Chlamydia trachomatis is the world's leading cause of preventable blindness. Also, C. trachomatis is considered the world's most common sexually transmitted bacterial pathogen. Many urogenital infections remain unnoticed, constituting a large reservoir of untreated individuals, a continuous threat for transmission of this pathogen. When not treated in time, infection with C. trachomatis can lead to infertility in women. C. trachomatis strains are discriminated by serotyping based on the antigenic difference between the major outer membrane proteins (MOMP). Nineteen serovars have been described: A, B, Ba, C (mainly seen among isolates from trachoma infections) D, Da, E, F, G, Ga, H, I, Ia, J, Ja, K, (urogenital infections) and L1, L2, L2a and L3 causing lymphogranuloma venereum (LGV). Among urogenital infections, serovars D - F are most frequently found . However, serotyping is laborious, needing culture and a large panel of antibodies [2, 3]. To overcome these drawbacks a PCR based RFLP of ompA was developed for the identification of genotypes corresponding to serovars [4–6]. Using this method genotypes were categorised into three geno-groups: the B group (B, E, D, Da, L1, L2, L2a), the C group (C, A, H, I, Ia, J, K, L3) and the intermediate group (F, G, Ga). Except for an immunological relationship between members of a group, the biological relevance of the geno-groups remains obscure.
Chlamydophila pneumoniae is a common cause of community-acquired pneumonia, bronchitis, pharyngitis and sinusitis . Although C. pneumoniae often causes mild or subclinical infections, its persistence in the host can lead to the establishment of chronic pathologies and an increasing number of reports indicate an association between persistent C. pneumoniae infections and arteriosclerosis  or coronary heart diseases [9, 10]. A robust typing scheme for C. pneumoniae is lacking.
Together with C. trachomatis, C. pneumoniae belongs to the family of Chlamydiaceae in the order of Chlamydiales. Based on phylogenetic analyses of 16S and 23S rRNA gene sequences, C. trachomatis, Chlamydia suis and Chlamydia muridarum all belong to the genus Chlamydia, while C. pneumoniae, Chlamydophila psittaci, Chlamydophila pecorum, Chlamydophila felis, Chlamydophila abortus, and Chlamydophila caviae all belong to the family of Chlamydophila [11–13]. Other family members of the order of Chlamydiales are Parachlamydiaceae and Simkaniaceae.
Currently, the typing scheme for C. trachomatis is based on epitopes in the major outer membrane protein (MOMP). Variants of this protein are subjected to selection and isolates of the same serovar may not be closely related [14, 15]. Here we present an MLST typing scheme using gene segment sequences of seven housekeeping genes. These genes were selected using the criteria that they are widely separated on the chromosome and not adjacent to putative outer membrane, secreted, or hypothetical proteins that might be under diversifying selection. In addition, each locus has a similar extent of nucleotide substitutions to ensure consistency . The results identified three sub-groupings within C. trachomatis, but no subdivision within C. pneumoniae. A phylogenetic tree based on the concatenated sequences of six of the housekeeping gene fragments is consistent with a tree based on 16S and 23S rRNA gene sequences.