Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature

Abstract

Chlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.

Keywords: Chlamydia trachomatis; inter-clade exchange; lymphogranuloma venereum (LGV); ompA; outbreak; recombination.

Fig. 1.

Confirmed cases of the outbreak-causing hybrid L2b/D-Da C. trachomatis strain. Schematic summary of the clinical data, co-infections, risk behaviours and laboratory typing results.

Fig. 2.

Phylogenetic integration of the hybrid L2b/D-Da outbreak-causing C. trachomatis strain in the genome-based species tree (a), ompA tree (b) and concatenated CT677–CT680-based tree (c). Represented strains reflect the species phylogenetic diversity [15] and are coloured by the genome-based phylogenetic clade (ocular, yellow; prevalent genital – T1, red; non-prevalent genital – T2, green; and LGV, black), as marked in (a).

Fig. 3.

Genome backbone and mosaic structure of the outbreak-associated C. trachomatis L2b/D-Da recombinant strain. (a) Genome backbone and recombination analysis of the L2b/D-Da C. trachomatis strain. The graph shows the number of genetic differences (SNPs and indels) detected among five complete or near-complete genomes of outbreak-associated L2b/D-Da clones when comparing with the genome (chromosome plus plasmid) sequence of the L2b/UCH-1/proctitis strain, which is a representative strain of the worldwide disseminated proctitis-associated outbreak of C. trachomatis L2b (a probable parental-like strain) occurring since 2003 (GenBank accession numbers: AM884177.2/NC_010280.2 for chromosome and AM886279.1 for the plasmid). Polymorphism is displayed as variant sites (SNPs or indels) in a window size and a step size of 10 000 bp each, where variants introduced by the main recombination event are highlighted in red. The 100 % conserved plasmid is present at the right side of the blue dashed line. Polymorphisms outside the recombinant fragment are detailed in Table S2. (b) Detail of the recombination event. The L2b/D-Da C. trachomatis strain is a recombinant strain resulting from the genetic import of the a ~4.2 kbp genomic fragment from a non-LGV D/Da strain (most likely belonging to T1 clade) by a typical proctitis-associated L2b strain. The recombination fragment (highlighted in red by both boxes and coloured genes) enrols ~75 % of CT681/ompA and four entire genes (CT677/frr, CT678/pyrH, CT679/tsf, CT680/rpsB) (positions 55221–59461 in the L2b/UCH-1 chromosome). Estimated recombination crossovers most likely involved the two following regions (shaded in orange): (i) a region with two contiguous tRNAs located between CT676 and CT677/rrf; and (ii) a conserved region (among serogroup B serovars: B/Ba, D/Da, E, L1 and L2) within ompA (5’- 3’ gene position 303-365). For scheme simplification, the core-genome-based phylogenetic reconstruction enrols sequences from C. trachomatis strains representing the main clades of the species tree [15] and from five outbreak-associated L2b/D-Da clones. Vertical pink lines reflect SNPs against the chromosome sequence of the parental-like L2b/UCH-1/proctitis strain (region spanning positions 54500–60000 bp; accession numbers AM884177.2/NC_010280.2) (highlighted by horizontal light blue lines). Gene orientation and annotation refers to the firstly released C. trachomatis genome, D/UW-3/CX strain (GenBank accession number NC_000117). (c) Schematic representation of the topology sketch of the recombinant MOMP, where the L2/L2b-like and D/Da-like non-transmembrane parts of the protein are coloured in black and red, respectively. MOMP is oriented from N-terminal to C-terminal (left to right). L1-L8 indicates protein loops (L) facing the outside, and include the four VDs (VDI–VDIV) of MOMP (shaded in blue). Amino acid sequence is detailed in Fig. S2. MOMP structure was drawn based on data from published work [25, 62].