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How likely is environmental or patient cross-contamination of Chlamydia trachomatis DNA to lead to false positive results in patients attending our clinic?
  1. Sum Yee Chan1,
  2. Sophie Jose2,
  3. Rebecca King1,
  4. Mark R Pakianathan1,
  5. Caroline Sabin2,
  6. S Tariq Sadiq3,
  7. Phillip E Hay1,
  8. Tim Planche4
  1. 1The Courtyard Clinic, St Georges Hospital, London, UK
  2. 2Department of Infection and Population Health, University College London, London, UK
  3. 3Department of Cellular and Molecular Medicine, St Georges University of London, London, UK
  4. 4Centre for Infection and Immunity, St Georges University of London, London, UK
  1. Correspondence to Dr Sum Yee Chan, The Courtyard Clinic, Blackshaw Road, Tooting, London SW17 0QT, UK; sumyeeyorkies{at}


Objectives Environmental contamination with DNA from Chlamydia trachomatis (CT) has previously been found in Genitourinary Medicine (GUM) clinics. There are no known cases of cross-contamination of clinical samples and no known nosocomial infections. We investigated whether diagnostic samples could become contaminated from the environment by running dummy sample and carrying out a patient-throughput analysis. A total of 29 748 patients attended clinics over a year. Of these, 2860 (9.6%) had a positive Chlamydia test result.

Method (1) A run of dummy samples (60 urine samples and 10 swabs) were processed as normal clinic specimens. (2) Patient-throughput analysis: Patient numbers attending the GUM clinic on a given day was categorised as low, moderate or high. χ2 Tests were used to look for associations between categorical variables and Chlamydia test positivity. A Poisson regression model was fitted to look at the effect of the number of people in the clinic on the number of positive results in a given day. As some clinics were only run on certain days of the week, a sensitivity analysis was later performed with attendances at non-daily clinics removed.

Results All dummy samples tested negative and we did not find evidence of an association between daily Chlamydia positivity and clinic attendance.

Conclusions It is unlikely that environmental or cross-contamination of CT has lead to significant numbers of false positive results. Laboratories check for possible cross-contamination routinely. The extension of this simple routine practice to all clinical areas could provide quality assurance, improving confidence in the results in clinics.

  • Chlamydia Trachomatis
  • Infection Control
  • Bacterial Infection
  • Chlamydia Infection
  • Genitourinary Medicine

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Environmental contamination with DNA from Chlamydia trachomatis (CT) and Neisseria gonorrhoeae detected by nucleic acid amplification tests has been found in Genitourinary Medicine (GUM) clinics, including our own (A Kakarla, R Lau, personal communications, Urine Chlamydia and risk of contamination, October 2007. Unpublished study from The Courtyard Clinic, St Georges Hospital).1–3 This raises the possibility of contamination of specimens during processing.3 CT may persist for up to 30 h on surfaces,4 with N gonorrhoeae persisting for 1–3 days.5 ,6 We hypothesise that if contamination occurs, it is more likely in clinics with high patient-throughput.

Specimen contamination resulting in misdiagnosis may lead to unnecessary antibiotic use, patient distress, relationship difficulties and a breakdown in patient/clinician trust.

We investigated environmental and cross-contamination of diagnostic samples in our clinic, attended by more than 29 000 patients a year. Routine diagnosis of CT was performed using the BD probeTec TM Qx assay on the BD viper platform (BD, Sparks, MD, USA).

Patient flow: The clinic opens on weekdays for different hours each day; daily attendance can exceed 150. Female swabs, taken by clinical staff in examination rooms, are laid out on a tray beforehand. Surfaces are routinely wiped with PDI Super Sani cloths (either alcohol- or soap-based) (Professional Disposables International, Aber Park, Flint, UK). Almost all male CT testing is performed on first-catch urine, voided directly into a 20 ml Universal container (Sterilin UK) and passed through a hatch from only one toilet in the clinic.


We investigated potential contamination in two ways.

