Chlamydia trachomatis genomes from rectal samples: description of new clade comprising ompA-genotype L4 from Argentina

Whole genome analysis has provided us with insights into the evolution of Chlamydia trachomatis and recently into circulating strains which cause lymphogranuloma venereum (LGV). A large LGV outbreak of a new ompA-genotype, L2b, was first reported in Europe in the early 2000s, primarily affecting men who have sex with men (MSM), and then expanded globally. More recent work shows this outbreak diversifying into variants of described ompA-genotypes, with the same L2b genomic backbone. This study extends the investigation of LGV cases to Argentina and Finland. In 2017, an LGV outbreak was described in Argentina characterized by distinct genomic features shown by both ompA-genotyping and MLST analysis. We have obtained whole genome sequences from cultured isolates and clinical samples via SureSelect (Agilent) target enrichment. Based on ompA and phylogenetic analyses, we describe further diversity within the ompA-genotype L2b clade, illustrating the transmission dynamics in both Argentina and Finland. A key finding is that of a novel clade of Argentinian samples, characterised by a proposed new ompA-genotype L4. Additionally, we present the genome sequence of a non-LGV strain associated with anorectal proctitis. These findings contribute to the investigation of LGV evolution, particularly with the presence of the novel L4 lineage, and provide insights into genomic diversity and transmission dynamics of C. trachomatis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/624510v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@3bd641org.highwire.dtl.DTLVardef@6f6866org.highwire.dtl.DTLVardef@2f1b6eorg.highwire.dtl.DTLVardef@b2137a_HPS_FORMAT_FIGEXP M_FIG C_FIG Impact statementThe phylogeny of C. trachomatis has been described in several publications and has been clear for a decade. The evolution of this STI in the intervening years also informs a great deal about the transmission opportunities and selective pressures that the intracellular bacterium is under. Through genome sequencing, also directly from clinical samples, we provide the first LGV genomes from Argentina and Finland, and describe further evidence of global circulation of the ompA-genotype L2b lineage. We describe a fully novel lineage of LGV C. trachomatis, from Argentina, proposed as ompA-genotype L4. We also find evidence of a strain causing proctitis from the urogenital lineage. Together, these provide significant new findings in the investigation of C. trachomatis. Data summaryAll illumina sequence data, with human read data removed using Hostile (1) and KrakenTools (https://github.com/jenniferlu717/KrakenTools), is deposited with the European Nucleotide Archive (ENA) under project number PRJEB72167.