ORIGINAL ARTICLE 10.1111/j.1469-0691.2004.01034.x Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum C. Arnold 1, L. Westland 1,2, G. Mowat 3, A. Underwood 1, J. Magee 3 and S. Gharbia 1 1 Genomics, Proteomics and Bioinformatics Unit, Centre for Infections, Health Protection Agency, London, UK, 2 Hogeschool van Utrecht, Faculteit Natuur & Techniek, Institute of Life Sciences and Chemistry, Utrecht, The Netherlands and 3 Regional Centre for Mycobacteriology, Health Protection Agency Newcastle Laboratory, Newcastle, UK ABSTRACT The rapid technique of pyrosequencing was used to examine 123 samples (in the form of DNA extracts and inactivated sputum) of Mycobacterium spp. Of 99 Mycobacterium tuberculosis samples investigated for single-nucleotide polymorphisms (SNPs), 68% of isoniazid-resistant isolates analysed had an AGC fi ACC mutation in katg at codon 315, resulting in the Ser fi Thr substitution associated previously with isoniazid resistance. Of the rifampicin-resistant isolates, 92% showed SNPs in rpob at codons 516, 531 or 526. Inactivated sputum samples and DNA extracts could both be analysed by pyrosequencing, and the method was able to differentiate rapidly between the closely related species of the M. tuberculosis complex (M. tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium canetti and Mycobacterium microti), except between M. tuberculosis, M. canetti and one of two M. africanum strains. This low-cost, high-throughput technique could be used as a rapid screen for drug resistance and as a replacement for some of the time-consuming tests used currently for species identification. Keywords resistance Antibiotic susceptibility testing, identification, Mycobacterium tuberculosis complex, pyrosequencing, Original Submission: 5 April 2004; Revised Submission: 2 September 2004; Accepted: 11 September 2004 Clin Microbiol Infect 2005; 11: 122 130 INTRODUCTION It has been estimated that one-third of the global population is infected with Mycobacterium tuberculosis, with c. 9 million cases of active tuberculosis (TB) and > 2 million deaths occurring each year [1,2]. These numbers are increasing, as is the number of individuals infected with strains resistant to first-line anti-tb drugs. In the UK, the current first-line treatment is a 2-month course of isoniazid, rifampicin and pyrazinamide, often with the addition of ethambutol, followed by isoniazid and rifampicin for a further 4 6 months. Aminoglycosides such as streptomycin and Corresponding author and reprint requests: C. Arnold, Genomics, Proteomics and Bioinformatics Unit, Health Protection Agency, 61 Colindale Avenue, London NW9 5HT, UK E-mail: catherine.arnold@hpa.org.uk amikacin, and fluoroquinolones such as ofloxacin and ciprofloxacin, are used as second-line agents. Drug resistance in M. tuberculosis occurs following spontaneous mutation in target genes such as katg, rpob and inha [3]. The mechanisms and the dominant mutations resulting in the drug resistance profiles have been well-documented [3 5]. Isoniazid resistance is often associated with mutation in a gene encoding catalase-peroxidase (katg), most frequently a Ser315Thr mutation [6]. Rifampicin inhibits transcription by binding to the RNA polymerase b-subunit, encoded by the rpob gene [7], with resistance resulting from mutations in the rifampicin resistance-determining region of rpob, an 81-bp region encoding amino-acids 507 533. The most common (70%) mutations are at codons 526 and 531, and are associated with high levels of resistance (> 100 mg L). Less frequent mutations, Ó 2004 Copyright by the European Society of Clinical Microbiology and Infectious Diseases
Arnold et al. Single-nucleotide polymorphisms in M. tuberculosis 123 particularly in codon 516, are associated with lower levels of resistance. The fluoroquinolones were considered to be alternative drugs, as they prevent transcription and cell division by suppressing DNA supercoiling [8]. DNA gyrase, encoded by gyrab, catalyses negative supercoiling of DNA. Mutations in the short quinolone resistance-determining region and at codon 94 of gyra overcome the DNA gyrase-blocking action of fluoroquinolones [8]. A rapid screening system for these mutations among isolates of M. tuberculosis is essential. A sequence-based method, rather than a DNA migration or a hybridisation approach, is ideal for the development of a fast, accurate