Genome Sequencing of Recent Clinical Chlamydia trachomatis Strains Identifies Loci Associated with Tissue Tropism and Regions of Apparent Recombination

Department of Biomedical Sciences, Oregon State University, Corvallis, Oregon 97331-4804, USA.
Infection and immunity (Impact Factor: 3.73). 03/2010; 78(6):2544-53. DOI: 10.1128/IAI.01324-09
Source: PubMed


The human pathogen Chlamydia trachomatis exists as multiple serovariants that have distinct organotropisms for different tissue sites. Culture and epidemiologic data have demonstrated that serovar G is more prevalent, while serovar E is less prevalent, for rectal isolates from men having sex with men (MSM). The relative prevalence of these serovars is the opposite for isolates from female cervical infections. In contrast, the prevalence of serovar J isolates is approximately the same at the different tissue sites, and these isolates are the only C-class strains that are routinely cultured from MSM populations. These correlations led us to hypothesize that polymorphisms in open reading frame (ORF) sequences correlate with the different tissue tropisms of these serovars. To explore this possibility, we sequenced and compared the genomes of clinical anorectal and cervical isolates belonging to serovars E, G, and J and compared these genomes with each other, as well as with a set of previously sequenced genomes. We then used PCR- and restriction digestion-based genotyping assays performed with a large collection of recent clinical isolates to show that polymorphisms in ORFs CT144, CT154, and CT326 were highly associated with rectal tropism in serovar G isolates and that polymorphisms in CT869 and CT870 were associated with tissue tropism across all serovars tested. The genome sequences collected were also used to identify regions of likely recombination in recent clinical strains. This work demonstrated that whole-genome sequencing along with comparative genomics is an effective approach for discovering variable loci in Chlamydia spp. that are associated with clinical presentation.

