{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:22:08Z","timestamp":1787962928026,"version":"build-2784847793"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,2,17]],"date-time":"2025-02-17T00:00:00Z","timestamp":1739750400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,4,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Objectives<\/jats:title>\n                  <jats:p>To survey genetic markers of potential antimicrobial resistance (AMR) to macrolides and fluoroquinolones among Chlamydia trachomatis\u2013positive samples from the collection of the Portuguese National Reference Laboratory for Sexually Transmitted Infections (STIs), and explore a multiplex PCR approach coupled with NGS to provide complementary information regarding a strain\u2019s genomic backbone.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>A total of 502 C. trachomatis\u2013positive samples, mostly anorectal exudates, were subjected to PCR and sequencing of five targets, including loci potentially driving AMR (23S rRNA, gyrA and parC) and loci potentially informative about a strain\u2019s genomic backbone with emphasis on differentiation of lymphogranuloma venereum (LGV)\/non-LGV and L2\/L2b (a 9\u2005bp insertion in pmpH, a 74\u2005bp insertion upstream from CT105 and the polymorphic CT442).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>No samples evidenced 23S rRNA mutations recognizably linked to macrolide resistance. Three samples harboured the Ser83Ile mutation in GyrA putatively driving fluoroquinolone resistance: two recombinant L2-L2b\/D-Da (0.4%) and one L2 (0.2%). The screened regions in pmpH, upstream CT105 and CT442 were fully concordant with LGV\/non-LGV differentiation. As expected, the pmpH L2b-specific genetic trait locus was detected in all L2b and recombinant L2-L2b\/D-Da ompA genotypes, but also in 96.0% of L2 specimens, which also likely possess an L2b genomic backbone. The insertion upstream from CT105 exhibited full LGV specificity, constituting a promising target for the development of rapid LGV diagnostic assays.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This study contributes to enhancing the knowledge of C. trachomatis molecular epidemiology, suggesting that the known genetic determinants of AMR are not disseminated in clinical C. trachomatis strains, and presents an exploratory approach that can be suitable for LGV\/non-LGV and L2\/L2b genomic background differentiation.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jac\/dkaf036","type":"journal-article","created":{"date-parts":[[2025,1,29]],"date-time":"2025-01-29T04:26:38Z","timestamp":1738124798000},"page":"1072-1079","source":"Crossref","is-referenced-by-count":4,"title":["Surveying genetic markers of antibiotic resistance and genomic background in <i>Chlamydia trachomatis<\/i>: insights from a multiplex NGS-based approach in clinical strains from Portugal"],"prefix":"10.1093","volume":"80","author":[{"given":"Zohra","family":"Lodhia","sequence":"first","affiliation":[{"name":"National Reference Laboratory (NRL) for Sexually Transmitted Infections (STI), Department of Infectious Diseases, National Institute of Health (Instituto Nacional de Sa\u00fade Doutor Ricardo Jorge, INSA, IP) , Lisbon ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Costa Da Silva","sequence":"additional","affiliation":[{"name":"National Reference Laboratory (NRL) for Sexually Transmitted Infections (STI), Department of Infectious Diseases, National Institute of Health (Instituto Nacional de Sa\u00fade Doutor Ricardo Jorge, INSA, IP) , Lisbon ,","place":["Portugal"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristina","family":"Correia","sequence":"additional","affiliation":[{"name":"National 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