Application of GeneXpert MTB/RIF technology in rifampicin resistance gene mutation of Mycobacterium tuberculosis / 中国热带医学

@#Abstract: Objective To analyze the accuracy and feasibility of GeneXpert MTB/RIF (GeneXpert) detection in the detection of Mycobacterium tuberculosis and the characteristics of rifampicin-resistant rpoB gene mutations. Methods A total of 4 234 sputum samples from suspected tuberculosis patients diagnosed in Sanya tuberculosis designated hospitals from 2015 to 2021 were selected and subjected to sputum smear, solid culture, drug sensitivity test by solid proportion method and GeneXpert detection. Results The positive detection rates of sputum smear, solid culture and GeneXpert of 4 234 sputum samples were 29.24% (1 238/4 234), 32.17% (1 362/4 234) and 35.40% (1 499/4 234), respectively. The positive detection rate of GeneXpert was higher than that of sputum smear, and the difference was statistically significant (χ2=36.775, P<0.01). It was slightly higher than solid culture, and the difference was not statistically significant (χ2=9.908, P=0.02). Taking solid culture results as the gold standard, the sensitivity and specificity of GeneXpert for detecting MTB were 91.04% (1 240/1 362) and 90.98% (2 613/2 872), respectively. According to the proportional drug susceptibility test results as the gold standard, the sensitivity and specificity of GeneXpert in detecting rifampicin resistance were 96.96% (96/99) and 98.86% (1 128/1 141), respectively, with the consensus rate of 98.71%. The accuracy of rifampicin resistance in GeneXpert group without probe mutation was significantly lower than that in group with probe mutation. There was a statistical difference in probe mutation frequency between newly treated and retreated cases. The analysis of rpoB gene mutation frequency characteristics showed: Probe E (50.00%) > Probe A (22.12%) > Probe D (14.42%) > Probe B (6.73%) > combined probe (5.77%) > Probe C (0.96%). Conclusions GeneXpert detection can quickly and effectively diagnose rifampicin-resistant tuberculosis, which is helpful for early clinical diagnosis and treatment. In this region, the rpoB gene mutation probes of rifampicin-resistant tuberculosis mainly occurr in Probe E and Probe A, with the least mutations in Probe C.

Construction of a High-Throughput Mutation Library of Mycobacterium Rifampin Resistance Gene rpoB / 中山大学学报(医学科学版)

ObjectiveTo establish a mutation library of rifampicin resistance gene rpoB. MethodsThe ΔrpoB attB：：rpoB strain of Mycobacterium smegmatis （M. smegmatis） be constructed by homologous recombination and L5 attB phage integration site exchange. Based on the L5 attB plasmid exchange system and resistance selection medium， 48 clones are selected to verify plasmid replacement efficiency. Degenerate primers are designed every 3 bases in the rifampicin resistance determining region （RRDR）， and a full-coverage mutation library of 81 bases in RRDR region is obtained by PCR amplification. The library fragments are seamlessly cloned into the vector and transformed into Escherichia coli （E. coli）to form an E. coli mutation library. Based on the principle of plasmid exchange， the mutant plasmid library is transformed into the M. smegmatis strain ΔrpoB attB：：rpoB， and the original L5 attB site plasmid is replaced to form the M. smegmatis mutant library. The genotype of the library are determined by genome extraction， library construction and high-throughput sequencing. ResultsCompared with the wild-type rpoB gene （5 600 bp）， the amplified fragment of the rpoB knockout strain is 2 200 bp， which proved that the ΔrpoB attB：：rpoB conditional knockout strain of M. smegmatis is successfully constructed. The success rate of plasmid replacement is 100%. There were 540 kinds of single amino acid mutations in both E. coli library and M. smegmatis library， 5 301 kinds of multi-point mutations in E. coli library， and 853 kinds of multi-point mutations in M. smegmatis library. The correlation coefficient between E. coli library and M. smegmatis library is 0.84. ConclusionsWe have developed a strategy to construct a library of mutants targeting the essential mycobacterial gene rpoB， and successfully established a mutant library of rifampicin resistance gene rpoB.

