlebrook, G. Isoniazid-resistance and catalase activity of tubercle bacilli; a preliminary report. Am. Rev. Tuberc. 1964; 69: 471–472.
  5. Tirunarayanan M.O., Vischer W.A. Relationship of isoniazid to the metabolism of mycobacteria; catalase and peroxidase. Am. Rev. Tuberc. 1957; 75: 62–70.
  6. Zhang Y., Garbe T., Young D. Transformation with katG restores isoniazid-sensitivity in Mycobacterium tuberculosis isolates resistant to a range of drug concentrations. Mol. Microbiol. 1993; 8: 521–524.
  7. Zhang Y., Heym B., Allen B., Young D., Cole S. The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature 1992; 358: 591–593.
  8. Timmins G.S., Deretic V. Mechanisms of action of isoniazid. Mol. Microbiol. 2006; 62: 1220–1227.
  9. Ferrazoli L., Palaci M., Telles M.A., i wsp. Catalase expression, katG, and MIC of isoniazid for Mycobacterium tuberculosis isolates from Sao Paulo, Brazil. J. Infect. Dis. 1995; 171: 237–240.
  10. Goto M., Oka S., Tachikawa N., i wsp. KatG sequence deletion is not the major cause of isoniazid resistance in Japanese and Yemeni Mycobacterium tuberculosis isolates. Mol. Cell. Probes 1995; 9: 433–439.
  11. Ramaswamy S.V., Reich R., Dou S.J. i wsp. Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 2003; 47: 1241–1250.
  12. Zhang M., Yue J., Yang Y.P. i wsp. Detection of mutations associated with isoniazid resistance in Mycobacterium tuberculosis isolates from China. J. Clin. Microbiol. 2005; 43: 5477–5482.
  13. Zwolska Z., Augustynowicz–Kopeć E., Klatt M. Pierwotna i nabyta lekooporność prątków gruźlicy w Polsce. Pneumonol. Alergol. Pol. 1999; 67: 536–545.
  14. van Embden J.D., Cave M.D., Crawford J.T. i wsp. Strain identification of Mycobacterium tuberculosis by DNA fingerprinting: recommendations for a standardized methodology. J. Clin. Microbiol. 1993; 31: 406–409.
  15. Youmans, G.P. The laboratory diagnosis of mycobacterial disease. Philadelphia: W. B. Saunders Co. 1979; 430–431.
  16. Cardoso R.F., Cooksey R.C., Morlock G.P. i wsp. Screening and characterization of mutations in isoniazid–resistant Mycobacterium tuberculosis isolates obtained in Brazil. Antimicrob. Agents Chemother. 2004; 48: 3373–3381.
  17. Coll P., Aragon L.M., Alcaide F. i wsp. Molecular analysis of isoniazid and rifampin resistance in Mycobacterium tuberculosis isolates recovered from Barcelona. Microb. Drug Resist. 2005; 11: 107–114.
  18. Guo H., Seet Q., Denkin S., Parsons L., Zhang Y. Molecular characterization of isoniazid-resistant clinical isolates of Mycobacterium tuberculosis from the USA. J. Med. Microbiol. 2006; 55: 1527–1531.
  19. Herrera L., Valverde A., Saiz P., Saez-Nieto J.A., Portero J.L., Jimenez M.S. Molecular characterization of isoniazid-resistant Mycobacterium tuberculosis clinical strains isolated in the Philippines. Int. J. Antimicrob. Agents 2004; 23: 572–576.
  20. Abate G., Hoffner S.E., ThomsenV.O., Miorner H. Characterization of isoniazid-resistant strains of Mycobacterium tuberculosis on the basis of phenotypic properties and mutations in katG. Eur. J. Clin. Microbiol. Infect. Dis. 2001; 20: 329–333.
  21. Abe C., Kobayashi I., Mitarai S. i wsp. Biological and molecular characteristics of Mycobacterium tuberculosis clinical isolates with low-level resistance to isoniazid in Japan. J. Clin. Microbiol. 2008; 46: 2263–2268.