and highthroughput system, as this will aid in the identification of alternative mutations in the regions analysed, as well as those characterised previously. The present study investigated the possibility of detecting the most common mutations by pyrosequencing, a short-read (c. 30 50 bp) sequencing technique based on the quantitative detection of pyrophosphate released following nucleotide incorporation into a growing DNA chain. The technology has also been used previously for single-nucleotide polymorphism (SNP) detection [9]. The slow-growing nature of M. tuberculosis means that several weeks can elapse before the susceptibility profile of an isolate is known and appropriately guided anti-tb chemotherapy can be put in place. Although genotypic testing cannot wholly replace phenotypic methods for the detection of antibiotic resistance, as not all mechanisms of action (and therefore specific mutations) are known for the different drugs used, a molecular screen capable of use on primary clinical samples to detect most mutations associated with resistance could be invaluable. This study therefore assessed pyrosequencing as a high-throughput, cost-effective genotypic screen for M. tuberculosis isoniazid resistance in which common mutations associated with resistance were detected in sputum samples and early cultures. Speciation of mycobacteria has been attempted previously by sequencing all or part of the 16S rrna gene [10], but this approach has failed to delineate this highly conserved genus. Other regions of the genome that are useful for mycobacterial speciation include rpob [11,12] and gyrb [13]. Therefore, the present study also assessed pyrosequencing as a rapid test for identifying members of the genus Mycobacterium, and specifically the M. tuberculosis complex (MTBC), using a composite assay of these three genes. As public health intervention strategies and transmission models may also benefit from the interpretation of data in the context of phylogenetically relevant genetic frameworks (genotypes) based on SNPs [14,15], a pyrosequencing assay to determine genotype was also developed. These three composite high-throughput assays, designed to be used on sputum samples and cultures in the early stages of growth to determine resistance profile, species and genotype, were applied to three groups of M. tuberculosis isolates to determine their utility in public health microbiology. MATERIALS AND METHODS Samples In total, 123 samples of mycobacteria were studied, of which 98 were M. tuberculosis nucleic acid extracts. Group 1 comprised 72 M. tuberculosis DNA extracts from three northwest London hospitals [16]. Seven (9.7%) of these extracted isolates were isoniazid-resistant (Table 1). There were six epidemiologically related groups of isolates (100 and 203; 113 and 128; 129 and 264; 139 and 140; 232, 251, 252 and 253; 1085 and 1086). Group 2 comprised 20 M. tuberculosis DNA extracts and seven inactivated sputum samples containing M. tuberculosis from northeast England (Newcastle) (Table 1). Fourteen of the extracted isolates were isoniazid- or isoniazid- and rifampicinresistant. The sputum samples, containing > 90 bacilli field, were inactivated by boiling in 1 M NaOH for 10 min following dithiothreitol liquefaction (Sputasol; Oxoid, Basingstoke, UK). Four of these samples yielded isoniazid-resistant M. tuberculosis isolates. A further four sputum samples contained mycobacterial species other than those causing TB, i.e., M. avium complex, M. malmoense and M. chelonae, which were isoniazid-resistant. Group 3 comprised 24 DNA extracts from 11 different Mycobacterium spp. (Table 2) obtained from K. Kremer (National Institute of Public Health and the Environment, Bilthoven, The Netherlands) [17]. Primer design Amplification and pyrosequencing primers were designed by visual comparison and confirmed with the use of on-line software (http://www.pyrosequencing.com). The sequence of M. tuberculosis H37Rv, ATCC 27294, was used as an in-silico template. Pyrosequencing primers were designed to detect resistance or species-associated SNPs (Fig. 1). Two of the regions analysed (katg 463 and gyra 95) were control regions that were not associated with drug resistance, but were associated with genotype assignation of M. tuberculosis [14], namely: CTG ACC = genotype I; CGG ACC = genotype II; and CGG AGC = genotype III (Table 1).
