One-step detection of the 2009 pandemic influenza A(H1N1) virus by the RT-SmartAmp assay and its clinical validation.

BACKGROUND: In 2009, a pandemic (pdm) influenza A(H1N1) virus infection quickly circulated globally resulting in about 18,000 deaths around the world. In Japan, infected patients accounted for 16% of the total population. The possibility of human-to-human transmission of highly pathogenic novel influenza viruses is becoming a fear for human health and society. METHODOLOGY: To address the clinical need for rapid diagnosis, we have developed a new method, the "RT-SmartAmp assay", to rapidly detect the 2009 pandemic influenza A(H1N1) virus from patient swab samples. The RT-SmartAmp assay comprises both reverse transcriptase (RT) and isothermal DNA amplification reactions in one step, where RNA extraction and PCR reaction are not required. We used an exciton-controlled hybridization-sensitive fluorescent primer to specifically detect the HA segment of the 2009 pdm influenza A(H1N1) virus within 40 minutes without cross-reacting with the seasonal A(H1N1), A(H3N2), or B-type (Victoria) viruses. RESULTS AND CONCLUSIONS: We evaluated the RT-SmartAmp method in clinical research carried out in Japan during a pandemic period of October 2009 to January 2010. A total of 255 swab samples were collected from outpatients with influenza-like illness at three hospitals and eleven clinics located in the Tokyo and Chiba areas in Japan. The 2009 pdm influenza A(H1N1) virus was detected by the RT-SmartAmp assay, and the detection results were subsequently compared with data of current influenza diagnostic tests (lateral flow immuno-chromatographic tests) and viral genome sequence analysis. In conclusion, by the RT-SmartAmp assay we could detect the 2009 pdm influenza A(H1N1) virus in patients' swab samples even in early stages after the initial onset of influenza symptoms. Thus, the RT-SmartAmp assay is considered to provide a simple and practical tool to rapidly detect the 2009 pdm influenza A(H1N1) virus.

Complete genome sequence of Mycoplasma pneumoniae type 2a strain 309, isolated in Japan.

Mycoplasma pneumoniae strain 309, a type 2a (subtype 2 variant) strain of this bacterium, has variations in the P1 protein, which is responsible for attachment of the bacterium to host cells. Here, we report the complete genome sequence of M. pneumoniae strain 309 isolated from a pneumonia patient in Japan.

Spread of a chromosomal cefixime-resistant penA gene among different Neisseria gonorrhoeae lineages.

In Neisseria gonorrhoeae, the mosaic type of penA, which encodes penicillin-binding protein 2 (PBP 2), is associated with reduced susceptibility to oral cephalosporins. To investigate the relatedness of N. gonorrhoeae clinical isolates with reduced susceptibility, we sequenced the penA genes of 32 isolates. Five different amino acid sequence types of PBP 2 were identified, but all seemed to be derivatives of pattern X of PBP 2 (PBP 2-X). However, multilocus sequence typing of the isolates showed that the isolates belonged to six different sequence types. As PBP 2-X was identified in three different sequence types, horizontal transfer of the penA allele encoding PBP2-X was suggested. We demonstrated that the penA gene could be transferred from an isolate with reduced susceptibility to a sensitive isolate by natural transformation. Comparison of the sequence of the penA-flanking regions of 12 transformants with those of the donor and the recipient suggested that at least a 4-kb DNA segment, including the penA gene, was transferred. During horizontal transfer, some of the penA alleles also acquired variations due to point mutations and genetic exchange within the allele. Our results provide evidence that the capacity for natural transformation in N. gonorrhoeae plays a role in the spread of chromosomal antibiotic resistance genes and the generation of diversity in such genes.

Three familial cases of drug-resistant Mycoplasma pneumoniae infection.

