This cross-sectional study was undertaken during August 23, 2016–September 27, 2017, at Melbourne Sexual Health Centre (MSHC), the only public sexual health clinic in Melbourne, a city of 4.5 million. MSM >18 years of age who were asymptomatic at both triage and clinician consultations and reported receptive anal sex within the preceding year were eligible to participate. To minimize the impact of this study on clinical and laboratory services, recruitment was restricted to 8 of 49 clinical staff members, who offered the study to consecutive eligible clients. To determine how representative participants were of all asymptomatic MSM attending MSHC, we compared positivity for rectal C. trachomatis and N. gonorrhoeae in recruited and nonrecruited MSM. We asked participants to complete a questionnaire about recent sexual risk practices and to record any anogenital symptoms experienced in the preceding week. Participants provided urine and a rectal swab specimen (self- or clinician-collected) for M. genitalium screening.

We agitated the rectal swabs in 0.6 mL of phosphate-buffered saline to release cellular material, vortexed them briefly, and centrifuged them at low speed (8,000 rcf, 10 min) to remove PCR inhibitors. This step was required to reduce inhibition that differentially affected rectal samples; in early evaluations, the internal control failed in 9 (20.5%) of 44 uncentrifuged rectal samples but in none of 106 samples subjected to centrifugation. We transferred 0.2 mL of supernatant for nucleic acid isolation using the MagNA Pure 96 DNA and viral small volume kit on the automated MagNA Pure 96 system (Roche Diagnostics, https://www.roche.com). We prepared urine samples as described previously (12). We detected M. genitalium and macrolide resistance mutations in the 23S rRNA gene using the ResistancePlus MG test (SpeeDx Pty Ltd, Australia, https://plexpcr.com). Published evaluations of this assay report specificity for the detection of M. genitalium of 100% and sensitivities of 94.9%, 98.5%, and 98.9% (13–15).

Participants provided additional samples for C. trachomatis and N. gonorrhoeae screening of the throat, urethra, and rectum; we performed serologic testing for syphilis and HIV as indicated. We tested samples for N. gonorrhoeae and C. trachomatis by transcription-mediated amplification (Aptima Combo 2, Hologic, https://www.hologic.com).

MSM who were recalled for treatment of M.genitalium completed another questionnaire about antimicrobial drug use. We also collected throat swab specimens from men with rectal M. genitalium infection so we could perform pharyngeal M. genitalium testing. Resources were not available for testing all participants, particularly since published studies have rarely detected M. genitalium at this site. However, we hypothesized that M. genitalium may be more common in the pharynx in men with rectal M. genitalium. We agitated the throat swabs in 0.6 mL of phosphate-buffered saline to release cellular material and performed nucleic acid isolation as described for the other samples.

During August 23, 2016–September 27, 2017, a total of 1,028 MSM were triaged as asymptomatic and invited to participate in the study. Of these, 17 declined: 3 declined the additional rectal swab specimen collection, and 14 declined for reasons unrelated to the study (distress or being unable to return to the clinic). Of the remaining 1,011, a total of 6 rectal swabs were unassessable (internal control failed), and 4 did not provide a urine sample. These 10 patients were excluded from the analysis, leaving 1,001 men with assessable samples from both collection sites.

Participants had a median age of 28.8 (interquartile range 24.3–34.1). A total of 107 (10.7%) were HIV positive, and 142 (15.9%) of the HIV-negative men were taking or commencing HIV preexposure prophylaxis medication (PrEP) (Table 1).

Of the 1,001 men, 95 (9.5% [95% CI 7.7%–11.5%]) had M. genitalium detected at any site. Twenty-seven (2.7% [95% CI: 1.8%–3.9%]) had M. genitalium detected in the urine and 70 (7.0% [95% CI 5.5%–8.8%]) in the rectum; 2 men were infected at both sites. C. trachomatis was detected in 91 (9.6% [95% CI 7.8%–11.7%]) of 948 men tested at both sites, and N. gonorrhoeae was detected in 64 (6.7% [95% CI 5.2%–8.5%]) of 952 men tested at both sites (Table 2). For urine samples, M. genitalium was detected in 2.7%, C. trachomatis in 1.7%, and N. gonorrhoeae in 0.7%: For rectal samples, M. genitalium was detected in 7.0%, C. trachomatis in 8.5%, and and N. gonorrhoeae in 6.2%.

