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.

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.

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.

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.

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.

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.

Molecular phylogenetic analysis of Vibrio cholerae O1 El Tor strains isolated before, during and after the O 139 outbreak based on the inter-genomic heterogeneity of the 16S-23S rRNA intergenic spacer regions.

We have cloned, sequenced and analysed all the five classes of the intergenic (16S-23S rRNA) spacer region (ISR) associated with the eight rrn operons (rrna-rrnh) of Vibrio cholerae serogroup O1 El Tor strains isolated before, during and after the O 139 outbreak. ISR classes 'a' and 'g' were found to be invariant, ISR-B (ISRb and ISRe) exhibited very little variation, whereas ISR-C (ISRc, ISRd, and ISRf) and ISRh showed the maximum variation. Phylogenetic analysis conducted with all three ISR classes (ISR-B, ISR-C and ISRh) showed that the pre-O 139 serogroup and post-O 139 serogroup O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C and ISR-h, instead of all five ISR classes, could be successfully used to study phylogeny in this organism.

Detection of Bartonella species from ticks, mites and small mammals in Korea

We investigated the prevalence of Bartonella infections in ticks, mites and small mammals (rodents, insectivores and weasels) collected during 2001 through 2004, from various military installations and training sites in Korea, using PCR and sequence analysis of 16S rRNA, 23S rRNA and groEL heat shock protein genes. The prevalence of Bartonella spp. was 5.2% (n = 1, 305 sample pools) in ticks, 19.1% (n = 21) in mesostigmatid mites and 13.7% (n = 424 individuals) in small mammals. The prevalence within the family Ixodidae was, 4.4% (n = 1, 173) in Haemaphysalis longicornis (scrub tick), 2.7% (n = 74) in H. flava, 5.0% (n = 20) in Ixodes nipponensis, 11.1% (n = 9) in I. turdus, 33.3% (n = 3) in I. persulcatus and 42.3% (n = 26) in Ixodes spp. ticks. In rodents, the prevalence rate was, 6.7% (n = 373) in Apodemus agrarius (striped field mouse) and 11.1% (n = 9) in Eothenomys regulus (Korean red-backed vole) and in an insectivore, Crocidura lasiura, 12.1% (n = 33). Neither of the two weasels were positive for Bartonella spp. Phylogenetic analysis based on amino acid sequence of a portion of the groEL gene amplified from one A. agrarius spleen was identical to B. elizabethae species. We demonstrated the presence of Bartonella DNA in H. longicornis, H. flava and I. nipponensis ticks, indicating that these ticks should be added to the growing list of potential tick vectors and warrants further detailed investigations to disclose their possible roles in Bartonella infection cycles.

Comparative studies on pheno- and genotypic properties of Staphylococcus aureus isolated from bovine subclinical mastitis in central Java in Indonesia and Hesse in Germany

In the present study, 35 Staphylococcal strain isolated from milk samples of 16 cows from eight farms of three different geographic locations in Central Java, Indonesia, and from milk samples of 19 cows from 19 farms of different geographic locations in Hesse, Germany, were compared pheno- and genotypically. On the basis of cultural and biochemical properties as well as by amplification of the 23S rRNA specific to Staphylococcus aureus, all isolates could be identified as S. aureus. In addition, all S. aureus isolates harboured the genes clfA and coa encoding staphylococcal clumping factor and coagulase, and the gene segments encoding the immunoglobulin G binding region and the X-region of protein A gene spa. By PCR amplification, the genes seb, seg, seh, and sei was observed for the S. aureus cultures isolated in Central Java, Indonesia and the genes sec, sed, seg, seh, sei, sej and tst for the S. aureus cultures isolated in Hesse, Germany. None of the S. aureus of both origins harboured the genes sea, see, eta and etb. All isolates were additionally positive for the genes nuc, fnbA, hla, and set1. The gene hlb was found for 6 cultures from Central Java, Indonesia and 16 cultures from Hesse, Germany. However, the gene fnbB and the gene segments cnaA and cnaB were not present among the strains isolated in Central Java, Indonesia and rare among the strains isolated in Hesse, Germany. It was of interest that most of the S. aureus isolated in Central Java, Indonesia harboured the gene cap5 and most of the strains isolated in Hesse, Germany the gene cap8. The phenotypic and genotypic results of the present study might help to understand the distribution of prevalent S. aureus clones among bovine mastitis isolates of both countries and might help to control S. aureus infections in dairy herds.

Use of restriction endonucleases for differentiation of pathogenic & saprophytic leptospires.

