In measurement of disease burden, rates are superior to case counts as they account for the underlying population at risk and provide a measure of disease intensity in a sub-population. Often MSM specific STI rates are difficult to calculate given that population estimates of MSM are often unavailable. Here we report on MSM and non-MSM racial/ethnic specific rates of STIs in San Francisco. Between 1999 and 2008, rates of MSM chlamydia and gonorrhea increased, while non-MSM rates of these STIs remained largely stable. These increases in STIs are consistent with previous reports in San Francisco and other cities [11, 14]. African-American, Hispanic, and White MSM had similar rates of chlamydia and gonorrhea while Asian/Pacific Islander MSM had the lowest rates during the study period. The MSM/non-MSM ratio was lowest for African-American men and highest for White and Asian/Pacific Islander men. While African-American MSM had comparable rates of chlamydia and gonorrhea to other racial/ethnic groups, African American non-MSM had rates up to five times higher than these groups.

Reducing racial disparities is a national public health priority. STIs, specifically gonorrhea, represent some of the largest racial/ethnic disparities among reportable conditions [4]. Our data highlight not only the disparities that exist across race and ethnicity, but also among subpopulations of MSM and non-MSM. These data identify important trends in chlamydia and gonorrhea morbidity that are often masked when all male morbidity is examined without regard to sexual behavior.

Furthermore, the data presented here suggest that the disparities paradigm be expanded to include sexual behavior. For all racial/ethnic groups, MSM had significantly higher rates of chlamydia and gonorrhea compared to non-MSM. In San Francisco, MSM are significantly burdened with STIs and these disparities warrant public health attention and resources.

San Francisco STD Prevention and Control Services recommends that all sexually active MSM be screened for syphilis, chlamydia, and gonorrhea every three to six months. In San Francisco, routine screening for gonorrhea and chlamydia at the urogenital, pharyngeal, and rectal sites is widely available for MSM and has been shown to lead to significantly higher rates of gonorrhea and chlamydia diagnoses, primarily through diagnosis of asymptomatic infections [15, 16]. After increased rates of syphilis were reported in 2001 and 2002, there have been multiple public health campaigns for routine STI screening of MSM which may partially explain the increased percentage of cases diagnosed in primary care offices during our study period. Additionally, San Francisco STD Prevention and Control Services has worked over the prior decade to ensure that STD screening is incorporated into routine HIV care for MSM in San Francisco.

Based on lower sexual risk behavior such screening is not routinely indicated in non-MSM and the higher rate of STIs among African-American non-MSM in San Francisco, while previously documented, is not well understood. Although several studies have shown that African-American MSM are less likely compared to other racial groups to self-identify as "gay" or "bisexual" we used data on gender of sex partners and not sexual identity to define MSM [17–19]. In addition, we found the percentage of African-American men classified as MSM was similar to that of white and Hispanic men, which would not support misclassification of sexual behavior as a sufficient explanation. Sexual networks, social context, and other contextual factors have been identified as important factors in racial STI disparities in other regions of the US [20–23]. It is unclear how these more macro level factors may function differently (if at all) between MSM and non-MSM.

Our analysis has several limitations worth noting. Our STI case rates and MSM/non-MSM ratios are dependent on estimation of population sizes for both MSM and non-MSM in San Francisco. Using the National NHBS and 2000 census data, we calculated a midpoint estimate and assume that the size of each population is relatively stable over the time period of analysis (1999-2008). Comparison of the 2000 census data to the 2006-2008 American Community Survey data for San Francisco County did not reveal any significant demographic shifts [24]. Furthermore, the NHBS sample size of MSM of color was too small to make meaningful comparisons between groups of MSM [25–29]. In the beginning of our study period, up to 81% of chlamydia cases and 70% of gonorrhea cases were diagnosed in the public STI clinic. There are data that STI rates among MSM attending public STI clinics are higher than other clinical sites which could lead to an over estimation of STI rates [30, 31]. However, we believe that the gonorrhea and chlamydia surveillance systems in San Francisco are robust, as electronic laboratory reporting has been integrated into routine surveillance activities. Additionally, our definition of MSM was considered fixed. If a male patient reported male partners in 1990 during an STD clinic visit or public health disease control interview, or on a morbidity report, all subsequent morbidity was classified as MSM. As a result, men who have not had recent male exposures would be misclassified as MSM. Finally, San Francisco is a unique urban environment and is residence to a large population of MSM. Therefore, these findings may have limited generalizibility. However, we believe the methods we employed could be used in other health jurisdictions to develop locally valuable measures of disease burden and disparity.