Statistical analysis of 484 Mycobacterium tuberculosis genomes reveals an association between single nucleotide polymorphisms on ponA1 gene and LAM and Haarlem lineages / Análisis estadístico de 484 genomas de Mycobacterium tuberculosis revela una asociación entre los polimorfismos de un solo nucleótido en el gen ponA1 y los linajes LAM y Haarlem

Abstract Objectives: Evaluate the association between rifampicin resistance and the presence of at least one SNP in the rpoB and ponA1 genes and the spoligotype defined lineages. Material and Methods: This study analyzed two databases of 484 genomes of M. tuberculosis from strains isolated from patients in the cities of Lima and Callao, for which the odds ratio (OR) was calculated considering belonging to a certain spoligotype defined lineages as an exposure factor. Results: No statistically significant association (ρ value> 0.05) was found between the presence of at least one SNP in the rpoB gene and the lineages included in the study (LAM, Haarlem, T and Beijing). However, a statistically significant association was found between the presence of at least one SNP in the ponA1 gene and the LAM and Haarlem lineages (ρ value <0.05). An association was found between the P631S SNP in the ponA1 gene and the LAM and Haarlem lineages; and the A516T SNP, of this same gene, presented an association with the LAM lineage. Likewise, an association was found between rifampicin resistance and the LAM lineage. Conclusions: The presence of SNPs in the ponA1 gene is associated with the LAM and Haarlem lineages.

Resumen Objetivos: Evaluar la asociación entre la resistencia a rifampicina y la presencia de al menos un SNP en los genes rpoB y ponA1 y los linajes definidos por espoli gotipos. Material y Métodos: Este estudio analizó dos bases de datos de 484 genomas de M. tuberculosis de cepas aisladas de pacientes de las ciudades de Lima y Callao, para lo cual se calculó el odds ratio (OR) considerando la pertenencia a determinado linaje definido por espoligotipos como un factor de exposición. Resultados: No se encontró una asociación estadísticamente significativa (valor de ρ >0.05) entre la presencia de al menos un SNP en el gen rpoB y los linajes incluidos en el estudio (LAM, Haarlem, T y Beijing). No obstante, se halló una asociación estadísticamente significativa entre la presencia de al menos un SNP en el gen ponA1 y los linajes LAM y Haarlem (valor de ρ <0.05). Se encontró una asociación entre el SNP P631S del gen ponA1 y los linajes LAM y Haarlem; y el SNP A516T, de este mismo gen, presentó una asociación con el linaje LAM. Asimismo, se halló una asociación entre la resistencia a rifampicina y el linaje LAM. Conclusiones: La presencia de SNPs en el gen ponA1 está asociada con los linajes LAM y Haarlem.

Development of molecular markers of Mycobacterium tuberculosis rifampicin resistance gene rpoB by PARMS technology / 生物工程学报

The purpose of this study is to provide a simple and reliable genetic typing approach for molecular drug susceptibility test of Mycobacterium tuberculosis, through the developing of fluorescence molecular marker of rifampicin resistance gene rpoB. Eleven fluorescent molecular markers of the rpoB gene were established by using the sequence difference between the amino acid positions 531, 526, 516, 511 and 513 of rpoB gene of rifampicin-resistant strains and the alleles of rifampicin-sensitive strains, combined with the PARMS technique (Penta-primer amplification refractory mutation system). We used 104 clinical isolates of Mycobacterium tuberculosis to validate this marker and it was verified by sequencing as 100% correct. These samples were also tested with proportional drug sensitivity test. The coincidence rate was 94.23%. The molecular markers had high reliability for genotyping of rpoB gene. It can also detect low-concentration drug-resistant samples (511/533 unit point mutations) whose phenotypic susceptibility cannot be detected. The eleven sets of fluorescent molecular markers could cover 92%-96% of rpoB gene mutation types of rifampicin-resistant strains, and provide new idea for rapid detection of rifampin-resistant Mycobacterium tuberculosis.