BACKGROUND & OBJECTIVES: PCR has been reported for amplification of the 482 bp genus specific region in 23S rRNA gene of Leptospira species. The sequence of this region was analyzed for specific restriction sites that could have yielded digestion products expected to provide differentiating banding profile for the pathogenic and the saprophytic group of leptospires. METHODS: Sixteen standard serovars of pathogenic group, two standard serovars of saprophytic group, 12 Leptospira isolates recovered from hospitalized patients with fever and jaundice or pyrexia of unknown origin and 23 isolates from different water sources were studied. Conventional tests, PCR methods and restriction digestion were used for confirming the identity of these isolates. RESULTS: All 12 isolates from patients and 1 from tap water source were identified as pathogenic and 22 isolates from water sources as saprophytic by the conventional tests and PCR. Of the 5 restriction endonuclease enzymes, viz, Apa I, Ban II, Hae III, Pst I and Sin I analyzed for digestion of PCR amplified 482 bp product, Apa I, Ban II, Pst I and Sin I provided fragments of different sizes providing distinct patterns for saprophytic and pathogenic leptospires. INTERPRETATION & CONCLUSION: The identity of a strain to genus Leptospira could be confirmed by PCR amplification of 482 bp region of 23S rRNA and with further restriction digestion a clear distinction into pathogenic or saprophytic group was achieved with the use of any of these 4 restriction enzymes.

Mutations in the 23S rRNA Gene of Helicobacter pylori Associated with Clarithromycin Resistance

Among 12 clarithromycin-resistant Helicobacter pylori strains isolated in Guri, Korea, 8 showed an adenine to guanine mutation at position 2143 (formerly A2144G or E. coli 2059) in the 23S rRNA gene by the PCR-restriction fragment length polymorphism (RFLP) method. The remaining 4 strains, digested by neither BsaI nor BbsI, showed a thymine to cytosine mutation at position 2182 (T2182C) by direct sequencing of the PCR products. The T2182C mutants showed a tendency of higher levels of minimum inhibitory concentration to clarithromycin than the A2143G mutants. In conclusion, either the A2143G or the T2182C mutation was present in 100% of clarithromycin-resistant H. pylori isolates examined. The PCR-RFLP technique with restriction enzymes BbsI and BsaI was a rapid and relatively simple method to detect the clarithromycin resistance. But undigested isolates were quite frequent among our isolates (33.3%), the PCR-RFLP method with restriction enzymes BbsI and BsaI should not be used alone, and development of other rapid detection method for clarithromycin resistance is mandatory.

Development of a 23S rRNA-based PCR assay for the detection of mycobacteria.

The partial nucleotide sequence of a recombinant plasmid containing the 23S rRNA gene of Mycobacterium tuberculosis was determined and an assay was developed for amplifying 23S rRNA gene sequences of mycobacteria. The PCR-based non-radioactive test enabled us to distinguish Mycobacterium from other closely related genera and was sensitive enough to detect 2 bacterial genome equivalents. The assay was extended to the detection of mycobacterial DNA in uncultured clinical specimens; 23S rRNA sequences were detected in thirty four of forty eight (70.8%) sputum and cerebrospinal fluid (CSF) specimens by the PCR assay, whereas direct smear examination and culture methods demonstrated a positivity rate of 29.2% and 16.7% respectively for the same specimens. A RNA-based PCR assay with a detection limit of 1 genome equivalent was also developed. These PCR assays should prove useful for the early and rapid detection of mycobacterial infection in uncultured clinical specimens.

Mechanism of ribosomal subunit association: oligodeoxynucleotides as probes.

From the kethoxal treatment data [Herr, W.; Chapman, N.M.; Noller, H.F. (1979) J. Mol. Biol. 130, 433-439] some regions of ribosomal RNAs are thought to be responsible for the association of 30S and 50S ribosomes of E. coli to form 70S ribosomes. In order to test this possibility about a dozen oligodeoxynucleotides complementary to the suspected regions of rRNAs were synthesised. Their association with ribosomes and naked rRNAs was tested by the gel filtration technique. In order to check the effects on the ribosomal subunit association or rRNA association either intact 30S and 50S ribosomes or naked 16S and 23S rRNAs were preincubated with the individual oligodeoxynucleotide and its effect was checked by density gradient centrifugation followed by UV absorbance monitoring. Some oligodeoxynucleotides interfered with either subunit association or 16S RNA and 23S RNA association, some with both. These data clearly indicate that RNA-RNA interaction plays the major role in ribosomal subunit association.