During the study period, 4,228 MSM were triaged as asymptomatic at MSHC and not offered the study but were tested for rectal C. trachomatis and N. gonorrhoeae at least once. After excluding repeat tests, positivity for C. trachomatis did not differ between nonrecruited (7.4%) and recruited (8.5%) MSM (p = 0.25), but N. gonorrhoeae was lower in nonrecruited (4.2%) than in recruited (6.2%) MSM (p = 0.006).

Detection of M. genitalium was significantly associated with younger age (odds ratio [OR] 0.96 [95% CI 0.93–0.99]) per year of increasing age. Detection of M. genitalium in the rectum was significantly associated with receptive anal sex with >2 partners within the past 3 months (OR 1.88 [95% CI 1.08–3.3]) and inconsistent condom use for receptive anal sex (OR 2.36 [95%CI 1.24–4.81]). M. genitalium was less common in HIV-infected men than in uninfected men (4.7% vs 10.1%, p = 0.08) but was not associated with taking or commencing PrEP.

The study population of 1,001 asymptomatic MSM completed a questionnaire about the presence of any anogenital or urethral symptoms in the week before presentation (all participants were asymptomatic at recruitment). Of these, 8.7% reported any recent symptoms in the urethra (itch, discomfort, discharge, or dysuria) and 25.5% in the anorectum (itch, discomfort, pain, or bleeding). Recent symptoms was not associated with detection of M. genitalium, C. trachomatis, or N. gonorrhoeae at either site (p>0.5 for all symptoms, individually or combined; Table 3).

We compared rectal test positivity for M. genitalium, C. trachomatis, and N. gonorrhoeae in the asymptomatic study population (n = 1,001) with rectal positivity in MSM who had symptoms of proctitis (n = 355) during the study period (Table 4). M. genitalium detection was similar in MSM with proctitis and asymptomatic MSM (5.6% for proctitis vs. 7.0% for asymptomatic; OR 0.79 [95% CI 0.45–1.35]; p = 0.38). However, rectal detection of both C. trachomatis (21.3% vs. 8.5%, OR 2.93 [95% CI 2.05–4.18]) and N. gonorrhoeae (28.4% vs. 6.2%, OR 5.97 [95% CI 4.15–8.61]) were significantly more common in MSM with symptoms of proctitis than in asymptomatic MSM.

We compared the urine test positivity for M. genitalium and C. trachomatis in the asymptomatic study population (n = 1,001) with the positivity in 1,019 MSM presenting with symptoms of NGU during the study period. Both M. genitalium (8.1% vs. 2.7%; OR 3.20 [95% CI 2.03–5.18]) and C. trachomatis (14.5% vs. 1.7%, OR 9.99 [95% CI 5.89–18.07]) were more commonly detected in MSM with symptoms of NGU than in asymptomatic MSM (Table 4).

We detected macrolide resistance mutations in 80 (84.2% [95% CI 75.3%–90.9%]) of 95 men who had positive M. genitalium tests (Table 5). We found no significant association between resistance and site of infection, and although these mutations were more common in MSM reporting recent use of antimicrobial drugs, particularly azithromycin, this difference was not significant. Macrolide resistance mutations were found in all HIV-negative men taking or commencing PrEP (p = 0.06).

Table 6 shows the proportion of asymptomatic MSM with M. genitalium who were co-infected with C. trachomatis and N. gonorrhoeae, by anatomic site. Rectal C. trachomatis and rectal N. gonorrhoeae were detected with similar frequency in MSM with rectal M. genitalium compared with men without rectal M. genitalium (C. trachomatis, 9.2% vs. 8.4%, p = 0.82; N. gonorrhoeae, 6.1% vs. 6.2%; p = 0.98). However, C. trachomatis and N. gonorrhoeae were detected significantly more often in the urine of asymptomatic men with M. genitalium compared with men without urethral M. genitalium (C. trachomatis, 7.4% vs. 1.5%, p = 0.03; N. gonorrhoeae, 7.4% vs. 0.5%, p = 0.002).

In contrast, in MSM with NGU, detection of C. trachomatis was uncommon in men with urethral M. genitalium (2.5%) compared with men without urethral M. genitalium (15.5%; p = 0.001). Overall, of 89 MSM with M. genitalium infection detected at any site and tested for all 3 infections, 15 (16.9% [95% CI 9.7–26.3]) were co-infected with either C. trachomatis or N. gonorrhoeae. Of 143 MSM with either C. trachomatis or N. gonorrhoeae, 15 (10.5% [95% CI 5.9%–16.7%]) were co-infected with M. genitalium.

