Band pattern analysis of mutations in rifampicin resistance strain of Mycobacterium tuberculosis by Line Probe assay in patients from Delhi, India

BACKGROUND

The GenoType MTBDRplus, a commercial Line Probe Assay (LPA) kit from Hain Lifescience, Germany, is endorsed by India's RNTCP Program for diagnosis of DRTB cases among smear-positive sputum samples. Although the LPA has been studied in several laboratories, there is a wide variation in existing M. tuberculosis strains across the globe, and false results can occur due to the presence of unique genetic mutations in different settings.

AIM AND OBJECTIVE

An attempt was made to carry out band pattern analysis using LPA and also to observe uncommon mutations in MDR strains.

MATERIALS AND METHODS

Sputum samples were collected from MDR suspects and transported to intermediate reference laboratory (IRL) at New Delhi Tuberculosis Centre in Delhi. Sputum decontamination, DNA extraction, amplification, hybridization, and band pattern analysis of Line Probe assay strips was performed as per manufacturer's instructions.

RESULTS

Among the 3000 samples with interpretable LPA strips, rifampicin drug resistance with or without isoniazid was observed in 600 samples. The most common mutation detected by LPA in the rpoB gene was Ser516Leu (29.0%). Novel mutations reported in this study include mutation from CAG (Gin) to CAT (His) at codon 517, AGC (Ser)-AGG (Arg) at codon 512, ACA (Thr) to GCA (Ala) at codon 526, TTG (Leu)-CTG (Leu)^s at codon 524.

CONCLUSION

High frequencies of uncommon mutations in rpoB gene by LPA were observed, highlighting possibility of those in-silico detected mutations that may not impart phenotypic resistance further.

Has universal screening with Xpert® MTB/RIF increased the proportion of multidrug-resistant tuberculosis cases diagnosed in a routine operational setting?

SETTING

Primary health services in Cape Town, South Africa where the introduction of Xpert® MTB/RIF (Xpert) enabled simultaneous screening for tuberculosis (TB) and drug susceptibility in all presumptive cases.

STUDY AIM

To compare the proportion of TB cases with drug susceptibility tests undertaken and multidrug-resistant tuberculosis (MDR-TB) diagnosed pre-treatment and during the course of 1st line treatment in the previous smear/culture and the newly introduced Xpert-based algorithms.

METHODS

TB cases identified in a previous stepped-wedge study of TB yield in five sub-districts over seven one-month time-points prior to, during and after the introduction of the Xpert-based algorithm were analysed. We used a combination of patient identifiers to identify all drug susceptibility tests undertaken from electronic laboratory records. Differences in the proportions of DST undertaken and MDR-TB cases diagnosed between algorithms were estimated using a binomial regression model.

RESULTS

Pre-treatment, the probability of having a DST undertaken (RR = 1.82)(p<0.001) and being diagnosed with MDR-TB (RR = 1.42)(p<0.001) was higher in the Xpert-based algorithm than in the smear/culture-based algorithm. For cases evaluated during the course of 1st-line TB treatment, there was no significant difference in the proportion with DST undertaken (RR = 1.02)(p = 0.848) or MDR-TB diagnosed (RR = 1.12)(p = 0.678) between algorithms.

CONCLUSION

Universal screening for drug susceptibility in all presumptive TB cases in the Xpert-based algorithm resulted in a higher overall proportion of MDR-TB cases being diagnosed and is an important strategy in reducing transmission. The previous strategy of only screening new TB cases when 1st line treatment failed did not compensate for cases missed pre-treatment.

Novel rapid PCR for the detection of Ile491Phe rpoB mutation of Mycobacterium tuberculosis, a rifampicin-resistance-conferring mutation undetected by commercial assays

OBJECTIVES

Neither the liquid medium-based Bactec MGIT, nor commercial molecular assays such as the Xpert MTB/RIF and the MTBDRplus V2.0 assays are capable of detecting up to 30% of rifampicin-resistant Mycobacterium tuberculosis strains in Swaziland because of the large proportion of the rpoB Ile491Phe mutations. In other countries, the frequency of this mutation is thought to be low.

