Linezolid Resistance in Methicillin-Resistant Staphylococcus aureus in Korea: High Rate of False Resistance to Linezolid by the VITEK 2 System

As various linezolid resistance mechanisms have been identified in methicillin-resistant Staphylococcus aureus (MRSA), we investigated the molecular characteristics of MRSA with elevated linezolid minimum inhibitory concentrations (MICs), using the VITEK 2 system (bioMérieux, Marcy-l'Étoile, France). Twenty-seven MRSA isolates from 14 patients exhibiting linezolid MICs ≥8 µg/mL were examined by broth microdilution (BMD) test as well as by sequencing for mutations in the 23S rRNA gene or ribosomal proteins (L3, L4, and L22) and the presence of the optrA, cfr, and cfr(B) genes. Of the 27 isolates, four (14.8%) from one patient were confirmed as linezolid resistant by BMD and harbored a 23S rRNA T2500A mutation. The remaining 23 were confirmed as linezolid susceptible, indicating that the linezolid-resistant results were major errors generated by VITEK 2. The most commonly detected mutation (19/27, 70.4%), L3 Gly152Asp, was detected in only linezolid-susceptible isolates. No isolates contained optrA, cfr, or cfr(B) or any L4 or L22 protein alterations. Our results show that the 23S rRNA T2500A mutation was mainly associated with linezolid resistance, while the L3 Gly152Asp mutation was not related to linezolid resistance. A confirmatory test is recommended for VITEK 2 linezolid-resistant results owing to the high probability of false resistant results.

Mutaciones del gen ARN ribosómico 23S de Helicobacter pylori asociadas con resistencia a claritromicina en pacientes atendidos en una unidad de endoscopia de Medellín, Colombia / Mutations in the Helicobacter pylori 23S rRNA gene associated with clarithromycin resistance in patients at an endoscopy unit in Medellín, Colombia

Resumen Introducción. La claritromicina es el antibiótico de primera línea para el tratamiento de la infección por Helicobacter pylori. La resistencia bacteriana se produce principalmente por mutaciones puntuales del gen ARN ribosómico 23S (ARNr 23S). Objetivo. Determinar la frecuencia de las mutaciones puntuales A2143G y A2142G del gen ARNr 23S asociadas con la resistencia de H. pylori a la claritromicina en muestras de pacientes con manifestaciones dispépticas en Medellín, región noroccidental de Colombia. Materiales y métodos. Se extrajo ADN a partir de muestras de biopsia gástrica obtenidas de pacientes con manifestaciones dispépticas atendidos en una unidad de endoscopia entre el 2016 y el 2017. Mediante reacción en cadena de la polimerasa (PCR), se amplificaron las regiones s y m del gen vacA y una región del gen ARNr 23S bacteriano. La presencia de las mutaciones A2142G y A2143G se determinó por la técnica de polimorfismos de longitud de fragmentos de restricción (RFLP) con las enzimas BbsI y BsaI, respectivamente. Resultados. Se encontró una prevalencia de infección de 44,2 % (175/396), según el informe de histopatología. En 143 de estas 175 muestras positivas se amplificaron las tres regiones del genoma bacteriano. Se identificaron las mutaciones A2143G y A2142G en 27 muestras (18,8 %; 27/143), la mutación más frecuente fue la A2143G (81,5 %; 22/27). Conclusiones. Hubo una gran prevalencia de mutaciones asociadas con la resistencia de H. pylori a la claritromicina en la población de estudio. Se requieren estudios adicionales para establecer la resistencia bacteriana en la población colombiana y, así, determinar los tratamientos de primera línea y de rescate.

