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Detection of Neisseria gonorrhoeae in the pharynx and saliva: implications for gonorrhoea transmission
  1. Eric P F Chow1,2,
  2. David Lee1,
  3. Sepehr N Tabrizi3,4,5,
  4. Samuel Phillips3,5,
  5. Anthony Snow1,
  6. Stuart Cook1,
  7. Benjamin P Howden6,
  8. Irene Petalotis1,6,
  9. Catriona S Bradshaw1,2,
  10. Marcus Y Chen1,2,
  11. Christopher K Fairley1,2
  1. 1Melbourne Sexual Health Centre, Alfred Health, Melbourne, Victoria, Australia
  2. 2Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
  3. 3Department of Microbiology and Infectious Diseases, The Royal Women's Hospital, Parkville, Victoria, Australia
  4. 4Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
  5. 5Murdoch Childrens Research Institute, Parkville, Victoria, Australia
  6. 6Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
  1. Correspondence to Dr Eric P F Chow, Melbourne Sexual Health Centre, Alfred Health, 580 Swanston Street, Carlton, VIC 3053, Australia; Echow{at}


Objectives This study aimed to determine the proportion of untreated pharyngeal swabs or saliva samples positive by culture or nucleic acid amplification tests (NAATs) for Neisseria gonorrhoeae up to 14 days after an initial culture-positive pharyngeal swab.

Methods Men who have sex with men who tested positive for pharyngeal gonorrhoea at Melbourne Sexual Health Centre (MSHC) and returned to MSHC for treatment within 14 days between 13 October 2014 and 25 March 2015 were included in this study. Pharyngeal swabs and saliva samples were collected for culture and NAAT.

Results Of 33 initially culture-positive pharyngeal swabs, 32 saliva samples and 31 pharyngeal swabs were positive by NAAT and 14 pharyngeal and 6 saliva samples were positive by culture within 14 days. There was a significant decline in the proportion of repeated pharyngeal culture samples positive by culture over time (p<0.001).

Conclusions The rapid decline suggests pharyngeal gonorrhoea is short-lived, and the finding of gonorrhoea commonly in the saliva implicates this body fluid in its transmission without direct throat inoculation.


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Gonorrhoea is common and its incidence is increasing in men who have sex with men (MSM), in many developed countries such as Australia1 as condom use falls. In this context, it is likely that new public health campaigns will be necessary for effective control. An integral part of any effective control programme is a better understanding of how it is transmitted between anatomical sites and which sites are most important for onward transmission in MSM.

Pharyngeal and rectal gonorrhoea is usually asymptomatic, while urethral gonorrhoea is predominantly symptomatic in men who seek healthcare soon after the onset of urethral discharge. The short duration of urethral gonorrhoea raises the possibility that this site may not be responsible for the majority of gonococcal transmission from the urethra to the pharynx or rectum because there may not be sufficient time to maintain ongoing community transmission. A previous Australian study has shown an association between reported oral–anal contact and rectal gonorrhoea after adjusting for other risks, suggesting that transmission occurs from the pharynx to the rectum.2 Transmission from the pharynx to the anus cannot occur through direct inoculation and would likely need to be mediated through saliva.

Only two studies, published over 30 years ago, have shown that gonorrhoea can be detected in saliva although the results were quite different. Both studies used culture and they showed marked differences in the proportion of positive culture in saliva (ie, 8% (2/24)3 vs 67% (34/51)4). The aim of this study was to estimate the proportion of culture-positive pharyngeal infections that were also positive on (1) culture of the saliva and (2) nucleic acid amplification tests (NAATs) of the saliva within 14 days of the initial positive pharyngeal culture.


