Use of a high-density DNA probe array for detecting mutations involved in rifampicin resistance in Mycobacterium tuberculosis

Cascade of deoxyribozymes for the colorimetric analysis of drug resistance in Mycobacterium tuberculosis

A visual cascade detection system has been applied to the detection and analysis of drug-resistance profile of Mycobacterium tuberculosis complex (MTC), a causative agent of tuberculosis. The cascade system utilizes highly selective split RNA-cleaving deoxyribozyme (sDz) sensors. When activated by a complementary nucleic acid, sDz releases the peroxidase-like deoxyribozyme apoenzyme, which, in complex with a hemin cofactor, catalyzes the color change of the sample's solution. The excellent selectivity of the cascade has allowed for the detection of point mutations in the sequences of the MTC rpoB, katG, and gyrA genes, which are responsible for resistance to rifampin, isoniazid, and fluoroquinolone, respectively. When combined with isothermal nucleic acid sequence based amplification (NASBA), the assay was able to detect amplicons of 16S rRNA and katG mRNA generated from 0.1 pg and 10 pg total RNA taken for NASBA, respectively, in less than 2 h, producing a signal detectable with the naked eye. The proposed assay may become a prototype for point-of-care diagnosis of drug resistant bacteria with visual signal output.

Could high-concentration rifampicin kill rifampicin-resistant M. tuberculosis? Rifampicin MIC test in rifampicin-resistant isolates from patients with osteoarticular tuberculosis

Purpose

Several studies have shown that the intralesional concentration of rifampicin in osteoarticular tuberculosis is typically at a subtherapeutic level. Sustained or controlled release by novel drug delivery systems has been investigated to maintain an effective rifampicin concentration, but the local administration of rifampicin remains controversial. Additionally, it is still unclear whether high-dose rifampicin could kill rifampicin-resistant Mycobacterium tuberculosis. The aim of this study was to assess the in vitro killing effect of high-concentration rifampicin on rifampicin-resistant M. tuberculosis isolated from patients with osteoarticular tuberculosis.

Methods

A set of 18 rifampicin-resistant M. tuberculosis isolates by the BACT/MGIT 960 system from patients with osteoarticular tuberculosis was collected for further study. The detection of rpoB gene mutations was performed using non-fluorescent, low-density DNA microarrays to determine the resistant mechanism. Following secondary culture, susceptibility to gradient concentrations of rifampicin (2 to 256 μg/ml) was tested; these concentrations are attainable for prolonged periods of local chemotherapy. The relationship between microbial killing by high-dose rifampicin and rpoB gene mutations was analyzed.

Results

Mutations in the rifampicin resistance-determining region (RRDR) of the rpoB gene were identified in 17 isolates (94.4%); one strain exhibited no mutations in this region. The most prevalent mutation sites were in codons 531 (55.56%), 516 (16.67%), 526 (11.11%), and 513 (11.11%). Isolates with mutations in the rpoB gene were highly resistant to rifampicin, 11 of which had minimal inhibitory concentrations (MICs) exceeding 256 μg/ml (not determined). The MICs for the remaining seven resistant isolates were between 32 and 256 μg/ml. Particularly in less rifampicin-resistant M. tuberculosis strains, growth was inhibited at high concentrations.

Conclusion

Increasing the rifampicin concentration may optimize this drug’s antituberculous effect, even against some rifampicin-resistant isolates, if systemic and local toxic effects can be minimized.

A systematic review of rapid drug susceptibility tests for multidrug-resistant tuberculosis using rifampin resistance as a surrogate

BACKGROUND

The emergence of multidrug-resistant tuberculosis (MDR-TB) has prompted the development of rapid drug susceptibility assays with a focus on rifampin in recent years. Systematic reviews with evaluation of predictive values for different assays are scarce.

METHOD

MEDLINE was searched on 6 September 2008 for English articles that contain concurrent original data for generating summary measures of sensitivity, specificity and likelihood ratios of rapid rifampin susceptibility assays.

RESULTS/CONCLUSIONS

Significant heterogeneity was found in likelihood ratios across studies of all assays except nitrate reductase assay and colorimetric assays. Although rapid assays are fairly reliable for ruling out MDR-TB, careful consideration of clinical risk factors is required before using these assays to rule in MDR-TB under different epidemiological settings.