Throat swabs were collected from 54 (77.1%) of 70 MSM with rectal M. genitalium, all 60 MSM with rectal N. gonorrhoeae, and 37 (45.7%) of 81 MSM with rectal C. trachomatis (routine clinic testing for pharyngeal C. trachomatis commenced halfway through the study). Only 1 (1.9% [95% CI 0.05–9.9]) of 54 MSM with rectal M. genitalium had pharyngeal M. genitalium. In contrast, 8 (21.6% [95% CI 9.8–38.2]) of 37 MSM with rectal chlamydia had pharyngeal chlamydia, and 21 (35% [95% CI 23.1–48.4]) of 60 MSM with rectal gonorrhea had pharyngeal gonorrhea. Thus, dual pharyngeal and rectal infection with M. genitalium was significantly less common than was observed for C. trachomatis (p = 0.002) and N. gonorrhoeae (p<0.001). Of all men tested, 12 (3.0%) of 407 had pharyngeal chlamydia and 62 (6.4%) of 963 had pharyngeal gonorrhea.

Almost 1 in 10 asymptomatic MSM attending a sexual health center in Melbourne, Victoria, Australia, during a 13-month period were infected with M. genitalium, and 84% of these infections were macrolide resistant. M. genitalium was detected in 7% of asymptomatic MSM at the rectum, 2.7% at the urethra, and only 0.2% at both sites. Overall, M. genitalium was as common as chlamydia and more common than gonorrhea in asymptomatic MSM. The proportion of asymptomatic MSM with M. genitalium in the rectum was no different from that in MSM with symptoms of proctitis during the same period. Co-infection with C. trachomatis or N. gonorrhoeae was common and present in 17% of M. genitalium infections. Screening MSM for C. trachomatis and N. gonorrhoeae will identify these infections, but if they are treated, asymptomatic M. genitalium infections, present in 10% of these cases, may be inadvertently exposed to azithromycin, exerting selection pressure for macrolide resistance, which may explain the rapid escalation of resistance in M. genitalium in MSM. The situation facing clinicians is challenging, because the recommended treatment for macrolide-resistant M. genitalium, moxifloxacin, is expensive, potentially toxic, and difficult to obtain and may generate further antimicrobial resistance, all of which should be considered before screening asymptomatic MSM for M. genitalium.

The detection of M. genitalium in 9.5% of asymptomatic MSM contrasts with a recent meta-analysis finding lower average prevalence estimates among MSM of 3.2% (95% CI 2.1%–5.1%) in 5 community-based studies and 3.7% (95% CI 2.4%–5.6%) in 4 clinic-based studies (16). This discrepancy may be because the meta-analysis included several studies that tested only urine, where M. genitalium is less common, or because of geographic or temporal differences. A recent Sydney study reported M. genitalium in 13.4% of MSM (rectum 8.9%, urine 4.7%) (17).

Rectal positivity for M. genitalium in men with symptoms of proctitis was no higher than in asymptomatic MSM. Furthermore, a report of mild anorectal symptoms over the preceding week was not associated with rectal M. genitalium and presumably reflected nonspecific self-limiting symptoms. In contrast, rectal C. trachomatis and N. gonorrhoeae were significantly associated with current symptoms of proctitis (OR 3 and 6, respectively). Two previous studies found no association between rectal M. genitalium and symptoms, whereas 1 reported a weak association of borderline significance (7,8,17). Other studies suggesting that M. genitalium may cause proctitis have not compared frequency of detection in symptomatic and asymptomatic patients (18,19).

The high proportion of cases with macrolide resistance in this study (84%) is consistent with recent MSHC data. MSHC has been using the same resistance assay for M. genitalium since June 20, 2016; by March 27, 2018, a total of 943 patients with NGU, cervicitis, PID, proctitis, or contacts of infection had M. genitalium detected. Macrolide resistance mutations were routinely detected in 265 (51.5% [95% CI 47.0–55.9]) of 515 heterosexual men and women compared with 349 (81.5% [95% CI 77.5–85.1]) of 428 MSM (p<0.0001). This difference between MSM and heterosexuals was also seen in a recent study in Spain, which reported macrolide resistance in 71% of MSM compared with 13% of heterosexuals (p<0.001); prior azithromycin exposure was a significant risk factor for resistance (20). Other recent studies in MSM report macrolide resistance in 74%–80% of M. genitalium infections (17,21). The high proportion of cases with resistance reduced our ability to identify risk factors; we detected resistance in 90% of infected men who recalled taking any antimicrobial drug within the previous 3 months and 100% of those who recalled taking azithromycin, but this difference was not significant.