Abstract Introduction: Clarithromycin is the first-line antibiotic for the treatment of Helicobacter pylori infection. Bacterial resistance is mainly due to the presence of specific mutations in the 23S ribosomal RNA (rRNA) gene. Objective: To determine the frequency of A2143G and A2142G specific mutations in the 23S rRNA gene associated with clarithromycin resistance of H. pylori in samples from patients with dyspeptic manifestations in Medellín, northwestern Colombia. Materials and methods: DNA was extracted from gastric biopsy samples of patients with dyspeptic manifestations seen at an endoscopy unit in Medellín between 2016 and 2017. PCR was performed to amplify the bacterial s and m vacA regions, and a region in the 23S rRNA gene. The presence of the A2142G and A2143G mutations was determined using the restriction fragment length polymorphism (RFLP) technique with the BbsI and BsaI enzymes, respectively. Results: The prevalence of infection was 44.2% (175/396), according to the histopathology report. The positive samples were analyzed and the three regions of the bacterial genome were amplified in 143 of the 175 samples. The A2143G and A2142G mutations were identified in 27 samples (18.8%, 27/143). The most frequent mutation was A2143G (81.5%, 22/27). Conclusions: We found a high prevalence of H. pylori mutations associated with clarithromycin resistance in the study population. Further studies are required to determine the bacterial resistance in the Colombian population in order to define first line and rescue treatments.

Susceptibilidad antimicrobiana y mutaciones en el gen ARNr 23S de Helicobacter pylori en pacientes dispépticos / Antimicrobial susceptibility and mutations in the 23S rRNA gen of Helicobacter pylori in dyspeptic patients

RESUMEN Con el objetivo de evaluar la susceptibilidad antimicrobiana y detectar mutaciones puntuales en el gen ARNr 23S en cepas de Helicobacter pylori se realizó un estudio transversal que incluyó a 95 pacientes con dispepsia atendidos en una clínica privada de Lima. Mediante endoscopía se colectaron biopsias de antro para el aislamiento de cepas de Helicobacter pylori para la evaluación de la susceptibilidad antimicrobiana empleando la técnica de microdilución en caldo. La detección de mutaciones puntuales se desarrolló mediante PCR-RFLP. El porcentaje de infección por Helicobacter pylori fue de 46,3%, se observaron valores de resistencia de 52,3% a claritromicina, 29,6% a metronidazol, 45,5% a levofloxacino y 4,6% a amoxicilina. El porcentaje de mutaciones puntuales A2142G y A2143G asociados a resistencia a claritromicina fue 43,5%. En conclusión, encontramos que las tasas de resistencia antimicrobiana y el porcentaje de cepas de Helicobacter pylori circulantes en una clínica privada de Lima fueron elevadas.

ABSTRACT In order to evaluate antimicrobial susceptibility and detect specific mutations in the 23S rRNA gene in Helicobacter pylori strains, a cross-sectional study was performed on 95 patients with dyspepsia treated in a private clinic in Lima. Antrum biopsies were collected by endoscopy for isolation and evaluation of antimicrobial susceptibility using the broth microdilution method. The detection of specific mutations was developed by PCR-RFLP. The percentage of infection by Helicobacter pylori was 46.3%. Resistance values of 52.3% to clarithromycin, 29.6% to metronidazole, 45.5% to levofloxacin, and 4.6% to amoxicillin were observed. The percentage of specific A2142G and A2143G mutations associated with clarithromycin resistance was 43.5%. In conclusion, we found that antimicrobial resistance rates and the percentage of Helicobacter pylori strains circulating in a private clinic in Lima were high.

Eradication Therapy for Helicobacter pylori with Diagnostic Test for Clarithromycin Resistance

Addressing the increasing antibiotic resistance, including clarithromycin resistance, which affects Helicobacter pylori (H. pylori) eradication therapy, is a challenge for clinicians. Antibiotic resistance is the main reason for H. pylori eradication failure and the resistance rate for clarithromycin may drastically increase, up to 38.5%, due to 23S ribosomal RNA point mutations. Therefore, the standard triple regimen is no longer suitable as the first-line treatment in most regions. However, there is a growing interest in personalized care for patients. Increased eradication rates of tailored therapy based on antibiotic susceptibility have been reported using nucleic acid-based techniques for clarithromycin resistance with a focus on the first-line eradication therapy of H. pylori infection. Herein, we discuss the eradication therapy for H. pylori, with a diagnostic test and appropriate treatment for clarithromycin resistance.

