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.

Whole-Genome Enrichment and Sequencing ofChlamydia trachomatisDirectly from Patient Clinical Vaginal and Rectal Swabs

“…Further, the detection of recombinant ompA, a known hotspot for recombination in the C. trachomatis genome, in these samples as part of an approximate 12kb exchange could have only been identified by WGS and not by Sanger sequencing alone, highlighting the genetic resolution achieved in this study to understand the evolution of contemporary C. trachomatis strains 40,43,55 . Some studies have reported recombinant forms of both ompA and pmpH, and tracking these and additional known recombinant variants may inform the field on the dynamics of current transmission networks and C. trachomatis tropism in general 9,53,79 . With that said, the high rates of recombination and limited genetic diversity within C. trachomatis strains indicates the need to include a large number of loci dispersed throughout the genome to circumvent false negativity of clinical strain typing, which can now be efficiently achieved by sequencing the whole genome.…”

“…Further, due to low genetic resolution, these methods fail to demonstrate precise inter-and intra-strain recombination events across the genome that contribute to strain diversity [40][41][42][43][44] . Recombination has been important in creating emerging strains of C. trachomatis such as L2b among MSM in many countries of the world and recombinant strains L2/D (termed L2c) and L2b/D-Da in the U.S. and Portugal, respectively 28,[40][41][42][43][44][45][46][47] .…”

“…trachomatis enrichment from rectal samples 53 . This RNA bait methodology has therefore been used to understand genomic diversity in circulating C. trachomatis ocular, urogenital and LGV lineages from clinical specimens but with varying success [53][54][55][56][57] .…”

Reduction of non-typeable results using a plasmid oriented Lymfogranuloma venereum PCR for typing of Chlamydia trachomatis positive samples

“…This was due to a CT strain in which part of the D/Da ompA gene was integrated by recombination in the L2b ompA gene in an L2 background CT genome. The variant LGV strain caused symptoms and was correctly diagnosed using another LGV typing test that targeted the pmpH gene [30]. We tested DNA from this recombinant ompA LGV strain and were able to detect <50 copies/μL, showing that the pgp3 LGV PCR is also able to detect this recombinant strain.…”

“…This strain was named the 'Swedish variant' since it was predominantly found in Sweden [28,29]. Recently Borges et al (2019) reported that some LGV strains were missed by using only ompA typing of CT in Portugal. This was due to a CT strain in which part of the D/Da ompA gene was integrated by recombination in the L2b ompA gene in an L2 background CT genome.…”