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.
Clarithromycin ; Diagnostic Tests, Routine ; Drug Resistance ; Drug Resistance, Microbial ; Helicobacter pylori ; Helicobacter ; Humans ; Point Mutation ; RNA, Ribosomal, 23S

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.
Bacillus subtilis ; genetics ; Genome, Bacterial ; Plasmids ; RNA, Ribosomal, 16S ; genetics ; RNA, Ribosomal, 23S ; genetics ; RNA, Ribosomal, 5S ; genetics ; Sequence Analysis, DNA

OBJECTIVETo explore the value of detecting bacterial 16S rRNA with 23S rRNA in the diagnosis of periprosthetic joint infection (PJI).

METHODSA 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.

RESULTSThe 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.

CONCLUSIONSThe 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.

Arthritis, Infectious ; diagnosis ; microbiology ; Arthroplasty, Replacement, Hip ; Humans ; Prospective Studies ; Prosthesis-Related Infections ; diagnosis ; microbiology ; RNA, Bacterial ; isolation & purification ; RNA, Ribosomal, 16S ; isolation & purification ; RNA, Ribosomal, 23S ; isolation & purification ; Real-Time Polymerase Chain Reaction ; Reoperation ; Sensitivity and Specificity

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.
Adult ; Aged ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Asian Continental Ancestry Group ; Clarithromycin/*therapeutic use ; DNA, Bacterial/analysis ; Drug Resistance, Bacterial/genetics ; Female ; Helicobacter Infections/*drug therapy/microbiology ; Helicobacter pylori/drug effects/genetics/*isolation & purification ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Mutation ; Polymerase Chain Reaction ; RNA, Ribosomal, 23S/genetics ; Republic of Korea ; Retrospective Studies ; Sequence Analysis, DNA

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.
Anti-Bacterial Agents/*pharmacology ; Child, Preschool ; Drug Resistance, Bacterial/*drug effects ; Female ; Humans ; Infant ; Infant, Newborn ; Macrolides/*pharmacology ; Male ; Mycoplasma pneumoniae/genetics/*isolation & purification ; Nasopharynx/microbiology ; Pneumonia, Mycoplasma/epidemiology/microbiology ; Primary Health Care ; RNA, Ribosomal, 23S/analysis ; Reagent Kits, Diagnostic ; Real-Time Polymerase Chain Reaction ; Tertiary Healthcare

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.
Adolescent ; Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Clarithromycin/*therapeutic use ; DNA, Bacterial/analysis ; Drug Resistance, Bacterial ; Female ; Gastroscopy ; Helicobacter Infections/*drug therapy ; Helicobacter pylori/drug effects/*genetics ; Humans ; Islands ; Male ; Middle Aged ; Point Mutation ; Polymerase Chain Reaction ; Proton Pump Inhibitors/therapeutic use ; RNA, Ribosomal, 23S/*genetics ; Republic of Korea ; Young Adult

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.
Anti-Bacterial Agents/pharmacology ; Child ; Child, Preschool ; Drug Resistance, Bacterial/drug effects ; Humans ; Macrolides/pharmacology ; Male ; Mutation ; Mycoplasma pneumoniae/*genetics/isolation & purification ; Pneumonia, Mycoplasma/*diagnosis/microbiology/radiography ; RNA, Ribosomal, 23S/*analysis ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, RNA ; Siblings

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.
Anti-Bacterial Agents ; Binding Sites ; RNA, Ribosomal, 23S ; Staphylococcus aureus ; Toll-Like Receptors

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.
Adult ; Antitubercular Agents/pharmacology ; Chromatography, High Pressure Liquid ; Female ; Humans ; Lung Diseases/*microbiology ; Microbial Sensitivity Tests ; Mycobacterium/classification/drug effects/*isolation & purification ; Mycobacterium Infections/microbiology ; Mycobacterium tuberculosis/genetics/isolation & purification ; Mycolic Acids/analysis ; Oligonucleotide Array Sequence Analysis ; Phylogeny ; RNA, Ribosomal, 16S/chemistry/genetics ; RNA, Ribosomal, 23S/chemistry/genetics ; Republic of Korea ; Sequence Analysis, DNA

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.
Anti-Bacterial Agents/*pharmacology ; Biopsy ; Clarithromycin/*pharmacology ; Drug Resistance, Bacterial ; Genotype ; Helicobacter Infections/*diagnosis/drug therapy/pathology ; Helicobacter pylori/drug effects/genetics/*isolation & purification ; Humans ; Microbial Sensitivity Tests ; Mutation ; Polymerase Chain Reaction ; RNA, Ribosomal, 23S/genetics