Whole Genome Sequence Determination and Analysis of Strain CGMCC 12426 / 中国医学科学院学报

Objective To describe the microbiological characteristics of ()CGMCC 12426 and determine and analyze its complete genome sequences.Methods strain CGMCC 12426 genomic DNA sequencing was performed on a single molecule real-time sequencing(SMRT)platform and the annotation was completed in the NCBI Prokaryotic Genomic Annotation Pipeline(pGAP).Results The complete genomic sequences of the released CGMCC 12426 consisted of a 4 138 265-bp circular chromosome and a 74 165-bp plasmid,which resulted in the prediction of 4581 genes including 4222 coding sequences,87 tRNAs,and 30 rRNAs(which included 5S rRNA,16S rRNA,and 23S rRNA).Conclusion The genome sequencing provided a basis for further investigations on the genetic background of and on the metabolic and regulatory mechanisms.

Value of detecting bacterial 16S and 23S rRNA in interface membrane in diagnosis of periprosthetic joint infection / 南方医科大学学报

<p><b>OBJECTIVE</b>To explore the value of detecting bacterial 16S rRNA with 23S rRNA in the diagnosis of periprosthetic joint infection (PJI).</p><p><b>METHODS</b>A prospective study was conducted among 67 patients with previous total hip arthroplasty (THA) undergoing a reoperation for infection (23 patients) or aseptic loosening (44 patients). Bacterial 16S rRNA and 23S rRNA in the interface membrane were detected by real-time PCR and their value in diagnosis of PJI was assessed.</p><p><b>RESULTS</b>The 16S rRNA and 23S rRNA showed no significant difference in their power in the diagnosis of PJI. The detection of 16S rRNA/23S rRNA showed a higher sensitivity and a greater negative predictive value in PJI diagnosis than the detection of 16S rRNA+23S rRNA (95.7% vs 52.2%, P<0.01; 97.6% vs 79.6%, P=0.01). The specificity, positive predictive value, and accuracy of the 4 diagnostic strategies were not significantly different.</p><p><b>CONCLUSIONS</b>The diagnostic power of 16S rRNA and 23S rRNA was similar in detecting PJI. Compared with the diagnostic strategy with 16S rRNA+23S rRNA, 16S rRNA/23S rRNA is more sensitive in detecting PJI.</p>

Detección de Mycoplasma canadense y Mycoplasma californicum en ganado lechero de Argentina / Detection of Mycoplasma canadense and Mycoplasma californicum in dairy cattle from Argentina

Diferentes especies del género Mycoplasma pueden afectar al ganado bovino y causar varias enfermedades. La técnica de PCR, secuenciación y posterior análisis de la región ITS 16S-23S ARNr ha mostrado que existe una importante variabilidad interespecies entre Mollicutes. Se realizó la amplificación (región ITS 16S-23S ARNr) de 16 aislamientos sospechosos de corresponder a alguna especie de Mycoplasma, que habían sido obtenidos de muestras de leche provenientes de rodeos lecheros. Catorce de esos aislamientos fueron PCR positivos. Para confirmar la identidad de Mycoplasma bovis, dichos aislamientos fueron evaluados por otra PCR especie-específica. Siete aislamientos dieron un resultado positivo. Los productos de la PCR de la ITS 16S-23S ARNr de un aislamiento identificado como M. bovis y de otros dos aislamientos identificados como no-M. bovis fueron seleccionados al azar, secuenciados y analizados. Las tres secuencias (A, B y C) mostraron 100 % de similitud con cepas de M. bovis, Mycoplasma canadense y Mycoplasma californicum, respectivamente

