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Prevalence and characteristics of gastrointestinal infections in men who have sex with men diagnosed with rectal chlamydia infection in the UK: an ‘unlinked anonymous’ cross-sectional study
  1. Gwenda Hughes1,
  2. Panida Silalang2,
  3. John Were1,
  4. Hemanti Patel3,
  5. Tristan Childs2,
  6. Sarah Alexander3,
  7. Stephen Duffell1,
  8. Cara Saxon4,
  9. Cathy Ison3,
  10. Holly Mitchell1,5,
  11. Nigel Field1,5,
  12. Claire Jenkins2
  1. 1 Department of HIV and STI, National Infection Service, Public Health England, London, UK
  2. 2 Gastrointestinal Infection Reference Service, Microbiology Services Centre, National Infection Service, Public Health England, London, UK
  3. 3 Sexually Transmitted Infection Reference Service, Microbiology Services Centre, National Infection Service, Public Health England, London, UK
  4. 4 Department of Sexual Medicine and HIV, University Hospitals of South Manchester NHS Foundation Trust, Manchester, UK
  5. 5 Research Department of Infection and Population Health, University College London, London, UK
  1. Correspondence to Dr Gwenda Hughes, Department of HIV and STI, National Infection Service, Public Health England, Colindale, London NW9 5EQ, UK;{at}


Introduction Gastrointestinal infections (GII) can cause serious ill health and morbidity. Although primarily transmitted through faecal contamination of food or water, transmission through sexual activity is well described, especially among men who have sex with men (MSM).

Methods We investigated the prevalence of GIIs among a convenience sample of MSM who were consecutively diagnosed with rectal Chlamydia trachomatis (CT) at 12 UK genitourinary medicine clinics during 10 weeks in 2012. Residual rectal swabs were coded, anonymised and tested for Shigella, Campylobacter, Salmonella, shiga toxin-producing Escherichia coli and enteroaggregative E. coli (EAEC) using a real-time PCR. Results were linked to respective coded and anonymised clinical and demographic data. Associations were investigated using Fisher's exact tests.

Results Of 444 specimens tested, overall GII prevalence was 8.6% (95% CI 6.3% to 11.6%): 1.8% (0.9% to 3.6%) tested positive for Shigella, 1.8% (0.9% to 3.6%) for Campylobacter and 5.2% (3.5% to 7.7%) for EAEC. No specimens tested positive for Salmonella or other diarrhoeagenic E. coli pathotypes. Among those with any GII, 14/30 were asymptomatic (2/7 with Shigella, 3/6 with Campylobacter and 9/17 with EAEC). Shigella prevalence was higher in MSM who were HIV-positive (4.7% (2.1% to 10.2%) vs 0.5%(0.1% to 3.2%) in HIV-negative MSM; p=0.01).

Conclusions In this small feasibility study, MSM with rectal CT appeared to be at appreciable risk of GII. Asymptomatic carriage may play a role in sexual transmission of GII.


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Gastrointestinal infections (GII) can cause serious ill health and morbidity, including diarrhoea, dehydration, bacteraemia, Reiter's syndrome and haemolytic uraemic syndrome. Transmission occurs through the faecal–oral route and is primarily associated with contaminated food or water. Sexual transmission is well described, especially among men who have sex with men (MSM), among whom it is usually associated with exposure through direct or indirect oroanal contact.1–5

In the last decade, there have been remarkable changes in the epidemiology of some GII in England.4 ,6 ,7 Diagnoses of non-travel associated Shigella flexneri, usually associated with travel to endemic areas, have risen sharply; non-travel associated cases now outnumber travel-associated cases.6 Control measures have focused on raising awareness among clinicians and patients to reduce spread in those with symptoms. However, these have made little impact on the Shigella spp. epidemics.6 It is unclear whether asymptomatic infection, which is an important characteristic for many STIs, plays a role in sexual transmission of GII.

The prevalence, incidence and transmission dynamics of GII in MSM is poorly understood because (1) surveillance data reflect the subset with acute infection presenting to clinical services, (2) sexual exposure is not routinely recorded for GII and (3) there is no simple method for routinely screening MSM for GII. We used a convenience sample of MSM diagnosed with rectal Chlamydia trachomatis (CT) at selected UK sexual health clinics to investigate whether rectal swabs from routine STI screens would make suitable specimens for GII testing and to provide crude estimates of GII prevalence in these men. Infection with rectal CT suggests a history of receptive condomless anal intercourse and identifies a group potentially at higher risk of GII from indirect oroanal contact. As such, MSM with rectal CT are an appropriate population for a feasibility study on GII.


Study population and study period

We used a convenience sample of MSM from a Lymphogranuloma venereum (LGV) case-finding study.8 The LGV study included only MSM who had been consecutively diagnosed with rectal CT at 12 clinics in the UK (in Brighton, Glasgow, London and Manchester) between 24 September 2012 and 7 December 2012, except those who had taken any antibiotics during the previous 6 weeks.8 The recruiting clinics serve large MSM populations; they undertake routine testing of MSM for rectal CT (using clinician or self-taken rectal swabs) regardless of symptoms and follow up some cases according to UK guidelines.9 Specimens were submitted to the Public Health England (PHE) Reference Laboratory for CT confirmation and LGV typing.8 Residual CT-positive specimens were included in the GII study.

