Narrative Review of Chlamydia trachomatis Culture, Viability Testing, and Sequencing Methods

Chlamydia trachomatis (CT) is the most commonly reported bacterial sexually transmitted infection in the United States and is routinely detected using nucleic acid amplification tests (NAATs). However, its obligate intracellular life cycle creates challenges for culture, viability determination, and antimicrobial susceptibility testing (AST). Despite these challenges, culture remains important for select applications, including strain typing, test-of-cure, sexual assault investigations, and resistance monitoring.

We conducted a systematic literature search across 5 electronic databases using defined terms to identify studies on CT culture methods, viability assays, and molecular or phenotypic approaches for antimicrobial resistance detection. Twenty-nine manuscripts met inclusion criteria and were synthesized narratively.

Our review found limited progress in CT culture techniques over the past decade. While several methods show promise for viability assessment and resistance detection, standardization and widespread implementation remain lacking. Phenotypic AST is restricted to specialized laboratories, and validated genotypic assays are not widely available. These gaps hinder accurate assessment of treatment failure and resistance trends.

The need for CT culture in routine clinical practice is declining, but culture continues to play a role in research, surveillance, and select clinical scenarios. Significant gaps in current technology include the inability to distinguish viable from nonviable organisms and lack of standardized AST protocols and genotypic resistance assays. Future research should prioritize development of clinical viability assays, consensus AST methods, and integrated genomic approaches to improve diagnostics and strengthen surveillance.