124 Clinical Microbiology and Infection, Volume 11 Number 2, February 2005 Table 1. Strain information for Mycobacterium tuberculosis isolates in groups 1 and 2: resistance profile, single-nucleotide polymorphism profile and genotype Identifier Resistance katg 315 (WT = AGC) rpob 516 (WT = GAC) rpob 526 (WT = CAC) rpob 531 (WT = TCG) gyra 94 (WT = GAC) katg 463 gyra 95 Genogroup Northwest London isolates (DNA extracts) WT profile 1 104, 124, 125, 126, WT AGC GAC CAC TCG GAC CTG ACC I 129, 131, 138, 142, 145, 149, 154, 157, 200, 208, 209, 212, 234, 241, 264, 267, 280, 282, 284, 285, 286, 982, 1010, 1023, 1026, 1053 WT profile 2 98, 100, 105, 106, WT AGC GAC CAC TCG GAC CGG ACC II 113, 114, 121, 122, 128, 136, 139, 140, 156, 203, 205, 218, 222, 223, 231, 237, 263, 269, 1002, 1022, 1030, 1054, 1062, CDC1551 WT profile 3 127, 229, 276, 1024, WT AGC GAC CAC TCG GAC CGG AGC III H37Rv WT profile 4 226, 1043 WT AGC GAC CAC TCG GAC Weak ACC I II Resistant profile 1 137, 232, 251, 252, INH ACC GAC CAC TCG GAC CTG ACC I 253, 1085, 1086 Newcastle isolates (DNA extracts) WT profile 1 16, 17 WT AGC GAC CAC TCG GAC CTG ACC I WT profile 2 12, 13 WT AGC GAC CAC TCG GAC CGG ACC II WT profile 3 14, 15 WT AGC GAC CAC TCG GAC CGG AGC III Resistant profiles 1 INH RIF ACC GAC CAC TTG GAC CTG ACC I 8 INH AGC GAC CAC TCG GAC CTG ACC I 9 INH AGC GAC CAC TCG GAC CGG AGC III 10 INH RIF EMB PZA ACC GCC CAC TCG GAC CTG ACC I 11 INH RIF EMB AGC GAC TCC Weak GAC CGG ACC II 22 INH RIF EMB ACC GAC CAC TTG GAC CTG ACC I 23 INH RIF PZA AGC GAC CAC TTG GAC CGG ACC II 24 INH RIF EMB AGC GAC TCC Weak GAC CGG ACC II 25 INH RIF ACC GAC GAC TCG GAC CGG ACC II 26 INH RIF EMB ACC GAC TAC TCG GAC CTG ACC I 27 INH RIF EMB ACC GAC GAC TCG GAC CGG ACC II 31 INH RIF EMB AGC GAC CAC TCG GAC CGG ACC II 33 INH RIF EMB ACC GAC CAC TTG GAC CTG ACC I 35 INH RIF ACC TAC CAC TCG GAC CTG ACC I Newcastle isolates (inactivated sputum) 36 INH AGC GAC CAC TCG ND CTG ND I 37 INH AGC GAC CAC TCG ND CTG ND I 38 INH ACC GAC CAC TCG ND CGG ND II III 39 INH ACC GAC CAC TCG ND CTG ND I 40 WT AGC ND ND ND ND CGG ND II III 41 WT AGC ND ND ND ND CTG ND I 42 WT AGC GAC CAC TCG ND CGG ND II III WT, wild-type; INH, isoniazid; RIF, rifampicin; EMB, ethambutol; PZA, pyrazinamide; ND not done. The rifampicin resistance detection assay and the rnpb species identification assay were designed by M. Krabbe (Pyrosequencing AB, Uppsala, Sweden). The rpob species identification assay was designed to generate c. 100-bp products by means of an alignment of sequences reported by Lee et al. [11]. The gyrb MTBC species identification assay targeted the MTBC-associated SNPs identified by Niemann et al. [13] and Kasai et al. [18], and was designed to distinguish M. tuberculosis, M. bovis, M. africanum and M. microti. PCR PCR was used to generate products from the rpob, katg, gyra, gyrb and rnpb genes in a final volume of 50 ll with c. 50 ng of extracted DNA or 1 ll of inactivated sputum, and 25 ll of PCR Ready Mix (Sigma-Aldrich, Poole, UK) containing 1.5 U of Taq polymerase, 10 mm Tris-HCl, 50 mm KCl, 1.5 mm MgCl 2, gelatine 0.001% v v, 0.2 mm dntps and stabilisers, and 10 pmol each of the forward and reverse primers (one of which was biotinylated; Fig. 1). PCR involved
Arnold et al. Single-nucleotide polymorphisms in M. tuberculosis 125 Table 2. Identification of Mycobacterium spp. in group 3 on the basis of single-nucleotide polymorphism and short-sequence data analysis Identifier Species rnpb ID assay rpob ID assay gyrb SNP position 675 gyrb SNP position 756 gyrb SNP position 1410 gyrb SNP position 1450 1 M. tuberculosis (H37Rv) MTBC MTBC C G C G 2 M. bovis BCG MTBC MTBC C A T T 3 M. canettii MTBC MTBC C G C G 4 M. canettii MTBC MTBC C G C G 5 M. africanum MTBC MTBC C G C T 6 M. africanum MTBC MTBC C G C G 7 M. microti MTBC MTBC T G C T 8 M. microti MTBC MTBC T G C T 9 M. bovis MTBC MTBC C A T T 10 M. bovis MTBC MTBC C A T T 11 M. avium M. avium M. avium