Genotyping of <it>Chlamydophila psittaci </it>using a new DNA microarray assay based on sequence analysis of <it>omp</it>A genes

<p>Abstract</p> <p>Background</p> <p>The currently used genotyping system for the avian zoonotic pathogen <it>Chlamydophila (C.) psittaci </it>has evolved from serology and is based on <it>omp</it>A sequence variations. It includes seven avian and two non-avian genotypes. Restriction enzyme cleavage of the amplified <it>omp</it>A gene and, less frequently, <it>omp</it>A sequencing are being used for examination, but, beside methodological limitations, an increasing number of recently tested strains could not be assigned to any established genotype.</p> <p>Results</p> <p>Comprehensive analysis of all available <it>omp</it>A gene sequences has revealed a remarkable genetic diversity within the species <it>C. psittaci</it>, which is only partially covered by the present genotyping scheme. We suggest adjustments and extensions to the present scheme, which include the introduction of subgroups to the more heterogeneous genotypes A, E/B and D, as well as six provisional genotypes representing so far untypable strains. The findings of sequence analysis have been incorporated in the design of a new DNA microarray. The ArrayTube™ microarray-based <it>omp</it>A genotyping assay has been shown to discriminate among established genotypes and identify so far untyped strains. Its high specificity, which allows detection of single-nucleotide polymorphisms, is due to the parallel approach consisting in the use of 35 hybridization probes derived from variable domains 2 and 4 of the <it>omp</it>A gene.</p> <p>Conclusion</p> <p>The traditional genotyping system does not adequately reflect the extent of intra-species heterogeneity in <it>omp</it>A sequences of <it>C. psittaci</it>. The newly developed DNA microarray-based assay represents a promising diagnostic tool for tracing epidemiological chains, exploring the dissemination of genotypes and identifying non-typical representatives of <it>C. psittaci</it>.</p>