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The Chlamydia trachomatis Plasmid Deletion Mutant —What Does it Mean to Us?

Schachter, Julius PhD

Sexually Transmitted Diseases: May 2007 - Volume 34 - Issue 5 - p 257
doi: 10.1097/OLQ.0b013e31805d0209

In an article in this issue of Sexually Transmitted Diseases, Ripa and Nilsson describe the detection of a Chlamydia trachomatis serovar E variant that has a 377-base pair deletion in the virtually ubiquitous cryptic plasmid.1 Although the function of the plasmid is not known, the fact that it is almost universal among C. trachomatis strains, and is present at multiple copies, has made it an attractive target for nucleic acid amplification tests (NAATs). Several of the tests that have been made commercially available have had regions in the plasmid DNA as targets. In Sweden, the existence of the deletion mutant was discovered because they were doing different NAATs on the same specimens. Discrepant results were seen between tests. Their routine test had a target in the plasmid, and results were often negative when a second NAAT, which had a chromosomal DNA (ompA) target, was positive. Over several months, approximately 20% of the chlamydial infections diagnosed with the ompA target were negative with the plasmid target. DNA sequencing studies identified the cause; a deleted region in the plasmid contained the target for the test yielding false-negative results. Ripa and Nilsson have developed a specific PCR assay that targets the DNA sequences that flank the deletion.

What does this mean to us? At the moment this observation seems to be fairly well localized to the Scandinavian population. Outside of southern Sweden, only 2 clinical specimens have been identified as containing this mutant. They were both in Norway and 1 specimen was collected from a visitor from Sweden.2 Thus, currently this observation does not seem to be important to C. trachomatis diagnostics in other settings. But potential implications for the future are obvious.

This observation could only have been made in a laboratory performing 2 different NAATs that targeted 2 different nucleic acid sequences. Any laboratory that is performing only 1 test might note a difference in prevalence or positivity rates, but that would be it. They would not know why. Some currently used tests would detect the variant, as they have different targets. These include BDProbeTec (Becton Dickinson, Sparks, MD), the APTIMA Combo 2 and APTIMA C. trachomatis assays (Gen-Probe, San Diego, CA), and the ARTUS C. trachomatis MOMP PCR (ARTUS GmbH, Hamburg, Germany). The Abbott M2000 RealTime PCR (Abbott Laboratories, Abbott Park, IL), currently only available in Europe, and the Roche AMPLICOR assays (Roche Molecular Systems, Branchburg, NJ) will not detect the variant.

There are 2 reasons to be concerned about such a variant. The obvious one is false negative test results. The second is that, assuming the mutant is at no biologic disadvantage, there would be a positive selective advantage to any microbe that would not be detected by screening tests.

There are no positive results from broad-based screening programs aimed at isolating or identifying the mutant.3,4 Certainly people are looking. One suspects that if the deletion mutants had been found, that would have been reported fairly quickly. We selected specimens in our archive that were positive in 1 NAAT and negative in another. They were sent to Kenneth Persson, in Sweden, who is also working on the mutant, but none were detected in our specimen collection. The bottom line is that we can still trust the results of our NAATs.

But this observation is a reminder as to how clever microbes are. Here the plasmid is cryptic and we do not have any known function; thus the relevant observation was the change in diagnostic test results. In other settings, changes in microbial chromosomal genes or acquisition of plasmids' nucleic acid sequences have lead to acquisition of antibiotic resistance, or pathogen's genes by commensals, or the addition or loss of enzyme functions that might have taxonomic or diagnostic implication. The bottom line is that we must be vigilant. Those bugs are clever little devils and they evolve; they don't stand still. This episode will certainly lead to some changes in NAATs for C. trachomatis.

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1. Ripa T, Nilsson PA. A Chlamydia trachomatis strain with a 377-bp deletion in the cryptic plasmid causing false-negative nucleic acid amplification tests. Sex Transm Dis 2007; 34:255–256.
2. Moghaddam A, Reinton N. Identification of the Swedish Chlamydia trachomatis variant among patients attending a STI clinic in Oslo, Norway. Euro Surveill 2007; 12(3).
3. van de Laar M, Ison C. Europe-wide investigation to assess the presence of new variant of Chlamydia trachomatis in Europe. Euro Surveill 2007 Feb 8; 12(2):E070208.4.
4. de Vries HJ, Catsburg A, van der Helm JJ, Beukelaar EC, Morre SA, Fennema JS, Theisbrummel H. No indication of Swedish Chlamydia trachomatis variant among STI clinic visitors in Amsterdam. Euro Surveill 2007 Feb 8; 12(2):E070208.3.
© Copyright 2007 American Sexually Transmitted Diseases Association