| 1. |
- Advani, Abdolreza
(författare)
-
Epidemiological characterisation of Bordatella pertussis in Sweden, 1970-2004
- 2007
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Worldwide, Bordetella pertussis causes some 50 million cases of pertussis, and an estimated 2-300,000 fatalities each year. In Sweden vaccination against pertussis was introduced in the 1950s using diphtheria-tetanus-whole-cell pertussis vaccine (DTPw) until 1979, when it was withdrawn due to concerns about effectiveness. Thereafter, there was a vaccination-free period until 1996 when diphtheria-tetanus-acellular pertussis vaccine (DTPa) was introduced. During the period without general vaccination, pertussis had become endemic, with an overall incidence of 120-150/100,000 person years. After the introduction of the acellular vaccines this trend was changed to 7-26/100,000 person years from 1998 through 2004. Nevertheless pertussis is still a health problem in Sweden, with more than 1000 reported cases each year. The primary aim of this study was to characterise the clinical isolates of B. pertussis collected during different vaccination periods in order to find possible shifts in circulating bacteria related to vaccination. A reference system for typing B. pertussis was established based on 1810 clinical isolates. Pulsed-Field Gel Electrophoresis (PFGE) was used as the main method in combination with fimbrial serotyping and gene sequencing of two other virulence factors, pertactin (PRN) and pertussis toxin (PT). We suggested 35 Swedish reference strains for PFGE traceability. This reference material is deposited at Culture Collection University of Gothenburg. Further characterisation of 1270 Swedish B. pertussis isolates collected during periods with different vaccination programs indicated shifts with respect to the PFGE profile, fimbrial serotype and prn genotype. A large number of PFGE profiles were identified but only a few were predominant during each period, and others replaced them over time. Shifts in fimbrial serotype occurred and were directly related to vaccination policy. In the DTPw or DTPa periods, Fim3 was significantly more prevalent and in the vaccination-free period Fim2. Prn1 was predominant during the DTPw period but was replaced by prn2 during the vaccine free period and DTPa period. Prn3 was sporadically observed through the study years with a peak in 1997-1998. The circulating strains differed from the vaccine strains in the studied markers and PFGE profiles. Changes in the B. pertussis population between three noted incidence peaks, in 1999-2000, 2002 and 2004, were investigated. The data showed that one profile, BpSR11, first seen in 1997, was dominating after 1999. Other BpSR11-related profiles, BpSR5 BpSR12, appeared with an increasing trend. Although vaccination with Pa has reduced disease, new variants have emerged in populations with high vaccination coverage. We compared Finnish (n=193) and Swedish (n=455) isolates circulating in 1998-2003 together with vaccine strains used in these neighbouring countries with different vaccination histories. The results suggest that the sequential epidemics were caused by clonal expansion of B. pertussis strains possibly transmitted from Sweden to Finland. BpSR11 was seen in the Swedish 1999 peak and later in the Finnish outbreak in 2003. As early as 1994, however, it was isolated in France. We analysed the association of PFGE profile and serotype to severity of disease for all children followed during the first seven years of a surveillance project. There were in all 927 children with both clinical information and strain characterisation data available. When two groups of strains characterised by PFGE profile or serotype were compared with clinical outcome, defined as duration of hospitalisation, spasmodic cough or complications, there were significantly more children with a long duration of hospital stay in the most frequent PFGE profile group (BpSR11) compared to the PFGE group of all other profiles (p=0.041). Our data indicate that the BpSR11 clone seems to have unique properties for spread and survival.
|
|
| 2. |
- Sandegren, Linus, et al.
(författare)
-
Genomic Stability over 9 Years of an Isoniazid Resistant Mycobacterium tuberculosis Outbreak Strain in Sweden
- 2011
-
Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:1, s. e16647-
-
Tidskriftsartikel (refereegranskat)abstract
- In molecular epidemiological studies of drug resistant Mycobacterium tuberculosis (TB) in Sweden a large outbreak of an isoniazid resistant strain was identified, involving 115 patients, mainly from the Horn of Africa. During the outbreak period, the genomic pattern of the outbreak strain has stayed virtually unchanged with regard to drug resistance, IS6110 restriction fragment length polymorphism and spoligotyping patterns. Here we present the complete genome sequence analyses of the index isolate and two isolates sampled nine years after the index case as well as experimental data on the virulence of this outbreak strain. Even though the strain has been present in the community for nine years and passaged between patients at least five times in-between the isolates, we only found four single nucleotide polymorphisms in one of the later isolates and a small (4 amino acids) deletion in the other compared to the index isolate. In contrast to many other evolutionarily successful outbreak lineages (e. g. the Beijing lineage) this outbreak strain appears to be genetically very stable yet evolutionarily successful in a low endemic country such as Sweden. These findings further illustrate that the rate of genomic variation in TB can be highly strain dependent, something that can have important implications for epidemiological studies as well as development of resistance.
|
|
| 3. |
|
|
| 4. |
- Storm, Martin, et al.
(författare)
-
Comparison of real-time PCR and pyrosequencing for typing Bordetella pertussis toxin subunit 1 variants
- 2006
-
Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 65:1, s. 153-158
-
Tidskriftsartikel (refereegranskat)abstract
- We describe two newly developed methods for rapid typing of the pertussis toxin subunit 1 gene (ptxS1). A real-time PCR assay based on hybridization probes and a Pyrosequencing assay were developed and the specificity, sensitivity, cost, hands-on time and post-assay data processing were compared to Sanger sequencing. Both methods enabled discrimination of all four allelic variants, correctly identified all ptxS1 alleles of 143 strains tested and proved suitable for large-scale screening of B. pertussis strains.
|
|
| 5. |
- Zheng, Zongli, et al.
(författare)
-
Titration-free 454 sequencing using Y adapters
- 2011
-
Ingår i: Nature Protocols. - : Springer Science and Business Media LLC. - 1754-2189 .- 1750-2799. ; 6:9, s. 1367-1376
-
Tidskriftsartikel (refereegranskat)abstract
- We describe a protocol for construction and quantification of libraries for emulsion PCR (emPCR)-based sequencing platforms such as Roche 454 or Ion Torrent PGM. The protocol involves library construction using customized Y adapters, quantification using TaqMan-MGB (minor groove binder) probe-based quantitative PCR (qPCR) and calculation of an optimal template-to-bead ratio based on Poisson statistics, thereby avoiding the need for a laborious titration assay. Unlike other qPCR methods, the TaqMan-MGB probe specifically quantifies effective libraries in molar concentration and does not require specialized equipment. A single quality control step prior to emulsion PCR ensures that libraries contain no adapter dimers and have an optimal length distribution. The presented protocol takes similar to 7 h to prepare eight barcoded libraries from genomic DNA into libraries that are ready to use for full-scale emPCR. It will be useful, for example, to allow analyses of precious clinical samples and amplification-free metatranscriptomics.
|
|
