Distribution of Chlamydia trachomatis ompA-genotypes over three decades (1990-2021) in Portugal - ompA sequence datasets

This repository includes sequence data from the study: "Distribution of Chlamydia trachomatis ompA-genotypes over three decades (1990-2021) in Portugal”, conducted by the National Reference Laboratory (NRL) for Sexually Transmitted Infections (STI), National Institute of Health Doutor Ricardo Jorge (INSA), Portugal.

The NRL performs molecular characterization (namely ompA-genotyping) of all C. trachomatis positive samples that receives. C. trachomatis ompA-genotyping technique was adapted from Lan, et al. [1]. Briefly, PCR and nested PCR were performed using primers NLO and NRO, and primers PCTM3 and SERO2A, respectively, as previously described [2]. Partial nucleotide sequencing of the ~1010 bp PCR product was performed with BigDye terminator v1.1 and capillary sequencing (3130XL Genetic Analyzer; Applied Biosystems),  using either two primers, as described elsewhere [2,3,4], or one primer (since ~2018), as described elsewhere [5]. Until 2018, LaserGene (DNASTAR) and MEGA (http://www.megasoftware.net) software were applied for sequence curation, alignment and phylogenetic reconstructions involving multiple reference sequences, as previously described [3]. Since ~2018, ompA genotypes have been determined by BLASTn-based comparison (using the ABRIcate tool [6]) directly from raw Sanger (AB1 format) sequences, with a custom database enrolling reference and variant sequences of all main ompA genotypes (https://github.com/insapathogenomics/ReporType/blob/main/databases/c_trachomatis.fasta) [3, 5, 7, 8], as currently implemented in ReporType (https://github.com/insapathogenomics/ReporType) [8]. When needed, MEGA software is then applied for fine genotype confirmation, namely for L2/L2b discrimination and confirmation of the hybrid ompA-profile of the recombinant L2b/D-Da [5].

This repository includes the following sequence datasets:

Dataset 1 - ompA sequences (curated FASTA) of C. trachomatis positive samples collected between 1991 and ~2018, as described above.

Dataset 2 - ompA sequences (raw Sanger sequences, converted from “ab1” format to FASTA) of C. trachomatis positive samples collected since ~2018 and 2021, as described above.

Note: The associated metadata is described in the Supplementary table 2 of the manuscript. These sequence datasets do not cover genotyped samples for which the ompA sequences were lost over the three decades of the laboratory's historical collection.

References

1. Lan J, Ossewaarde JM, Walboomers JM, Meijer CJ, van den Brule AJ. Improved PCR sensitivity for direct genotyping of Chlamydia trachomatis serovars by using a nested PCR. J Clin Microbiol. 1994;32(2):528-530. doi:10.1128/jcm.32.2.528-530.1994;

2. Gomes JP, Bruno WJ, Borrego MJ, Dean D. Recombination in the genome of Chlamydia trachomatis involving the polymorphic membrane protein C gene relative to ompA and evidence for horizontal gene transfer. J Bacteriol 2004;186:4295–4306;

3. Nunes A, Borrego MJ, Nunes B, Florindo C, Gomes JP. Evolutionary dynamics of ompA, the gene encoding the Chlamydia trachomatis key antigen. J Bacteriol. 2009 Dec;191(23):7182-92. doi: 10.1128/JB.00895-09. Epub 2009 Sep 25. PMID: 19783629; PMCID: PMC2786549;

4. Nunes A, Nogueira PJ, Borrego MJ, Gomes JP. Adaptive evolution of the Chlamydia trachomatis dominant antigen reveals distinct evolutionary scenarios for B- and T-cell epitopes: worldwide survey. PLoS One. 2010 Oct 5;5(10):e13171. doi: 10.1371/journal.pone.0013171. PMID: 20957150; PMCID: PMC2950151.

5. Borges V, Cordeiro D, Salas AI, et al. Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signature. Microb Genom. 2019;5(11):e000313. doi:10.1099/mgen.0.000313;

6. Seemann T. ABRIcate. https://github.com/tseemann/abricate

7 Nunes A, Nogueira PJ, Borrego MJ, Gomes JP. Adaptive evolution of the Chlamydia trachomatis dominant antigen reveals distinct evolutionary scenarios for B- and T-cell epitopes: worldwide survey. PLoS One. 2010 Oct 5;5(10):e13171. doi: 10.1371/journal.pone.0013171. PMID: 20957150; PMCID: PMC2950151.

8. Cruz H, Pinheiro M, Borges V. ReporType: a flexible bioinformatics tool for targeted loci screening and typing of infectious agents (https://github.com/insapathogenomics/ReporType). Int J Mol Sci. 2024;25:3172. https://doi.org/10.3390/ijms25063172