| 1. |
- Eriksson, Lorraine, 1990-, et al.
(författare)
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Whole-Genome Sequencing of Emerging Invasive Neisseria meningitidis Serogroup W in Sweden
- 2018
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Ingår i: Journal of Clinical Microbiology. - : American Society for Microbiology. - 0095-1137 .- 1098-660X. ; 56:4
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Tidskriftsartikel (refereegranskat)abstract
- Invasive disease caused by Neisseria meningitidis serogroup W (MenW) has historically had a low incidence in Sweden, with an average incidence of 0.03 case/100,000 population from 1995 to 2014. In recent years, a significant increase in the incidence of MenW has been noted in Sweden, to an average incidence of 0.15 case/100,000 population in 2015 to 2016. In 2017 (1 January to 30 June), 33% of invasive meningococcal disease cases (7/21 cases) were caused by MenW. In the present study, all invasive MenW isolates from Sweden collected in 1995 to June 2017 (n = 86) were subjected to whole-genome sequencing to determine the population structure and to compare isolates from Sweden with historical and international cases. The increase of MenW in Sweden was determined to be due to isolates belonging to the South American sublineage of MenW clonal complex 11, namely, the novel U.K. 2013 lineage. This lineage was introduced in Sweden in 2013 and has since been the dominant lineage of MenW.
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| 2. |
- Jacobsson, Susanne, 1974-, et al.
(författare)
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Neisseria meningitidis carriage in Swedish teenagers associated with the serogroup W outbreak at the World Scout Jamboree, Japan 2015
- 2018
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Ingår i: Acta Pathologica, Microbiologica et Immunologica Scandinavica (APMIS). - : Wiley-Blackwell Publishing Inc.. - 0903-4641 .- 1600-0463. ; 126:4, s. 337-341
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Tidskriftsartikel (refereegranskat)abstract
- The aims of the study were to estimate the carrier state of Neisseria meningitidis in Swedish teenagers and its association with an outbreak at the World Scout Jamboree in 2015 as well as to compare sensitivity of throat versus nasopharyngeal swab for optimal detection of carriage. In total, 1 705 samples (cultures n = 32, throat swabs n = 715, nasopharyngeal swabs n = 958) from 1 020 Jamboree participants were collected and sent to the National Reference Laboratory for Neisseria meningitidis for culture and molecular analysis. The overall positivity for N. meningitidis was 8% (83/1 020), whereas 2% (n = 22) belonged to a known sero/genogroup while the majority (n = 61) were non-groupable. Throat sample is clearly the sampling method of choice, in 56 individuals where both throat and nasopharynx samples were taken, N. meningitidis was detected in both throat and nasopharynx in eight individuals, in 46 individuals N. meningitidis was only detected in the throat and in two individuals only in the nasopharynx. Carriage studies are important to provide knowledge of the current epidemiology and association between carrier isolates and disease-causing isolates in a given population. Therefore, planning for a carriage study in Sweden is in progress.
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| 3. |
- Stenmark, Bianca, 1987-, et al.
(författare)
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Methylome comparison of two meningococcal sub-lineages of serogroup Y cc23
- 2018
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Konferensbidrag (refereegranskat)abstract
- Introduction: A significant increase in invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (MenY) ST-23 clonal complex (cc23) emerged in the United States during the 1990s, spreading to Europe shortly thereafter. The largest increase was observed in Sweden with incidence proportions up to 53%. Genome analysis of all MenY isolates causing IMD between 1995 to 2012 in Sweden revealed that a distinct strain (YI) and more specifically a subtype (1) of this strain was found to be responsible for the increase of MenY IMD in Sweden [1]. In this study, we compared the methylomes of subtype 1 to the less successful subtype 2, using Single Molecule Real-Time (SMRT) sequencing technology.Methods: Ten genomes belonging to subtype 1 (n=7) and 2 (n=3) and one MenY genome without connection to a specific lineage were sequenced using SMRT sequencing on a PacBio®RS II. The analysis platform SMRT Portal v2 was used to identify modified positions and for the genome-wide analysis of modified motifs. DNA methyltransferase genes associated with the different methyltransferase recognition motifs identified were searched using SEQWARE. The modification-dependent restriction endonucleases MspJI and FspEI were used to determine the m5C recognition sites of the active m5C methylases in the strains.Results: The genome-wide analysis of the methylomes identified two m6A modified motifs: GATC and CACNNNNNTAC, but the latter was only found in isolates belonging to subtype 2 due to a transposase inserted in the candidate gene in subtype 1 strains: a Type I restriction system specificity protein (NEIS2535). The motif CACNNNNNTAC was only found in one other meningococcal isolate in REBASE, belonging to cc23, suggesting that this is a cc23 specific motif. Eleven putative restriction modification (RM) systems were found when comparing the sequences of all 11 genomes to DNA methyltransferase genes in REBASE. Five m5C genes were predicted, however, only three of these corresponding to the motifs: GCRYGC, GGNNCC and CCAGR were confirmed as active using MspJI and FspEI cleavage. The apparent CCAGR motif may be the result of two methylases, one recognizing CCWGG and the other CCAGA, but this will have to be verified.Conclusion: These results are consistent with previous studies [2] that have shown that the composition of different RM systems are clade specific suggesting that the unique RM system of cc23 isolates will most likely result in a specific DNA methylation pattern unique to this particular cc. However, although the majority of methyltransferases were shared between the two subtypes, there was one difference in a m6A modified motif between these two highly similar cc23 subtypes, which may lead to an altered gene expression pattern.
