Background Prevalence of Mycoplasma genitalium is higher in vulnerable populations of women in low-resource settings; predictors for infection, however, are not well understood. This study aimed to determine the prevalence of Mycoplasma genitalium and its associated risk factors among female sex workers in Nairobi, Kenya.

Methods A total of 350 FSW aged 18–50 years old participated in this cross-sectional study from 2009 to 2011. A questionnaire was administered at baseline to obtain information on sociodemographics and sexual behaviours. Physician-collected cervical samples were tested for M. genitalium mRNA and other sexually transmitted infections using transcription-mediated amplification-based APTIMA assays (Hologic/Gen-Probe Inc.). Cervical cytology was conducted using physician-collected specimens and classified according to the Bethesda criteria.

Results The median age in the study was 28 (range: 18–48). Prevalence of M. genitalium was 12.7%. In the multivariate model, younger age was associated with a higher risk of M. genitalium, whereby women greater than 30 years old were less likely to have infection (OR [95% confidence interval] = 0.3 [0.1.0.9] versus women less than 30 years old). Women who reported using condoms at least “most of the time” were more likely to be infected with M. genitalium than women who reported using condoms “half the time or less.” Relative to those with normal cytology, women with cytology results of either high-grade squamous intraepithelial lesions or squamous cell carcinoma had a higher prevalence of M. genitalium (23.1% vs. 16.2%), although effect estimates were relatively imprecise.

Conclusions Younger women within a vulnerable population appear to be at greater risk of M. genitalium infection. The reverse association between condom use and M. genitalium may be due to social desirability bias. Further investigation of the association between M. genitalium infection and high-grade cervical cytology is warranted.