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High Resolution Genotyping of Chlamydia trachomatis
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Chlamydia trachomatis is an obligate intracellular bacterium of major human health concern, causing urogential chlamydia infections, lymphogranuloma venereum (LGV) and trachoma. Chlamydia is one of the most common sexually transmitted infections worldwide and can cause infertility.

In the first four papers described herein we used a high resolution multilocus sequence typing (MLST) system to investigate the epidemiology of C. trachomatis, and showed that MLST is superior to conventional ompA genotyping with respect to resolution. In the fifth paper we simplified the methodology by developing and validating a multilocus typing (MLT) DNA microarray based on the MLST system.

In more detail, MLST analysis of consecutive specimens from 2006 in Örebro County in Sweden, and comparison to specimens from 1999-2000, showed that the new variant C. trachomatis (nvCT) is monoclonal and likely has appeared in recent years.

MLST analysis of LGV specimens from men who have sex with men (MSM) showed that the increase of LGV in Europe in the last decade indeed was a clonal outbreak, contrary to the USA where LGV might have been present all along.

In the third paper, clinical symptoms could not be correlated with the MLST genotypes, suggesting, together with the combined results of all previous studies, that bacterial factors, if important, need to be understood in the context of host factors.

MLST analysis of specimens from a high incidence C. trachomatis area in North Norway revealed interesting epidemiological details concerning unusual genetic variants, the nvCT and MSM, but found no significant difference in genetic diversity compared to two other geographic areas in Norway.

Lastly, we developed a MLT array that provides high resolution while being rapid and cost-effective, which makes it an interesting alternative for C. trachomatis genotyping.

In conclusion, the MLST system and the MLT array have proven to be useful tools and should now be applied in further investigations to improve our understanding of C. trachomatis epidemiology.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis , 2011. , 48 p.
Series
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 690
Keyword [en]
Chlamydia trachomatis: multilocus sequence typing: MLST: genotyping: lymphogranuloma venereum: new variant C. tracomatis: nvCT: multilocus typing DNA microarray: MLT array
National Category
Microbiology in the medical area
Research subject
Medical Science
Identifiers
URN: urn:nbn:se:uu:diva-156751ISBN: 978-91-554-8121-6 (print)OAI: oai:DiVA.org:uu-156751DiVA: diva2:433170
Public defence
2011-09-29, Hörsalen, Klinisk mikrobiologi, Akademiska sjukhuset, Dag Hammarskjöldsväg 17, Uppsala, 09:15 (English)
Opponent
Supervisors
Available from: 2011-08-30 Created: 2011-08-09 Last updated: 2011-09-08
List of papers
1. Characterisation of Chlamydia trachomatis by ompA sequencing and multilocus sequence typing in a Swedish county before and after identification of the new variant
Open this publication in new window or tab >>Characterisation of Chlamydia trachomatis by ompA sequencing and multilocus sequence typing in a Swedish county before and after identification of the new variant
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2010 (English)In: Sexually Transmitted Infections, ISSN 1368-4973, E-ISSN 1472-3263, Vol. 86, no 1, 56-60 p.Article in journal (Refereed) Published
Abstract [en]