UNLABELLED: Mycoplasma pneumoniae infection is believed to result from defective host immune response rather than from direct cell injury by the organism itself. In this context, emergence of drug-resistant M. pneumoniae may provide us with special opportunities to study the pathogenesis from a clinical point of view. In this report, three patients with intrafamilial M. pneumoniae infection are presented. M. pneumoniae was isolated with a Hayflick pleuropneumonia-like organism diphasic medium. Minimal inhibitory concentrations of antibiotics were determined by a broth microdilution method. Polymerase chain reaction and restriction fragment length polymorphism analysis were done to determine point mutation in domain V of the 23S rRNA gene. As a result, all three strains from the three intrafamilial cases had the same drug-resistant point mutation, specifically A-to-G transition at position 2063. However, their clinical courses were quite different; a 6-year-old girl suffered severe pneumonia, a 5-year-old girl had mild pneumonia, and a 3-year-old boy had only a fever of 1-day duration without pneumonia. CONCLUSIONS: Our clinical and laboratory observations strongly support the idea that the host immune maturity, rather than a virulence factor of the organism, is a major determinant factor of disease severity of M. pneumoniae infection and that drug resistance does not necessarily lead to a serious clinical outcome.

Genotyping analysis of Mycoplasma pneumoniae clinical strains in Japan between 1995 and 2005: type shift phenomenon of M. pneumoniae clinical strains.

Mycoplasma pneumoniae clinical isolates obtained between 1995 and 2005 were examined to determine the prevalent genotype. One hundred and twenty-seven strains isolated from bronchitis and pneumonia patients were genotyped by a PCR-RFLP method based on nucleotide sequence polymorphisms of the p1 gene, which encodes the major adhesin protein. The typing results established that 66 of the isolates were group I strains, 45 were group II strains and 16 were group II variants. Analysis of the annual occurrence of these isolates showed a predominance of group II strains between 1995 and 2001 (n=37). No group I strain was found during this period. However, group I strains appeared in the isolates from 2002 (2/5 isolates, 40 %) and increased in specimens taken after 2003, thereby constituting a large proportion of the isolates. In 2004 and 2005, no group II strains were found among the isolates (n=49), although there were nine group II variants. Throat swabs and sputum samples obtained from patients with respiratory infections between 1997 and 2005 were also analysed by PCR-RFLP or a new nested PCR to detect the p1 gene DNA. Typing analysis of these p1 gene DNAs also showed that the group I p1 gene was not present in specimens taken before 2000, but was present and dominant in specimens taken after 2001. These results indicate that, in Japan, the prevalent type of M. pneumoniae changed from a group II strain to a group I strain around 2002.

[Antibiotic susceptibility of Neisseria meningitidis from healthy and diseased persons in Japan].

We examined the susceptibilities of 100 Neisseria meningitidis strains isolated between 1990 and 2004 to 12 antimicrobial agents, finding the MIC50 to be 0.031 microg/mL and that of MIC90 of benzylpenicillin (PCG), a type of penicillin, to be 0.063 microg/mL. Two strains showed intermediate resistance (MIC of 0.125-0.25 microg/mL). Two strains of the same origin also showed intermediate resistance (0.25-1 microg/mL) to ampicillin (ABPC). For cephems, MIC50 and MIC90 of cefotaxime (CTX) were both 0.004 microg/mL, while the MICs of ceftriaxone (CTRX) were all 0.004 microg/mL, showing the strongest antibacterial spectrum. The three carbapenems surveyed meropenem (MEPM), panipenem (PAPM), and imipenem (IPM) also had a strong antibacterial spectrum in ascending order, with the MIC50 and MIC90 of MEPM, which was lowest, being 0.008 microg/mL and 0.016 microg/mL. Some 97% of MICs for ciprofloxacin (CPFX) were 0.004 microg/mL but 3 strains showed resistance (0.125 microg/mL). No difference was seen between MICs of N. meningitidis strains originated from meningitis patients, patients other than meningitis, and healthy carriers. No difference was seen in MICs by serogroup (A, B, C, Y, W135 and NG).

Clinical evaluation of macrolide-resistant Mycoplasma pneumoniae.