METHODS

We designed a real-time multiplex allele-specific PCR assay to identify the rpoB Ile491Phe mutation responsible for these undetected resistant M. tuberculosis strains.

RESULTS

The technique showed 100% similarity with rpoB sequencing on a panel of 78 strains from Swaziland.

CONCLUSIONS

We propose that the detection of the rpoB Ile491Phe rpoB mutation should complement commercial assays for the diagnosis of rifampicin-resistant M. tuberculosis in routine conditions, particularly in countries where this specific mutation is frequent. The technique proposed in this paper is adapted for most reference laboratories.

Decreased Time to Treatment Initiation for Multidrug-Resistant Tuberculosis Patients after Use of Xpert MTB/RIF Test, Latvia

This test decreased time to treatment initiation by 66%–84%.

Few studies have examined whether the Xpert MTB/RIF test improves time to treatment initiation for persons with multidrug-resistant tuberculosis (MDR TB). We determined the impact of this test in Latvia, where it was introduced in 2010. After descriptive analyses of pulmonary MDR TB patients in Latvia during 2009–2012, time to treatment initiation was calculated, and univariate and multivariable accelerated failure time models were constructed. Univariate results showed strong evidence of an association between having rifampin-resistant TB detected by Xpert MTB/RIF and reduced time to treatment initiation versus the test not being used. A multivariable model stratifying by previous TB showed similar results. Our finding that in Latvia, time to treatment initiation was decreased for MDR TB cases that were rifampin-resistant TB by XpertMTB/RIF has implications for the use of this test in other settings with a high burden of MDR TB in which rifampin resistance is highly predictive of MDR TB.

Fermentation, isolation, purification and characterization of an antitubercular antibiotic from Streptomyces luridus MTCC 4402

Tuberculosis, caused by Mycobacterium tuberculosis, continues to be a serious public health problem around the world, and it urges the need for development of new antitubercular drugs. An antibiotic producing strain, Streptomyces luridus (MTCC 4402) was earlier isolated from soil by our group. In this work, the phylogenic status was established by 16S rRNA gene sequence analysis. The strain was found to be active against clinically resistant strains. The culture was grown in shake flasks in a medium containing cornsteep liquor, glucose, CaCO(3), soyabean meal and starch. Antibiotic production reached maximum at the end of 72 h. and fermentation profile was obtained. The active compound was extracted into ethyl acetate and was subjected to activity guided purification by column chromatography using silica gel, TLC and HPLC methods. The pure compound eluted at 16.7 min. by gradient elution was subjected to (1)H, (13)C NMR and mass spectral analyses. The acquired data was compared with that of natural products’ data base and found to be a known antibiotic, spiramycin. The purified compound was studied for mutagenic, cytotoxicity, antitubercular activities. It was non mutagenic at the concentration of 1000 μg/mL, non cytotoxic and active as antitubercular agent at a concentration of 64 mg/mL and was comparable to rifampicin.

Graft Infectivity of Rifampin and Silver-Bonded Polyester Grafts to MRSA Contamination