Molecular Identification of 22 Species of Lauraceae by DNA Barcoding / 中国实验方剂学杂志

Objective:DNA barcodes suitable for Lauraceae plants were screened，and 22 Lauraceae plants were identified and classified. Method:The DNA of 22 species of Lauraceae was extracted and amplified by polymerase chain reaction（PCR） with different DNA barcoding primers，followed by electrophoresis and sequencing. Codon Code Aligner was used to proofread，splice， and remove the forward and reverse primer sequences. The sequence was imported into DNAMAN for multiple sequence alignment，and the base mutation sites were analyzed. The Kimura 2-Parameter（K2P） distance of different plants was calculated by MEGA，and the variation degree was analyzed according to the genetic distance. The phylogenetic tree was constructed based on the adjacency method. Result:Three pairs of DNA barcoding primers were used to amplify and sequence the DNA of 22 species of Lauraceae，and 20 species were identified by comparing the specific base sites of gene sequences<bold>.</bold> Conclusion:Four <italic>Litsea</italic> plants could be identified by <italic>matK</italic>， three <italic>Phoebe</italic> plants except for<italic> Cinnamomum validinerve </italic>by<italic> rbcL</italic>， and 20 Lauraceae plants by the combination of<italic> matK</italic>， <italic>rbcL</italic>， and <italic>rpoB</italic>，which provided a theoretical basis for the identification and development of Lauraceae plants. Among them，<italic>matK</italic> was predominant in the identification of Lauraceae plants，and the results also showed that the combination of sequences for plant identification could achieve a better result in DNA barcoding. This study investigated the genetic relationship between Lauraceae plants at the molecular level，aiming at providing a basis for the investigation，cultivation，development，protection， and utilization of medicinal plant resources.

Molecular prophage typing of Staphylococcus aureus isolates from bovine mastitis

Staphylococcus aureus is one of the major pathogens causing bovine mastitis and foodborne diseases associated with dairy products. To determine the genetic relationships between human and bovine or bovine isolates of S. aureus, various molecular methods have been used. Previously we developed an rpoB sequence typing (RSTing) method for molecular differentiation of S. aureus isolates and identification of RpoB-related antibiotic resistance. In this study, we performed spa typing and RSTing with 84 isolates from mastitic cows (22 farms, 72 cows, and 84 udders) and developed a molecular prophage typing (mPPTing) method for molecular epidemiological analysis of bovine mastitis. To compare the results, human isolates from patients (n = 14) and GenBank (n = 166) were used for real and in silico RSTing and mPPTing, respectively. Based on the results, RST10-2 and RST4-1 were the most common rpoB sequence types (RSTs) in cows and humans, respectively, and most isolates from cows and humans clearly differed. Antibiotic resistance-related RSTs were not detected in the cow isolates. A single dominant prophage type and gradual evolution through prophage acquisition were apparent in most of the tested farms. Thus, RSTing and mPPTing are informative, simple, and economic methods for molecular epidemiological analysis of S. aureus infections.

Molecular identification of coagulase-negative staphylococci by rpoB sequence typing / 대한수의학회지

Bovine mastitis (BM) has resulted in enormous economic loss in the dairy industry and coagulase-negative staphylococci (CNS) have caused subclinical BM. Although VITEK 2 GP ID card (VITEK 2) has been used for CNS identification, the probability of identification varies. The rpoB sequence typing (RSTing) method has been used for molecular diagnosis and epidemiology of bacterial infections. In this study, we undertook RSTing of CNS and compared the results with those of VITEK2 and 16S rRNA gene sequencing. As compared VITEK2, the molecular-based methods were more reliable for species identification; moreover, RSTing provided more molecular epidemiological information than that from 16S rRNA gene sequencing.

Direct detection of rpoB and katG gene mutations of Mycobacterium tuberculosis in clinical samples

Objectives: To study the rpoB and katG gene mutation rate and its markers. Methods: Cross-sectional study methods were used to study Tuberculosis. A total of 45 sputum samples were collected from Annapurna Neurological Institute and Allied sci-ences. Then, acid fast bacilli staining were performed. Positive and negative samples were carried for conventional polymerase chain reaction identification and electrophoresis. Results: Out of 45 samples, 3 were acid fast bacilli positive and the rest were negative. Male participants were more as compare to female participants and the mutation in rpoB and katG gene was found similar i.e. 6.66％among the total samples. Conclusions: We can conclude that genetic mutation in Mycobacterium tuberculosis can be identified directly from the clinical samples. However, we have carried this study in less sample size and to validate research on large number of sample is recommended.

