Rapid detection of rpoB mutations in rifampin resistant M. tuberculosis from sputum samples by denaturing gradient gel electrophoresis

Hesperetin Inhibits Expression of Virulence Factors and Growth of Helicobacter pylori

Helicobacter pylori (H. pylori) is a bacterium known to infect the human stomach. It can cause various gastrointestinal diseases including gastritis and gastric cancer. Hesperetin is a major flavanone component contained in citrus fruits. It has been reported to possess antibacterial, antioxidant, and anticancer effects. However, the antibacterial mechanism of hesperetin against H. pylori has not been reported yet. Therefore, the objective of this study was to determine the inhibitory effects of hesperetin on H. pylori growth and its inhibitory mechanisms. The results of this study showed that hesperetin inhibits the growth of H. pylori reference strains and clinical isolates. Hesperetin inhibits the expression of genes in replication (dnaE, dnaN, dnaQ, and holB) and transcription (rpoA, rpoB, rpoD, and rpoN) machineries of H. pylori. Hesperetin also inhibits the expression of genes related to H. pylori motility (flhA, flaA, and flgE) and adhesion (sabA, alpA, alpB, hpaA, and hopZ). It also inhibits the expression of urease. Hespereti n downregulates major virulence factors such as cytotoxin-associated antigen A (CagA) and vacuolating cytotoxin A (VacA) and decreases the translocation of CagA and VacA proteins into gastric adenocarcinoma (AGS) cells. These results might be due to decreased expression of the type IV secretion system (T4SS) and type V secretion system (T5SS) involved in translocation of CagA and VacA, respectively. The results of this study indicate that hesperetin has antibacterial effects against H. pylori. Thus, hesperetin might be an effective natural product for the eradication of H. pylori.

Evaluation of denaturing gradient gel electrophoresis for the detection of mycobacterial species and their potential association with waterborne pathogens

The versatility of denaturing gradient gel electrophoresis (DGGE) protocol provides enough grounds for its wide application over an array of microorganisms. This work was designed to evaluate DGGE for the detection and confirmation of mycobacteria and their association, if any, with waterborne pathogens. A total of 76 samples comprising raw untreated water, schmutzdecke, floccules and final treated water obtained from a common water source, and two water treatment works (WTW1 and WTW2), were analysed. Thirty-five species were identified from the overall samples, with 7% (5/76), 13% (10/76) and 26% (20/76) from the common raw water source, WTW1 and WTW2 respectively. The majority of the species were Cyanobacteria, with high dominance in the raw water entering WTW2. In the final treated water of WTW1 Eutreptiella braarudii was found, and that of WTW2 contained Anabaena nereformis, Anabaena torulosa and Podocarpus nerrifolius. Furthermore, one Mycobacterium species was found in the raw water of WTW1 aside from the detection of Mycobacterium avium ssp. paratuberculosis by the technique. No association between mycobacteria and the other species was observed. This implies DGGE may be employed to study the diversity of other akin mycobacterial species from various sources, and not as a direct means of elucidating microbial associations.

PCR Multipleks untuk Identifikasi Mycobacterium tuberculosis Resisten terhadap Isoniazid dan Rifampisin pada Galur Lokal Balai Laboratorium Kesehatan Provinsi Jawa Barat

The incidence of multidrug-resistant tuberculosis (MDR-TB) cases has become the biggest source of the problem in the effort to eradicate tuberculosis (TB) disease in Indonesia. MDR-TB is a resistant TB bacteria to the two, at least, first-line TB drugs, e.g., rifampin and isoniazid. Unfortunately, the current diagnostics methods to identify the MDR-TB are still slow, unspecific, and inaccurate. The purpose of this study is to identify the isoniazid- and rifampin-resistant M. tuberculosis (local strain Balai Laboratorium Kesehatan Provinsi Jawa Barat) by using multiplex PCR method. The TB bacteria colonies were cultivated in Middlebrook 7h9 broth media, which followed by the isolation of chromosomal DNA. The best PCR condition was achieved by optimizing the annealing temperature, the concentration of magnesium chloride, and a number of the cycle. Multiplex PCR was conducted with inhA1-inhA2, rpoB1- rpoB2, katG1- katG2, and B1-B2 pair primers. Furthermore, the PCR product was characterized on 2% gel agarose electrophoresis which stained by using ethidium bromide. The result showed that isoniazid- and rifampin-resistant M. tuberculosis sample could be identified using multiplex PCR, producing DNA fragments with a size of 71 bp, 124 bp 186 bp, and 200 bp. A non-MDR-TB only produced one DNA fragments with a size of 200 bp. Therefore, it can be concluded that MDR-TB and non-MDR-TB can be distinguished using multiplex PCR with a combination of four pair primers.  