OBJECTIVES: In 2006 a new variant of Chlamydia trachomatis (nvCT), with a deletion in the cryptic plasmid, was reported in Sweden. This deletion included the targets for the genetic diagnostic systems used in many clinical laboratories and resulted in thousands of false-negative results. The aim of this study was to characterise consecutive Chlamydia tissue culture-positive samples from 2006 in Orebro County, after identification of the nvCT, and to compare the results from samples collected in the same county in 1999-2000. The study also aimed to evaluate the discriminatory capacity of multilocus sequence typing (MLST) compared with ompA sequencing. METHODS: ompA sequencing and MLST was used to characterise 100 consecutive Chlamydia tissue culture-positive samples. RESULTS: A significant (p<0.001) increase of genotype E, from 47% in 1999-2000 to 69% in 2006, was detected. All 41 nvCT isolates from 2006 displayed an identical ompA genotype E and MLST profile. Excluding the nvCT isolates, the distribution of ompA genotypes is similar to the genotyping results from 1999-2000. Among the wild-type genotype E isolates from 2006, 14 unique MLST sequence types were obtained from 26 isolates while they were identical in ompA genotyping. The discriminatory power (D) of C trachomatis strains in this material was 83.5% using the MLST system compared with 49.5% utilising ompA sequencing. CONCLUSION: In all, MLST enables improved studies of the molecular epidemiology of C trachomatis. All nvCT isolates from 2006 displayed an identical ompA genotype E and MLST profile, which strongly indicates a clonal spread of the nvCT.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-125330 (URN)10.1136/sti.2009.037572 (DOI)000274525800014 ()19837730 (PubMedID)
Available from: 2010-05-17 Created: 2010-05-17 Last updated: 2017-12-12Bibliographically approved
2. Typing of Lymphogranuloma Venereum Chlamydia trachomatis Strains
Open this publication in new window or tab >>Typing of Lymphogranuloma Venereum Chlamydia trachomatis Strains
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2010 (English)In: Emerging Infectious Diseases, ISSN 1080-6040, E-ISSN 1080-6059, Vol. 16, no 11, 1777-1779 p.Article in journal (Refereed) Published
Abstract [en]

We analyzed by multilocus sequence typing 77 lymphogranuloma venereum Chlamydia trachomatis strains from men who have sex with men in Europe and the United States. Specimens from an outbreak in 2003 in Europe were monoclonal. In contrast, several strains were in the United States in the 1980s, including a variant from Europe.

National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-135357 (URN)10.3201/eid1611.100379 (DOI)000283699700023 ()
Available from: 2010-12-07 Created: 2010-12-06 Last updated: 2017-12-11Bibliographically approved
3. Multilocus sequence typing of urogenital Chlamydia trachomatis from patients with different degrees of clinical symptoms
Open this publication in new window or tab >>Multilocus sequence typing of urogenital Chlamydia trachomatis from patients with different degrees of clinical symptoms
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2011 (English)In: Sexually Transmitted Diseases, ISSN 0148-5717, E-ISSN 1537-4521, Vol. 38, no 6, 490-494 p.Article in journal (Refereed) Published
Abstract [en]

Background: In the past, contradictory results have been obtained linking Chlamydia trachomatis serovars (ompA gene) to different clinical courses of infection.

Methods: A high resolution multilocus sequence typing (MLST) system was used to genotype 6 genetic regions, including ompA, in 70 Dutch urogenital C. trachomatis strains from patients with different degrees of defined clinical symptoms (asymptomatic, symptomatic, and lower abdominal pain), to determine if MLST genotypes correlated with clinical manifestations of infection.

Results and conclusions: We identified 46 MLST types, with only a small overlap to Swedish MLST types. This study found no correlation between MLST profiles and symptomatology. To understand the clinical course of infection, future studies should not only consider bacterial factors but also look on the immunogenetics of the host.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-138699 (URN)10.1097/OLQ.0b013e31820b8be0 (DOI)000290561200005 ()
Available from: 2010-12-17 Created: 2010-12-17 Last updated: 2017-12-11Bibliographically approved
4. Multilocus Sequence Typing of Genital Chlamydia trachomatis in Norway Reveals Multiple New Sequence Types and a Large Genetic Diversity
Open this publication in new window or tab >>Multilocus Sequence Typing of Genital Chlamydia trachomatis in Norway Reveals Multiple New Sequence Types and a Large Genetic Diversity
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2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 3, e34452- p.Article in journal (Refereed) Published
Abstract [en]

Background: The Chlamydia trachomatis incidence rate in Finnmark, the most northern and sparsely populated county in Norway, has been twice the national average. This population based cross-sectional study among Finnmark high school students had the following aims: i) to examine distribution of multilocus sequence types (STs) of C. trachomatis in a previously unmapped area, ii) to compare chlamydia genetic diversity in Finnmark with that of two urban regions, and iii) to compare discriminatory capacity of multilocus sequence typing (MLST) with conventional ompA sequencing in a large number of chlamydia specimens.