The purpose of this study was to evaluate the ability of vascular polyester grafts with antibacterial properties to resist colonization following surface contamination by methicillin-resistant Staphylococcus aureus(MRSA) in an experimental canine model or aortic graft infection. Twenty-four pathogen-free dogs underwent replacement of the infrarenal aorta with either a rifampin-soaked (30 mg/mL) or silver-impregnated (Ag-acetate) woven polyester graft. Following implantation, the external graft surface was inoculated with 2 mL of 107 colonyforming units/mL (CFU) of MRSA. Preoperative antibiotic prophylaxis consisted of a single intravenous dose of 500 mg of sodium cefazolin. Four grafts of each type were explanted at 3, 7, and 14 days after implantation. Quantitative cultures (CFU/specimen) of perigraft fluid (1 mL), graft material (1 cm segment), and adjacent aorta (1 cm segment) were performed. Differences between grafts are expressed as% mean log reduction in recoverable CFU compared to the inoculation solution concentration of 107 CFUs. At 3 days, explanted rifampinsoaked grafts exhibited no MRSA growth (4 of 4 grafts) and a =97% mean log reduction of MRSA CFUs from the adjacent aorta and perigraft fluid (PGF). At 3 days, all silver-bonded grafts exhibited signs of infection and a mean log CFU reduction of MRSA ranging from 68% (absolute range 101–103 recoverable CFU) for the graft, 79% (absolute range 101–103 recoverable CFU) for the aorta, and 86% (absolute range 101–104 recoverable CFU) for PGF. The 7-day rifampin group had an average log reduction in MRSA CFU of 72% (graft), 58% (PGF), 75% (aorta). Quantitative cultures of 14-day rifampin grafted demonstrated continued bacterial growth suppression with mean MRSA CFU log reductions of 82%, graft; 72%, PGF; 89%, aorta. Silver-bonded grafts demonstrated <50% mean CFU reduction in MRSA growth at 7 days (absolute range 105–107 recoverable CFU) and 14 days (absolute range 103–107 recoverable CFU). No animal died from sepsis or anastomotic hemorrhage. Neither rifampin nor silverbonded grafts demonstrated prolonged resistance to surface MRSA contamination. Rifampinsoaked polyester grafts exhibited a marked but transient resistance MRSA colonization likely the result of high antibiotic concentration in the perigraft tissue. While both types of grafts failed to eradicate the MRSA infection future research with silver-bonded grafts that have an additional antibiotic attached may have a place in the treatment of MRSA infection.

Rifamycins, Alone and in Combination

Rifamycins inhibit RNA polymerase of most bacterial genera. Rifampicin remains part of combination therapy for treating tuberculosis (TB), and for treating Gram-positive prosthetic joint and valve infections, in which biofilms are prominent. Rifabutin has use for AIDS patients in treating mycobacterial infections TB and Mycobacterium avium complex (MAC), having fewer drug-drug interactions that interfere with AIDS medications. Rifabutin is occasionally used in combination to eradicate Helicobacter pylori (peptic ulcer disease). Rifapentine has yet to fulfill its potential in reducing time of treatment for TB. Rifaximin is a monotherapeutic agent to treat gastrointestinal (GI) disorders, such as hepatic encephalopathy, irritable bowel syndrome, and travelers' diarrhea. Rifaximin is confined to the GI tract because it is not systemically absorbed on oral dosing, achieving high local concentrations, and showing anti-inflammatory properties in addition to its antibacterial activity. Resistance issues are unavoidable with all the rifamycins when the bioburden is high, because of mutations that modify RNA polymerase.

Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance

A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs such as D-cycloserine. Here we used the whole-genome sequences from 498 strains of M. tuberculosis to identify new resistance-conferring genotypes. By combining association and correlated evolution tests with strategies for amplifying signal from rare variants, we found that loss-of-function mutations in ald (Rv2780), encoding L-alanine dehydrogenase, were associated with unexplained drug resistance. Convergent evolution of this loss of function was observed exclusively among multidrug-resistant strains. Drug susceptibility testing established that ald loss of function conferred resistance to D-cycloserine, and susceptibility to the drug was partially restored by complementation of ald. Clinical strains with mutations in ald and alr exhibited increased resistance to D-cycloserine when cultured in vitro. Incorporation of D-cycloserine resistance in novel molecular diagnostics could allow for targeted use of this toxic drug among patients with susceptible infections.