Modified genome comparison method: a new approach for identification of specific targets in molecular diagnostic tests using Mycobacterium tuberculosis complex as an example

BACKGROUND

The first step of designing any genome-based molecular diagnostic test is to find a specific target sequence. The modified genome comparison method is one of the easiest and most comprehensive ways to achieve this goal. In this study, we aimed to explain this method with the example of Mycobacterium tuberculosis complex and investigate its efficacy in a diagnostic test.

METHODS

A specific target was identified using modified genome comparison method and an in-house PCR test was designed. To determine the analytical sensitivity and specificity, 10 standard specimens were used. Also, 230 specimens were used to determine the clinical sensitivity and specificity.

RESULTS

The identity and query cover of our new diagnostic target (5KST) were ≥ 90% with M. tuberculosis complex. The 5KST-PCR sensitivity was 100% for smear-positive, culture-positive and 85.7% for smear-negative, culture-positive specimens. All of 100 smear-negative, culture-negative specimens were negative in 5KST-PCR (100% clinical specificity). Analytical sensitivity of 5KST-PCR was approximately 1 copy of genomic DNA per microliter.

CONCLUSIONS

Modified genome comparison method is a confident way to find specific targets for use in diagnostic tests. Accordingly, the 5KST-PCR designed in this study has high sensitivity and specificity and can be replaced for conventional TB PCR tests.

Rapid detection of mutations in erm(41) and rrl associated with clarithromycin resistance in Mycobacterium abscessus complex by denaturing gradient gel electrophoresis

Clarithromycin resistance is increasing dramatically among Mycobacterium abscessus complex. The main resistance mechanisms are mutations in the erm(41) and rrl genes. Here we report PCR-based denaturing gradient gel electrophoresis (DGGE) as an alternative method for rapidly detection of mutations in erm(41) and rrl among M. abscessus isolates. Four primer sets targeting the full-length erm(41) gene and a 354bp fragment of the rrl gene were designed. A combination of 16 different DGGE patterns were observed for erm(41) gene, including 16 in M. abscessus subsp. abscessus and 1 in M. abscessus subsp. massiliense. Six DGGE patterns were obtained for rrl gene. Mutations in the erm(41) and rrl detected by DGGE were 100% identical to mutations detected by DNA sequencing. This is the first report to identify PCR-based DGGE as a practical, relatively inexpensive technique for rapidly detecting mutations in the erm(41) and rrl genes associated with clarithromycin resistance in M. abscessus complex.

Comparison of Xpert MTB/RIF with line probe assay for detection of rifampin-monoresistant Mycobacterium tuberculosis

