Spread of a new Chlamydia trachomatis variant from men who have sex with men to the heterosexual population after replacement and recombination in ompA and pmpH genes

Rodríguez-Domínguez, Mario; González-Alba, José Marı́a; Puerta, Teresa; Martínez-García, Laura; Menéndez, Blanca; Romero, Jorge del; Galán, Juan Carlos

doi:10.1016/j.cmi.2017.03.009

Cited by 9 publications

(6 citation statements)

References 21 publications

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“…Further, the identification of ST58 (most common in cases of LGV) in two samples containing genotype D suggests recombination between LGV and genotype D strains, or coinfection with strains of both genotypes. Cases of recombination of LGV with other genotypes have been reported previously in Spain [ 38 , 39 ].…”

Section: Discussionmentioning

confidence: 99%

Genetic Characterization of Non-Lymphogranuloma venereum Chlamydia trachomatis Indicates Distinct Infection Transmission Networks in Spain

Piñeiro

Villa

Salmerón

et al. 2023

IJMS

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Chlamydia trachomatis infection is an important public health problem. Our objective was to assess the dynamics of the transmission of this infection, analysing the distribution of circulating ompA genotypes and multilocus sequence types of C. trachomatis in Spain as a function of clinical and epidemiological variables. During 2018 and 2019, we genetically characterized C. trachomatis in tertiary hospitals in six areas in Spain (Asturias, Barcelona, Gipuzkoa, Mallorca, Seville and Zaragoza), with a catchment population of 3.050 million people. Genotypes and sequence types were obtained using polymerase chain reaction techniques that amplify a fragment of the ompA gene, and five highly variable genes (hctB, CT058, CT144, CT172 and pbpB), respectively. Amplicons were sequenced and phylogenetic analysis was conducted. We obtained genotypes in 636/698 cases (91.1%). Overall and by area, genotype E was the most common (35%). Stratifying by sex, genotypes D and G were more common among men, and genotypes F and I among women (p < 0.05). Genotypes D, G and J were more common in men who have sex with men (MSM) than in men who have sex with women (MSW), in whom the most common genotypes were E and F. The diversity index was higher in sequence typing (0.981) than in genotyping (0.791), and the most common sequence types were ST52 and ST108 in MSM, and ST30, ST148, ST276 and ST327 in MSW. Differences in genotype distribution between geographical areas were attributable to differences in population characteristics. The transmission dynamics varied with sexual behaviour: the predominant genotypes and most frequent sequence types found in MSM were different to those detected in MSW and women.

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Section: Discussionmentioning

confidence: 99%

Genetic Characterization of Non-Lymphogranuloma venereum Chlamydia trachomatis Indicates Distinct Infection Transmission Networks in Spain

Piñeiro

Villa

Salmerón

et al. 2023

IJMS

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“…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.…”

Section: Discussionmentioning

confidence: 99%

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

Bowden

Joseph

Cartee

et al. 2020

Preprint

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Chlamydia trachomatis is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. U.S. cases have been steadily increasing for more than a decade in both the urogenital tract and rectum. C. trachomatis is an obligate intracellular bacterium that is not easily cultured, limiting the capacity for genome studies to understand strain diversity and emergence among various patient populations globally. While Agilent SureSelectXT target-enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival and rectal samples, efficiencies are only 60-80% for >95-100% genome coverage. We therefore re-designed and expanded the RNA bait library to augment enrichment of the organism from clinical samples to improve efficiency. We describe the expanded library, the limit of detection for C. trachomatis genome copy input, and the 100% efficiency and high-resolution of generated genomes where genomic recombination among paired vaginal and rectal specimens from four patients was identified. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, among geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.

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“…Recombination is a driver of C. trachomatis evolution [9,12,31]; clinical isolates with recombinations between LGV and urogenital strains have been described [28,30,32], including a recent L2b-D/Da hybrid strain identified in Portugal, which resulted from a recombination across ompA in an L2b genomic background [30]. Therefore, a plausible hypothesis for this observation of these pmpH-ompA discrepancies is that recombination between the genomes of ompA-genotype L2b and ompA-genotype L2 has occurred.…”

Section: Impact Statementmentioning

confidence: 99%

Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains

et al. 2021

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Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) Chlamydia trachomatis , is caused by strains from the LGV biovar, most commonly represented by ompA-genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (n=321) from eight countries collected between 2011 and 2017 (Spain n=97, Netherlands n=67, Switzerland n=64, Australia n=53, Sweden n=37, Hungary n=31, Czechia n=30, Slovenia n=10) were genotyped for pmpH and ompA variants. All were found to contain the 9 bp insertion in the pmpH gene, previously associated with ompA-genotype L2b. However, analysis of the ompA gene shows ompA-genotype L2b (n=83), ompA-genotype L2 (n=180) and several variants of these (n=52; 12 variant types), as well as other/mixed ompA-genotypes (n=6). To elucidate the genomic diversity, whole genome sequencing (WGS) was performed from selected samples using SureSelect target enrichment, resulting in 42 genomes, covering a diversity of ompA-genotypes and representing most of the countries sampled. A phylogeny of these data clearly shows that these ompA-genotypes derive from an ompA-genotype L2b ancestor, carrying up to eight SNPs per isolate. SNPs within ompA are overrepresented among genomic changes in these samples, each of which results in an amino acid change in the variable domains of OmpA (major outer membrane protein, MOMP). A reversion to ompA-genotype L2 with the L2b genomic backbone is commonly seen. The wide diversity of ompA-genotypes found in these recent LGV samples indicates that this gene is under immunological selection. Our results suggest that the ompA-genotype L2b genomic backbone is the dominant strain circulating and evolving particularly in men who have sex with men (MSM) populations.

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Spread of a new Chlamydia trachomatis variant from men who have sex with men to the heterosexual population after replacement and recombination in ompA and pmpH genes

Cited by 9 publications

References 21 publications

Genetic Characterization of Non-Lymphogranuloma venereum Chlamydia trachomatis Indicates Distinct Infection Transmission Networks in Spain

Genetic Characterization of Non-Lymphogranuloma venereum Chlamydia trachomatis Indicates Distinct Infection Transmission Networks in Spain

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

Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains

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