INTRODUCTION Human papillomaviruses and Chlamydia trachomatis are the most frequent causes of sexually transmitted infections. Although the association between some human papillomavirus genotypes and cervical cancer has been demonstrated and Chlamydia trachomatis infection is the most common cause of female infertility, Cuba has no national baseline studies on the circulation and co-circulation of these agents, the synergistic effect of which may be a risk factor for occurrence and development of precancerous cervical lesions. Additionally, few local studies have examined risk factors for infection.

OBJECTIVE Determine the frequency of infection by human papillomavirus and Chlamydia trachomatis and their association with sociodemographic, clinical and epidemiological variables in women seeking routine Pap smears or other medical services at the primary care level in Cuba.

METHODS A cross-sectional study was conducted among 500 women aged 16–67 years (100 from Havana, 200 from Villa Clara and 200 from Holguín Provinces, Cuba), from August through December 2015. Chlamydia trachomatis infection was detected by real-time polymerase chain reaction and 35 genotypes of human papillomavirus by low-density microarray. We then examined the association of infection with sociodemographic, clinical and epidemiological variables.

RESULTS Human papillomavirus was detected in 14.8% (74/500) of the women. Of the 29 genotypes identified, 79.7% (59/74) were oncogenic high-risk types. Type 16 was the most frequently identified (23%; 17/74), followed by type 31 (10.8%; 8/74) and then by types 33, 53, 61 and 66 in equal proportions (8.1%; 6/74). Infection frequency was greater in women aged ≤25 years (38.8%; 31/80), students (46.7% 7/15), single (23.0%; 40/174) and among those who reported having more than 3 sexual partners in the last 2 years (41.0%; 17/41). Differences were found among provinces for circulating genotypes and infection-related variables. Human papillomavirus infection from genotypes 16, 31, 33, 53, 61, 66, 68 and 89 was associated with the 7.9% (30/382) of women who had positive Pap tests. Infection from Chlamydia trachomatis was positive in 1% (5/500) of women, all aged ≤25 years. Coinfection by Chlamydia trachomatis and HPV was found in one woman infected with human papillomavirus genotype 61.

CONCLUSIONS Frequency of human papillomavirus is high in the three Cuban provinces studied, with greater frequency of genotype 16 and other oncogenic high-risk types. For both agents, infection is more frequent in young women and adolescents. Positive Pap tests are frequently associated with HPV infection. Prevalence findings from this study could be used as a baseline for future research or interventions.

KEYWORDS Human papillomavirus, microarrays, genotypes, Chlamydia trachomatis, real-time polymerase chain reaction, women, Cuba