Prevalence of Chlamydia trachomatis, associated reproductive factors, and comparison of molecular specimen types among pregnant women attending a tertiary hospital in Malaysia

Abstract Objectives Genital Chlamydia trachomatis infection during pregnancy is frequently asymptomatic and is associated with adverse maternal and perinatal outcomes. Chlamydia trachomatis screening—defined here as nucleic acid amplification test (NAAT)–based testing of pregnant women to identify largely asymptomatic infection—is essential for preventing adverse maternal and perinatal outcomes. In Malaysia, data on the burden of infection, associated risk factors, and optimal diagnostic specimen types in pregnancy remain limited. Methods This cross-sectional study evaluated the prevalence, risk factors, and diagnostic performance of different specimen types for C. trachomatis detection among pregnant women in Malaysia. A total of 100 pregnant women were recruited at a tertiary hospital, and endocervical, vaginal, and first-void urine samples were analyzed using nested polymerase chain reaction (PCR) targeting the major outer membrane protein (MOMP) gene. In the absence of a single definitive diagnostic test, a composite molecular reference conclusion was used to classify infection status. Results Thirty-six participants were classified as infected, yielding a prevalence of 36%. A history of pregnancy loss was significantly associated with current infection (OR 2.72, p = 0.03). Using a composite reference conclusion as the gold standard, endocervical samples demonstrated the highest sensitivity (61.1%), followed by vaginal (47.2%) and urine specimens (41.7%). Pairwise agreement between specimen types was fair (κ = 0.27–0.33), with no statistically significant directional differences. Conclusion This study demonstrates a substantial burden of undiagnosed C. trachomatis infection among pregnant women attending a tertiary care setting in Malaysia and identifies prior pregnancy loss as a potential risk marker for infection. Endocervical sampling showed the highest diagnostic sensitivity, although vaginal sampling represents a feasible alternative where self-collection may improve screening uptake. Larger, multicenter studies are needed to confirm these findings and to inform antenatal screening strategies in similar settings.