Drug-susceptibility testing in TB: current status and future prospects

The rising number of resistant and multidrug-resistant Mycobacterium tuberculosis strains and the emergence of extensively drug-resistant strains substantiate the urgent demand for rapid and reliable techniques for the detection of drug-resistant TB. In recent years, a multitude of techniques for rapid drug-susceptibility testing have been designed and evaluated. Two different strategies for the assessment of drug resistance can be followed; phenotypic determination has been common practice for years, whereas more recently the genetic detection of mutations that confer for drug resistance has been established. Novel liquid culture-based drug-susceptibility testing techniques have been evaluated; several of them have proved their reliability and accuracy, while others need more evaluation or a different performance due to biosafety risks. Among the molecular tests, line-probe assays seem to be the most promising tools for a rapid and very specific and sensitive detection of multidrug-resistant M. tuberculosis.

Visual detection of rpoB mutations in rifampin-resistant Mycobacterium tuberculosis strains by use of an asymmetrically split peroxidase DNAzyme

Multidrug-resistant Mycobacterium tuberculosis is resistant to two first-line antituberculosis drugs, isoniazid and rifampin, resulting in the relapse of tuberculosis. M. tuberculosis grows very slowly, and thus traditional examination methods take time to test its drug resistance and cannot meet clinical needs. The use of a DNA probe makes it possible to test rifampin resistance. We developed an asymmetrical split-assembly DNA peroxidase assay to detect drug-resistant mutation of rifampin-resistant M. tuberculosis in the rpoB gene rapidly and visibly. A new strategy was also designed to eliminate the adverse effects caused by the complicated secondary structure of the target DNA and to improve the efficiency of the probes. This detection system consists of five group detections, covers rifampin-resistant determination region of the rpoB gene, and tests 40 kinds of mutations, including the most common mutations at codons 531 and 526. Every group detection or individual mutant allele detection can distinguish corresponding mutant DNA sequences from the wild-type DNA sequences.

Rapid detection of isoniazid, rifampin, and ofloxacin resistance in Mycobacterium tuberculosis clinical isolates using high-resolution melting analysis

A high-resolution melting analysis (HRMA) assay was developed to detect isoniazid, rifampin, and ofloxacin resistance in Mycobacterium tuberculosis by targeting resistance-associated mutations in the katG, mabA-inhA promoter, rpoB, and gyrA genes. A set of 28 (17 drug-resistant and 11 fully susceptible) clinical M. tuberculosis isolates was selected for development and evaluation of HRMA. PCR amplicons from the katG, mabA-inhA promoter, rpoB, and gyrA genes of all 28 isolates were sequenced. HRMA results matched well with 18 mutations, identified by sequencing, in 17 drug-resistant isolates and the absence of mutations in 11 susceptible isolates. Among 87 additional isolates with known resistance phenotypes, HRMA identified katG and/or mabA-inhA promoter mutations in 66 of 69 (95.7%) isoniazid-resistant isolates, rpoB mutations in 51 of 54 (94.4%) rifampin-resistant isolates, and gyrA mutations in all of 41 (100%) ofloxacin-resistant isolates. All mutations within the HRMA primer target regions were detected as variant HRMA profiles. The corresponding specificities were 97.8%, 100%, and 98.6%, respectively. Most false-positive results were due to synonymous mutations, which did not affect susceptibility. HRMA is a rapid, sensitive method for detection of drug resistance in M. tuberculosis which could be used routinely for screening isolates in countries with a high prevalence of tuberculosis and drug resistance or in individual isolates when drug resistance is suspected.

Recombination and population structure in Salmonella enterica

Salmonella enterica is a bacterial pathogen that causes enteric fever and gastroenteritis in humans and animals. Although its population structure was long described as clonal, based on high linkage disequilibrium between loci typed by enzyme electrophoresis, recent examination of gene sequences has revealed that recombination plays an important evolutionary role. We sequenced around 10% of the core genome of 114 isolates of enterica using a resequencing microarray. Application of two different analysis methods (Structure and ClonalFrame) to our genomic data allowed us to define five clear lineages within S. enterica subspecies enterica, one of which is five times older than the other four and two thirds of the age of the whole subspecies. We show that some of these lineages display more evidence of recombination than others. We also demonstrate that some level of sexual isolation exists between the lineages, so that recombination has occurred predominantly between members of the same lineage. This pattern of recombination is compatible with expectations from the previously described ecological structuring of the enterica population as well as mechanistic barriers to recombination observed in laboratory experiments. In spite of their relatively low level of genetic differentiation, these lineages might therefore represent incipient species.