  22. Ahmad S., Mokaddas E. Contribution of AGC to ACC and other mutations at codon 315 of the katG gene in isoniazid-resistant Mycobacterium tuberculosis isolates from the Middle East. Int. J. Antimicrob. Agents 2004; 23: 473–479.
  23. Baker L.V., Brown T.J., Maxwell O. i wsp. Molecular analysis of isoniazid-resistant Mycobacterium tuberculosis isolates from England and Wales reveals the phylogenetic significance of the ahpC-46A polymorphism. Antimicrob Agents Chemother. 2005; 49: 1455–1464.
  24. Bakonyte D., Baranauskaite A., Cicenaite J., Sosnovskaja A., Stakenas P. Molecular characterization of isoniazid-resistant Mycobacterium tuberculosis clinical isolates in Lithuania. Antimicrob. Agents Chemother. 2003; 47: 2009–2011.
  25. Clemente W.T., Soares Lima S.S., Palaci M. i wsp. Phenotypic and genotypic characterization of drug–resistant Mycobacterium tuberculosis strains. Diagn. Microbiol. Infect. Dis. 2008; 62: 199–204.
  26. Hazbon, M.H., Brimacombe, M., Bobadilla del Valle, M. i wsp. Population genetics study of isoniazid resistance mutations and evolution of multidrug-resistant Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 2006; 50: 2640–2649.
  27. Lavender C., Globan M., Sievers A., Billman-Jacobe H., Fyfe J. Molecular characterization of isoniazid-resistant Mycobacterium tuberculosis isolates collected in Australia. Antimicrob. Agents Chemother. 2005; 49: 4068–4074.
  28. Musser J.M., Kapur V., Williams D.L., Kreiswirth B.N., van Soolingen D., van Embden J.D. Characterization of the catalase-peroxidase gene (katG) and inhA locus in isoniazid-resistant and susceptible strains of Mycobacterium tuberculosis by automated DNA sequencing: restricted array of mutations associated with drug resistance. J. Infect. Dis. 1996; 173: 196–202.
  29. Shemyakin I.G., Stepanshina V.N., Ivanov I.Y. i wsp. Characterization of drug-resistant isolates of Mycobacterium tuberculosis derived from Russian inmates. Int. J. Tuberc. Lung Dis. 2004; 8: 1194–1203.
  30. Zakerbostanabad S., Titov L.P., Bahrmand A.R. Frequency and molecular characterization of isoniazid resistance in katG region of MDR isolates from tuberculosis patients in southern endemic border of Iran. Infect. Genet. Evol. 2008; 8: 15–19.
  31. Zhang S.L., Qi H., Qiu D.L. i wsp. Genotypic analysis of multidrug--resistant Mycobacterium tuberculosis isolates recovered from central China. Biochem. Genet. 2007; 45: 281–290.
  32. Kiepiela P., Bishop K.S., Smith A.N., Roux L., York D.F. Genomic mutations in the katG, inhA and aphC genes are useful for the prediction of isoniazid resistance in Mycobacterium tuberculosis isolates from Kwazulu Natal, South Africa. Tuber. Lung Dis. 2000; 80: 47–56.
  33. Mokrousov I., Narvskaya O., Otten T., Limeschenko E., Steklova L., Vyshnevskiy B. High prevalence of KatG Ser315Thr substitution among isoniazid–resistant Mycobacterium tuberculosis clinical isolates from northwestern Russia, 1996 to 2001. Antimicrob. Agents Chemother. 2002; 46: 1417–1424.
  34. Tracevska T., Jansone I., Broka L., Marga O., Baumanis V. Mutations in the rpoB and katG genes leading to drug resistance in Mycobacterium tuberculosis in Latvia. J. Clin. Microbiol. 2002; 40: 3789–792.
  35. Silva M.S., Senna S.G., Ribeiro M.O. i wsp. Mutations in katG, inhA, and ahpC genes of Brazilian isoniazid-resistant isolates of Mycobacterium tuberculosis. J. Clin. Microbiol. 2003; 41: 4471–4474.