Direct detection of rpoB and katG gene mutations of Mycobacterium tuberculosis in clinical samples

Objectives To study the rpoB and katG gene mutation rate and its markers. Methods Cross-sectional study methods were used to study Tuberculosis. A total of 45 sputum samples were collected from Annapurna Neurological Institute and Allied sciences. Then, acid fast bacilli staining were performed. Positive and negative samples were carried for conventional polymerase chain reaction identification and electrophoresis. Results Out of 45 samples, 3 were acid fast bacilli positive and the rest were negative. Male participants were more as compare to female participants and the mutation in rpoB and katG gene was found similar i.e. 6.66% among the total samples. Conclusions We can conclude that genetic mutation in Mycobacterium tuberculosis can be identified directly from the clinical samples. However, we have carried this study in less sample size and to validate research on large number of sample is recommended.

Identifation methods of Brucella Melitensis / 中华地方病学杂志

Objective To establish genotyping methods for rapid identification of Brucella melitensis (B.melitensis) biovar 1,2 and 3 and to verify these method.Methods Single nucleotide polymorphism of RpoB gene and tandem repeat sequence (TRS) Bru42 of standard reference strain 16M were used to design primers,then the RpoB-PCR and TRS-PCR method were established for identification of B.melitensis standard reference strains,these two methods were used to identify clinical isolates of B.melitensis and compared with the conventional methods.Results The results of B.melitensis standard reference strains (biotype 1,2,3) identified by RpoB-PCR and TRS-PCR were consistent with those of the conventional identification methods.Totally 50 clinical isolates [including B.melitensis biovar 1 (17),2 (3) and 3 (30)] were identified as RpoB-2 genotype,only one B.melitensis biovar 1 strain was identified as RpoB-3 genotype.Genotype identification results of standard reference strains and clinical isolates with the same biotype were not exactly the same.Fothermore,TRS-PCR experiment displayed that 51 clinical isolates were all genotype 2 of B.melitensis (genotype TRS-2).Conclusions There is no clear relationship between biovars and genotypes within B.melitensis,and significant difference exists between B.melitensis standard reference strains and clinical isolates within RpoB gene.Bru42 can not be used for genotyping clinical isolates of B.melitensis.

Identifation methods of Brucella Melitensis / 中华地方病学杂志

Objective To establish genotyping methods for rapid identification of Brucella melitensis (B.melitensis) biovar 1,2 and 3 and to verify these method.Methods Single nucleotide polymorphism of RpoB gene and tandem repeat sequence (TRS) Bru42 of standard reference strain 16M were used to design primers,then the RpoB-PCR and TRS-PCR method were established for identification of B.melitensis standard reference strains,these two methods were used to identify clinical isolates of B.melitensis and compared with the conventional methods.Results The results of B.melitensis standard reference strains (biotype 1,2,3) identified by RpoB-PCR and TRS-PCR were consistent with those of the conventional identification methods.Totally 50 clinical isolates [including B.melitensis biovar 1 (17),2 (3) and 3 (30)] were identified as RpoB-2 genotype,only one B.melitensis biovar 1 strain was identified as RpoB-3 genotype.Genotype identification results of standard reference strains and clinical isolates with the same biotype were not exactly the same.Fothermore,TRS-PCR experiment displayed that 51 clinical isolates were all genotype 2 of B.melitensis (genotype TRS-2).Conclusions There is no clear relationship between biovars and genotypes within B.melitensis,and significant difference exists between B.melitensis standard reference strains and clinical isolates within RpoB gene.Bru42 can not be used for genotyping clinical isolates of B.melitensis.