Basic concepts of microarrays and potential applications in clinical microbiology

The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.

Recent advances in the diagnosis and treatment of multidrug-resistant tuberculosis

Tuberculosis (TB) is a major infectious disease killing nearly two million people, mostly in developing countries, every year. The increasing incidence of resistance of Mycobacterium tuberculosis strains to the most-effective (first-line) anti-TB drugs is a major factor contributing to the current TB epidemic. Drug-resistant strains have evolved mainly due to incomplete or improper treatment of TB patients. Resistance of M. tuberculosis to anti-TB drugs is caused by chromosomal mutations in genes encoding drug targets. Multidrug-resistant (resistant at least to rifampin and isoniazid) strains of M. tuberculosis (MDR-TB) evolve due to sequential accumulation of mutations in target genes. Emergence and spreading of MDR-TB strains is hampering efforts for the control and management of TB. The MDR-TB is also threatening World Health Organization's target of tuberculosis elimination by 2050. Proper management of MDR-TB relies on early recognition of such patients. Several diagnostic methods, both phenotypic and molecular, have been developed recently for rapid identification of MDR-TB strains from suspected patients and some are also suitable for resource-poor countries. Once identified, successful treatment of MDR-TB requires therapy with several effective drugs some of which are highly toxic, less efficacious and expensive. Minimum treatment duration of 18-24 months is also long, making it difficult for health care providers to ensure adherence to treatment. Successful treatment has been achieved by supervised therapy with appropriate drugs at institutions equipped with facilities for culture, drug susceptibility testing of MDR-TB strains to second-line drugs and regular monitoring of patients for adverse drug reactions and bacteriological and clinical improvement.

Molecular epidemiology and prevalence of mutations conferring rifampicin and isoniazid resistance in Mycobacterium tuberculosis strains from the southern Ukraine

Understanding the molecular epidemiology of tuberculosis (TB) and mutations in genes associated with drug resistance may contribute to the development of appropriate interventions to improve tuberculosis control. A structured questionnaire was used to collect basic epidemiological data from 589 patients with radiologically confirmed TB in the Odessa and Nikolaev regions of the Ukraine in 2003-2004. A non-commercial reverse hybridisation assay and DNA sequencing were used to detect mutations associated with rifampicin and isoniazid resistance. Genotyping was performed using multilocus variable number tandem repeat (VNTR) typing and spoligotyping. Mutations conferring rifampicin and isoniazid resistance were detected in 32.9% and 44.0%, respectively, of 225 Mycobacterium tuberculosis isolates from individual consecutive patients. Mutations in codon 531 and codon 315 of the rpoB and katG genes, respectively, were predominant among drug-resistant isolates. Multidrug (MDR) resistance rates were significantly higher among former prison inmates compared with non-prisoners (54.8% vs. 27.3%; RR 2.01; 95% CI 1.35-2.97) and the prevalence of mutations was higher in Beijing strains sharing the VNTR signature 223325173533424 than in other Beijing strains (71.4% vs. 45.7%; RR 1.74; 95% CI 1.17-2.57), suggesting that this group may be responsible for rapid transmission of MDR TB in the southern Ukraine.

Resistance levels and rpoB gene mutations among in vitro-selected rifampin-resistant Mycobacterium tuberculosis mutants

The distribution and resistance levels of 189 in vitro-selected rifampin-resistant Mycobacterium tuberculosis mutants of Beijing and other genotypes were determined. Apart from a higher amount of codon 522 point mutations and large deletions, a spread of mutations similar to that reported for clinical isolates was seen. Most mutations were correlated with high-level resistance; a lower level, or a MIC of <16 mg/liter, was associated with codon 522 mutations. Multiple mutations were detected in two Beijing mutants.