Different species of Mycoplasma can affect bovine cattle, causing several diseases. PCR sequencing and further analysis of the 16S-23S rRNA ITS region have shown a significant interspecies variability among Mollicutes. Sixteen suspected isolates of Mycoplasma spp. obtained from milk samples from dairy herds were amplified (16S-23S rRNA ITS region). Fourteen out of those 16 suspected Mycoplasma spp. isolates were PCR-positive. To confirm the identity of Mycoplasma bovis, these 14 isolates were tested by another species-specific PCR. Seven of the isolates rendered a positive result. The products of 16S-23S rRNA ITS PCR from one isolate that was identified as M. bovis and from two other isolates, identified as non- M. bovis were randomly selected, sequenced and analyzed. The three sequences (A, B and C) showed 100% similarity with M. bovis, Mycoplasma canadense and Mycoplasma californicum respectively

Clarithromycin-Based Standard Triple Therapy Can Still Be Effective for Helicobacter pylori Eradication in Some Parts of the Korea

We evaluated the antibiotic resistance rates and eradication rates of clarithromycin based triple therapy from 2005 to 2010 retrospectively. In addition, we investigated the mechanism of clarithromycin resistance in Helicobacter pylori strains isolated from Korean patients. Two hundred and twelve strains of H. pylori were isolated from 204 patients. H. pylori ATCC 43504 was used as the standard strain. The eradication rates of H. pylori from 2005 to 2010 were 89.3%, 82.6%, 86.3%, 87.7%, 81.8%, and 84.2%, respectively. Total eradication rate was 84.9%. DNA sequences of the 23S RNA gene in clarithromycin-resistant strains were determined. The resistance rates of H. pylori to amoxicillin, clarithromycin, metronidazole, tetracycline, ciprofloxacin, moxifloxacin, and levofloxacin were 9.0%, 8.5%, 36.3%, 0%, 14.2%, 14.2%, and 14.2%, respectively. The multidrug resistance rate of H. pylori was 16.5%. Sequence analysis of clarithromycin-resistant strains showed an A2144G mutation in 8 of 14 strains (57.1%), a T2183C mutation in 5 of 14 strains (35.7%), and double mutations of both A2144G and T2183C in 1 of 14 strains (7.1%). In the present study, triple therapy may still be an effective eradication therapy for H. pylori infections in Korea. The A2144G and T2183C mutations are mainly present in clarithromycin-resistant isolates.

Clarithromycin-resistant Helicobacter pylori Associated with 23S rRNA Point Mutations in Jeju Island / 대한소화기학회지

BACKGROUND/AIMS: The point mutations in 23S rRNA gene accounts for the majority of the clarithromycin resistance of Helicobacter pylori. This study aimed to investigate the association between the clarithromycin-resistance of H. pylori and the failure of primary H. pylori eradication therapy in Jeju Island. METHODS: Between April 2011 and October 2012, 6,937 patients underwent endoscopy, and H. pylori infection was evaluated in 2,287 patients (33.0%). Total of 110 patients with H. pylori infection were treated with proton pump inhibitor (PPI)-based triple therapy. The result of eradication was evaluated with urea breath test, histology and PCR which were conducted 4 weeks from the last dose of medicine. RESULTS: The patients who had point mutations were 33 (26.0%). A2142G and A2143G mutations were observed in 10 patients (7.9%) and 23 patients (18.1%). Among 110 patients treated with PPI-based triple therapy, the success rate of the eradication therapy was 52.7% (58/110) and 70.7% (58/82) by intention-to-treat and per-protocol analysis, respectively. Fifteen of the 24 patients who failed the eradication therapy showed point mutations; 1 patient (4.2%) showed A2142G mutation and 14 patients (58.3%) showed A2143G mutation. Patients with A2143G mutation H. pylori showed higher failure rate of 87.5%. Patients with A2142G mutation H. pylori showed similar failure rate compared to those of the patients with wild type H. pylori. CONCLUSIONS: In Jeju Island, the frequency of 23S rRNA point mutations is similar (26.0%) with other regions of Korea (15.8-31.3%). A2143G mutation is associated with the failure of H. pylori eradication.