Frequency and Type of Disputed rpoB Mutations in Mycobacterium tuberculosis Isolates from South Korea / 결핵및호흡기질환

BACKGROUND: A disputed rpoB mutation is a specific type of rpoB mutation that can cause low-level resistances to rifampin (RIF). Here, we aimed to assess the frequency and types of disputed rpoB mutations in Mycobacterium tuberculosis isolates from South Korea. METHODS: Between August 2009 and December 2015, 130 patients exhibited RIF resistance on the MTBDRplus assay at Asan Medical Center. Among these cases, we identified the strains with disputed rpoB mutation by rpoB sequencing analysis, as well as among the M. tuberculosis strains from the International Tuberculosis Research Center (ITRC). RESULTS: Among our cases, disputed rpoB mutations led to RIF resistance in at least 6.9% (9/130) of the strains that also exhibited RIF resistance on the MTBDRplus assay. Moreover, at the ITRC, sequencing of the rpoB gene of 170 strains with the rpoB mutation indicated that 23 strains (13.5%) had the disputed mutations. By combining the findings from the 32 strains from our center and the ITRC, we identified the type of disputed rpoB mutation as follows: CTG511CCG (L511P, n=8), GAC516TAC (D516Y, n=8), CTG533CCG (L533P, n=8), CAC526CTC (H526L, n=4), CAC526AAC (H526N, n=3), and ATG515GTG (M515V, n=1). CONCLUSION: Disputed rpoB mutations do not seem to be rare among the strains exhibiting RIF resistance in South Korea.

Comparison phenotypic and genotypic identification of Staphylococcus species isolated from bovine mastitis / Comparação da identificação fenotípica e genotípica de espécies do gênero Staphylococcus isoladas de mastite bovina

In addition to Staphylococcus aureus nowadays other coagulase-positive staphylococci (CoPS) and coagulase-negative staphylococci (CoNS), earlier considered of minor importance, are now accepted as relevant pathogens for humans and animals. The involvement of these microorganisms in bovine mastitis etiology and the possibility their transmission through milk to humans justify the requirement of developing reliable methods for identification of the most frequent species among them. The purpose of this study was to compare the phenotypic techniques with the genotypic method carried out by sequencing of the rpoB gene in identification of several species of the genus Staphylococcus isolated from bovine mastitis. A total of 300 staphylococci isolates of bovine mastitis cases from several Brazilian dairy herds were studied by phenotypic and genotypic techniques, respectively: 150 CoPS and 150 CoNS strains. A total of 18 CoNS different species and 4 CoPS species were identified. Among the CoNS the following species were recognized: 48 (32%) Staphylococcus warneri, 22(15%) S. epidermidis, 20(13%) S. hyicus, 10(7%) S. xylosus, 7(5%) S. haemolyticus, 6(4%) S. simulans, 6(4%) S. schleiferi subsp schleiferi, 6(4%) S. hominis, 5(3%) S. pasteuri, 4(2.7%) S. cohnii, 3(2%) S. saprophyticus subsp. saprophyticus 3(2%) S. chromogenes 3(2%) S. sciuri, 2(1%) S. saccharolyticus, 2(1%) S. lugdunensi, 1(0,7%) S. auricularis, 1(70%) S. saprophyticus subsp. bovis, 1(0.7%) S. capitis. And among the 150 CoPS were identified respectively: 105 (70%) S. aureus, 21(14%), S. hyicus, 19(13%) S. intermedius e 5(3%) S. schleiferi subsp coagulans. Considering the 150 CoNS isolates, the identifications performed by phenotypic and genotypic tests presented 96.7% of concordance, kappa coefficient of agreement = 0.933, SE (standard error) of kappa=0.021 (95% confidence interval: 0.893 to 0.974), Pearson's correlation coefficient (r) = 0.9977, (confidence interval 95%: 0.9938 a 0.9992) and in relation to 150 CPS isolates it was detected an agreement of 98.7%, kappa = 0.960, SE of kappa = 0.016, (95% confidence interval: 0.929 to 0.992) Pearson's correlation coefficient (r) = 0.9994 (95% confidence interval: 0.9681 to 1.0000). The verified agreement strength between the identification methods can be considered as excellent. These results assure that according to laboratory resources any of them will be suitable to perform the staphylococci identification.(AU)

