Hypervirulent Chlamydia trachomatis Clinical Strain Is a Recombinant between Lymphogranuloma Venereum (L ₂ ) and D Lineages

Abstract

Chlamydia trachomatis is an obligate intracellular bacterium that causes a diversity of severe and debilitating diseases worldwide. Sporadic and ongoing outbreaks of lymphogranuloma venereum (LGV) strains among men who have sex with men (MSM) support the need for research on virulence factors associated with these organisms. Previous analyses have been limited to single genes or genomes of laboratory-adapted reference strain L2/434 and outbreak strain L2b/UCH-1/proctitis. We characterized an unusual LGV strain, termed L2c, isolated from an MSM with severe hemorrhagic proctitis. L2c developed nonfusing, grape-like inclusions and a cytotoxic phenotype in culture, unlike the LGV strains described to date. Deep genome sequencing revealed that L2c was a recombinant of L2 and D strains with conserved clustered regions of genetic exchange, including a 78-kb region and a partial, yet functional, toxin gene that was lost with prolonged culture. Indels (insertions/deletions) were discovered in an ftsK gene promoter and in the tarp and hctB genes, which encode key proteins involved in replication, inclusion formation, and histone H1-like protein activity, respectively. Analyses suggest that these indels affect gene and/or protein function, supporting the in vitro and disease phenotypes. While recombination has been known to occur for C. trachomatis based on gene sequence analyses, we provide the first whole-genome evidence for recombination between a virulent, invasive LGV strain and a noninvasive common urogenital strain. Given the lack of a genetic system for producing stable C. trachomatis mutants, identifying naturally occurring recombinants can clarify gene function and provide opportunities for discovering avenues for genomic manipulation.

Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen

“…The L2C genome inherited a serotype D region encoding a partial yet functional toxin that might contribute to the hypervirulent phenotype associated with this strain and that is notably absent from other sequenced LGV strains. An increasing number of LGV-causing serovars (L1, L2, L3, L2a, L2b, and L2C) have been identified (122)(123)(124). These strains predominantly infect monocytes and macrophages and disseminate to inguinal lymph nodes, leading to their classification as a biovar (LGV) distinct from the noninvasive urogenital and ocular serovars (trachoma biovars) (125).…”

2013 European guideline on the management of lymphogranuloma venereum

“…A new LGV variant originating from a recombination of L2 and D C. trachomatis lineages has been reported but the extent of transmission of this hybrid organism within the community needs further investigation. 3 In contrast to serovars A-K which remain confined to the mucosa, serovar L strains are invasive organisms that disseminate via underlying connective tissue and spread to regional lymph nodes. 2 Worldwide, LGV is thought to account for 2-10% of genito-ulcerative disease in areas such as India and Africa.…”

Chlamydial Intracellular Survival Strategies

“…Such in vivo recombinant strains can have significant clinical implications. For instance, a hypervirulent C. trachomatis strain (L 2 c) isolated from a patient with severe hemorrhagic proctitis represents a recombination event between serovar L2 and serovar D strains (Somboonna et al 2011).…”