A molecular platform for the diagnosis of multidrug-resistant and pre-extensively drug-resistant tuberculosis based on single nucleotide polymorphism mutations present in Colombian isolates of Mycobacterium tuberculosis

Developing a fast, inexpensive, and specific test that reflects the mutations present in Mycobacterium tuberculosis isolates according to geographic region is the main challenge for drug-resistant tuberculosis (TB) control. The objective of this study was to develop a molecular platform to make a rapid diagnosis of multidrug-resistant (MDR) and extensively drug-resistant TB based on single nucleotide polymorphism (SNP) mutations present in therpoB, katG, inhA,ahpC, and gyrA genes from Colombian M. tuberculosis isolates. The amplification and sequencing of each target gene was performed. Capture oligonucleotides, which were tested before being used with isolates to assess the performance, were designed for wild type and mutated codons, and the platform was standardised based on the reverse hybridisation principle. This method was tested on DNA samples extracted from clinical isolates from 160 Colombian patients who were previously phenotypically and genotypically characterised as having susceptible or MDR M. tuberculosis. For our method, the kappa index of the sequencing results was 0,966, 0,825, 0,766, 0,740, and 0,625 forrpoB, katG, inhA,ahpC, and gyrA, respectively. Sensitivity and specificity were ranked between 90-100% compared with those of phenotypic drug susceptibility testing. Our assay helps to pave the way for implementation locally and for specifically adapted methods that can simultaneously detect drug resistance mutations to first and second-line drugs within a few hours.

Piloting Upfront Xpert MTB/RIF Testing on Various Specimens under Programmatic Conditions for Diagnosis of TB & DR-TB in Paediatric Population

BACKGROUND

India accounts for one-fifth of the global TB incidence. While the exact burden of childhood TB is not known, TB remains one of the leading causes of childhood mortality in India. Bacteriological confirmation of TB in children is challenging due to difficulty in obtaining quality specimens, in the absence of which diagnosis is largely based on clinical judgement. While testing multiple specimens can potentially contribute to higher proportion of laboratory confirmed paediatric TB cases, lack of high sensitivity tests adds to the diagnostic challenge. We describe here our experiences in piloting upfront Xpert MTB/RIF testing, for diagnosis of TB in paediatric population in respiratory and extra pulmonary specimens, as recently recommended by WHO.

METHOD

Xpert MTB/RIF testing was offered to all paediatric (0-14 years) presumptive TB cases (both pulmonary and extra-pulmonary) seeking care at public and private health facilities in the project areas covering 4 cities of India.

RESULTS

Under this pilot project, 8,370 paediatric presumptive TB & presumptive DR-TB cases were tested between April and-November 2014. Overall, 9,149 specimens were tested, of which 4,445 (48.6%) were non-sputum specimens. Xpert MTB/RIF gave 9,083 (99.2%, CI 99.0-99.4) valid results. Of the 8,143 presumptive TB cases enrolled, 517 (6.3%, CI 5.8-6.9) were bacteriologically confirmed. TB detection rates were two fold higher with Xpert MTB/RIF as compared to smear microscopy. Further, a total of 60 rifampicin resistant TB cases were detected, of which 38 were detected among 512 presumptive TB cases while 22 were detected amongst 227 presumptive DR-TB cases tested under the project.

CONCLUSION

Xpert MTB/RIF with advantages of quick turnaround testing-time, high proportion of interpretable results and feasibility of rapid rollout, substantially improved the diagnosis of bacteriologically confirmed TB in children, while simultaneously detecting rifampicin resistance.

Unraveling Comparative Anti-Amyloidogenic Behavior of Pyrazinamide and D-Cycloserine: A Mechanistic Biophysical Insight

Amyloid fibril formation by proteins leads to variety of degenerative disorders called amyloidosis. While these disorders are topic of extensive research, effective treatments are still unavailable. Thus in present study, two anti-tuberculosis drugs, i.e., pyrazinamide (PYZ) and D-cycloserine (DCS), also known for treatment for Alzheimer's dementia, were checked for the anti-aggregation and anti-amyloidogenic ability on Aβ-42 peptide and hen egg white lysozyme. Results demonstrated that both drugs inhibit the heat induced aggregation; however, PYZ was more potent and decelerated the nucleation phase as observed from various spectroscopic and microscopic techniques. Furthermore, pre-formed amyloid fibrils incubated with these drugs also increased the PC12/SH-SY5Y cell viability as compare to the amyloid fibrils alone; however, the increase was more pronounced for PYZ as confirmed by MTT assay. Additionally, molecular docking study suggested that the greater inhibitory potential of PYZ as compare to DCS may be due to strong binding affinity and more occupancy of hydrophobic patches of HEWL, which is known to form the core of the protein fibrils.