Macrolide-resistant Mycoplasma pneumoniae (MR M. pneumoniae) has been isolated from clinical specimens in Japan since 2000. A comparative study was carried out to determine whether or not macrolides are effective in treating patients infected with MR M. pneumoniae. The clinical courses of 11 patients with MR M. pneumoniae infection (MR patients) treated with macrolides were compared with those of 26 patients with macrolide-susceptible M. pneumoniae infection (MS patients). The total febrile days and the number of febrile days during macrolide administration were longer in the MR patients than in the MS patients (median of 8 days versus median of 5 days [P = 0.019] and 3 days versus 1 day [P = 0.002], respectively). In addition, the MR patients were more likely than the MS patients to have had a change of the initially prescribed macrolide to another antimicrobial agent (63.6% versus 3.8%; odds ratio, 43.8; P < 0.001), which might reflect the pediatrician's judgment that the initially prescribed macrolide was not sufficiently effective in these patients. Despite the fact that the febrile period was prolonged in MR patients given macrolides, the fever resolved even when the initial prescription was not changed. These results show that macrolides are certainly less effective in MR patients.

Characterization and molecular analysis of macrolide-resistant Mycoplasma pneumoniae clinical isolates obtained in Japan.

In recent years, Mycoplasma pneumoniae strains that are clinically resistant to macrolide antibiotics have occasionally been encountered in Japan. Of 76 strains of M. pneumoniae isolated in three different areas in Japan during 2000 to 2003, 13 strains were erythromycin (ERY) resistant. Of these 13 strains, 12 were highly ERY resistant (MIC, > or =256 microg/ml) and 1 was weakly resistant (MIC, 8 microg/ml). Nucleotide sequencing of domains II and V of 23S rRNA and ribosomal proteins L4 and L22, which are associated with ERY resistance, showed that 10 strains had an A-to-G transition at position 2063 (corresponding to 2058 in Escherichia coli numbering), 1 strain showed A-to-C transversion at position 2063, 1 strain showed an A-to-G transition at position 2064, and the weakly ERY-resistant strain showed C-to-G transversion at position 2617 (corresponding to 2611 in E. coli numbering) of domain V. Domain II and ribosomal proteins L4 and L22 were not involved in the ERY resistance of these clinical M. pneumoniae strains. In addition, by using our established restriction fragment length polymorphism technique to detect point mutations of PCR products for domain V of the 23S rRNA gene of M. pneumoniae, we found that 23 (24%) of 94 PCR-positive oral samples taken from children with respiratory infections showed A2063G mutation. These results suggest that ERY-resistant M. pneumoniae infection is not unusual in Japan.

Observation of CO(2) in Fourier transform infrared spectral measurements of living Acholeplasma laidlawii cells.

In monitoring the time course of conformational disorder by Fourier transform infrared spectroscopy for intact Acholeplasma laidlawii cells grown at 37 degrees C on binary fatty acid mixtures containing oleic acid and for cells grown on pure palmitic acid, an absorption band at 2343 cm(-1) was observed. The band intensity was found to increase with time. This band was not observed in the spectra for isolated membranes. It is suggested that the 2343 cm(-1) band is due to CO(2) dissolved in water, most likely produced at the final point of fermentation of amino acid by this microorganism.

Novel observation of hot-cold-hot hemolysis exhibited by group B streptococci.

Six human isolates of group B streptococci (GBS) were cultured on blood agar anaerobically at 37 degrees C for 18 h and then at 4 degrees C for 6 h and reincubated anaerobically at 37 degrees C for 6 h. Three of the strains showed a marked enlargement of the hemolysis zone compared with that obtained after hot-only (37 degrees C for 18 h) or hot-cold (37 degrees C for 18 h and then 4 degrees C for 6 h) treatment. Subsequent broth culture experiments revealed that enhanced hemolytic activity due to hot-cold-hot treatment was observed in all 6 GBS strains when cultured in the presence of starch.