{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T01:39:12Z","timestamp":1760060352604,"version":"build-2065373602"},"reference-count":33,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T00:00:00Z","timestamp":1755820800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Instituto Nacional de Medicina Legal e Ci\u00eancias Forenses, Portugal"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Sexual assault is a global public health and human rights concern, with serious physical, psychological and reproductive consequences for survivors. Among these, sexually transmitted infections are particularly relevant due to their frequently asymptomatic nature and potential for long-term complications. The detection of sexually transmitted infections in forensic settings is crucial for clinical management of victims and for evidentiary support in forensic sexual crimes investigations. This study aimed to evaluate the applicability of real-time polymerase chain reaction for detecting Chlamydia trachomatis, Trichomonas vaginalis, Neisseria gonorrhoeae, and Treponema pallidum in biological samples collected from victims of sexual assault and stored under routine forensic conditions, in some cases, for up to 18 years. A total of 231 swabs from 116 individuals collected between 2004 and 2017 were analysed using real-time PCR with pathogen-specific primers and fluorescent probes. The analysis revealed 13 positive samples of T. vaginalis (5.6%) and 11 of C. trachomatis (4.8%). No positive results were obtained for N. gonorrhoeae or T. pallidum. These findings demonstrate the usefulness of real-time polymerase chain reaction for detecting sexually transmitted infections in long-term preserved forensic samples. Moreover, the ability to identify pathogen DNA in archived samples highlights the potential role of molecular diagnostics in the retrospective investigation of sexual crimes, including cold cases. It underscores the value of molecular methods as a complementary tool in forensic proceedings and survivor care.<\/jats:p>","DOI":"10.3390\/ijms26178124","type":"journal-article","created":{"date-parts":[[2025,8,22]],"date-time":"2025-08-22T12:31:26Z","timestamp":1755865886000},"page":"8124","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Sexually Transmitted Infections: Usefulness of Molecular Methods for Microorganism Detection in Stored Sexual Assault Samples"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6542-4256","authenticated-orcid":false,"given":"Laura","family":"Cain\u00e9","sequence":"first","affiliation":[{"name":"National Institute of Legal Medicine and Forensic Sciences, I.P., Centre Branch, 3000-548 Coimbra, Portugal"},{"name":"Faculty of Medicine, Porto University, 4200-319 Porto, Portugal"},{"name":"LAQV&REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-9384-8088","authenticated-orcid":false,"given":"Ana","family":"Eira","sequence":"additional","affiliation":[{"name":"National Institute of Legal Medicine and Forensic Sciences, I.P., Centre Branch, 3000-548 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7593-1059","authenticated-orcid":false,"given":"Jennifer","family":"Fadoni","sequence":"additional","affiliation":[{"name":"LAQV&REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"},{"name":"National Institute of Legal Medicine and Forensic Sciences, I.P., North Branch, 4050-202 Porto, Portugal"}]},{"given":"Magda","family":"Franco","sequence":"additional","affiliation":[{"name":"National Institute of Legal Medicine and Forensic Sciences, I.P., Centre Branch, 3000-548 Coimbra, Portugal"}]},{"given":"Helena","family":"Correia Dias","sequence":"additional","affiliation":[{"name":"National Institute of Legal Medicine and Forensic Sciences, I.P., Centre Branch, 3000-548 Coimbra, Portugal"},{"name":"Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal"},{"name":"Laboratory of Forensic Anthropology, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7506-4426","authenticated-orcid":false,"given":"Ant\u00f3nio","family":"Amorim","sequence":"additional","affiliation":[{"name":"National Institute of Legal Medicine and Forensic Sciences, I.P., Centre Branch, 3000-548 Coimbra, Portugal"},{"name":"LAQV&REQUIMTE, Laboratory of Applied Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal"},{"name":"Faculty of Sciences, Lisbon University, 1749-016 Lisboa, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2025,8,22]]},"reference":[{"key":"ref_1","unstructured":"World Health Organisation (2025, August 04). Sexually Transmitted Infections. Available online: https:\/\/www.who.int\/data\/gho\/data\/themes\/topics\/global-and-regional-sti-estimates."