Data collection

Data on symptom presentation in study participants were systematically recorded by clinicians during the consultation and submitted to PHE through a secure web portal. The proforma covered CT-related or LGV-related symptoms and included a free-text field to record non-specific symptoms (eg, diarrhoea, loose stools).8 Patients presenting with symptoms at any attendance associated with a single STI care episode (typically 2–4 weeks duration) were defined as symptomatic. (In the original study, only three patients were initially asymptomatic, but subsequently symptomatic during the same care episode.) Data on HIV status were available for patients in England (97%) from the national electronic STI surveillance system.8 ,10

Unlinked anonymous testing protocol

As the GII testing protocol was not part of patients' clinical care, to comply with the Data Protection Act, all residual specimens were irreversibly unlinked and anonymised prior to GII testing, a technique originally developed to monitor HIV prevalence.11 A unique GII study number was assigned to each specimen and associated clinical data, and a ‘GII study dataset’ created. Patient ID numbers in the GII study dataset were irreversibly deleted as were GII study numbers in all source datasets. Clinical data in the GII study dataset were restricted and summarised to prevent deductive disclosure of patients into the following groups: (1) region of residence (London/non-London), (2) symptom status (symptomatic/asymptomatic), (3) HIV status (positive/negative), (4) LGV status (positive/negative). As only one patient presented with symptoms consistent with GII, GII symptoms were grouped with CT and LGV-related symptoms.

DNA extraction and GII testing

Residual rectal swabs, which had been tested for CT/LGV as part of the LGV case-finding study and which had been stored at −20°C, were used for GII testing. DNA was extracted using the QIAsymphony DSP DNA Mini Kit (Qiagen) according to manufacturer's instructions. Specimens were tested for Shigella sp., Campylobacter sp., Salmonella sp., shiga toxin-producing Escherichia coli and enteroaggregative E. coli (EAEC) using a real-time PCR on a Rotor-Gene (Qiagen). The amplification parameters were 95°C for 5 min, followed by 95°C for 15 s and 60°C for 60 s. The cycle threshold was set at 0.05 for all targets. Details of the primers, probes and gene targets are listed in the web table.

supplementary web table

Data analysis

Summary clinical data were linked to the GII PCR test result using the GII study number. We estimated GII prevalence with 95% CIs and used Fisher's exact tests to compare test results by patient characteristics, for each GII, and for all GII combined.

Ethical statement

No individual patient consent was required or sought as PHE has authority to handle patient data for public health monitoring and infection control under section 251 of the UK National Health Service Act of 2006 (previously section 60 of the Health and Social Care Act of 2001).


Of 489 stored rectal specimens, 444 (91%) had DNA successfully extracted for PCR testing. Of these, 38 (8.5%) tested positive for any GII: 8 (1.8%) tested positive for Shigella sp., 8 (1.8%) for Campylobacter sp. and 23 (5.2%) for EAEC (table 1). No specimens tested positive for Salmonella sp. or the other diarrhoeagenic E. coli pathotypes. One patient was coinfected with Shigella sp. and EAEC.

Table 1

Gastrointestinal infection (GII) PCR test results on rectal swabs taken from men who have sex with men diagnosed with rectal Chlamydia trachomatis at selected STI clinics in the UK: prevalence with 95% CIs and association with selected patient characteristics (N=444)

Among those with GII, 30/38 were London residents (8/8 with Shigella sp., 7/8 Campylobacter sp. and 16/23 EAEC infections), 14/30 were asymptomatic (2/7 with Shigella sp., 3/6 with Campylobacter sp. and 9/17 with EAEC infections) and 16/30 were HIV-positive (6/7 with Shigella sp., 4/6 with Campylobacter sp. and 6/17 with EAEC infections).

GII prevalence was weakly associated with symptom presentation (13.1% in symptomatic vs 6.4% in asymptomatic; p=0.05) and in those who were HIV-positive (12.6% in HIV-positive vs 6.3% in HIV-negative; p=0.05) (table 1). The prevalence of Shigella sp. was significantly higher in MSM who were HIV-positive (4.7% vs 0.5% in HIV-negative MSM, p=0.01; table 1).


To our knowledge, this is the first study to estimate GII prevalence in MSM with rectal CT attending STI clinics, much of which is likely to have been sexually transmitted. We show that 9% of MSM infected with rectal CT were coinfected with a GII; 13%, if they were HIV-positive. Although not directly comparable, in a cohort of over 700 people attending UK general practice, who developed GII symptoms, Shigella sp. was not detected, and the detection rate of EAEC was lower, suggesting the burden of GII experienced by some MSM may be appreciable.12 We have also demonstrated the feasibility of using rectal swabs for GII testing. Rectal swabs are routinely taken for STI screening in sexual health clinics and might provide a practicable and acceptable method for investigating prevalence, clinical presentation and risk factors of GII in MSM to inform the public health response. Aside from bacterial GII, MSM have historically been at risk of various protozoan and viral GII, including Giardia spp., Entamoeba spp. and hepatitis A.13 ,14 We are exploring whether our approach can be used to identify a broader range of pathogens. Whether rectal swabs might replace faecal specimens for clinical diagnosis requires further investigation to validate test performance and determine whether swabs would facilitate organism culture for typing and antimicrobial resistance profiling. Even if feasible and acceptable, further research on the clinical and public health benefit is needed before introducing routine testing of asymptomatic MSM for GII in STI clinics.