C G C G 12 M. avium M. avium M. avium C G C G 13 M. kansasii M. kansasii M. kansasii C G C G 14 M. kansasii M. kansasii M. kansasii C G C G 15 M. gordonae Unclear M. gordonae C G C T 16 M. gordonae Unclear M. gordonae C G C T 17 M. smegmatis M. smegmatis M. smegmatis C G C G 18 M. smegmatis M. smegmatis M. smegmatis C G C G 19 M. xenopi M. xenopi M. xenopi C No data C No data 20 M. xenopi M. xenopi M. xenopi C No data C No data 21 M. tuberculosis MTBC MTBC C G C G 22 M. tuberculosis MTBC MTBC C G C G 23 M. tuberculosis MTBC MTBC C G C G 24 M. tuberculosis MTBC MTBC C G C G MTBC, Mycobacterium tuberculosis complex. denaturation at 94 C for 2 min, followed by 35 cycles of 94 C for 30 s, 60 C for 30 s and 72 C for 1 min, followed by a final extension at 72 C for 10 min. Amplification products were checked on a 96-well Ready-To-Run agarose gel (Amersham Biosciences, Chalfont St Giles, UK). When PCR performed directly on sputum samples resulted in low yields, 1 ll of the initial product was re-amplified to generate sufficient product for sequencing. Pyrosequencing Pyrosequencing was performed with the SQA kit (Pyrosequencing AB) and the pyrosequencing primers shown in Fig. 1. Briefly, 20 ll of biotinylated PCR product was bound to streptavidin-coated sepharose beads and denatured. After washing, the products were transferred to a 96-well microtitre plate and 20 qmol of pyrosequencing primer was annealed in a 45-lL reaction volume. Once the reaction cartridge was loaded with dntps, enzyme and substrate from the kit, the cartridge and reaction plate were placed in the instrument (Pyrosequencing AB) for analysis. Depending on the number of nucleotide additions (each nucleotide addition cycle takes 1 min to complete), 96 reactions were completed in c. 10 15 min. RESULTS Resistance mutations The most frequent mutations associated with isoniazid, rifampicin and fluoroquinolone resistance were detected with the primers described in Fig. 1. PCR products were generated from all 99 M. tuberculosis samples tested (both extracted nucleic acid and sputum samples). In group 1, an AGC fi ACC mutation in katg at codon 315, resulting in a Ser fi Thr substitution (Fig. 2), was identified in all of the isoniazid-resistant extracts (Table 1). Two groups (n =4; n = 2) of these samples were related epidemiologically. In group 2, the same mutation was identified in ten of the 18 isoniazid-resistant samples (Table 1). Mutations associated with resistance at gyra codon 94 were not detected, although PCR products and pyrosequence data were generated from all samples, and all replicates gave identical pyrosequence data. In group 2, the rpob positions analysed showed mutations, compared to the wild-type, in 11 of the 12 extracts of isoniazid- and rifampicin-resistant isolates. Point mutations were identified at codon 516 in two samples (10 and 35), at codon 526 in five samples (11, 24 27), and at codon 531 in four samples (1, 22, 23 and 33) (Table 1). No mutations were identified at gyra codon 95. PCR products were not amplified from the four inactivated sputum samples containing Mycobacterium spp. other than those causing TB. However, in group 2, a katg codon 315 mutation was identified in two of the four inactivated sputum samples containing isoniazid-resistant MTBC (determined by resistance ratio testing [19]) (Table 1). Genotyping SNPs at katg codon 463 and gyra codon 95 are not associated with resistance, but were used to
