ABSTRACT
Capnocytophaga canimorsus and C. cynodegmi are gram negative bacteria that can be transmitted to humans from dogs or cats and cause serious infections. Routine bacteriological methods, including fermentation and phenotypic tests are insufficient to correctly identify C. canimorsus or C. cynodegmi. The aim of this study was to evaluate the performance of VITEK2 and MALDI-TOF in identification of these bacteria. Twenty two isolates that were identified as C. canimorsus / C. cynodegmi by 16S rRNA sequencing were included in the study and were further investigated with VITEK2 and MALDI-TOF. A Capnocytophaga species-specific PCR was used as the reference method. Out of 22 included isolates, the species-specific PCR identified six blood isolates as C. canimorsus and 14 wound isolates as C. cynodegmi. Two isolates could not be identified with the reference method. VITEK2 identified 10/20 isolates correctly to Capnocytophaga spp. MALDI-TOF analysis correctly identified 6/6 C. canimorsus and 13/14 C. cynodegmi isolates. The mean time to identification with VITEK2 was 6 hours whereas MALDI-TOF required approximately 10 minutes per sample. Here we show that MALDI-TOF rapidly identified C. canimorsus and C. cynodegmi and thus constitutes a valuable diagnostic tool in the clinical laboratory.
Subject(s)
Blood-Borne Pathogens/isolation & purification , Blood/microbiology , Capnocytophaga/isolation & purification , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Wound Infection/microbiology , Adult , Aged , Bacterial Typing Techniques , Bites and Stings/microbiology , Capnocytophaga/genetics , Female , Genes, rRNA , Humans , Male , Middle Aged , Polymerase Chain Reaction , RNA, Ribosomal, 16S/analysis , RNA, Ribosomal, 16S/genetics , Reagent Kits, Diagnostic , Sensitivity and Specificity , Time FactorsABSTRACT
In this study, we have applied and evaluated a modified cDNA representational difference analysis (RDA) protocol based on magnetic bead technology to study the molecular effects of a candidate drug (N,N'-diacetyl-L-cystine, DiNAC) in a model for atherosclerosis. Alterations in a gene expression profile induced by DiNAC were investigated in a human monocytic cell line (THP-1) differentiated into macrophage-like cells by lipopolysaccharide and further exposed to DiNAC. Three rounds of subtraction have been performed and the difference products from the second and third rounds have been characterized in detail by analysis of over 1000 gene sequences. Two protocols for analysis of the subtraction products have been evaluated, a shotgun approach and size selection of both distinct fragments and band-patterned smear. We demonstrate that in order to obtain a representative view of the most abundant gene fragments, the shotgun procedure is preferred. The obtained sequences were analyzed against the UniGene and Expressed Gene Anatomy Database (EGAD) databases and the results were visualized and analyzed with the ExProView software enabling rapid pair-wise comparison and identification of individual genes or functional groups of genes with altered expression levels. The identified differentially expressed gene sequences were comprised of both genes with known involvement in atherosclerosis or cholesterol biosynthesis and genes previously not implicated in these processes. The applicability of a solid-phase shotgun RDA protocol, combined with virtual chip monitoring, results in new starting points for characterization of novel candidate drugs.
Subject(s)
Cystine/analogs & derivatives , DNA, Complementary/genetics , Gene Expression Profiling , Arteriosclerosis/genetics , Arteriosclerosis/prevention & control , Cell Line , Cystine/pharmacology , Gene Expression Regulation/drug effects , Humans , Nucleic Acid Hybridization/methods , Polymerase Chain Reaction/methods , Reproducibility of Results , Reverse Transcriptase Polymerase Chain Reaction , SoftwareABSTRACT
OBJECTIVES: To analyze the early gene expression in macrophages accompanying the phenotypic changes into foam cells upon exposure to oxidized low-density lipoprotein. To identify candidate genes and markers for further studies into the pathogenesis of atherosclerosis. METHODS: Cells of the monocytic cell line THP-1 were activated by PMA and exposed to oxidized low-density lipoprotein. Gene expression profiles were investigated after 24 h, using a solid phase cDNA representational difference analysis (RDA) method and shotgun sequencing. Results were verified by microarray hybridization, and analyzed in the virtual chip display of a novel software tool for transcript profile exploration. RESULTS: By comparing transcript profiles of exposed/unexposed cells, 1,984 transcript sequences, representing a total of 921 genes with altered expression levels in response to oxidized low-density lipoprotein exposure, were identified. Genes that are central to cell cycle control and proliferation, inflammatory response, and of pathways not previously implicated in atherosclerosis were identified. The data obtained is also made available on-line at http:// biobase.biotech.kth.se/thp1a for further exploration. CONCLUSION: The identification of new candidate genes for atherosclerotic disease through RDA-based transcript profiling facilitates further functional genomic studies in coronary artery disease. Candidate genetic polymorphism markers of potential clinical relevance can be identified by filtering information in genome variation databases through the virtual chip analysis of the transcript profiles and subsequently tested in association studies.