Use of a convenience sample to estimate GII prevalence introduces obvious limitations to our study. The men in the study had been diagnosed with rectal CT and do not represent all MSM attending STI clinics, they only represent those with a history of condomless receptive anal intercourse represent. Testing MSM with specific sexual risk behaviours has likely led to higher GII prevalence. Conversely, repeating DNA extraction from stored swabs for the GII study is likely to have reduced DNA quantity and quality and therefore test sensitivity, leading to underestimation of GII prevalence. Furthermore, we had no information on specific practices associated with GII acquisition, and the small sample size limited statistical power.

Despite these limitations, the study provides important insights into GII epidemiology in MSM. Although numbers were small, 14 of 30 MSM with GII were asymptomatic, suggesting asymptomatic carriage may play a role in infection transmission. Our findings further strengthen the association between Shigella sp. transmission and HIV-positive MSM, and suggest that a similar association may exist for Campylobacter sp.5 ,7 The factors underlying this relationship may be associated with HIV seroadaptive behaviours (choosing to have condomless sex with partners according to their perceived HIV status), as has been observed in other STI epidemics among MSM, and the effect of HIV infection on biological susceptibility and shedding of Shigella sp.15 ,16

The clinical and public health response to sexual transmission of Shigella spp. and other GII has been inadequate, partly because the role of asymptomatic and persistent infections in maintaining transmission remains unclear. This study contributes to our understanding of GII in MSM and demonstrates the potential value of using rectal swabs to detect GII in studies addressing these questions.

Key messages

  • About 9% of men who have sex with men with rectal chlamydia were coinfected with a gastrointestinal infection (GII); 13%, if they were HIV-positive.

  • Among those with GII, 14 of 30 were asymptomatic, suggesting asymptomatic carriage may play a role in sexual transmission of GII.

  • Testing rectal swabs may be a feasible and acceptable method for detecting GIIs.


The authors gratefully acknowledge current and past members of the UK LGV Case-Finding Group who contributed data, specimens and expertise: Sameena Ahmad (University Hospitals of South Manchester National Health Service (NHS) Foundation Trust, Manchester, UK); Nadia Ahmed, Patrick French (Central and North West London NHS Foundation Trust, London, UK); Pamela Saunders and Sinan Turkaslan (Sexually Transmitted Bacteria Reference Unit, Public Health England, Colindale, London); Tristan Childs, Stephen Duffell, Rishma Maini, Chinelo Obi, Parnam Seyan (Centre for Infectious Disease Surveillance and Control, PHE Colindale); Sara Day, Jamie Hardie, Ken McKlean, Alan McOwan, Christopher Scott, Richard Stack, Ann Sullivan (Chelsea and Westminster Hospital NHS Foundation Trust, London); Gillian Dean, Mohammed Hassan-Ibrahim, Gary Homer (Brighton and Sussex University Hospitals NHS Trust, Brighton, UK); Kirstine Eastick (Scottish Bacterial Sexually Transmitted Infections Reference Laboratory, Health Protection Scotland, Edinburgh, Scotland, UK); Laura Greaves, Maria Sampson, Merle Symonds (Barts Health NHS Trust, London); Rory Gunson, Anthony Rea, Andrew Winter (NHS Greater Glasgow and Clyde Health Board, Glasgow, Scotland, UK); Peter Horne, Daniel Krahe, Iain Reeves (Homerton University Hospital NHS Foundation Trust, London); Monica Rebec, Javier Rubio, Dawn Wilkinson (Imperial College Healthcare NHS Trust, London); Gabriel Schembri, Peter Tilston, Andrew Turner (Central Manchester University Hospitals NHS Foundation Trust); Simon Stevenson (University College London Hospitals NHS Foundation Trust); Helen Ward (Imperial College London); John White (Guy's and St Thomas' NHS Foundation Trust, London).



  • Handling editor Jackie A Cassell

  • Twitter Follow Sarah Alexander @sarah1alexander and Nigel Field @fienige

  • Contributors GH, CJ, NF and CI devised the study and developed the protocol. PS, HP and SA processed laboratory specimens and undertook all testing, overseen by CJ and CI. JW, TC, CS, SD and GH developed and undertook the data anonymisation and linkage protocol, and JW and GH performed the data analysis. GH wrote the first draft of the manuscript. All authors read the manuscript and provided comments.

  • Funding Undertaken as part of PHE-funded public health surveillance.

  • Competing interests None declared.

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