126 Clinical Microbiology and Infection, Volume 11 Number 2, February 2005 Fig. 1. Location of single-nucleotide polymorphisms (SNP) and pyrosequencing primers in PCR amplicons. SNPs of interest are shown in bold, and pyrosequencing primers are shown in italics. Products generated with a biotinylated forward primer (i.e., sequenced in the opposite direction) are marked with asterisks. separate genotypes I III. The results are shown in Table 1. Identification DNA sequences of all rpob and rnpb fragments generated were compared with sequences generated previously for mycobacteria [11,12]. Both the rnpb and the rpob short (25 30 bp) sequence assays correctly identified all of the mycobacterial species tested, with the exception of M. gordonae, which failed to produce a clean sequence with the rnpb assay (Table 2). As expected, neither of these assays could separate members of the MTBC. However, the gyrb SNP assays correctly differentiated between the various species, except between M. tuberculosis, M. canetti and one of the two M. africanum strains (Table 2). For the MTBC only, SNP position 675 was always C except for M. microti (T), position 756 was always G except for M. bovis (A), position 1410 was always C except for M. bovis (T), and position 1450 was always T except for M. tuberculosis, M. canetti and M. africanum type II (G). A schematic diagram showing the identification algorithm used is given in Fig. 3.
Arnold et al. Single-nucleotide polymorphisms in M. tuberculosis 127 Fig. 2. (A) A pyrogram of the wild type for katg Ser315. The sequence reads GCGGCATC. (B) A pyrogram of a mutation conferring isoniazid resistance (AGC fi ACC) at katg 315. The sequence reads CCGGCATC. (N.B. The first nucleotide in this codon (A) is the last base in the pyrosequencing primer). rpob ID MOTT MTBC gyrb ID1 gyrb ID2 SNP 675 SNP 756 SNP 1410 SNP 1450 C>T G>A C>T T>G =M. microti = M. bovis = M. bovis = M. tuberculosis or M. canetti or M. africanum type II Fig. 3. Schematic algorithm for the Mycobacterium tuberculosis pyrosequencing identification assay. DISCUSSION In the UK, molecular tests for multidrug resistance (MDR) are carried out only following consideration of epidemiological factors such as nationality or close contact with an individual known to be infected with multidrug-resistant TB. Nationally, < 1% of isolates are multidrug-resistant [20], although isoniazid resistance is more common (6 10%). Inappropriate prescription of isoniazid to patients infected with an isoniazidresistant strain can cause liver damage and may drive mutation to MDR by the so-called amplifier effect, whereby resistant TB strains gain additional resistance to further anti-tb drugs. Correct treatment with first-line drugs usually prevents development of drug resistance in most patients, but it aggravates drug resistance in patients harbouring resistant strains, so that previous anti-tb treatment is a risk factor for MDR [20]. Antibiotic susceptibility testing is carried out on isolates from all new TB cases in the UK. The katg gene is the most commonly targeted region involved in isoniazid resistance, with mutations at codon 315 occurring in 30 90% of isoniazidresistant isolates, depending on geographical distribution [7,21 23]. Recently, real-time molecular assays have been developed to detect mutations associated with antibiotic resistance in M. tuberculosis. These include the use of specific hybridisation probes for use with the LightCycler, a line probe assay and PCR restriction fragment length polymorphism analysis [24 26]. The real-time PCR methods are fast, but DNA is extracted from cultured clinical isolates, which adds to the cost and time of the assay, and data interpretation can be subjective. Line probe assays are also carried out on DNA extracted from cultures, and the assay can take 1 2 days to complete [25]. PCR restriction fragment length polymorphism analysis requires DNA extraction, amplification, a 4-h restriction endonuclease digestion period and polyacrylamide gel electrophoresis. In M. tuberculosis samples from the UK, the AGC fi ACC mutation in katg at codon 315, resulting in a Ser fi Thr substitution, was detected by pyrosequencing in 68% of isoniazid-resistant isolates. Among the 12 isoniazid- and rifampicin-resistant isolates analysed, point mutations at codons 516, 531 or 526 were identified in 11 (92%) cases. Importantly, it was possible