  36. van Soolingen D., de Haas P.E., van Doorn H.R., Kuijper E., Rinder H., Borgdorff M.W. Mutations at amino acid position 315 of the katG gene are associated with high-level resistance to isoniazid, other drug resistance, and successful transmission of Mycobacterium tuberculosis in the Netherlands. J. Infect. Dis. 2000; 182: 1788–1790.
  37. Garcia de Viedma D., del Sol Diaz Infantes M., Lasala F., Chaves F., Alcala L., Bouza E. New real-time PCR able to detect in a single tube multiple rifampin resistance mutations and high-level isoniazid resistance mutations in Mycobacterium tuberculosis. J. Clin. Microbiol. 2002; 40: 988–995.
  38. Rindi L., Bianchi L., Tortoli E., Lari N., Bonanni D., Garzelli C. Mutations responsible for Mycobacterium tuberculosis isoniazid resistance in Italy. Int. J. Tuberc. Lung Dis. 2005; 9: 94–97.
  39. Rouse D.A., Li Z., Bai G.H., Morris S.L. Characterization of the katG and inhA genes of isoniazid-resistant clinical isolates of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 1995; 39: 2472–2477.
  40. Pretorius G.S., van Helden P.D., Sirgel F., Eisenach K.D., Victor T.C. Mutations in katG gene sequences in isoniazid-resistant clinical isolates of Mycobacterium tuberculosis are rare. Antimicrob. Agents Chemother. 1995; 39: 2276–2281.
  41. Sajduda A., Brzostek A., Popławska M. i wsp. Molecular characterization of rifampin- and isoniazid-resistant Mycobacterium tuberculosis strains isolated in Poland. J. Clin. Microbiol. 2004; 42: 2425–2431.
  42. Wojtyczka R.D., Dworniczak S., Pacha J. i wsp. PCR-RFLP analysis of a point mutation in codons 315 and 463 of the katG gene of Mycobacterium tuberculosis isolated from patients in Silesia, Poland. Pol. J. Microbiol. 2004; 53: 89–93.
  43. Wengenack N.L., Uhl J.R., St Amand A.L. i wsp. Recombinant Mycobacterium tuberculosis KatG (S315T) is a competent catalase-peroxidase with reduced activity toward isoniazid. J. Infect. Dis. 1997; 176: 722–727.
  44. Zhao X., Yu H., Yu S., Wang F., Sacchettini J.C., Magliozzo R.S. Hydrogen peroxide-mediated isoniazid activation catalyzed by Mycobacterium tuberculosis catalase-peroxidase (KatG) and its S315T mutant. Biochemistry 2006; 45: 4131–4140.
  45. Pym A.S., Saint-Joanis B., Cole S.T. Effect of katG mutations on the virulence of Mycobacterium tuberculosis and the implication for transmission in humans. Infect. Immun. 2002; 70: 4955–4960.
  46. Marttila H.J., Soini H., Eerola E. i wsp. A Ser315Thr substitution in KatG is predominant in genetically heterogeneous multidrug-resistant Mycobacterium tuberculosis isolates originating from the St. Petersburg area in Russia. Antimicrob. Agents Chemother. 1998; 42: 2443–2445.
  47. Marín M., García de Viedma D., Ruíz-Serrano M.J., Bouza E. Rapid direct detection of multiple rifampin and isoniazid resistance mutations in Mycobacterium tuberculosis in respiratory samples by real-time PCR. Antimicrob. Agents Chemother. 2004; 48: 4293–4300.
  48. Piatek A.S., Telenti A., Murray M.R. i wsp. Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing. Antimicrob. Agents Chemother. 2000; 44: 103–110.
  49. van Doorn H.R., de Haas P.E., Kremer K., Vandenbroucke-Grauls C.M., Borgdorff M.W., van Soolingen D. Public health impact of isoniazid-resistant Mycobacterium tuberculosis strains with a mutation at amino-acid position 315 of katG: a decade of experience in The Netherlands. Clin. Microbiol. Infect. 2006; 12: 769–775.
  50. Gagneux S., Burgos M.V., DeRiemer K. i wsp. Impact of bacterial genetics on the transmission of isoniazid-resistant Mycobacterium tuberculosis. PLoS Pathog. 2006; 2: 61.

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