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In Japan it was reported that about 9% of sexually active female teenagers had Chlamydia trachomatis. Most of them were asymptomatic, which may lead to continuing spread of the infection. Like C trachomatis, Mycoplasma genitalium is a pathogen in male non-gonococcal urethritis. However, few studies of the prevalence of M genitalium in the general population have been reported. The objective of this study was to determine the prevalence of M genitalium infection among younger females and to determine risk factors for this infection.The study was conducted between October 2005 and January 2006 using first voided urine specimens and questionnaires from female students of three vocational schools in the Miyazaki prefecture, Japan. C trachomatis was detected with Amplicor™ PCR. M genitalium was detected with inhibitor controlled real-time TaqMan™ PCR detecting the MgPa adhesion gene and with a PCR detecting the 16S rRNA. Risk factors associated with infection of M genitalium or C trachomatis were analysed with Fisher’s exact test.Among 298 female, 249 (84%) had had experience of sexual intercourse. The prevalence of M genitalium was 2.8% (95% CI 0.76% to 4.86%) and the prevalence of C trachomatis was 8.8% (95% CI 5.31% to 12.36%).The risk factors of infection with M genitalium were more than five lifetime sexual partners and co-infection with C trachomatis.