to sequence PCR products amplified from all sputum samples containing M. tuberculosis, although samples containing Mycobacterium spp. other than those causing TB were not amplified. The latter finding may be a result of a lower bacterial load or a reduced specificity of primers. Moreover, the mutations conferring isoniazid resistance in atypical mycobacteria are not necessarily related to those in M. tuberculosis. The ability to use clinical samples without the need for expensive and timeconsuming DNA extraction procedures would enable this method to be used more widely than is possible at present. As the whole assay is
128 Clinical Microbiology and Infection, Volume 11 Number 2, February 2005 conducted in a high-throughput, 96-well format, hundreds of isolates could be analysed in < 6 h. The longest step in the process is the PCR (a step required in all molecular detection assays described so far), while the pyrosequencing technique itself, including the PCR clean-up, takes c. 20 min for 96 samples and costs c. 2.70 euro for each SNP analysed. The pyrosequencing method produced clear and objective sequence data. These assays are based on short-read sequences, designed to give control sequence data following or preceding the SNPs of interest. This objectivity is extremely useful for applications in medical microbiology, as the technique does not therefore require the skilled interpretation of bands or peaks required with other methods. In the PCR restriction fragment length polymorphism study by Leung et al. [26], it was observed that a particular SNP position in katg at codon 463, thought previously to be associated with isoniazid resistance [27], was found primarily in isolates from the south China region. Of 375 (102 isoniazid-resistant and 273 isoniazid-susceptible) isolates, 317 (85%) had Leu463, compared with the major wild-type Arg463 associated with isolates from the western world. This particular SNP is associated with genotype I, thought to be evolutionarily old, and was described first by Sreevatsan et al. [14] and in more detail by Gutacker et al. [15]. Sreevatsan et al. observed that clusters of cases were caused by genotypic groups I and II, but not group III organisms, as the newly emergent group III organisms were associated with sporadic cases, suggesting that the pathogen was evolving towards a state of reduced transmissibility or virulence. The study in northwest London [16] also revealed epidemiologically related groups of isolates, all of which were either genotype I or II, supporting the hypothesis that genotypes I and II were associated with increased transmissibility or virulence. However, in a separate study of related infections in the northeast of England, a genotype III cluster was identified in four unrelated clusters (data not shown). The ability to perform the pyrosequencing assay on inactivated sputum samples has considerable advantages, including the fact that the speed of this high-throughput assay means that genotypic resistance screening of all newly diagnosed infections in the UK is achievable. The advantages of identifying isoniazid resistance easily and cheaply in a single day, rather than weeks or months, for the individual patient and in the wider context of preventing MDR are clear, and antibiotic resistance screening is recommended for all new M. tuberculosis infections. Phenotypic tests are available for the identification of Mycobacterium spp., but are time-consuming and may lack discriminatory power [11]. Several molecular tests have been developed, mostly based on 16S rrna sequence analysis. However 16S rrna sequencing fails to differentiate species belonging to the MTBC. Both of the short-sequence assays described here, based on rnpb and rpob, identified the different Mycobacterium spp. tested, although some sequence data from the rnpb assay were unreadable, presumably because of a lack of complementarity of the primers