Effects of Introducing Xpert MTB/RIF on Diagnosis and Treatment of Drug-Resistant Tuberculosis Patients in Indonesia: A Pre-Post Intervention Study

Background

In March 2012, the Xpert MTB/RIF assay (Xpert) was introduced in three provincial public hospitals in Indonesia as a novel diagnostic to detect tuberculosis and rifampicin resistance among high risk individuals.

Objective

This study assessed the effects of using Xpert in place of conventional solid and liquid culture and drug-susceptibility testing on case detection rates, treatment initiation rates, and health system delays among drug-resistant tuberculosis (TB) patients.

Methods

Cohort data on registration, test results and treatment initiation were collected from routine presumptive patient registers one year before and one year after Xpert was introduced. Proportions of case detection and treatment initiation were compared using the Pearson Chi square test and median time delays using the Mood’s Median test.

Results

A total of 975 individuals at risk of drug-resistant TB were registered in the pre-intervention year and 1,442 in the post-intervention year. After Xpert introduction, TB positivity rate increased by 15%, while rifampicin resistance rate reduced by 23% among TB positive cases and by 9% among all tested. Second-line TB treatment initiation rate among rifampicin resistant patients increased by 19%. Time from client registration to diagnosis was reduced by 74 days to a median of a single day (IQR 0–4) and time from diagnosis to treatment start was reduced by 27 days to a median of 15 days (IQR 7–51). All findings were significant with p<0.001.

Conclusion

Compared to solid and liquid culture and drug-susceptibility testing, Xpert detected more TB and less rifampicin resistance, increased second-line treatment initiation rates and shortened time to diagnosis and treatment. This test holds promise to improve rapid case finding and management of drug-resistant TB patients in Indonesia.

[DETERMINATION OF CRITICAL CONCENTRATION OF CHEMOTHERAPY DRUGS FOR MYCOBACTERIUM TUBERCULOSIS SENSITIVITY EVALUATION USING Sensititre MyCoTB TEST SYSTEM]

AIM

Determination of critical concentration for chemotherapy drugs, widely used for tuberculosis treatment, for use in Mycobacterium tuberculosis drug sensitivity results evaluation by Sensititre MycoTB test-system.

MATERIALS AND METHODS

Minimal inhibiting concentration (MIC) of isoniazid, rifampicin, streptomycin, ethambutol, amikacin, kanamycin, ofloxacin and moxifloxacin against conditionally sensitive and conditionally resistant strains of tuberculosis mycobacteria (TBM), isolated from various diagnostic material, obtained from patients with various forms of lung tuberculosis being treated in MCSPCTC hospital and dispensaries for tuberculosis control of Moscow, were studied in Sensititre MycoTB test system.

RESULTS

Critical concentration of chemotherapy drugs for MycoTB test system was determined as a result of the obtained MIC values analysis as the minimal concentration that suppressed growth of 95% of sensitive strains and does not obstruct growth of 95% of resistant. The following MIC values were established: streptomycin--1.0, isoniazid--0.25, rifampicin--1.0, ethambutol--4.0, ofloxacin--2.0, moxifloxacin--0.25, kanamycin--2.5 and amikacin- 1.0 µg/ml.

CONCLUSION

The developed critical concentration of the mentioned preparations is currently used for evaluation of sensitivity/ resistance of TBM clinical isolates from MCSPCTC.

