In principle, sequencing of the ompA gene can also be used to identify the genotype of C. psittaci, as well as C. trachomatis. However, there are no generally agreed criteria in terms of sequence similarity, so that the assignment remains somewhat arbitrary. Detailed analysis of ompA sequence data deposited at the GenBank database led Sachse et al. [14] to the conclusion that at least 15 ompA genotypes of C. psittaci are occurring in nature. A summary of this classification in Table 1 shows that the more heterogeneous types A, D, and E/B can be further divided into subtypes. The host range of the proposed new genotypes 1V, 6N, Mat116, R54, YP84, and CPX0308 is not yet fully known, but they seem to occur predominantly in wildlife birds.

The fact that genotype-specific sites of C. psittaci are located in ompA’s variable domains (VD) 2 and 4 allows a molecular definition of individual genotypes at the nucleotide level.

In this situation, the use of DNA microarray technology can provide added value because of its potential to simultaneously exploit minor sequence differences at multiple target sites. In the present chapter, we describe a rapid genotyping assay using the ArrayStrip™ (AS) platform that was shown to work with clinical samples under the conditions of routine diagnosis [14, 15]. The AS platform is open and flexible, so that iterative adaptation of probes and extension beyond the currently covered genotypes will always be possible, for instance, in the case of newly emerging types. Comments on the platform’s major performance parameters and comparison with PCR-RFLP and ompA sequencing are given in Note 1 . While both sensitivity and specificity of the microarray assay are high, its main assets include rapidity, ease of operation, and the possibility of mixed genotype identification, as well as high-throughput and moderate costs. An AS unit consists of eight connected plastic vessels in microtiter format, each of which carrying a microarray chip on the bottom.

The present genotyping procedure is based on target DNA being amplified using duplex PCR with 5′-biotinylated primers to generate a 418-bp product encompassing VD1 and VD2, as well as a 570-bp fragment covering VD3 and VD4. Subsequently, the amplification products are subjected to hybridization on the microarray. Based on the analysis of ompA sequences described above, 35 hybridization probes derived from the discriminatory sites of VD2 and VD4 were selected. They had an average size of 26 nt (22–30), average melting temperature of 60.3 °C (59.7–61.2), and G + C contents of 46.0 mol % (37.0–59.0).

Similarly, an ompA genotyping microarray assay was developed for C. trachomatis [16]. Variable domains 1, 2, and 4 of the ompA locus were amplified using a multiplex PCR with biotinylated primers. A total of 61 oligonucleotide probes representing genotype-specific polymorphisms in the same variable domains were included.