  1. A run of dummy samples processed as normal: 60 dummy urine samples, 10 dummy swabs.

  2. A patient-throughput analysis to detect possible increases in positive CT results on busy days.

Dummy specimens: Two vials of sterile water and a universal container were taken into the toilet which was flushed with the container open. The sterile water was emptied into the container and then processed identically to routine specimens by nursing and laboratory staff. Dummy (unused) CT swabs were placed open on a tray in examination rooms for a week.

Patient-throughput analysis: Patient attendance at the Genitourinary Medicine clinic on any given day was categorised as low (<100), moderate (100–149) or high (>150). χ2 Tests assessed associations of sex, age, day of week, clinic-type and number of attendees with number of positive CT results. Poisson regression determined the association between the risk of a positive result on busy compared with quiet days (adjusted for confounders). As some clinic-types occurred only on certain week days, a sensitivity analysis was performed after excluding attendances at these non-daily clinics.


Dummy specimens: 60 dummy urines and 10 swabs all tested negative for CT (95% CI 0% to 5%). The swabs were exposed for a total of 50 clinic days.

Patient-throughput analysis (see table 1): Of 29 748 new patient attendances over 1 year (252 clinic days), 2860 (9.6%) had a positive CT result with similar proportions between men and women (9.9% and 9.4%, respectively), but a lower proportion in those aged over 25 (<40: 3.4%; 25–40: 7.3%) than in those under 25 (16.7%). Although fewest patients attended on Wednesdays (12.4%), the proportion of positive tests on Wednesdays was higher than on other days (relative risk 1.26; 95% CI 1.12 to 1.42). Approximately 11% of tests performed on low attendance days were positive compared with 9.0% and 9.7% of tests on moderate and high attendance days, respectively.

Table 1

Poisson regression model

After adjustment for age, sex, clinic-type and day of week days, busy- and moderate-throughput did not have significantly higher rates of positive results than quiet days (see table 1). As expected, CT positivity was associated with younger age (p<0.0001); an association was also seen with male gender in adjusted analyses only (p=0.04). The significance of increase in positive results on Wednesdays did not remain after adjustment for age.

After exclusion of attendances at non-daily clinics, 24 115 tests remained, of which 2394 (9.9%) were positive. Again the number of clinic attendees on a given day was not associated with the proportion of positive results.


As DNA contamination occurs as a two-stage process, environmental contamination and sample contamination from the environment, we hypothesised that contamination was more likely on busier days due to high-throughput. In this small study, we found no evidence of dummy sample contamination or a significant association between daily CT positivity rate and patient-throughput. These findings provide some reassurance that significant specimen contamination on busier days is unlikely.

While we did not detect a significant increase in the rate of positive results with higher patient attendance, our relatively wide CIs means we cannot rule out the possibility of an increase in risk of up to 30%. A larger study would provide greater power to detect any such effects. Furthermore, CT DNA can survive on surfaces for prolonged periods, so specimen contamination may also occur on subsequent days. These results apply to one routine clinic using the BD probeTec TM Qx assay. It is routine practice in diagnostic laboratories to check for possible cross-contamination. The extension of this simple routine practice to all clinical areas as we have done could provide quality assurance, improving confidence in results in the clinic setting.


Despite previous reports of environmental contamination of CT DNA, there was no evidence in our study of any detectable cross-contamination.

Key messages

  • Environmental contamination with DNA from Chlamydia trachomatis (CT) and Neisseria gonorrhoeae has been found in Genitourinary Medicine clinics.

  • A run of dummy samples, processed identically to normal clinic specimens, tested negative for CT.

  • There was no association between daily CT positive rate and clinic attendance on busy days.

  • False positive results due to specimen contamination are unlikely in our clinic.


The authors would like to thank the doctors and nursing staff in the Courtyard clinic, St Georges Hospital, London.



  • Contributors SYC conceived the study, collected data and drafted the manuscript. SJ carried out statistical analysis and drafted the statistical parts of the manuscript. RK collected samples. TS and MP participated in study design. PH and TP designed the study and helped to draft the manuscript. CS supervised the statistical analysis and helped to draft the manuscript. All authors contributed towards the revision of the manuscript.

  • Competing interests None.

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