[New methods of diagnosis in tuberculosis]

Bacteriological diagnosis of tuberculosis has benefited in recent years from many technological advances to improve rapidity and sensitivity of the techniques. Thus, new LED fluorescence microscopes are in the process of replacing the optical microscopes and the Ziehl-Neelsen technique, making the examination more precise, faster and easier. The manual and automatic liquid culture has improved Lowenstein-Jensen culture and helped shorten antibiotic sensitivity test, allowing appropriate management of patients. The development and standardization of molecular biology methods led to the rapid detection and identification of mycobacterium directly in clinical samples but also of resistance genes for early diagnosis of MDR-TB and dealing with them quickly. However, the performance of these techniques does not sufficiently cover the diagnosis of smear-negative tuberculosis, extrapulmonary forms, children- and immune-compromised tuberculosis where sensitivity is limited. The diagnosis of latent tuberculosis is reinforced by the in vitro release testing of gamma interferon overcoming the lack of specificity of the tuberculin skin test. Despite considerable progress, more amelioration is still needed to improve these techniques in order to extend them to the paucibacillary tuberculosis and to facilitate their access to low-resource countries.

Molecular interactions of rifabutin with membrane under acidic conditions

This work focuses on the interaction of the anti-tuberculosis (anti-TB) drug, rifabutin (RFB) with cell membrane models formed by 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). The experiments were performed under acidic conditions (i.e., pH 5.0) taking into account the pH conditions that RFB may find in the course of its in vivo pharmacological activity. The partition of the drug to the membrane was quantified through the partition coefficient (Kp). Fluorescence quenching studies were performed to predict the drug's location across the cell membrane model. The effect of RFB on the biophysical parameters of the cell membrane model was studied by steady-state anisotropy and small-angle X-ray scattering (SAXS). The overall results point to a marked interaction of RFB with cell membranes under acidic pH, which may be related with its pharmacological effects. The in vivo success of RFB may be associated with the drug's disordering effect of the membranes under acidic pH values environments, and consequently drug accumulation in the gastric infected tissues and inside phagolysosomes. On the other hand, the present study allowed establishing important correlations with the gastrointestinal side effects caused by RFB.

Clinical Experience With Minocycline and Rifampin-Impregnated Central Venous Catheters in Bone Marrow Transplantation Recipients: Efficacy and Low Risk of Developing Staphylococcal Resistance

In this retrospective evaluation of the 4-year clinical use of minocycline and rifampin-impregnated catheters in bone marrow transplantation (BMT) patients, we report low risk of development of staphylococcal resistance to the antibiotics coating the catheters and efficacy in preventing primary staphylococcal bloodstream infections.

In vitro activity of rifampicin and verapamil combination in multidrug-resistant mycobacterium tuberculosis

The aim of the present study was to evaluate the effect of the combination of rifampicin (RIF) and verapamil (VP) against the Mycobacterium tuberculosis H37Rv reference strain and six multidrug-resistant (MDR) M. tuberculosis clinical isolates by determining Time-Kill Curves and the ability to efflux drug by fluorometry. The RIF+VP combination showed synergism in one MDR clinical isolate. For the other five MDR clinical isolates, the drug combination showed no interaction. The MDR clinical isolate had lower ethidium bromide (EtBr) accumulation when exposed to the RIF+VP combination, compared with RIF and VP exposure alone. The other MDR clinical isolates showed no significant difference in EtBr accumulation. These results suggest greater efflux action in one of the MDR clinical isolates compared with the M. tuberculosis H37Rv reference strain. The other five MDR isolates may have additional mechanisms of drug resistance to RIF. The use of the RIF+VP combination made one MDR bacillus more susceptible to RIF probably by inhibiting efflux pumps, and this combination therapy, in some cases, may contribute to a reduction of resistance to RIF in M. tuberculosis.