The MTBDRplus line probe assay (LPA) and Xpert MTB/RIF have been endorsed by the World Health Organization for the rapid diagnosis of drug-resistant tuberculosis. However, there is no clarity regarding the superiority of one over the other. In a double-blinded prospective study, we evaluated the efficacy of the Xpert MTB/RIF on samples that were first tested by LPA under the revised national tuberculosis control program of India. A total of 405 sputum samples from suspected drug-resistant tuberculosis patients were included. Of these, 285 smear-positive samples were subjected to LPA. Seventy-two (25.8%) samples showed multidrug resistance, 62 (22.2%) showed rifampin monoresistance, 29 (10.3%) showed isoniazid monoresistance, and 116 (41.5%) were pan-susceptible. Six (2.1%) of the samples gave invalid results. Of the 62 rifampin-monoresistant samples by LPA, 38 (61.4%) showed rifampin resistance, while 21 (33.8%) were found susceptible to rifampin by Xpert MTB/RIF using cartridge version G4. Three (4.8%) samples gave an error. Of the 116 pan-susceptible samples, only 83 were available for Xpert MTB/RIF testing; 4 (5.1%) were rifampin resistant, 74 (94.8%) were susceptible, and 5 (6.0%) showed an error. The 25 discrepant samples were further subjected to MGIT960 drug susceptibility testing. The MGIT960 results showed 100% agreement with LPA results but only 64.4% agreement with Xpert MTB/RIF results. Sequencing analysis of discrepant samples showed 91.3% concordance with LPA but only 8.7% concordance with the Xpert MTB/RIF assay. These findings indicate that by using Xpert MTB/RIF testing we might be underestimating the burden of drug-resistant tuberculosis and indicate that country-specific probes need to be designed to increase the sensitivity of the Xpert MTB/RIF.

High prevelance of rifampin-monoresistant tuberculosis: a retrospective analysis among Iranian pulmonary tuberculosis patients

We determined the prevalence of rifampin-monoresistant tuberculosis (RMR-TB) in Iran. Because development of RMR-TB is not common, we also identified the major risk factors associated with RMR-TB reported from different provinces of Iran. Data for 3,020 TB patients who remained or became smear positive after two, four, six, and nine months of standard first-line chemotherapy were retrospectively analyzed. Of 3,020 patients, 1,242 patients (41.1%) were culture and DNA positive for Mycobacterium tuberculosis. Of these patients, 73 (7.4%) patients had monoresistant isolates to rifampin, which was significantly higher than that for multidrug-resistant TB (5.8%). The average rate of RMR-TB in the studied population ranged from 5% to 10%. Classical investigation showed that 33.6% of patients had either a previous or family history of TB. Molecular epidemiology methods (i.e., spoligotyping and Mycobacterium interspersed repetitive unit-variable number tandem repeat), defined transmission link in three clusters (13%). These results outline the urgent need for a comprehensive plan for detection and treatment of RMR-TB cases.

Resistance profiles and rpoB gene mutations of Mycobacterium tuberculosis isolates in Taiwan

BACKGROUND/PURPOSE

The rifampicin resistance of Mycobacterium tuberculosis is caused by mutations in the 81-base pair region of the rpoB gene encoding the β-subunit of RNA polymerase. Sequences of the rpoB gene of 68 isolates were analyzed to identify the mutations and to compare the mutations with their related susceptibilities.

METHODS

Susceptibility tests of 68 M. tuberculosis isolates, collected in Taiwan during the period from 1999 to 2011, were performed by the modified agar proportion method according to Clinical and Laboratory Standards Institute recommendations. Sequences of the rpoB gene and the resistance profiles were analyzed and compared with the data from different geographic regions.

RESULTS

Seven alleles were identified. Among 47 isolates of allele 1 (without mutations of rpoB), 46 were rifampicin-susceptible. The other 21 isolates (alleles 2 to 7, with mutations of rpoB) were rifampicin-resistant, including 18 isolates that were multidrug-resistant. Five mutated alleles demonstrated a single mutation. The mutations occurred in the codons 531 (68.2%), 513 (9.1%), 533 (9.1%), 516 (4.5%), and 526 (4.5%). The sensitivity and specificity of rpoB mutations for predicting the rifampicin-resistance of M. tuberculosis were 95.5% and 100%, respectively.

CONCLUSION

The most prevalent mutations of the rpoB gene were missense mutations in the critical codons, encoding Ser-531, Gln-513, Leu-533, Asp-516, and His-526. These mutations had high sensitivity and specificity for predicting the rifampicin-resistance of M. tuberculosis isolates. The resistance profiles and the frequencies of mutated codons of the rpoB gene varied in different geographic regions, indicating that resistance evolved under the selective pressure of the therapeutic regimens and the spread of different genetic clones.