Macrolide Resistance of Mycoplasma pneumoniae and Its Detection Rate by Real-Time PCR in Primary and Tertiary Care Hospitals

BACKGROUND: This study aimed to evaluate the prevalence of Mycoplasma pneumoniae in primary and tertiary care hospitals and its macrolide resistance rate. METHODS: Nasopharyngeal swabs were collected from 195 pediatric patients in primary and tertiary care hospitals from October to November 2010. The AccuPower MP real-time PCR kit (Bioneer, Korea) was used for the detection of M. pneumoniae. Direct amplicon sequencing was performed to detect point mutations conferring resistance to macrolides in the 23S rRNA gene. RESULTS: Among the 195 specimens, 17 (8.7%) were M. pneumoniae positive, and 3 of the strains (17.6%) obtained from these 17 specimens displayed the A2063G mutation in 23S rRNA. Three macrolide-resistant M. pneumoniae isolates were isolated from patients hospitalized at the primary care hospital. The positive rates of M. pneumoniae for the primary and tertiary care hospitals were 12.1% (15/124) and 2.8% (2/71), respectively (P=0.033). CONCLUSIONS: The positive rate of M. pneumoniae in the primary care hospital was higher than that in the tertiary care hospital. Simultaneous detection of M. pneumoniae and macrolide-resistant mutation genes in the 23S rRNA by real-time PCR is needed for rapid diagnosis and therapy of M. pneumoniae infections.

Two Cases of Mycoplasma pneumoniae Pneumonia with A2063G Mutation in the 23S rRNA Gene in Siblings

We describe 2 cases of pneumonia caused by the same macrolide-resistant Mycoplasma pneumoniae in siblings. M. pneumoniae was identified using real-time PCR. Direct sequence analysis of the 23S rRNA gene revealed a point mutation in V domain (A2063G) of the 23S rRNA gene.

Lung Infection Caused by Mycobacterium riyadhense Confused with Mycobacterium tuberculosis: The First Case in Korea

A slowly growing, non-chromogenic mycobacterial strain was isolated from sputum and bronchial lavage fluid samples of a patient presenting with productive cough, blood-tinged sputum, low-grade fever, and weakness. A positive acid-fast bacilli sputum smear result prompted the initiation of an anti-tuberculosis regimen. Multiplex real-time PCR showed a negative result for Mycobacterium tuberculosis complex and a positive result for nontuberculous mycobacteria. The DNA chip test confirmed this organism as a member of the genus Mycobacterium, but could not specify the species. Interestingly, the mycolic acid patterns obtained by HPLC nearly overlapped with those of M. simulans. The sequences of the Mycobacterium 16S rRNA gene and 16S-23S internal transcribed spacer region were unique and were found to have 100% similarity with those of M. riyadhense. After a review of the literature, we report this case as the first Korean case of M. riyadhense lung infection.

Bacterial 23S Ribosomal RNA, a Ligand for Toll-like Receptor 13

Toll-like receptors are required for detection of pathogen-associated molecular patterns and play critical roles in protection of host from infection. Murine TLR13 was recently reported to be involved in recognition of bacterial 23S ribosomal RNA sequence that is the binding site of different antibiotics.

A Comparison Analysis on the Diagnosis of Helicobacter pylori Infection and the Detection of Clarithromycin Resistance according to Biopsy Sites / 대한진단검사의학회지