Comparison of a conventional antimicrobial susceptibility assay to an oligonucleotide chip system for detection of drug resistance in Mycobacterium tuberculosis isolates

An oligonucleotide chip (Combichip Mycobacteria chip) detecting specific mutations in the rpoB, katG, and inhA genes of Mycobacterium tuberculosis was compared with conventional antimicrobial susceptibility results. The probes detecting drug resistance were as follows: 7 wild-type and 13 mutant probes for rifampin and 2 wild-type and 3 mutant probes for isoniazid. Target DNA of M. tuberculosis was amplified by PCR, followed by hybridization and scanning. Direct sequencing was performed to verify the results of the oligonucleotide chip. One-hundred seven of 115 rifampin-resistant strains (93%) had mutations in the rpoB gene. Eighty-five of 119 isoniazid-resistant strains (71%) had mutations in the katG gene or inhA gene. The diagnostic oligonucleotide chip with mutation-specific probes is a reliable and useful tool for the rapid and accurate diagnosis of resistance against rifampin and isoniazid in M. tuberculosis isolates.

Application of oligonucleotide arrays to high-content genetic analysis

The scope of single nucleotide polymorphism genotyping for genetic association studies has expanded recently from the use of relatively small numbers of candidate genes and markers, to include hypothesis-free, whole-genome approaches using hundreds of thousands of polymorphisms. The ability to perform such large-scale association studies has been dependant on the development of highly parallel and cost-effective genotyping platforms, of which those based on oligonucleotide arrays have proved to be the most scalable and widely adopted. It is to be expected that the new array-based genotyping methods will not only greatly expand the scope of genetic studies, but, as further content is added to arrays, will also form part of an integrated set of DNA, RNA and proteomic analyses enabling the detailed, multilayered study of complex disease-linked phenotypes.

Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest

Environmental screening of bacteria for the presence of genes of interest is a challenging problem, due to the high variability of the nucleotide sequence of a given gene between species. Here, we tackle this general issue using a particularly well-suited model system that consists of the nodulation gene nodC, which is shared by phylogenetically distant rhizobia. 41mer and 50mer oligonucleotides featuring the nucleotide diversity of two highly conserved regions of the NodC protein were spotted on glass slides and cross hybridized with the radioactive-labeled target genomic DNA under low-stringency conditions. Statistical analysis of the hybridization patterns allowed the detection of known, as well as new, nodC sequences and classified the rhizobial strains accordingly. The microarray was successfully used to type the nodC gene directly from legume nodules, thus eliminating the need of cultivation of the endosymbiont. This approach could be extended to a panel of diagnostic genes and constitute a powerful tool for studying the distribution of genes of interest in the environment, as well as for bacteria identification.

Evaluation of hybridisation on oligonucleotide microarrays for analysis of drug-resistant Mycobacterium tuberculosis

A molecular approach was developed to identify drug-resistant strains of Mycobacterium tuberculosis by means of biochips with oligonucleotides immobilised in polyacrylamide gel pads. The technique was based on multiplex PCR, followed by hybridisation on an oligonucleotide microarray, and detected > 95% of rifampicin-resistant and c. 80% of isoniazid-resistant M. tuberculosis isolates within 12 h. In total, 220 drug-resistant isolates and 131 clinical samples were tested using biochips. The sensitivity and specificity of the developed method were comparable with those of standard bacteriological testing of M. tuberculosis drug resistance.

Novel technology and the development of pharmacogenetics within the pharmaceutical industry

This article focuses on the role of pharmacogenetics (PGx) technology across the drug development pipeline. Recent technology developments in three main areas are discussed: the discovery of polymorphisms or other variants in genes of interest; genotyping technologies used in PGx research (both for candidate gene analyses and for a whole-genome association approach); and the use of genotyping in patients prior to prescription (diagnostics). Finally, the associated issues of genetic data management and analysis are addressed, and the challenges facing the pharmaceutical industry in storing, manipulating and exploiting the large and complex data sets that will be generated from emerging PGx platforms are discussed. In conclusion, it is demonstrated that, despite the failures of some technology development programs and the slow rate of progress of others, there has, in fact, been steady progress toward the implementation of PGx within the pharmaceutical industry.