Takashi Hirama

Peptide nucleic acid-locked nucleic acid polymerase chain reaction clamp-based detection test for gefitinib-refractory T790M epidermal growth factor receptor mutation

Mutations in the epidermal growth factor receptor (EGFR) are observed in a fraction of non‐small‐cell lung cancers (NSCLS). EGFR mutation‐positive NSCLS responds to gefitinib. Secondary T790M mutation confers gefitinib resistance to NSCLS. A detection test for the T790M mutation was designed based on the peptide nucleic acid–locked nucleic acid polymerase chain reaction clamp method. The specificity and sensitivity of the test were both greater than 0.99. The test revealed that only a small population of the PC‐13 cells carried the T790M mutation. The test also revealed that the T790M mutation was found in none of 151 NSCLC specimens obtained before gefitinib treatment, whereas it was found in four of four specimens obtained from NSCLS that had become refractory to gefitinib. In one patient in whom the L858R‐positive EGFR allele was amplified to multiple copies, an L858R‐T790M double‐mutant allele emerged during the gefitinib therapy. This allele was expressed highly. The T790M mutation detection test based on the peptide nucleic acid–locked nucleic acid polymerase chain reaction clamp method is sensitive and specific, and is applicable to clinical practice. It detects T790M‐positive cells in the course of gefitinib treatment, and thus will help to devise therapies effective for T790M‐positive NSCLS. (Cancer Sci 2008; 99: 595–600)

Prediction of the Pathogens That Are the Cause of Pneumonia by the Battlefield Hypothesis

Commensal organisms are frequent causes of pneumonia. However, the detection of these organisms in the airway does not mean that they are the causative pathogens; they may exist merely as colonizers. In up to 50% cases of pneumonia, the causative pathogens remain unidentified, thereby hampering targeting therapies. In speculating on the role of a commensal organism in pneumonia, we devised the battlefield hypothesis. In the “pneumonia battlefield,” the organism-to-human cell number ratio may be an index for the pathogenic role of the organism. Using real-time PCR reactions for sputum samples, we tested whether the hypothesis predicts the results of bacteriological clinical tests for 4 representative commensal organisms: Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas spp., and Moraxella catarrhalis. The cutoff value for the organism-to-human cell number ratio, above which the pathogenic role of the organism was suspected, was set up for each organism using 224 sputum samples. The validity of the cutoff value was then tested in a prospective study that included 153 samples; the samples were classified into 3 groups, and each group contained 93%, 7%, and 0% of the samples from pneumonia, in which the pathogenic role of Streptococcus pneumoniae was suggested by the clinical tests. The results for Haemophilus influenzae, Pseudomonas spp., and Moraxella catarrhalis were 100%, 0%, and 0%, respectively. The battlefield hypothesis enabled legitimate interpretation of the PCR results and predicted pneumonia in which the pathogenic role of the organism was suggested by the clinical test. The PCR reactions based on the battlefield hypothesis may help to promote targeted therapies for pneumonia. The prospective observatory study described in the current report had been registered to the University Hospital Medical Information Network (UMIN) registry before its initiation, where the UMIN is a registry approved by the International Committee of Medical Journal Editors (ICMJE). The UMIN registry number was UMIN000001118: A prospective study for the investigation of the validity of cutoff values established for the HIRA-TAN system (April 9, 2008).

Tuberculosis screening programme using the QuantiFERON®-TB Gold test and chest computed tomography for healthcare workers accidentally exposed to patients with tuberculosis

Healthcare workers (HCWs) have an increased incidence of tuberculosis (TB). Periodic and as-needed screenings of HCWs exposed to patients with TB are important. We integrated chest computed tomography (CT) and the QuantiFERON-TB Gold (QFT-G) test into our TB screening programme for HCWs. First, contacts were tested using the QFT-G test. Those positive for the QFT-G test were investigated by CT and classified as having active, latent (LTBI), or old TB. Between April 2005 and April 2010, 11 patients who had not been diagnosed with active TB on admission were found to have the disease. A total of 512 close or high risk contacts were identified, and underwent screening. Out of those, 34 (6.64%) were QFT-G positive, whereas 478 (93.36%) were negative. Of the 34 QFT-G-positive HCWs, four had CT findings compatible with active TB and received multidrug treatment; 24 showed no findings of active TB and received isoniazid for six months. All completed their regimens without any adverse effects. The TB screening programme integrating CT and the QFT-G test was safe and feasible. The efficacy of the programme needs to be confirmed by large scale clinical trials.

