Genotype-Specific Distribution of High-Risk Human Papillomavirus (HPV) and Microbial Co-Detections in HPV-Positive Women from Southern Croatia

Background/Objectives: High-risk human papillomavirus (HPV) is the principal etiological agent of cervical cancer, with distinct genotype-specific oncogenic potential. While HPV type 16 is most frequently implicated in carcinogenesis, the role of other genotypes and their interaction with sexually transmitted infections and cervico-vaginal dysbiosis is gaining recognition. This study aimed to assess the genotype-specific distribution of high-risk HPV among HPV-positive women from Southern Croatia and examine associations with age and co-infections with selected microbial pathogens. Methods: We conducted a retrospective cross-sectional study on 1211 HPV-positive women (out of 3098 tested) from Split and Dalmatia County between 2023 and 2024. Cervico-vaginal swabs were tested using molecular and culture-based methods for 14 high-risk HPV genotypes and several pathogens, including Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, Gardnerella vaginalis, and other microorganisms. In the analysis, each detected HPV genotype was also treated as a distinct line-level observation. Genotypes were grouped by phylogenetic and carcinogenic profiles, and statistical analyses—including chi-square tests and multinomial logistic regression—were performed to evaluate associations with age and co-infections. Results: Among high-risk HPV-positive women, the most frequently detected high-risk HPV genotypes were HPV 16 (23.3%), HPV 31 (22.4%), and HPV 51 (13.5%). Notably, HPV 18 was less prevalent (8.1%) and occurred at a similar frequency to HPV 58 and 68. Although younger age was significantly associated with high-risk HPV positivity (p < 0.001), no significant differences in HPV genotype group distribution were observed between age groups; however, C. trachomatis and Streptococcus agalactiae were significantly more prevalent in women aged ≤29 years (p < 0.001 and p = 0.029, respectively). Multinomial regression revealed that C. trachomatis was negatively associated with 16-related and lower-risk genotypes, while G. vaginalis showed a positive association with 16-related types. Conclusions: There is a complex interplay between high-risk HPV genotypes and microbial co-infections, which means the broader cervico-vaginal microbiome has to be considered in HPV risk assessment. The findings highlight the need for extended genotyping and microbial screening to inform regional prevention strategies.