},{"key":"ref_2","first-page":"168","article-title":"Definitions and Epidemiology Sexual Assault of Women","volume":"103","author":"Farahi","year":"2021","journal-title":"Am. Fam. Physician"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Sigurdardottir, S., and Halldorsdottir, S. (2021). Persistent suffering: The serious consequences of sexual violence against women and girls, their search for inner healing and the significance of the #metoo movement. Int. J. Environ. Res. Public Health, 18.","DOI":"10.3390\/ijerph18041849"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e235","DOI":"10.1016\/S1473-3099(17)30310-9","article-title":"Sexually transmitted infections: Challenges ahead","volume":"17","author":"Unemo","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Fasciana, T., Capra, G., Lipari, D., Firenze, A., and Giammanco, A. (2022). Sexually Transmitted Diseases: Diagnosis and Control. Int. J. Environ. Res. Public Health, 19.","DOI":"10.3390\/ijerph19095293"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.yfpn.2024.02.002","article-title":"Sexually Transmitted Infections Update","volume":"6","author":"Pair","year":"2024","journal-title":"Adv. Fam. Pract. Nurs."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1","DOI":"10.5101\/nbe.v2i1.p1-7","article-title":"Rapid Whole Blood Bioassays using Microwave-Accelerated Metal-Enhanced Fluorescence","volume":"2","author":"Aslan","year":"2010","journal-title":"Nano Biomed. Eng."},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Rodrigues, R., Sousa, C., and Vale, N. (2022). Chlamydia trachomatis as a Current Health Problem: Challenges and Opportunities. Diagnostics, 12.","DOI":"10.3390\/diagnostics12081795"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1128\/CMR.11.2.300","article-title":"Clinical and microbiological aspects of Trichomonas vaginalis","volume":"11","author":"Petrin","year":"1998","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1007\/s15010-015-0860-0","article-title":"Trichomonas vaginalis: Pathogenicity and potential role in human reproductive failure","volume":"44","author":"Mielczarek","year":"2016","journal-title":"Infection"},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Rogstad, K.E. (2024). Sexually Transmitted Infections Following Sexual Assault. Forensic and Legal Medicine: Clinical and Pathological Aspects, CRC Press.","DOI":"10.1201\/9781003138754-85"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"365674","DOI":"10.1155\/2015\/365674","article-title":"Biological Evidence Management for DNA Analysis in Cases of Sexual Assault","volume":"2015","author":"Silva","year":"2015","journal-title":"Sci. World J."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1016\/j.scijus.2022.09.005","article-title":"Novel recovery methods for biological materials in cases of alleged sexual assault: A word of caution","volume":"62","author":"Murphy","year":"2022","journal-title":"Sci. Justice"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.bpobgyn.2012.08.020","article-title":"The forensic aspects of sexual violence","volume":"27","author":"Newton","year":"2013","journal-title":"Best Pract. Res. Clin. Obstet. Gynaecol."},{"key":"ref_15","unstructured":"C\u0103t\u0103lin, M., Andrei, A., and Mitra\u015fca, O. (2025, April 12). Modern Methods of Collection and Preservation of Biological Evidence for Human Identification by DNA Analysis. Available online: https:\/\/www.abacusdiagnostics.com\/Modern_Methods_of_Collection.pdf."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Artika, I.M., Dewi, Y.P., Nainggolan, I.M., Siregar, J.E., and Antonjaya, U. (2022). Real-Time Polymerase Chain Reaction: Current Techniques, Applications, and Role in COVID-19 Diagnosis. Genes, 13.","DOI":"10.3390\/genes13122387"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1292","DOI":"10.1093\/nar\/30.6.1292","article-title":"Real-time PCR in virology","volume":"30","author":"Mackay","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"ref_18","unstructured":"Sachs, C.J., Ladd, M., and Thomas, B. (2025). Sexual Assault Infectious Disease Prophylaxis. [Updated 2023 September 9]. StatPearls [Internet], StatPearls Publishing. Available online: https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK482239\/."