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Available from: Brendan M Jeffrey, Jan 17, 2014
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    • "We focused on tissue tropism in cervical, urethral, vaginal, anorectal and pharyngeal infections that are primarily caused by the anogenital genovars D to K, and the LGV genovars L1 to L3. Recent studies reported on several pathogen and host genes related to disease severity and tissue tropism [5, 21–24], but these studies focused primarily on the molecular basis underlying the disparities between ocular, genital, and LGV associated genovars. Although we did not find any indication for tissue tropism within the urogenital strains, the possible role of tissue tropism on the prevalence of anorectal LGV infections could not be determined, as our study did not include urogenital samples from MSM. "
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    ABSTRACT: Background Previous studies showed that C. trachomatis strains found in MSM are different from those in heterosexuals. This study investigates whether the differences in strain distribution between MSM and heterosexuals are due to tissue tropism. Methods C. trachomatis positive samples were collected from MSM (anorectal) and women (anorectal, cervical, vaginal, pharyngeal) visiting the STI outpatient clinic of Amsterdam between 2008 and 2013. All samples were typed using multilocus sequence typing (MLST). Epidemiological data were derived from electronic patient records. Results We obtained full MLST data for C. trachomatis from 207 MSM and 185 women, all with anorectal infections. Six large clusters were identified of which 3 consisted predominantly of samples from women (89%-100%), whereas the other 3 consisted predominantly of samples from MSM (97%-100%). Furthermore, we obtained full MLST data from 434 samples of 206 women with concurrent infections at multiple anatomical locations. No association was observed between C. trachomatis cluster and the anatomical location of infection. Conclusion We found no indication for tissue tropism in urogenital, pharyngeal and anorectal C. trachomatis infections. Combined with results from previously conducted studies, we hypothesize that MSM and heterosexuals have different distributions of C. trachomatis strains due to their separate sexual networks.
    BMC Infectious Diseases 08/2014; 14(1):464. DOI:10.1186/1471-2334-14-464 · 2.61 Impact Factor
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    • "have all the necessary recombination machinery despite an inclusion-confined lifestyle (Zhang et al., 1995; Demars et al., 2007; Joseph et al., 2011; Harris et al., 2012). Recombination has been documented between strains with different tissues tropisms, the lymphogranuloma venereum with the urogenital biovars, and within different genital strains in vitro and in vivo (Jeffrey et al., 2010, 2013; Harris et al., 2012). Whole genome sequencing analyses with a collection of diverse clinical isolates and laboratory strains have revealed that the recombination or mutation events often occur in several regions of the chromosome encoding surface-exposed proteins, such as MOMP, Pmps and the T3S system effector Tarp (Gomes et al., 2004; Brunelle and Sensabaugh, 2006; Gomes et al., 2006; Joseph et al., 2011; Harris et al., 2012). "
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    ABSTRACT: Bacteria have evolved specific adaptive responses to cope with changing environments. These adaptations include stress response phenotypes with dynamic modifications of the bacterial cell envelope and generation of membrane vesicles (MVs). The obligate intracellular bacterium, Chlamydia trachomatis, typically has a biphasic lifestyle, but can enter into an altered growth state typified by morphologically aberrant chlamydial forms, termed persistent growth forms, when induced by stress in vitro. How C. trachomatis can adapt to a persistent growth state in host epithelial cells in vivo is not well understood, but is an important question, since it extends the host-bacterial relationship in vitro and has thus been indicated as a survival mechanism in chronic chlamydial infections. Here, we review recent findings on the mechanistic aspects of bacterial adaptation to stress with a focus on how C. trachomatis remodels its envelope, produces MVs, and the potential important consequences of MV production with respect to host-pathogen interactions. Emerging data suggest that the generation of MVs may be an important mechanism for C. trachomatis intracellular survival of stress, and thus may aid in the establishment of a chronic infection in human genital epithelial cells.
    Frontiers in Cellular and Infection Microbiology 06/2014; 4:73. DOI:10.3389/fcimb.2014.00073 · 3.72 Impact Factor
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    • "There are data in the literature suggesting that recombination hotspots might be present within or around ompA[7,11,12], and also at other locations in the genome [34]. Our genome sequencing has added some support for this premise, as the D(s)/2923 genome discussed by Jeffrey et al. [10] has a hybrid D/E OmpA sequence, and apparent recombination sites within this strain are at or very near sites seen in other, independently isolated, clinical strains [9,11]. Other investigators have proposed and debated the concept of chlamydial recombination hotspots using analysis of chlamydial genome sequences from laboratory-generated or clinical strains [8,24,35]. "
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    ABSTRACT: Pre-genomic and post-genomic studies demonstrate that chlamydiae actively recombine in vitro and in vivo, although the molecular and cellular biology of this process is not well understood. In this study, we determined the genome sequence of twelve Chlamydia trachomatis recombinants that were generated in vitro under antibiotic selection. These strains were used to explore the process of recombination in Chlamydia spp., including analysis of candidate recombination hotspots, and to correlate known C. trachomatis in vitro phenotypes with parental phenotypes and genotypes. Each of the 190 examined recombination events was the product of homologous recombination, and no candidate targeting motifs were identified at recombination sites. There was a single deletion event in one recombinant progeny that resulted in the removal of 17.1 kilobases between two rRNA operons. There was no evidence for preference for any specific region of the chromosome for recombination, and analyses of a total of over 200 individual recombination events do not provide any support for recombination hotspots in vitro. Two measurable phenotypes were analyzed in these studies. First, the efficiency of attachment to host cells in the absence of centrifugation was examined, and this property segregated to regions of the chromosome that carry the polymorphic membrane protein (Pmp) genes. Second, the formation of secondary inclusions within cells varied among recombinant progeny, but this did not cleanly segregate to specific regions of the chromosome. These experiments examined the process of recombination in C. trachomatis and identified tools that can be used to associate phenotype with genotype in recombinant progeny. There were no data supporting the hypothesis that particular nucleotide selected sequences are preferentially used for recombination in vitro. Selected phenotypes can be segregated by analysis of recombination, and this technology may be useful in preliminary analysis of the relationship of genetic variation to phenotypic variation in the chlamydiae.
    BMC Microbiology 06/2013; 13(1):142. DOI:10.1186/1471-2180-13-142 · 2.73 Impact Factor
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