Diagnostic accuracy of the Xpert MTB/RIF assay for extrapulmonary and pulmonary tuberculosis when testing non-respiratory samples: a systematic review

BACKGROUND

Although the evidence base regarding the use of the Xpert MTB/RIF assay for diagnosis of pulmonary tuberculosis (TB) when testing respiratory samples is well established, the evidence base for its diagnostic accuracy for extrapulmonary and sputum-scarce pulmonary TB when testing non-respiratory samples is less clearly defined.

METHODS

A systematic literature search of 7 electronic databases (Medline, EMBASE, ISI Web of Science, BIOSIS, Global Health Database, Scopus and Cochrane Database) was conducted to identify studies of the diagnostic accuracy of the Xpert assay when testing non-respiratory samples compared with a culture-based reference standard. Data were extracted and study quality was assessed using the QUADAS-2 tool. Sensitivities and specificities were calculated on a per-sample basis, stratified by sample type and smear microscopy status and summarised using forest plots. Pooled estimates were calculated for groups with sufficient data.

RESULTS

Twenty-seven studies with a total of 6,026 non-respiratory samples were included. Among the 23 studies comparing Xpert and culture done on the same samples, sensitivity was very heterogeneous with a median sensitivity of 0.83 (IQR, 0.68-0.94) whereas specificities were typically very high (median, 0.98; IQR, 0.89-1.00). The pooled summary estimates of sensitivity when testing smear-positive and smear-negative samples were 0.95 (95% CI 0.91-1.00) and 0.69 (95% CI 0.60-0.80), respectively. Pooled summary estimates of sensitivity varied substantially between sample types: lymph node tissue, 0.96 (95% CI, 0.72-0.99); tissue samples of all types, 0.88 (95% CI, 0.76-0.94); pleural fluid, 0.34 (95% CI, 0.24-0.44); gastric aspirates for diagnosis of sputum-scarce pulmonary TB, 0.78 (IQR, 0.68 - 0.85). Median sensitivities when testing cerebrospinal fluid and non-pleural serous fluid samples were 0.85 (IQR, 0.75-1.00) and 0.67 (IQR, 0.00-1.00), respectively.

CONCLUSION

Xpert detects with high specificity the vast majority of EPTB cases with smear-positive non-respiratory samples and approximately two-thirds of those with smear-negative samples. Xpert is a useful rule-in diagnostic test for EPTB, especially when testing cerebrospinal fluid and tissue samples. In addition, it has a high sensitivity for detecting pulmonary TB when using gastric aspirate samples. These findings support recent WHO guidelines regarding the use of Xpert for TB diagnosis from non-respiratory samples.

Characterisation of a putative AraC transcriptional regulator from Mycobacterium smegmatis

MSMEG_0307 is annotated as a transcriptional regulator belonging to the AraC protein family and is located adjacent to the arylamine N-acetyltransferase (nat) gene in Mycobacterium smegmatis, in a gene cluster, conserved in most environmental mycobacterial species. In order to elucidate the function of the AraC protein from the nat operon in M. smegmatis, two conserved palindromic DNA motifs were identified using bioinformatics and tested for protein binding using electrophoretic mobility shift assays with a recombinant form of the AraC protein. We identified the formation of a DNA:AraC protein complex with one of the motifs as well as the presence of this motif in 20 loci across the whole genome of M. smegmatis, supporting the existence of an AraC controlled regulon. To characterise the effects of AraC in the regulation of the nat operon genes, as well as to gain further insight into its function, we generated a ΔaraC mutant strain where the araC gene was replaced by a hygromycin resistance marker. The level of expression of the nat and MSMEG_0308 genes was down-regulated in the ΔaraC strain when compared to the wild type strain indicating an activator effect of the AraC protein on the expression of the nat operon genes.