This was a cross-sectional study among MSM screened for pharyngeal gonorrhoea who attended Melbourne Sexual Health Centre (MSHC) between 13 October 2014 and 25 March 2015. On the day of screening, a pharyngeal swab was taken by clinicians from both tonsillar fossae and the posterior oropharynx (hereafter termed pharyngeal specimens) for gonorrhoea using cotton-tipped swabs and immediately plated onto GC Agar medium in the consulting room and then taken within minutes to the onsite laboratory for culture. We excluded patients who were transgender individuals, treated with antibiotics since the initial positive pharyngeal swab or returned to MSHC more than 14 days after the pharyngeal swab.

On the day of treatment, two pharyngeal specimens (from both tonsillar fossae and the posterior oropharynx) were obtained from the patients by the clinicians (DL, AS and SC). One pharyngeal swab was taken using a cotton-tipped swab and plated onto GC Agar medium for culture; a second pharyngeal swab was rotated in 0.4 mL of phosphate-buffered saline and was placed in −80°C until NAAT testing. Patients were also asked to accumulate saliva for 60 s and spit into a sterile plastic screw-topped jar. A swab was used to plate the saliva onto GC Agar medium for culture. An aliquot of 0.2 mL of saliva was also placed in −80°C for NAAT. We randomly alternated the sampling order for saliva and the two pharyngeal swabs in a 1:1 ratio. All patients were then treated with ceftriaxone 500 mg as a single intramuscular injection plus azithromycin 1 g as a single dose.

All specimens were immediately taken to the clinic's onsite laboratory for testing and storage. Inoculated culture plates were incubated at 36°C in 5% carbon dioxide for 48 h. An aliquot of 0.2 mL of saliva and cells obtained from swab was extracted using the MagNA Pure 96 and eluted DNA was used to perform three PCR reactions targeting: (1) β globin gene to assess sample adequacy;w1 (2) N. gonorrhoeae opa genew2 and (3) N. gonorrhoeae porA.w3 The 95% confidence interval (CI) of the proportion positive were calculated based on the ‘exact’ binomial distribution. The χ2 trend test was used to examine the trend of positivity of gonorrhoea by culture in the pharynx within 14 days. The McNemar test was used to compare the positivity of gonorrhoea by culture versus NAAT. All analyses were performed using Stata V.13.1 (Stata Corp., College Station, Texas, USA).


The median age of the 33 participants was 27 years (IQR 25–34). Participant returned to the clinic between 3 and 14 days for treatment (see online supplementary figure S1), with a median day of return visit of 7 days (IQR 6–8). Of the 33 participants who tested culture positive for gonorrhoea at baseline, 60.6% (95% CI 42.1% to 77.1%) had positive pharyngeal swabs by day 7 and 42.4% (25.5% to 60.8%) had positive swabs by day 14 (ptrend<0.001) (see online supplementary figure S1) using culture. However, 31 of 33 (93.9%; 79.8% to 99.3%) men had positive pharyngeal swabs by NAAT by day 14 (see online supplementary table S1). In contrast, only 18.2% (7.0% to 35.5%; 6/33) of men had a positive saliva sample by culture but 97.0% (84.2% to 99.9%; 32/33) had a positive saliva sample by NAAT (p<0.001) within 14 days. Pharyngeal swabs were significantly more likely to be culture positive than saliva specimens (McNemar test; p=0.01). There were no significant differences in gonorrhoea positivity by which specimen (pharyngeal swab/saliva) was taken first.

Of the 14 men who were culture positive for gonorrhoea in the pharynx on the day of treatment, 6 (42.9%; 17.7% to 71.1%) men were also culture positive in saliva (table 1). All 31 men who were NAAT positive in the pharynx were also NAAT positive in saliva.

Table 1

Comparison between gonorrhoea positivity in the pharynx and saliva by culture at day 14 among men who have sex with men


Our study highlighted a number of important findings relevant to pharyngeal gonorrhoea. First, we showed that almost half of the patients (43%) that were culture positive in the pharynx also had a positive saliva sample by culture, which was midway between the only two previous estimates (ie, 8%3 vs 67%4). These differences may be because no saliva samples were taken on day 0 in our study. Second, we found a significant decline in the proportion of repeated pharyngeal culture samples positive for gonorrhoea to 42% within 14 days after the initial culture positive but despite the fall in culture positivity, NAAT remained positive in the pharynx and saliva in most of the participants (94–97%) for up to 14 days after the initial culture-positive sample. The significance of these findings is that direct inoculation of the penis to the pharynx is presumably not necessary because saliva contains viable culture-positive gonorrhoea. Similarly, saliva used for oral–anal sex would also contain viable gonorrhoea.