Além de Staphylococcus aureus atualmente outros estafilococos coagulase positiva (SCP) e estafilococos coagulase-negativos (SCN), anteriormente considerados de menor relevância, são reconhecidos como importantes patógenos para humanos e animais. O envolvimento desses micro-organismos na etiologia da mastite bovina e a possibilidade da sua transmissão através do leite aos humanos justifica a utilização de métodos confiáveis para a identificação das espécies mais frequentes. O objetivo deste estudo foi comparar as técnicas fenotípicas com o método genotípico realizada por sequenciamento do gene rpoB na identificação de espécies do gênero Staphylococcus spp. isolados de mastite bovina. Um total de 300 estafilococos isolados de casos de mastite bovina em diferentes rebanhos leiteiros brasileiros foram estudados por técnicas fenotípicas e genotípicas, respectivamente: 150 linhagens de SCP e 150 linhagens de SCN. Foram identificados um total de 18 espécies de SCN e 4 espécies SCP. Entre os SCN as seguintes espécies identificadas: 48 (32%) Staphylococcus warneri, 22 (15%) S. epidermidis, 20 (13%) S. hyicus, 10 (7%) S. xylosus, 7 (5%) S. haemolyticus, 6 (4%) S. simulans, 6 (4%) S. schleiferi subsp schleiferi, 6 (4%) S. hominis, 5 (3%) S. pasteuri, 4 (2,7%) S. cohnii, 3 (2%) S. saprophyticus subsp. saprophyticus, 3 (2%) S. chromogenes, 3 (2%) S. sciuri, 2 (1%) S. saccharolyticus, 2 (1%) S. lugdunensi, 1 (0,7%) S. auricularis, 1 (70 %) S. saprophyticus subsp. bovis, 1 (0,7%) S. capitis. E entre as 150 SCP foram identificados, 105 (70%) S. aureus, 21 (14%), S. hyicus, 19 (13%) S. intermedius e 5 (3%) S. schleiferi subsp coagulans. Considerando-se os 150 SCN isolados, as identificações realizadas por testes fenotípicos e genotípicos apresentaram 96,7% de concordância, coeficiente de concordância kappa = 0,933, SE (erro padrão) de kappa = 0,021 (95% intervalo de confiança: 0,893-0,974), coeficiente de correlação de Pearson (r) = 0,9977, (intervalo de confiança de 95%: 0,9938 a 0,9992) e em relação a 150 SCP isolados foi observado uma concordância de 98,7%, kappa = 0,960, sE de kappa = 0,016, (95% de intervalo de confiança: 0,929 a 0,992) coeficiente de correlação de Pearson (r) = 0,9994 (95% intervalo de confiança: 0,9681-1,0000). A correlação entre os métodos de identificação pode ser considerada como excelente. Esses resultados demonstraram que de acordo com os recursos disponíveis no laboratório, poderia ser utilizada qualquer uma das metodologias.(AU)

Early detection of multidrug resistant (MDR) Mycobacterium tuberculosis in a single tube with in-house designed fluorescence resonance energy transfer (FRET) probes using real-time PCR.

Rapid and correct diagnosis is crucial for the management of multidrug resistance (MDR) in Mycobacterium tuberculosis (MTB). The present study aims at rapid diagnosis for identification of multidrug resistance tuberculosis (MDR-TB) using real-time PCR. FRET hybridization probes targeting most prominent four selected codons for rpoB526 and 531 and for katG314 and 315 genes were designed and evaluated on 143 clinical MTB isolates and paired sputa for rapid detection of MDR-TB. The results of real-time PCR were compared with gold standard L-J proportion method and further validated by DNA sequencing. Of the 143 MTB positive cultures, 85 and 58 isolates were found to be ‘MDR’ and ‘pan susceptible’, respectively by proportion L-J method. The sensitivity of real-time PCR for the detection of rifampicin (RIF) and isoniazid (INH) were 85.88 and 94.11%, respectively, and the specificity of method was found to be 98.27%. DNA sequencing of 31 MTB isolates having distinct melting temperature (Tm) as compared to the standard drug susceptible H37Rv strain showed 100% concordance with real-time PCR results. DNA sequencing revealed the mutations at Ser531Leu, His526Asp of rpoB gene and Ser315Thr, Thr314Pro of katG gene in RIF and INH resistance cases. This real-time PCR assay that targets limited number of loci in a selected range ensures direct and rapid detection of MDR-TB in Indian settings. However, future studies for revalidation as well as refinement are required to break the limitations of MDR-TB detection.