HIRA-TAN: A real-time PCR-based system for the rapid identification of causative agents in pneumonia

UNLABELLED Identification of the causative pathogen(s) of pneumonia would allow the selection of effective antibiotics and thus reduce the mortality rate and the emergence of drug-resistant pathogens. To identify such pathogens and to obtain these benefits, it is necessary that a clinical test is rapid, accurate, easily performed, and cost-effective. Here, we devised a PCR-based test, named HIRA-TAN, which is able to discriminate therapeutic targets from commensal organisms (e.g. Streptococcus pneumoniae or Haemophilus influenzae) and to detect foreign organisms (e.g. Mycoplasma pneumoniae or Legionella pneumophila) in the sputum. The utility of this system was validated in a prospective study, using sputum samples from patients with pneumonia. 568 patients were enrolled and the HIRA-TAN assay identified the causative pathogens with an accuracy of 96.7% for H. influenzae; 93.2% for Pseudomonas aeruginosa; 80.6% for Klebsiella pneumoniae; 90.9% for Moraxella catarrhalis; 87.5% for Escherichia coli; 78.1% for MRSA and 91.6% for S. pneumoniae. Overall the HIRA-TAN procedure was able to identify the causative pathogens of pneumonia in 60% of the cases. Additionally, this procedure was able to determine when the pneumonia-causing organism was a commensal organism or a foreign organism in a single assay. The HIRA-TAN approach yielded reproducible results and provided valuable information to plan the course of treatment of pneumonia. Through the rapid identification of the causative pathogens, the HIRA-TAN will promote targeted treatments for pneumonias. CLINICAL TRIALS REGISTRATION UMIN000001694.

PCR-Based Rapid Identification System Using Bridged Nucleic Acids for Detection of Clarithromycin-Resistant Mycobacterium avium-M. intracellulare Complex Isolates

ABSTRACT The nontuberculous mycobacteria (NTM) cause miscellaneous disorders in humans, especially in the lungs, which present with a variety of radiological features. To date, knowledge of the pathogenic role of the Mycobacterium avium-intracellulare complex (MAC) in the human lung and the definitive criteria for initiating multidrug therapy are still lacking. However, there is little doubt that clarithromycin is the most efficacious drug among the various treatment regimens for lung NTM. In this study, with the use of a bridged nucleic acid (BNA) probe a detection system based on a real-time PCR (BNA-PCR) for the identification of the point mutations at position 2058 or 2059 in domain V of the 23S rRNA gene responsible for clarithromycin resistance was developed and has been assessed using MAC isolates from clinical samples. Out of 199 respiratory specimens, the drug susceptibility test demonstrated 12 strains resistant to clarithromycin, while the BNA-PCR showed 8 strains carrying the point mutation at position 2058 or 2059 of the 23S rRNA gene. This system revealed that there were mycobacterial strains resistant to clarithromycin which do not carry previously identified resistance genes. This paper documents a novel system for detecting clarithromycin-resistant strains and demonstrates that although these mutations are tacitly assumed to account for >90% of the reported resistant mutants, there is a significant fraction of resistant mutants that do not harbor these mutations. Therefore, unknown mechanisms affecting clarithromycin resistance remain to be elucidated.

A pressure-driven column-based technique for the efficient extraction of DNA from respiratory samples.

Currently molecular techniques are a broadly accepted tool for diagnosis and are able to benefit patients in clinical practice. The polymerase chain reaction (PCR) has been especially incorporated into practical applications that are already in widespread use across the globe. With regard to the initial DNA extraction from clinically relevant samples, a number of commercially available kits are commonly used and are also designed to be easy to handle and less labor-intensive. In this study, the pressure system extracting DNA in column-based kit was developed, and its utility was compared with the centrifuge method using sputum from patients who were diagnosed with pneumonia. Also, due to the compact size and rapid processing time, the practical application of the pressure-based system incorporated into an automated pipetting machine was evaluated through clinical study. Our data suggests that DNA extraction by pressure was capable of serving as a substitute for the centrifuge method, and the compact and automatic nature of the pressure system device provided rapid and valuable information for clinical practice.

The Quantiferonî-TB Gold In-Tube Assay Detects Interferon- ReleaseResponses to Mycobacterium Tuberculosis Antigens for Extended Periodsof Time

The development and wide usage of interferon (IFN)-γ release assays (IGRAs) brought remarkable advances in the diagnosis of tuberculosis (TB). QuantiFERON®-TB Gold In-Tube (QFT-GIT), one of the IGRAs, employs three TB antigens, ESAT-6, CFP-10, and TB7.7, to which cell-mediated immune responses are measured in a single tube. In this regard, the QFT-GIT in patients with active TB was hypothesized to detect TB positivity for a longer period after the initiation of treatment. The change of IFN-γ values in patients with pulmonary TB serially registered to the study was examined with QFT-GIT before initiating anti-TB drugs, after completion of treatment and 12 months after the cessation of treatment. The data demonstrates that the IFN-γ levels remained consistently positive for a period of one year after treatment.