Introduction Nucleotide sequencing of the ompA gene, encoding the outer membrane protein MOMP, divides C. trachomatis into 15 main genovars comprising three biovars associated with different disease phenotypes along with distinct tissue tropisms. The extra chromosomal plasmid of Chlamydia trachomatis is suggested to encode genes essential for chlamydial infection and transmission. Using an in silico plasmid MLST scheme, the clustering of C. trachomatis isolates was investigated in association with previously defined ompA biovars.

Methods: In silico analysis using publicly available whole genome sequence data (WGS) of C. trachomatis isolates deposited in the Chlamydiales pubMLST database (http://pubmlst.org/chlamydiales/) was performed. Only data from WGS were investigated ensuring that complete sequence data in all eight known plasmid genes and ompA, were included. An in silico plasmid MLST scheme was developed to assign allele numbers and plasmid sequence types to all included isolates. Clustering of C. trachomatis plasmids was assessed using minimum spanning tree analysis. Moreover, we performed a polymorphism analysis of each plasmid gene.

Results Using the in silico plasmid MLST scheme, plasmid alleles and sequence types were successfully assigned to 157 C . trachomatis isolates. Overall, 47 unique plasmid sequence types were detected. Minimum spanning tree analysis identified 5 large clusters, which showed clustering of C. trachomatis plasmids according to the ompA defined biovars. Further analysis of individual plasmid genes showed that besides specific STs, each biovar also had distinct plasmid alleles. Moreover, analysis of the polymorphic variation of plasmid genes confirmed that the C. trachomatis plasmid was highly conserved with all isolates sharing >99% sequence identity.

Conclusion: In silico multilocus sequence typing of C. trachomatis plasmids showed clustering of isolates according to biovars, suggesting that the C. trachomatis plasmid along with specific plasmid genes may play a role in the distinct disease phenotypes found in C. trachomatis infections.