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High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
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2007 (English)In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 45, no 5, 1410-1414 p.Article in journal (Refereed) Published
Abstract [en]

Genotyping of Chlamydia trachomatis is limited by the low sequence variation in the genome, and no adequatemethod is available for analysis of the spread of chlamydial infections in the community. We have developeda multilocus sequence typing (MLST) system based on five target regions and compared it with analysis ofompA, the single gene most extensively used for genotyping. Sequence determination of 16 reference strains,comprising all major serotypes, serotypes A to L3, showed that the number of genetic variants in the fiveseparate target regions ranged from 8 to 16. The genetic variation in 47 clinical C. trachomatis isolates ofrepresentative serotypes (14 serotype D, 12 serotype E, 11 serotype G, and 10 serotype K strains) was analyzed;and the MLST system detected 32 variants, whereas 12 variants were detected by using ompA analysis.Specimens of the predominant serotype, serotype E, were differentiated into seven genotypes by MLST but intoonly two by ompA analysis. The MLST system was applied to C. trachomatis specimens from a population ofmen who have sex with men and was able to differentiate 10 specimens of one predominant ompA genotype Gvariant into four distinct MLST variants. To conclude, our MLST system can be used to discriminate C.trachomatis strains and can be applied to high-resolution molecular epidemiology.

Place, publisher, year, edition, pages
2007. Vol. 45, no 5, 1410-1414 p.
National Category
Medical and Health Sciences
Identifiers
URN: urn:nbn:se:uu:diva-13844DOI: 10.1128/JCM.02301-06ISI: 000246600300005PubMedID: 17329456OAI: oai:DiVA.org:uu-13844DiVA: diva2:41614
Available from: 2008-12-03 Created: 2008-12-03 Last updated: 2017-12-11Bibliographically approved
In thesis
1. Chlamydia trachomatis: Development of molecular typing methods and applications in epidemiology
Open this publication in new window or tab >>Chlamydia trachomatis: Development of molecular typing methods and applications in epidemiology
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

A general aim was to combine molecular typing methods with clinical background information to increase epidemiological knowledge about Chlamydia trachomatis infections.

An outbreak of Lymfogranuloma venereum (LGV), caused by a more invasive variant of C. trachomatis, was reported from the Netherlands in 2003 among men who have sex with men (MSM). All Chlamydia positive specimens from a venereal disease clinic for MSM in Stockholm during one year were genotyped. No spread of LGV was found, apart from three symptomatic cases. The same ompA genotypes were found among MSM in Melbourne, but the genotype distribution was different compared to findings among the heterosexual population in Sweden.

The standard method for genotyping of Chlamydia is ompA-sequencing, but it has low resolution because one genotype predominates. A multilocus sequence typing (MLST) system based on five targets was developed. In a sample of 47 specimens, 32 variants were found with MLST, but only 12 variants with ompA-sequencing. The polymorphisms in the hctB gene, one MLST target, are caused by an element of 108 bp that is present in two to four repetitions and in different variants. Although the DNA-binding function of Hc2 that is encoded by hctB has been studied, our findings of a considerable size variation show that new studies are needed.

In 2006, specimens with a 377 bp deletion in the cryptic plasmid covering the target region for diagnostic test systems from Abbott and Roche were discovered in Sweden. Applying MLST to these specimens indicated that there was a single clone, denoted nvCT. The proportion of nvCT in all detected Chlamydia cases was higher (20% to 65%) in counties using Abbott/Roche compared to counties using the BectonDickinson test system (7% to 20%). The proportions of nvCT converge in counties with high or low levels when detection systems were adjusted to detect nvCT.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2009. 71 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 488
Keyword
Chlamydia trachomatis, Lymphogranuloma venereum, Genotyping, MLST, nvCT, hctB, Hc2
National Category
Microbiology in the medical area
Research subject
Clinical Bacteriology
Identifiers
urn:nbn:se:uu:diva-108930 (URN)978-91-554-7625-0 (ISBN)
Public defence
2009-11-20, Hörsalen, Klinisk Mikrobiologi, Akademiska Sjukhuset, Dag Hammarskjöldsväg 17, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2009-10-30 Created: 2009-10-05 Last updated: 2009-10-30Bibliographically approved
2. Methods and Applications in Comparative Bacterial Genomics
Open this publication in new window or tab >>Methods and Applications in Comparative Bacterial Genomics
2007 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Comparative studies of bacterial genomes, now counting in the hundreds, generate massive amounts of information. In order to support a systematic and efficient approach to genomic analyses, a database driven system with graphic visualization of genomic properties was developed - GenComp. The software was applied to studies of obligate intracellular bacteria. In all studies, ORFs were extracted and grouped into ORF-families. Based on gene order synteny, orthologous clusters of core genes and variable spacer ORFs were identified and extracted for alignments and computation of substitution frequencies.

The software was applied to the genomes of six Chlamydia trachomatis strains to identify the most rapidly evolving genes. Five genes were chosen for genotyping, and close to a 3-fold higher discrimination capacity was achieved than that of serotypes.

With GenComp as the backbone, a massive comparative analysis were performed on the variable gene set in the Rickettsiaceae, which includes Rickettsia prowazekii and Orientia tsutsugamushi, the agents of epidemic and scrub typhus, respectively. O. tsutsugamushi has the most exceptional bacterial genome identified to date; the 2.2 Mb genome is 200-fold more repeated than the 1.1 Mb R. prowazekii genome due to an extensive proliferation of conjugative type IV secretion systems and associated genes. GenComp identified 688 core genes that are conserved across 7 closely related Rickettsia genomes along with a set of 469 variably present genes with homologs in other species. The analysis indicates that up to 70% of the extensively degraded and variably present genes represent mobile genetic elements and genes putatively acquired by horizontal gene transfer. This explains the paradox of the high pseudogene load in the small Rickettsia genomes. This study demonstrates that GenComp provides an efficient system for pseudogene identification and may help distinguish genes from spurious ORFs in the many pan-genome sequencing projects going on worldwide.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2007. 66 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 381
Keyword
Biology, Biologi
Identifiers
urn:nbn:se:uu:diva-8398 (URN)978-91-554-7061-6 (ISBN)
Public defence
2008-02-01, Zootissalen, Evolutionsmusset, Villavägen 9, Uppsala, 10:00 (English)
Opponent
Supervisors
Available from: 2008-01-10 Created: 2008-01-10 Last updated: 2010-03-16Bibliographically approved

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Klint, MarkusFuxelius, Hans-HenrikHerrmann, Björn

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