Asymptomatic urethral co-infections with C. trachomatis and N. gonorrhoeae were significantly associated with detection of M. genitalium, but this association was not seen with rectal co-infections. Although the association between M. genitalium and urethral co-infections was significant, we found only 4 cases of co-infection. Specific host factors might possibly lead some men to tolerate, and therefore accumulate, urethral infections. The proportion of asymptomatic men with M. genitalium detected in their urine was higher than for C. trachomatis and for N. gonorrhoeae, again consistent with the hypothesis that M. genitalium might be less pathogenic than C. trachomatis or N. gonorrhoeae.

Pharyngeal M. genitalium is reported as rare (22–26), so to optimize detection, we limited pharyngeal testing to MSM with rectal infection because other pharyngeal sexually transmitted infections (STIs) are commonly concurrent with rectal infections. Of patients with rectal M. genitalium, only 1.9% had pharyngeal M. genitalium, which was much lower than for pharyngeal C. trachomatis (22%) and N. gonorrhoeae (35%) in MSM with these rectal infections. However, C. trachomatis and N. gonorrhoeae were detected by transcription mediated amplification. A recent Sydney study using the ResistancePlus PCR assay also found no pharyngeal M. genitalium infections in 508 MSM (rectal prevalence 8.9%), providing further evidence that M. genitalium is rarely detected in pharyngeal specimens (17).

Of concern, 17% of MSM with M. genitalium were co-infected with C. trachomatis or N. gonorrhoeae, predominantly reflecting rectal infections. The rectum appears likely to be a reservoir for asymptomatic M. genitalium, and treatment of concurrent STIs promotes macrolide resistance, which is estimated to develop de novo in 12% of wild-type cases exposed to single-dose azithromycin (6). The high proportion of macrolide-resistant M. genitalium in MSM may be caused by the combination of a high background prevalence of asymptomatic rectal M. genitalium, a high frequency of concurrent chlamydia or gonorrhea, and the resulting use of azithromycin in this population.

This study has limitations, including reliance on recall of antimicrobial drug exposure, recruitment from a sexual health center where findings may not reflect MSM elsewhere, and restricted testing for pharyngeal M. genitalium. Centrifugation to remove PCR inhibitors was undertaken on rectal samples because of higher levels of inhibition, which could have reduced the sensitivity of rectal M. genitalium detection. Furthermore, we were unable to approach all MSM attending the clinic. The study population had a higher proportion with rectal gonorrhea, but not chlamydia, compared with those who were not recruited, possibly because our inclusion criteria required receptive anal sex in the previous year and the nonrecruited group included MSM attending an express service for lower-risk men. This difference suggests that the study population may have had a slightly elevated risk of infection, which should be considered alongside our findings. Diagnoses of nongonococcal urethritis and proctitis were predominantly clinical, based on symptoms and sexual risk, which is likely to lead to a lower prevalence of STIs in these groups compared with studies that required microscopic criteria for case definitions. However, clinical diagnoses are commonly used in primary care and are supported by the strong associations we observed between detection of C. trachomatis and N. gonorrhoeae and the symptom-based definitions of proctitis and urethritis.

We detected M. genitalium in 9.5% of asymptomatic MSM; although it was as common as chlamydia or gonorrhoea, 84% of these infections were macrolide resistant. The high proportion of MSM with macrolide-resistant M. genitalium might be considered a reason to screen for this infection but would not meet the criteria for screening established by Wilson and Jungner (27). For example, the natural history of M. genitalium infection, particularly in the rectum, is poorly understood. Testing is not widely available and the high prevalence of antimicrobial drug resistance also limits the availability of treatment. If we screened this population, 8% of MSM (84% of 9.5%) would require moxifloxacin or a similar agent. Moxifloxacin is expensive, difficult to obtain in many parts of the world, and associated with uncommon but concerning toxicities. Resistance to quinolone antimicrobial drugs is now detected in 16% of patients coming to MSHC (mixed heterosexual and MSM population) in ongoing unpublished work (G.L. Murray, unpub. data). Increasing the use of moxifloxacin as a result of screening would be expected to generate more resistance.

Rectal M. genitalium infection may not warrant treatment. It was not associated with current anorectal symptoms in this study; most published literature suggests no association or only a weak association. No prospective studies have associated M. genitalium with increased risk for HIV infection in MSM, in contrast to women; such an association may become less critical when HIV PrEP and treatment are widely used. Therefore, screening asymptomatic MSM for M. genitalium would result in considerable expense and adverse events for uncertain benefit. Although M. genitalium has been identified in cases of proctitis, it is predominantly asymptomatic in the rectum, and there appears to be insufficient evidence to suggest that M. genitalium is a cause of proctitis.