Methodology: ompA sequencing and a high-resolution MLST system based on PCR amplification and DNA sequencing of five highly variable genetic regions were used. Eighty chlamydia specimens from adolescents aged 15-20 years in Finnmark were collected in five high schools (n = 60) and from routine clinical samples in the laboratory (n = 20). These were compared to routine clinical samples from adolescents in Tromso (n = 80) and Trondheim (n = 88), capitals of North and Central Norway, respectively.

Principal Findings: ompA sequencing detected 11 genotypes in 248 specimens from all three areas. MLST displayed 50 STs providing a five-fold higher resolution. Two-thirds of all STs were novel. The common ompA E/Bour genotype comprised 46% and resolved into 24 different STs. MLST identified the Swedish new variant of C. trachomatis not discriminated by ompA sequencing. Simpson's discriminatory index (D) was 0.93 for MLST, while a corrected D-c was 0.97. There were no statistically significant differences in ST genetic diversity between geographic areas. Finnmark had an atypical genovar distribution with G being predominant. This was mainly due to expansion of specific STs of which the novel ST161 was unique for Finnmark.

Conclusions/Significance: MLST revealed multiple new STs and a larger genetic diversity in comparison to ompA sequencing and proved to be a useful tool in molecular epidemiology of chlamydia infections.

Keyword
Chlamydia trachomatis epidemiology: multilocus sequence typing: novel genotypes: Swedish new variant of Chlamydia trachomatis
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-156747 (URN)10.1371/journal.pone.0034452 (DOI)000304489000111 ()
Note
Manuscript title: High-resolution Multilocus Sequence Typing of Chlamydia trachomatis reveals multiple new genotypes in North and Central NorwayAvailable from: 2011-08-09 Created: 2011-08-09 Last updated: 2017-12-08Bibliographically approved
5. High-Resolution Genotyping of Chlamydia trachomatis by Use of a Novel Multilocus Typing DNA Microarray
Open this publication in new window or tab >>High-Resolution Genotyping of Chlamydia trachomatis by Use of a Novel Multilocus Typing DNA Microarray
Show others...
2011 (English)In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 49, no 8, 2838-2843 p.Article in journal (Refereed) Published
Abstract [en]

Typing of Chlamydia trachomatis is important to understandingits epidemiology. Currently used methods such as DNA sequencingof the ompA gene and multilocus sequence typing (MLST) eitheroffer limited epidemiological resolution or are laborious andexpensive, or both. DNA microarray technology using the ArrayStripformat is an affordable alternative for genotyping. In thisstudy, we developed a new multilocus typing (MLT) DNA microarray,based on the target regions of a high-resolution MLST systemas well as software for easy analysis. Validation of the arraywas done by typing 80 previously MLST-typed clinical specimensfrom unselected adolescents in school. The MLT array showed100% specificity and provided 2.4-times-higher resolution thanompA sequencing, separating the commonly predominating ompAE/Bour genotype into 7 MLT array genotypes. The MLT array reproducedepidemiological findings revealed by the MLST system and showedsufficient sensitivity to work with clinical specimens. Comparedto MLST analysis, the expenses needed for testing a sample withthe MLT array are considerably lower. Moreover, testing canbe completed within 1 working day rather than 3 or 4 days, withdata analysis not requiring highly specialized personnel. Thepresent MLT array represents a powerful alternative in C. trachomatisgenotyping.

Keyword
Chlamydia trachomatis, genotyping, microarray, MLT array, multilocus sequence typing (MLST), multilocus typing array, ompA
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-156746 (URN)10.1128/JCM.00883-11 (DOI)000293221900009 ()
Available from: 2011-08-09 Created: 2011-08-09 Last updated: 2017-12-08Bibliographically approved

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