Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries

Abstract

eThe Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses. Chlamydia trachomatis is one of the most common sexually transmitted infections (STIs) worldwide (1), and besides urogenital infections, it also causes lymphogranuloma venereum (LGV), which is a rare but more invasive sexually transmitted disease. In addition, C. trachomatis causes the eye infection trachoma, which is the major infectious cause of preventable blindness worldwide. Severe sequelae from urogenital chlamydia infections include ectopic pregnancy and infertility (2). In spite of testing, treatment, partner notification, and counseling, huge public health efforts have not been able to control urogenital chlamydia infections. Current knowledge about the role of repeated infections and transmission in sexual networks is still limited and needs to be extended to achieve a reduction in the rate of infections.In this context, it is important to have adequate tools for genotyping to understand the epidemiology of chlamydia infections. Traditional typing of C. trachomatis was based on serotyping of the major outer membrane protein (MOMP) and, later on, genotyping of the ompA gene, which encodes MOMP. However, neither MOMP nor ompA provides sufficient discriminatory power for epidemiological purposes (3). In most countries, almost half of all urogenital chlamydia infections are of serotype E, and within this serotype the ompA E/Bour genotype predominates (4-8). Therefore, other typ...

European Chlamydia abortus livestock isolate genomes reveal unusual stability and limited diversity, reflected in geographical signatures

“…Two molecular typing schemes exist, using either multiple locus variable number tandem repeat analysis (MLVA), which has only identified seven MLVA sequence types (MTs) [19, 20], or multiple locus sequence typing (MLST) [19, 21], where only six MLST sequence types (STs) have been defined. This is in sharp contrast to greater diversity in other species of Chlamydia [21–23]. Studies on limited numbers of samples suggest that C. abortus isolates in livestock appear to be largely monomorphic: low diversity is observed throughout the genome, even within the plasticity zone (PZ), a region of high genomic variation in other chlamydial species [6, 9, 18].…”

Highly diverse MLVA-ompA genotypes of rectalChlamydia trachomatisamong men who have sex with men in Brighton, UK and evidence for an HIV-related sexual network

“…Furthermore, genome sequencing data reveals that omp A must not be relied on solely as a marker for genotyping, as recombination of all or parts of this gene within and between biovars is evident 15. There are now several very highly discriminating multilocus molecular typing systems, including multi locus sequence typing (MLST), for C. trachomatis that allow differentiation and subgrouping of isolates within a genotype 13 16 17 . W4–6 The multilocus variable number tandem repeat (VNTR) analysis plus analysis of the omp A gene (MLVA- omp A) high-resolution genotyping system of Pedersen et al ,13 has been successfully evaluated,18 and recent work has shown that the VNTR marker sequences are stable and therefore ideal for genotyping 19.…”

Spread of a new Chlamydia trachomatis variant from men who have sex with men to the heterosexual population after replacement and recombination in ompA and pmpH genes

“…In recent years, we have acquired a more complete view of the complex epidemiology of C. trachomatis [18,19]. In this study, we describe for the first time an onsite ecological displacement of a previous variant, and this replacement could also help to spread the infection more easily.…”

“…On the other hand, several authors defined clusters of transmission, identifying nodes with only G genotypes in MSM [22]. Furthermore, these publications consistently reported clusters with G and J genotypes in the MSM population, and they also found genotype J in the heterosexual population [19,23]. These results suggest that genotype J could be a 'bridge genotype'.…”