with genomic DNA from some of the more diverse species, or possibly because of sequence-specific looping of the single-stranded DNA template. The use of single-stranded binding protein or the addition of NNN (where N is any base) to the 5 -end of the non-biotinylated PCR primer during its synthesis may counteract this effect. The SNPs used in this assay to differentiate members of the MTBC were first identified by Kasai et al. [18] and described in more detail by Niemann et al. [13]. These SNPs were able to differentiate between the members of the MBTC, except for the three most closely related species, namely M. tuberculosis, M. canetti and M. africanum. The present assay discriminated between one of the M. africanum isolates and M. tuberculosis. It is likely that the M. africanum isolate identical (G) to M. tuberculosis at SNP position 1450 belongs to type II, whereas the other M. africanum isolate tested belongs to type I. Niemann et al. [13] were able to discriminate between the two M. africanum types by analysing a fifth SNP at gyrb position 1311. Although the differentiation of M. tuberculosis, M. canetti and M. africanum type II was not achieved with pyrosequencing, and therefore remains based on phenotypic characteristics or the use of methods such as deletion analysis and amplified fragment length polymorphism analysis [28,29], it is likely that other SNPs that can be used to separate these closely related species will be identified. Indeed, Goh et al. [30] have already published data indicating the use of a particular SNP to differentiate M. canetti from other members of the MBTC.
Arnold et al. Single-nucleotide polymorphisms in M. tuberculosis 129 In summary, the present study succeeded in developing and piloting rapid, high-throughput, short-sequence and SNP-based assays to speciate and screen for drug resistance in this important human pathogen. These low-cost assays can be used to complement current techniques, and may be used to replace some of the time-consuming biochemical tests used currently for identification, and also as a rapid screen for the detection of drug resistance in M. tuberculosis infections in the UK. The ability to obtain sequence data directly from sputum samples containing M. tuberculosis suggests that the assays described here could indicate species or drug resistance much more rapidly than methods used currently, and therefore that they could have a considerable impact on public health intervention strategies. ACKNOWLEDGEMENTS The authors would like to acknowledge M. Krabbe for design of the rnpb identification assay and Pyrosequencing AB for software modification. REFERENCES 1. Chan ED, Iseman MD. Current medical treatment for tuberculosis. BMJ 2002; 325: 1282 1286. 2. World Health Organization. Tuberculosis fact sheet number 104. Geneva: WHO, 2002. 3. Riska PF, Jacobs WR, Alland D. Molecular determinants of drug resistance in tuberculosis. Int J Tuberc 2000; 4: S4 S10. 4. Ramaswamy SV, Reich R, Dou S-J, Jasperse L, Pan X, Wanger A. Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2003; 47: 1241 1250. 5. Somoskovi A, Parsons LM, Salfinger M. The molecular basis of resistance to isoniazid, rifampin and pyrazinamide in Mycobacterium tuberculosis. Respir Res 2001; 2: 164 168. 6. Zhang Y, Heym B, Allen B, Young D, Cole S. The catalaseperoxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature 1992; 358: 591 593. 7. Ramaswamy SV, Musser JM. Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tuberc Lung Dis 1998; 79: 3 29. 8. Van Doorn HR, Kuijper EJ, Van Ende A et al. The susceptibility of Mycobacterium tuberculosis to isoniazid and the Arg > Leu mutation at codon 463 are not associated. J Clin Microbiol 2001; 39: 1591 1594. 9. Ronaghi I, Nygren M, Lundeberg J, Nygren P. Analyses of secondary structures in DNA by pyrosequencing. Anal Biochem 1999; 267: 65 71. 