The Swedish new variant of Chlamydia trachomatis: genome sequence, morphology, cell tropism and phenotypic characterization

Abstract

Chlamydia trachomatis is a major cause of bacterial sexually transmitted infections worldwide. In 2006, a new variant of C. trachomatis (nvCT), carrying a 377 bp deletion within the plasmid, was reported in Sweden. This deletion included the targets used by the commercial diagnostic systems from Roche and Abbott. The nvCT is clonal (serovar/genovar E) and it spread rapidly in Sweden, undiagnosed by these systems. The degree of spread may also indicate an increased biological fitness of nvCT. The aims of this study were to describe the genome of nvCT, to compare the nvCT genome to all available C. trachomatis genome sequences and to investigate the biological properties of nvCT. An early nvCT isolate (Sweden2) was analysed by genome sequencing, growth kinetics, microscopy, cell tropism assay and antimicrobial susceptibility testing. It was compared with relevant C. trachomatis isolates, including a similar serovar E C. trachomatis wild-type strain that circulated in Sweden prior to the initially undetected expansion of nvCT. The nvCT genome does not contain any major genetic polymorphisms - the genes for central metabolism, development cycle and virulence are conserved - or phenotypic characteristics that indicate any altered biological fitness. This is supported by the observations that the nvCT and wild-type C. trachomatis infections are very similar in terms of epidemiological distribution, and that differences in clinical signs are only described, in one study, in women. In conclusion, the nvCT does not appear to have any altered biological fitness. Therefore, the rapid transmission of nvCT in Sweden was due to the strong diagnostic selective advantage and its introduction into a high-frequency transmitting population.

Fig. 1.

Phylogenetic relationships within C. trachomatis. Comparison of tree topologies produced by maximum-likelihood analyses of plasmid (right) and full genome (left) sequences. The serotypes (serovars/genovars) are indicated. Bars, number of substitutions per SNP site. Numbers on nodes represent numbers of SNPs occurring on that branch.

Fig. 2.

Comparison of the PZ in C. trachomatis nvCT (Sweden2, serovar E), Jali20 (serovar B) and D/UW-3/CX (serovar D). The grey lines indicate forward and reverse reading frames of sequenced genomes, with predicted CDSs superimposed. The red bars indicate regions of 95–100 % nucleotide identity. Brown CDSs denote pseudogenes. The phospholipase D locus (purple) contains pseudogenes in all strains. The cytotoxin locus (yellow) in D/UW-3/CX produces an active cytotoxin (Belland et al., 2001). This locus is identical in the nvCT, except for an SNP causing a putative 35 aa N-terminal truncation in the leftmost CDS. The trp operon (green) is complete in strains D/UW-3/CX and the nvCT, but has pseudogene trpA in Jali20. The nvCT carries an insertion of 307 bp in a CDS encoding a hypothetical protein downstream of the trp operon, causing an N-terminal extension of 127 aa. Additionally, an SNP in the nvCT relative to D/UW-3/CX causes read-through of CDSs encoding two conserved hypothetical proteins to create one CDS of 247 aa (dark blue). Other CDSs are turquoise.

Fig. 3.

Iodine-stained inclusions of the C. trachomatis strains nvCT [Sweden2 (a)], Sweden3 [wtCT (b)], E/Bour [prototype reference E strain (c)] and C599 [plasmid-free E strain (d)] in McCoy cells. Bar, 4 μm. Stained inclusions containing glycogen are dark brown, as seen in (a)–(c).

Fig. 4.

TEM of the C. trachomatis strains nvCT [Sweden2 (a) and (b)] and E/Bour [prototype reference E strain (c) and (d)] in BGMK cells. Electron micrographs were taken at 24 h [mid stage of developmental cycle (a) and (c)] and 48 h [mature inclusions (b) and (d)], and showed no major differences between the strains. The enlarged images in the lower right corner of (b) and (d) show EBs with membrane blebs.