We also found that there was a substantial and rapid decline in the proportion of pharyngeal swabs that were culture positive over 14 days, suggesting that the load of bacteria is falling over time, while remaining positive by NAAT. While it is not possible to know if the NAAT positive samples were viable or not, the observation that only one of 33 was negative in saliva suggests at least some of the culture-negative samples contained low levels of viable organisms. There have been only two previous studies of untreated pharyngeal gonorrhoea and both occurred more than 30 years ago. One study by Hutt and Judson4 showed only 45% remained culture positive after 7 days. Wallin and Siegel5 showed that pharyngeal gonorrhoea persisted on average for 6 weeks with no infections lasting longer than 12 weeks using culture. Taken collectively, these data suggest the gonorrhoea infectious load may fall relatively quickly. If the average duration of pharyngeal gonorrhoea is substantially less than 3 months, annual screening for gonorrhoea among MSM will fail to detect most cases of pharyngeal gonorrhoea.w4 w5

This study has several limitations. First, we acknowledged that the sampling technique may have varied between different clinicians. It has been shown that the detection of pharyngeal gonorrhoea using culture is highly associated with the frequent induction of the gag reflex by patients when collecting pharyngeal specimens6; however, the collection method was standardised and done by three well-trained research nurses only to minimise the sampling variation. Second, we used a relatively small quantity of saliva, and that larger quantities, more typical of sexual acts, may improve the chance of identifying culture-positive samples. Third, culture has a 100% specificity compared with NAAT, but its sensitivity is poor when compared with NAAT detection for pharyngeal gonorrhoea.7

Sexual practices among MSM lend themselves to saliva playing a role in gonorrhoea transmission, although saliva use during sex has not been well studied. Indeed, kissing has been reported to be the most common sexual behaviour among MSM;8 it is, therefore, possible that gonorrhoea could be transmitted from pharynx to pharynx via ‘wet kissing’.9 Oral–anal contact (‘rimming’) is also common among MSM.8 Previous Australian studies have showed that MSM who performed rimming are more likely to have pharyngeal gonorrhoea,9 and MSM who received rimming have a higher risk of rectal gonorrhoea.2 Also, saliva is commonly used as a lubricant for anal intercourse (87%) among MSM10 and could be pushed into the rectum by the penis during penile–anal intercourse. Furthermore, a previous Australian study showed that some MSM with urethral gonorrhoea reported no insertive anal sex.11


Supplementary materials

  • Supplementary Data

    This web only file has been produced by the BMJ Publishing Group from an electronic file supplied by the author(s) and has not been edited for content.


  • Handling editor Jackie A Cassell

  • Contributors CKF conceived the idea that saliva and kissing may play a key role in the transmission of gonorrhoea in MSM. EPFC, DL and CKF designed the study. EPFC and DL undertook the analysis. DL, AS and SC involved in the study recruitment. SNT, SP and IP performed the laboratory analyses. SNT and BPH were involved in interpretation of the laboratory data. EPFC prepared the first draft of the manuscript. All authors contributed to the interpretation of the study findings and contributed to the drafting of the manuscript.

  • Funding This work was supported by the National Health and Medical Research Council (NHMRC) programme grant (no.: 568971).

  • Competing interests EPFC is supported by the Early Career Fellowships from the Australian NHMRC (no.: 1091226).

  • Patient consent Obtained.

  • Ethics approval The ethics committee of Alfred Hospital, Melbourne, Australia (number 316/14).

  • Provenance and peer review Not commissioned; externally peer reviewed.