Genotypic Detection of rpoB and katG Gene Mutations Associated with Rifampicin and Isoniazid Resistance in Mycobacterium Tuberculosis Isolates: A Local Scenario (Kelantan)

Background: Drug resistant tuberculosis (DR-TB) remains a public health issue that is of major concern on a global scale. The characterisation of clinical isolates may provide key information regarding the underlying mechanisms of drug resistance, and helps to augment therapeutic options. This study aims to evaluate the frequency of gene mutations associated with Rifampicin (RIF) and Isoniazid (INH) resistance among nine clinical isolates. Methods: A total of nine drug resistant Mycobacterium tuberculosis clinical isolates were screened for genetic mutations in rpoB and katG using polymerase chain reaction (PCR) amplification and DNA sequencing. Genotypic analysis was performed to detect the mutations in the sequence of the target genes. Results: Our findings reveal that 80% of the isolates possess mutations at codon 119 (His119Tyr) and 135 (Arg135Trp and Ser135Leu) within the rpoB gene; and 70% possess mutations in the katG gene at codon 238 with amino acid change (Leu238Arg). Conclusion: Findings from this study provide an overview of the current situation of RIF and INH resistance in a hospital Universiti Sains Malaysia (HUSM) located in Kelantan, Malaysia, which could facilitate molecular-based detection methods of drug-resistant strains. Further information regarding the molecular mechanisms involved in resistance in RR-/MDR-TB should be addressed in the near future.

Development of Quantitative Real-Time PCR Primers for Detection of Streptococcus sobrinus

The purpose of this study was to develop Streptococcus sobrinus-specific qPCR primers based on the nucleotide sequence of the RNA polymerase β-subunit gene (rpoB). The specificity of the primers was determined by conventional polymerase chain reaction (PCR) with 12 strains of S. sobrinus and 50 strains (50 species) of non-S. sobrinus bacteria. The sensitivity of the primers was determined by quantitative real-time PCR (qPCR) with serial dilutions of the purified genomic DNAs (40 ng to 4 fg) of S. sobrinus ATCC 33478(T). The specificity data showed that the S. sobrinus-specific qPCR primers (RTSsob-F4/RTSsob-R4) detected only the genomic DNAs of S. sobrinus strains with a detection limit of up to 4 fg of S. sobrinus genomic DNA. Our results suggest that the RTSsob-F4/RTSsob-R4 primers are useful in detecting S. sobrinus with high sensitivity and specificity for epidemiological studies of dental caries.

Molecular profiling of drug resistant isolates ofMycobacterium tuberculosis in the state of Santa Catarina, southern Brazil

Drug resistance is a global threat and one of the main contributing factors to tuberculosis (TB) outbreaks. The goal of this study was to analyse the molecular profile of multidrug-resistant TB (MDR-TB) in the state of Santa Catarina in southern Brazil. Fifty-three MDR Mycobacterium tuberculosisclinical isolates were analysed by spoligotyping and a partial region of therpoB gene, which is associated with rifampicin resistance (RMP-R), was sequenced. Some isolates were also distinguished by their mycobacterial interspersed repetitive units (MIRU). S531L was the most prevalent mutation found within rpoBin RMP-R isolates (58.5%), followed by S531W (20.8%). Only two MDR isolates showed no mutations withinrpoB. Isolates of the Latin American Mediterranean (LAM) family were the most prevalent (45.3%) found by spoligotyping, followed by Haarlem (9.4%) and T (7.5%) families. SIT106 was found in 26.4% of isolates and all SIT106 isolates typed by MIRU-12 (5 out of 14) belong to MIT251. There was a high correlation between the S531W mutation and the LAM family mainly because all SIT2263 (LAM9) isolates carry this mutation. Among isolates with the S531W mutation in rpoB MIRU demonstrates a cluster formed by four isolates (SIT2263 and MIT163) and very similar profiles were observed between eight of the nine isolates. Better characterisation of TB isolates may lead to new ways in which to control and treat TB in this region of Brazil.