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Kebbi-Beghdadi, C., Aeby, S., Baud, D., and Greub, G. (2022). Evaluation of a Multiplex Real-Time PCR Assay for Detecting Chlamydia trachomatis in Vaginal Samples. Diagnostics, 12.","DOI":"10.3390\/diagnostics12051141"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.mimet.2006.08.002","article-title":"Trichomonas vaginalis detection using real-time TaqMan PCR","volume":"68","author":"Schirm","year":"2007","journal-title":"J. Microbiol. Methods"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1080\/10647440500068248","article-title":"Real-time PCR improves detection of Trichomonas vaginalis infection compared with culture using self-collected vaginal swabs","volume":"13","author":"Caliendo","year":"2005","journal-title":"Infect. Dis. Obstet. Gynecol."},{"key":"ref_22","first-page":"7","article-title":"Trichomoniasis: A brief review of diagnostic methods and our experience with real-time PCR for detecting infection","volume":"24","year":"2015","journal-title":"Acta Dermatovenerol. Alp. Pannonica et Adriat."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1007\/s00580-011-1402-5","article-title":"Real-time PCR improve detection of Trichomonas vaginalis compared to conventional techniques","volume":"22","year":"2013","journal-title":"Comp. Clin. Pathol."},{"key":"ref_24","first-page":"252","article-title":"Diagnostic efficacy of a real time-PCR assay for Chlamydia trachomatis infection in infertile women in north India","volume":"140","author":"Dhawan","year":"2014","journal-title":"Indian J. Med. Res."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"254","DOI":"10.1080\/01443615.2020.1736014","article-title":"Prevalence of Neisseria gonorrhoeae and Trichomonas vaginalis in Portuguese women of childbearing age","volume":"41","author":"Silva","year":"2020","journal-title":"J. Obstet. Gynaecol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"778","DOI":"10.1111\/j.1600-051X.2005.00740.x","article-title":"Comparison of culture and real-time PCR for detection and quantification of five putative periodontopathogenic bacteria in subgingival plaque samples","volume":"32","author":"Koltzscher","year":"2005","journal-title":"J. Clin. Periodontol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"598","DOI":"10.5897\/AJMR2013.6459","article-title":"Comparison of three DNA extraction methods for polymerase chain reaction (PCR) analysis of bacterial genomic DNA","volume":"8","author":"Omar","year":"2014","journal-title":"Afr. J. Microbiol. Res."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Uwiringiyeyezu, T., El Khalfi, B., Saile, R., Belhachmi, J., and Soukri, A. (2022). Comparability of CMV DNA Extraction Methods and Validation of Viral Load. Methods Protoc., 5.","DOI":"10.3390\/mps5010006"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1111\/j.1198-743X.2004.00722.x","article-title":"Real-time PCR in the microbiology laboratory","volume":"10","author":"Mackay","year":"2004","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Sellami, H., Znazen, A., Sellami, A., Mnif, H., Louati, N., Ben Zarrouk, S., Keskes, L., Rebai, T., Gdoura, R., and Hammami, A. (2014). Molecular detection of Chlamydia trachomatis and other sexually transmitted bacteria in semen of male partners of infertile couples in Tunisia: The effect on semen parameters and spermatozoa apoptosis markers. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0098903"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1128\/JCM.00720-09","article-title":"Clinical value of Treponema pallidum real-time PCR for diagnosis of syphilis","volume":"48","author":"Heymans","year":"2010","journal-title":"J. Clin. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1233","DOI":"10.1111\/j.1469-0691.2006.01566.x","article-title":"Specific and sensitive diagnosis of syphilis using a real-time PCR for Treponema pallidum","volume":"12","author":"Koek","year":"2006","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.3201\/eid2608.201246","article-title":"US CDC Real-Time Reverse Transcription PCR Panel for Detection of Severe Acute Respiratory Syndrome Coronavirus 2","volume":"26","author":"Lu","year":"2020","journal-title":"Emerg. Infect. Dis."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/17\/8124\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:33:35Z","timestamp":1760034815000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/26\/17\/8124"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,22]]},"references-count":33,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2025,9]]}},"alternative-id":["ijms26178124"],"URL":"https:\/\/doi.org\/10.3390\/ijms26178124","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2025,8,22]]}}}