Comparison of automated microarray detection with real-time PCR assays for detection of respiratory viruses in specimens obtained from children.

Respiratory virus infections are a major health concern and represent the primary cause of testing consultation and hospitalization for young children. We developed and compared two assays that allow the detection of up to 23 different respiratory viruses that frequently infect children. The first method consisted of single TaqMan quantitative real-time PCR assays in a 96-well-plate format. The second consisted of a multiplex PCR followed by primer extension and microarray hybridization in an integrated molecular diagnostic device, the Infiniti analyzer. Both of our assays can detect adenoviruses of groups A, B, C, and E; coronaviruses HKU1, 229E, NL63, and OC43; enteroviruses A, B, C, and D; rhinoviruses of genotypes A and B; influenza viruses A and B; human metapneumoviruses (HMPV) A and B, human respiratory syncytial viruses (HRSV) A and B; and parainfluenza viruses of types 1, 2, and 3. These tests were used to identify viruses in 221 nasopharyngeal aspirates obtained from children hospitalized for respiratory tract infections. Respiratory viruses were detected with at least one of the two methods in 81.4% of the 221 specimens: 10.0% were positive for HRSV A, 38.0% for HRSV B, 13.1% for influenzavirus A, 8.6% for any coronaviruses, 13.1% for rhinoviruses or enteroviruses, 7.2% for adenoviruses, 4.1% for HMPV, and 1.5% for parainfluenzaviruses. Multiple viral infections were found in 13.1% of the specimens. The two methods yielded concordant results for 94.1% of specimens. These tests allowed a thorough etiological assessment of respiratory viruses infecting children in hospital settings and would assist public health interventions.

Automation of complex assays: pharmacogenetics of warfarin dosing.

AutoGenomics, Inc. (Carlsbad, CA, USA) have developed a multiplex microarray assay for genotyping both VKORC1 and CYP2C9 using the INFINITI(™) Analyzer. Multiple alleles in each DNA sample are analyzed by polymerase chain reaction amplification, followed by detection primer extension using the INFINITI Analyzer. The INFINITI Analyzer performs single-nucleotide polymorphism (SNP) analysis using universal oligonucleotides immobilized on the biochip. To genotype broader ethnic groups, genomic DNA from whole blood was tested for nine SNPs for VKORC1 and six for CYP2C9 genotypes. Information related to all 15 SNPs is needed to determine dosing of population of diverse ethnic origin. The INFINITI system provides genotyping information for same day dosing of warfarin.

Characterization of a novel group of mycobacteria and proposal of Mycobacterium sherrisii sp. nov.

We describe here the characterization of five isolates of Mycobacterium simiae-like organisms representing a novel group based on whole-cell fatty acid analysis and genotypic evaluation. Two of the five isolates in this study, W55 and W58, were previously considered to belong to M. simiae serotype 2. Analysis of cellular fatty acids by gas-liquid chromatography indicated a close clustering of this group, which was well differentiated from the other M. simiae-like species. Molecular characterization was performed by nucleic acid sequencing of the small subunit rRNA gene and the gene encoding the 65-kDa heat shock protein and genomic DNA hybridization. Sequence analysis of the entire 16S rRNA gene showed a unique sequence most closely related to those of M. triplex and M. simiae. The hsp65 partial gene sequence was identical for the five isolates, with 97% identity to the M. simiae type strain. However, qualitative whole genomic DNA hybridization analysis confirmed that this group is genetically distinct from M. simiae and M. triplex. Antimicrobial susceptibilities for this group resemble those of M. simiae and M. lentiflavum. We conclude that this group represents a unique Mycobacterium species for which we propose the name Mycobacterium sherrisii sp. nov.

A novel thiocationic liposomal formulation of antisense oligonucleotides with activity against Mycobacterium tuberculosis.

This study describes the development of a novel thiocationic (OBEHYTOP) lipid-based formulation of phosphorothioate antisense oligonucleotides (PAOs) showing inhibitory activity against mycobacterium tuberculosis (mTB) as measured by an in vitro BACTEC 460TB assay. PAOs were designed based on sequences complementary to essential regions of the mycobacterial genome from published nucleic acid databases in GenBank. These included the superoxide dismutase sod A gene (TBS3), catalase-peroxidase katG gene (TBK1, TBK10), RNA polymerase beta-subunit rpo B gene (TBR5) and diaminopimelate decarboxylase lys A gene (TBL5). The effect of PAOs (TBS3, K1, K10, R5 and L5) alone on mTB was not significant compared with the no-drug control over a period of exposure of 150 h (ranges of -11.8 to +23.58% at 72 h; 15.26 to +25.82% at 96 h and -5.51 to +24.00% at 150 h). Liposomal formulations (10:5:2 OBEHYTOP:oleic acid:vitamin D3) of PAOs resulted in statistically significant (p < 0.05 in all cases) inhibition (ranges of -51.45 to -63.00% at 72 h; -56.75 to -67.96% at 96 h; -51.45 to -60.26% at 150 h) compared with PAOs alone, thiocationic liposomal control and liposomal components. Positive controls of streptomycin and isoniazid used at their minimum inhibitory concentrations of 2.00 and 0.10 microM, respectively, resulted in average % inhibition values of -94% and -97.36%, respectively, indicating that these thiocationic lipid-formulated PAOs showed inhibitory activity directed against mTB in vitro.