Identification of Leptospira serovars by RFLP of the RNA polymerase beta subunit gene (rpoB)

Leptospires are usually classified by methods based on DNA-DNA hybridization and the conventional cross-agglutination absorption test, which uses polyclonal antibodies against lipopolysaccharides. In this study, the amplification of the rpoB gene, which encodes the beta-subunit of RNA polymerase, was used as an alternative tool to identify Leptospira. DNA extracts from sixty-eight serovars were obtained, and the hypervariable region located between 1990 and 2500-bp in the rpoB gene was amplified by polymerase chain reaction (PCR). The 600-bp amplicons of the rpoB gene were digested with the restriction endonucleases TaqI, Tru1I, Sau3AI and MslI, and the restriction fragments were separated by 6% polyacrylamide gel electrophoresis. Thirty-five fragment patters were obtained from the combined data of restriction fragment length polymorphism (PCR-RFLP) analysis and used to infer the phylogenetic relationships among the Leptospira species and serovars. The species assignments obtained were in full agreement with the established taxonomic classifications. Twenty-two serovars were effectively identified based on differences in their molecular profiles. However, the other 46 serovars remained clustered in groups that included more than one serovar of different species. This study demonstrates the value of RFLP analysis of PCR-amplified rpoB as an initial method for identifying Leptospira species and serovars.

The characteristics of the genes mutations in rifampin and isoniazid resistant Mycobacterium tuberculosis clinical isolates from Baise district, Guangxi autonomous region / 实用医学杂志

Objective To analyze the characteristics of the rpoB, KatG and inhA genes mutations in rifampin and isoniazid resistant Mycobacterium tuberculosis (MTB) clinical isolates in Baise district, Guangxi autonomous region. Methods 128 MTB clinical strains were collected and isolated for drug susceptibility testing, and drug resistant strain DNA was subtracted for rpoB, KatG and inhA genes mutation analysis. Results 75%(27/36)isolates carried mutations in the rpoB gene,and 59.3%(16/27)isolates carried mutations in 531 sites. 44.1%(15/34) isolates carried mutations in KatG or inhA, and 66.7%(10/15) isolates appeared in KatG 315 site, with two new mutations found in KatG 279 and 427 site. In these mutation isolates, 13.3%(2/15) mutations appeared in inhA 5, 6.7%(1/15) in inhA 16, and 20%(3/15) in both katG and inhA. Conclusions The mutation of rpoB, katG and inhA genes in TB is highly correlated with its resistance to rifampin and isoniazid in Baise district, Guangxi autonomous region. The study will provide a basis for further understanding the anti-bacterium mechanism and quick diagnostic methods for drug-resistant tuberculosis.

In vitro activity of rifampin against and rpoB mutations in Chlamydia trachomatis clinical isolates / 中华皮肤科杂志

Objective To evaluate the susceptibility of Chlamydia trachomatis clinical isolates to rifampin, and assess the relationship between rpoB mutations and antibiotic resistance in them.Methods A microculture method was used to determine the minimal inhibitory concentration (MIC) of rifampin in 52 Chlamydia trachomatis clinical isolates.The rpoB gene was amplified from all the clinical isolates and a standard strain of Chlamydia trachomatis followed by single-strand conformation polymorphism (SSCP)analysis.Sequencing of PCR products was carried out for two clinical isolates.Results No rifampin-resistant strain was found among these clinical isolates.The MIC of rifampin varied from 0.004 to 0.030 mg/L Neither SSCP analysis nor sequencing showed rpoB mutations.Conclusions No rpoB mutations were found in Chlamydia trachomatis isolates from patients unresponsive to rifampin.The unresponsiveness to rifampin may be attributed to multiple factors.