BACKGROUND: This study was performed to determine the biopsy sites that are suitable for the diagnosis of Helicobacter pylori infection and to assess the sensitivity of culture, histology, and dual-priming oligonucleotide (DPO)-based multiplex PCR. Moreover, we evaluated the usefulness of PCR for the detection of 23S rRNA mutations, which are responsible for the clarithromycin resistance of H. pylori. METHODS: From 90 patients, we obtained biopsy specimens for culture, histology, and Seeplex(R) ClaR-H. pylori PCR (Seegene Inc., Korea). Phenotypic susceptibility to clarithromycin was evaluated using the E-test (AB Biodisk, Sweden). RESULTS: H. pylori was detected in 48 of 90 patients. The positive rates of infection in the antrum and body were higher than those in the biopsies obtained from the duodenal bulb. The positive rates in histology, PCR, and culture were 46.7%, 42.2%, and 34.4%, respectively. Using histology or PCR, we identified H. pylori in 46 of the 48 patients. 23S rRNA mutations were detected in 8 patients. The clarithromycin E-test showed that all the 10 wild-type patients were susceptible. However, the results of the PCR and E-test of 3 of the 8 mutation-positive patients were discrepant. CONCLUSIONS: We observed that a combination of histology and PCR affords a high detection rate of H.pylori infection and that DPO-based PCR can be practically used for the diagnosis of H. pylori infection and the determination of clarithromycin resistance. These techniques were useful for biopsy sampling simultaneously from the antrum and body for the detection of clarithromycin resistance of multiple strain infection or heteroresistance.

A Report of Cat Scratch Disease in Korea Confirmed by PCR Amplification of the 16S-23S rRNA Intergenic Region of Bartonella henselae / 대한진단검사의학회지

We report a case of cat scratch disease in an 8-yr-old girl who presented with fever and enlargement of both axillary lymph nodes. Both aerobic and anaerobic cultures of the lymph node aspirate were negative for microbial growth. Gram staining and Warthin-Starry silver staining did not reveal any organism. Purified DNA from the PCR-amplicon of the 16S-23S rRNA intergenic region was sequenced and showed 99.7% identity with the corresponding sequence of Bartonella henselae strain Houston-1. Our findings suggest that the internal transcribed spacer is a reliable region for PCR identification of Bartonella species. In patients with lymphadenitis, a history of contact with cats or dogs necessitates the use of diagnostic approaches that employ not only the conventional staining and culture but also molecular methods to detect B. henselae.

Detection of marine pathogenic bacterial Vibrio species by multiplex polymerase chain reaction (PCR).

Polymerase chain reactions (PCR) were performed to accomplish quick and accurate detection of Vibrio species. The primers prepared with 16S-23S rDNA intergenic spacer (IGS) region exhibited an excellent species-specificity for Vibrio sp and detected Vibrio sp more successfully than the conventional culture method. Multiplex PCR was also fruitful not only forthe identification of the 5 standard Vibrio sp simultaneously but also for the detection of Vibrio spin the samples collected from the natural environment.

Using oligonucleotide suspension arrays for laboratory identification of bacteria responsible for bacteremia / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

The aim of this study was to develop and validate an oligonucleotide suspension array for rapid identification of 15 bacterial species responsible for bacteremia, particularly prevalent in Chinese hospitals. The multiplexed array, based on the QIAGEN LiquiChip Workstation, included 15 oligonucleotide probes which were covalently bound to different bead sets. PCR amplicons of a variable region of the bacterial 23S rRNA genes were hybridized to the bead-bound probes. Thirty-eight strains belonging to 15 species were correctly identified on the basis of their corresponding species-specific hybridization profiles. The results show that the suspension array, in a single assay, can differentiate isolates over a wide range of strains and species, and suggest the potential utility of suspension array system to clinical laboratory diagnosis.

Detection and identification of seven clinical common pathogenic bacteria by oligonucleotide microarray / 中华流行病学杂志

