Prevalence, antimicrobial resistance, and diagnostic performance of lower genital tract infections in women in Antananarivo, Madagascar

Lower genital tract infections (LGTIs) are a major public health concern in sub-Saharan Africa, with serious implications for women’s reproductive health. In Madagascar, data on aetiological profiles, antimicrobial resistance (AMR), and diagnostic performance remain scarce. This study aimed to determine the prevalence, aetiology, antimicrobial resistance patterns, and diagnostic performance of direct microscopy for lower genital tract infections among women in Antananarivo. We conducted a retrospective cross-sectional study at the microbiology laboratory of CHU-JRA, Antananarivo, including all cervico-vaginal swabs from women between January 2021 and December 2023. LGTI was defined as a positive culture and/or detection of Trichomonas vaginalis by direct microscopy. Logistic regression identified associated factors. Diagnostic performance of direct microscopy (yeast, clue cells, leukocytes) was assessed against culture as the gold standard. Among 495 records, the prevalence of LGTI was 53.1% (263/495). The proportion of positive cases diagnosed in 2023 (48.3%) was higher than in 2021 (23.2%; adjusted OR = 2.1, 95% CI 1.4–3.3, p < 0.001). Women under 25 years had higher odds of infection (aOR = 2.1, 95% CI 1.3–3.2, p = 0.001). The most frequent pathogens were Gardnerella vaginalis (11.5%), Candida albicans (7.5%), and coagulase-negative Staphylococcus (6.3%). Co-infections occurred in 20.5% of cases. Direct microscopy showed high specificity (81.5–95.3%) but low sensitivity (33.5–52.1%) for all markers. High AMR was observed, particularly in E. coli against tetracycline (86.7%) and cotrimoxazole (80.0%). LGTIs are highly prevalent in Antananarivo, especially among young women. The high levels of AMR challenge empirical treatment, while the limited sensitivity of microscopy underscores the need for better diagnostic tools. Strengthening antimicrobial stewardship and updating national guidelines are urgently required.