Testing the role of genetic background in parallel evolution using the comparative experimental evolution of antibiotic resistance

Parallel evolution is the independent evolution of the same phenotype or genotype in response to the same selection pressure. There are examples of parallel molecular evolution across divergent genetic backgrounds, suggesting that genetic background may not play an important role in determining the outcome of adaptation. Here, we measure the influence of genetic background on phenotypic and molecular adaptation by combining experimental evolution with comparative analysis. We selected for resistance to the antibiotic rifampicin in eight strains of bacteria from the genus Pseudomonas using a short term selection experiment. Adaptation occurred by 47 mutations at conserved sites in rpoB, the target of rifampicin, and due to the high diversity of possible mutations the probability of within-strain parallel evolution was low. The probability of between-strain parallel evolution was only marginally lower, because different strains substituted similar rpoB mutations. In contrast, we found that more than 30% of the phenotypic variation in the growth rate of evolved clones was attributable to among-strain differences. Parallel molecular evolution across strains resulted in divergent phenotypic evolution because rpoB mutations had different effects on growth rate in different strains. This study shows that genetic divergence between strains constrains parallel phenotypic evolution, but had little detectable impact on the molecular basis of adaptation in this system.

[What Hansen's disease research learned from tuberculosis research: from molecular biological aspect]

As for the Mycobacterium leprae which is a causative agent of Hansen's disease, many studies had been done since it was identified in 1873. However, those studies, at the same time, experienced many struggles because of the difficulty of culture of M. leprae on the artificial growth media. Hence, the study of Hansen's disease progressed by taking the knowledge from the study of tuberculosis caused by the bacteria belonging to the same genus, genus Mycobacterium. For instance, the knowledge of mutations in specific genes responsible for rifampicin- and quinolone-resistance in M. tuberculosis led the elucidation of drug-resistant acquisition mechanism of M. leprae. Similarly, it is necessary for the researcher of Hansen's disease to get important information from the latest topic of the tuberculosis study and utilize them to the study of the disease.

Genotype MTBDR plus (Hain) test in suspected MDR-TB patients

BACKGROUND

Incidence ofMDR-TB in Thailand is higher Diagnosis ofmulti-drug resistance (MDR-TB) is often delayed because of insufficient investigations. Therefore, there is a need to introduce an efficient testing method. Genotype MTBDR plus (Hain test) is a new technology of line probe assay (LPAs) In general practice, it had questionable benefit on negative and positive direct smear specimens.

OBJECTIVE

Evaluate the accuracy of the Hain test as compared to the conventional culture and drug susceptibility test (DST), and evaluate the judgment of the physician on starting MDR-TB treatment after receiving the result of the Hain test.

MATERIAL AND METHOD

An observational prospective study was done of 100 suspected MDR-TB patients who visited the Central Chest Institute of Thailand between September and December 2012. Ninety-four patients were included in the present study. They were assessed by direct sputum smear test, Hain test, sputum conventional culture, and drug-susceptibility test (DST) in the first visit. Followed-up treatment until cure/definite treatment were observed for definite diagnosis.

RESULTS

Hain tests identified 65 (69%) MTB positives, 25 (26%) MTB negatives, andfour (4%) Non-tuberculous Mycobacteria (NTM), respectively. Fourteen of 17 negative direct smear but positive Hain test samples were culture negative. We followed these 14 patients. Four patients with TB treatment were cured. Six patients received MDR treatment and improved. Two patients were misdiagnosed CA. Two patients had old scar TB lesion. Sensitivity, specificity, and accuracy ofHain test for MDR-TB detection compared to standard conventional culture were 95%, 86%, and 88%, respectively. Twelve patients were NTMculture positive. Most of them (75%) were M abscessus. Sixty-three percent of chest physicians used the result of the Hain testfor extended treatment ofstandard regimen in non-IR resistance or changing ofTB regimen. There was correlation between judgments of starting MDR-TB treatment and results of Hain test (p = 0.001), no correlation between judgments of physician and pattern (default/relapse/failure) ofprevious TB treatment history (p = 0.6), and periods oftime from first diagnosis of TB to develop suspected MDR-TB (p = 0.09) were demonstrated.

CONCLUSION

We recommend Hain test to diagnose MDR-TB in highly suspected cases, and to wait for conventional culture results to confirm NTM. Hain test has benefit in negative direct smear