<p><b>OBJECTIVE</b>Using 16S rDNA and 23S rDNA genes as the target sequences to develop a system based on oligonucleotide microarray and to detect the seven clinical pathogenic bacteria, commonly seen.</p><p><b>METHODS</b>Double polymerase chain reaction (PCR) was applied to amplify the segments of 16S rDNA and 23S rDNA genes of the target bacteria. An oligonucleotide microarray was constructed to simultaneously detect EHEC O157:H7, Vibrio parahaemolyticus, Salmonella sp., Vibrio cholerae, Listeria monocytogenes, Campylobacter jejuni and Shigella sp. Specificity, sensitivity and reproducibility of the microarray during detection were checked. And then microarray was used to detect the microbes in stool specimens of 81 patients with diarrhea and vomiting.</p><p><b>RESULTS</b>The double PCR method could simultaneously amplify the target sequences of 16S rDNA and 23S rDNA genes of the seven pathogens. The sensitivity of the developed oligonucleotide microarray could reach 10(3) cfu/ml but no positive results were presented for non-targeted bacteria. The coefficients of differentiation in one lot or among different lots of the microarray slices were 3.89% - 5.81%. The positive detection rate of the stool specimens by oligonucleotide microarray was 39.5% (32/81), with a coincidence of 96.3% (78/81) for the patients and another coincidence of 96.8% (31/32) for bacterial genus or species identification, when comparing to the results by routine bacteriological examinations.</p><p><b>CONCLUSION</b>The established assay in this study based on oligonucleotide microarray to detect the seven pathogenic bacteria has many advantages such as convenient, rapid, accurate, stable and high flux, which is suitable for clinical specimen examination and epidemiological field investigation.</p>

Application of nested PCR and sequencing technique to detect point mutations of the 23S rRNA gene of Mycoplasma pneumoniae / 中华儿科杂志

<p><b>OBJECTIVE</b>To establish a quick method to detect drug resistance of Mycoplasma pneumoniae (MP) and study the condition of drug resistance in MP infection.</p><p><b>METHODS</b>MP 23S rRNA target gene in throat swab specimens from 200 patients with suspected MP infection was detected by using nested PCR and DNA sequencing. The result of 23S rRNA gene detection was confirmed by MP isolation and drug susceptibility test in vitro for reliability.</p><p><b>RESULTS</b>Of the 200 clinical specimens, 64 were proved to be positive for MP through MP-IgM antibody, MP specific 16S rRNA nested PCR and MP isolation . The 23S rRNA gene was amplified and the gene sequence was compared with MP reference strain in Genbank, 26 were identical to the reference strain, 38 had a point mutation in 23S rRNA. Among them, 35 had A to G mutation at position 2063, 1 had A to C mutation at position 2063 and 2 had A to G mutation at position 2064, the percentage of drug resistance was 59.4%. The sensitivity of the gene detection method was 10(2) ccu/ml and it was confirmed to be reliable by MP isolation and drug susceptibility test.</p><p><b>CONCLUSIONS</b>The gene detection method could detect MP drug resistant gene directly from clinical specimen, which has the advantages of high specificity, high sensitivity and quickness. It is of great significance for diagnosis of MP infection because MP isolation is difficult and time-consuming.</p>

Rapid identification of mycobacteria by gene amplification restriction analysis technique targeting 16S-23S ribosomal RNA internal transcribed spacer & flanking region.

BACKGROUND & OBJECTIVE: Conventional identification of a clinical isolate of mycobacteria primarily based on culture characteristics and biochemical tests needs several weeks and may remain inconclusive. This study was undertaken to develop a new rapid method to identify the mycobacterial isolates at species level by gene amplification restriction analysis using primers encoding 16S-23S rRNA internal transcribed spacer (ITS) region and flanking parts of the 16S as well as 23S rRNA gene. METHODS: This system is based on the amplification of approximately 1.8 kb fragment encoding 16S-23S rRNA spacer region and flanking parts of the 16S as well as 23S rRNA gene. This assay was applied on 13 reference strains and 480 clinical isolates of mycobacteria to validate the technique. Restriction was carried out with three restriction endonucleases Hha I, Hinf I and Rsa I. RESULTS: Distinct gene amplification restriction analysis patterns were obtained by restriction of amplicons with three distinct restriction endonucleases (Hha I, Hinf I and Rsa I) which could differentiate various mycobacterial species. INTERPRETATION & CONCLUSION: Restriction patterns with the enzymes used in this study could clearly distinguish Mycobacterium tuberculosis complex from other non chromogenic clinically important species M. avium and M. intracellulare. Results indicated this assay to be a simple, rapid and reproducible method to identify clinically relevant mycobacteria.