10. Rogall T, Flohr T, Bottger E. Differentiation of mycobacterial species by direct sequencing of amplified DNA. J Gen Microbiol 1990; 136: 1915 1920. 11. Lee H, Bang H-E, Bai GH-J, Cho S-N. Novel polymorphic region of the rpob gene containing Mycobacterium speciesspecific sequences and its use in identification of mycobacteria. J Clin Microbiol 2003; 41: 2213 2218. 12. Herrmann B, Pettersson B, Everett KD, Mikkelsen NE, Kirsebom LA. Characterization of the rnpb gene and RNase P RNA in the order Chlamydiales. Int J Syst Evol 2000; 50: 149 158. 13. Niemann S, Harmsen D, Rusch-Gerdes S, Richter E. Differentiation of clinical Mycobacterium tuberculosis complex isolates by gyrb DNA sequence polymorphism analysis. J Clin Microbiol 2000; 38: 3231 3234. 14. Sreevatsan S, Pan X, Stockbauer KE et al. Restricted gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination. Proc Natl Acad Sci USA 1997; 94: 9869 9874. 15. Gutacker MM, Smoot JC, Lux Migliaccio CA et al. Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains. Genetics 2002; 162: 1533 1543. 16. Kumar D, Saunders N, Watson JM et al. Clusters of new tuberculosis cases in north-west London: a survey from three hospitals based on IS6110 RFLP typing. J Infect 2000; 40: 132 137. 17. Kremer K, Frothingham R, Haas WH et al. Comparison of methods based on different molecular epidemiological markers for typing of Mycobacterium tuberculosis complex strains: interlaboratory study of discriminatory power and reproducibility. J Clin Microbiol 1999; 37: 2607 2618. 18. Kasai H, Ezaki T, Harayama S. Differentiation of phylogenetically related slowly growing mycobacteria by their gyrb sequences. J Clin Microbiol 2000; 38: 301 308. 19. Heifets LB, Cangelosi GA. Drug susceptibility testing of Mycobacterium tuberculosis: a neglected problem at the turn of the century. Int J Tuberc Lung Dis 1999; 7: 564 581. 20. Fodor T, Vadasz I, Lorinczi I. Drug-resistant tuberculosis in Budapest. Int J Tuberc Lung Dis 1998; 2: 732 735. 21. Piatek AS, Telenti A, Murray MR et al. Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing. Antimicrob Agents Chemother 2000; 44: 103 110. 22. Haas WH, Schilke K, Brand J et al. Molecular analysis of katg gene mutations in strains of Mycobacterium tuberculosis complex from Africa. Antimicrob Agents Chemother 2000; 41: 1601 1603. 23. Van Soolingen D, de Haas PEW, Van Doorn HE, Kuijper E, Rinder H, Borgdorff MW. 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. 24. Rindi L, Bianchi L, Tortoli E, Lari N, Bonanni D, Garzelli C. A real-time PCR assay for detection of isoniazid resistance in Mycobacterium tuberculosis clinical isolates. J Microbiol Meth 2003; 55: 797 800. 25. Johansen IS, Lundgren B, Sosnovskaja A, Thomsen VO. Direct detection of multi-drug resistant Mycobacterium tuberculosis in clinical specimens in low- and high-incidence
130 Clinical Microbiology and Infection, Volume 11 Number 2, February 2005 countries by line probe assay. J Clin Microbiol 2003; 41: 4454 4456. 26. Leung E, Kam K-M, Chiu A et al. Detection of katg Ser315Thr substitution in respiratory specimens from patient with isoniazid-resistant Mycobacterium tuberculosis using PCR-RFLP. J Med Microbiol 2003; 52: 999 1003. 27. Cockerill FR, Uhl JR, Temesgen Z et al. Rapid identification of a point mutation of the Mycobacterium tuberculosis catalase-peroxidase (katg) gene associated with isoniazid resistance. J Infect Dis 1995; 171: 240 245. 28. Huard RC, de Oliveira Lazzarini LC, Butler WR, Van Soolingen D, Ho JL. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol 2003; 41: 1637 1650. 29. Van den Braak N, Simons G, Gorkink R et al. A new highthroughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganism Mycobacterium tuberculosis. J Microbiol Meth 2004; 56: 49 62. 30. Goh KS, Legrand E, Sola C, Rastogi N. Rapid differentiation of Mycobacterium canettii from other Mycobacterium tuberculosis complex organisms by PCR-restriction analysis of the hsp65 gene. J Clin Microbiol 2001; 39: 3705 3708.