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: 4.16). 03/2010; 78(6):2544-53. DOI: 10.1128/IAI.01324-09
Source: PubMed

ABSTRACT 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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    • "Obtaining these data rapidly is a new challenge , particularly pertinent in the study of difficult-to-culture or fastidious bacteria. Until now, cell culture has been necessary to generate sufficient C. trachomatis DNA for genome sequencing (Stephens et al. 1998; Carlson et al. 2005; Thomson et al. 2008; Seth-Smith et al. 2009; Jeffrey et al. 2010; Unemo et al. 2010; Somboonna et al. 2011; Harris et al. 2012; Joseph et al. 2012). Using clinical samples as a starting material, several months of passaging is often required . "
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    ABSTRACT: The use of whole-genome sequencing as a tool for the study of infectious bacteria is of growing clinical interest. Chlamydia trachomatis is responsible for sexually transmitted infections and the blinding disease trachoma, which affect hundreds of millions of people worldwide. Recombination is widespread within the genome of C. trachomatis, thus whole-genome sequencing is necessary to understand the evolution, diversity, and epidemiology of this pathogen. Culture of C. trachomatis has, until now, been a prerequisite to obtain DNA for whole-genome sequencing; however, as C. trachomatis is an obligate intracellular pathogen, this procedure is technically demanding and time consuming. Discarded clinical samples represent a large resource for sequencing the genomes of pathogens, yet clinical swabs frequently contain very low levels of C. trachomatis DNA and large amounts of contaminating microbial and human DNA. To determine whether it is possible to obtain whole-genome sequences from bacteria without the need for culture, we have devised an approach that combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification. Using IMS-MDA in conjunction with high-throughput multiplexed Illumina sequencing, we have produced the first whole bacterial genome sequences direct from clinical samples. We also show that this method can be used to generate genome data from nonviable archived samples. This method will prove a useful tool in answering questions relating to the biology of many difficult-to-culture or fastidious bacteria of clinical concern.
    Genome Research 03/2013; 23(5). DOI:10.1101/gr.150037.112 · 13.85 Impact Factor
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    • "In fact, it has been shown that several IGRs exhibit the same phylogenetic signal as neighboring genes (Nunes et al. 2008). Finally, although mutation events likely constitute the C. trachomatis major evolutionary driving force (Nunes et al. 2008), phenomena of genome-dispersed recombination have been recently described, seemingly related to tissue tropism and antigenic variability (Millman et al. 2001; Gomes et al. 2007; Jeffrey et al. 2010). Accordingly , we applied the widely used robust bioinformatic platform ClonalFrame (Didelot and Falush 2007) to several data sets encompassing loci that may differently impact the estimation of recombination and mutation rates, namely, (i) HKs from a recently developed MLST scheme (Dean et al. 2009); (ii) positively selected genes (PSG); (iii) five groups of loci strictly ranked by their number of alleles; and (iv) intergenic regions. "
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    ABSTRACT: The knowledge of the frequency and relative weight of mutation and recombination events in evolution is essential for understanding how microorganisms reach fitted phenotypes. Traditionally, these evolutionary parameters have been inferred by using data from multilocus sequence typing (MLST), which is known to have yielded conflicting results. In the near future, these estimations will certainly be performed by computational analyses of full-genome sequences. However, it is not known whether this approach will yield accurate results as bacterial genomes exhibit heterogeneous representation of loci categories, and it is not clear how loci nature impacts such estimations. Therefore, we assessed how mutation and recombination inferences are shaped by loci with different genetic features, using the bacterium Chlamydia trachomatis as the study model. We found that loci assigning a high number of alleles and positively selected genes yielded nonconvergent estimates and incongruent phylogenies and thus are more prone to confound algorithms. Unexpectedly, for the model under evaluation, housekeeping genes and noncoding regions shaped estimations in a similar manner, which points to a nonrandom role of the latter in C. trachomatis evolution. Although the present results relate to a specific bacterium, we speculate that microbe-specific genomic architectures (such as coding capacity, polymorphism dispersion, and fraction of positively selected loci) may differentially buffer the effect of the confounding factors when estimating recombination and mutation rates and, thus, influence the accuracy of using full-genome sequences for such purpose. This putative bias associated with in silico inferences should be taken into account when discussing the results obtained by the analyses of full-genome sequences, in which the "one size fits all" approach may not be applicable.
    G3-Genes Genomes Genetics 07/2012; 2(7):761-8. DOI:10.1534/g3.112.002923 · 2.51 Impact Factor
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    • "and were shown to be expressed as variant surface antigens and to be important adhesins mediating the binding of the EB to human epithelial cells via their GGA[ILV] and FXXN repeats (Tan et al., 2009; Molleken et al., 2010). There is also evidence for a role of Pmp in tissue tropism (Jeffrey et al., 2010). Using TrichDB 48 TvPmp entries positive for the InterPro profile IPR003368:Chlamydia_PMP were identified. "
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