The diagnosis of syphilis can be complicated when it is based on diverse clinical manifestations, dark-field microscopy, and serology. In the present study, therefore, we examined the additional clinical value of a Treponema pallidum real-time TaqMan PCR for the detection of primary and secondary syphilis. The additional value of the T. pallidum real-time PCR for the diagnosis of primary syphilis was evaluated by the use of three different algorithms: (i) a head-to-head comparison of the dark-field microscopy result and the T. pallidum real-time PCR result, (ii) comparison of the clinical diagnosis made in a sexually transmitted infection clinic (STI) (including by dark-field microscopy) and the T. pallidum real-time PCR result, and (iii) comparison of the clinical diagnosis made in a general practitioner's office (without dark-field microscopy) and the T. pallidum real-time PCR result. A fourth algorithm was used to determine the performance of the T. pallidum real-time PCR regarding the detection of secondary syphilis. From December 2006 to April 2008, 716 patients with suspected cases of primary syphilis and 133 patients with suspected cases of secondary syphilis were included in the study. A kappa value of 0.601 was found for the agreement between dark-field microscopy and the T. pallidum real-time PCR. Good agreement was found between the T. pallidum real-time PCR and both the diagnosis of the general practitioner (kappa = 0.745) and the diagnosis of the STI clinic (kappa = 0.769). The sensitivity with respect to the STI clinic diagnosis was 72.8%, the specificity was 95.5%, the positive predictive value was 89.2%, and the negative predictive value was 95.0%. The T. pallidum real-time PCR is a fast, efficient, and reliable test for the diagnosis of primary syphilis in an STI outpatient clinic and a general practitioner setting, but it has no added diagnostic value for the diagnosis of secondary syphilis.

Genovar distributions of Chlamydia trachomatis based on ompA typing differ between men who have sex with men (MSM) and heterosexuals. We investigated clonal relationships using a high resolution typing method to characterize C. trachomatis types in these two risk groups. C. trachomatis positive samples were collected at the STI outpatient clinic in Amsterdam between 2008 and 2010 and genotyped by multilocus sequence typing. Clusters were assigned using minimum spanning trees and these were combined with epidemiological data of the hosts. We typed 526 C. trachomatis positive samples: 270 from MSM and 256 from heterosexuals. Eight clusters, containing 10–128 samples were identified of which 4 consisted of samples from MSM (90%–100%), with genovars D, G, J, and L2b. The other 4 clusters consisted mainly of samples from heterosexuals (87%–100%) with genovars D, E, F, I, and J. Genetic diversity was much lower in the MSM clusters than in heterosexual clusters. Significant differences in number of sexual partners and HIV-serostatus were observed for MSM–associated clusters. C. trachomatis transmission patterns among MSM and heterosexuals were largely distinct. We hypothesize that these differences are due to sexual host behavior, but bacterial factors may play a role as well.

Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. WGS data from 157 Ct isolates deposited in the Chlamydiales pubMLST database ( http://pubMLST.org/chlamydiales/ ) were annotated with 902 genes including the core and accessory genome. Plasmid associated genes were annotated and a plasmid MLST scheme was defined allowing plasmid sequence types to be determined. Plasmid allelic variation was investigated. Phylogenetic relationships were examined using the Genome Comparator tool available in pubMLST. Phylogenetic analyses identified four distinct Ct core genome clusters and six plasmid clusters, with a strong association between the chromosomal genotype and plasmid. This in turn was linked to ompA genovars and disease phenotype. Horizontal genetic transfer of plasmids was observed for three urogenital-associated isolates, which possessed plasmids more commonly found in isolates resulting from ocular infections. The pgp3 gene was identified as the most polymorphic plasmid gene and pgp4 was the most conserved. A strong association between chromosomal genome, plasmid type and disease was observed, consistent with previous studies. This suggests co-evolution of the Ct chromosome and their plasmids, but we confirmed that plasmid transfer can occur between isolates. These data provide a better understanding of the genetic diversity occurring across the Ct genome in association with the plasmid content.