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| 4. |
- Stenmark, Bianca, 1987-, et al.
(författare)
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Whole genome sequencing of the emerging invasive Neisseria meningitidis serogroup W in Sweden
- 2017
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Ingår i: 14th Congress of the EMGM, European Meningococcal and Haemophilus Disease Society. - Prague : EMGM. - 9788090666238 ; , s. 7-8
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Introduction: The incidence of Neisseria meningitidisserogroup W (MenW) causing invasive meningococcal disease has historically been low. In 2015 an increase in MenW was observed in Sweden when an incidence of 0.1/100,000 population (10 cases) was reported, compared to an incidence of 0.02 (2 cases), in 2014. In 2016 the number of cases had almost doubled (18 cases, incidence of 0.2). England and Wales have also reported an increase of MenW from 2009 which was determined to be due to a sublineage in the South American/UK strain, called novel UK-2013 strain1. Both the South American/UK strain cluster and the novel UK-2013 strain belong to clonal complex (cc) 11, which consists of different strains from different serogroups associated with outbreaks that have occurred around the world2.Aim: The aim was to determine the population structure of MenW in Sweden compared to historical and international cases.Material and methods: All invasive MenW isolates collected in Sweden between 1995 and 2016 (n=71) were whole genome sequenced on the MiSeq (Illumina) using Nextera XT library preparation kit (Illumina) and MiSeq reagent Kit v3, 600 cycles. Reads were de novo assembled using Velvet within SeqSphere (Ridom GmbH). Genomes were uploaded to the Neisseria PubMLST database and genome comparison was performed with the genome comparator tool within pubMLST, comparing 1605 species specific core genes. The generated distance matrices were visualized using SplitsTree4 V4.Results: The most common fine type among the Swedish isolates was P1.5-2: F1-1: ST-11 (cc11) (n=31). Theisolates belonged to four different clonal complexes: cc11, cc22, cc60 and cc174, and the majority of isolates (39/71) belonged to cc11. No particular clonal complex dominated during the investigated time period except for cc11 since 2014. Core genome comparison showed that the majority of Swedish MenW isolates clustered with the South American/UK strain (n=26), six isolates clustered with the Hajj-associated strain and seven isolates were not associated to any strain. The majority of Swedish isolates in the South American/UK strain cluster, were from 2015 to 2016 and more specifically belonged to the UK sublineages: 23 isolates in the novel UK-2013 strain and three isolates in the original UK-strain.Conclusion: In conclusion, the increase of MenW in Sweden is comprised of isolates belonging to the South American/UK sublineage, more specifically the novel UK-2013 strain currently increasing in England and Wales.References:1 Lucidarme J, Scott KJ, Ure R, Smith A, Lindsay D, Stenmark B, et al. An international invasive meningococcal disease outbreak due to a novel and rapidly expanding serogroup W strain, Scotland and Sweden, July to August 2015. Euro Surveill. 2016;21(45):pii=303952 Lucidarme J, Hill DM, Bratcher HB, Gray SJ, du Plessis M, Tsang RS, et al. Genomic resolution of an aggressive, widespread, diverse and expanding meningococcal serogroup B, C and W lineage. The Journal of infection. 2015;71(5):544-52
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| 5. |
- Säll, Olof, 1980-, et al.
(författare)
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Etiology of Central Nervous System Infections in a Rural Area of Nepal Using Molecular Approaches
- 2019
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Ingår i: American Journal of Tropical Medicine and Hygiene. - : HighWire Press. - 0002-9637 .- 1476-1645. ; 101:1, s. 253-259
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Tidskriftsartikel (refereegranskat)abstract
- The etiology of infections of the central nervous system (CNS) in Nepal often remains unrecognized because of underdeveloped laboratory facilities. The aim of this study was to investigate the etiology of CNS infections in a rural area of Nepal using molecular methods. From November 2014 to February 2016, cerebrospinal fluid (CSF) was collected from 176 consecutive patients presenting at United Mission Hospital in Tansen, Nepal, with symptoms of possible CNS infection. After the CSF samples were stored and transported frozen, polymerase chain reaction (PCR) was performed in Sweden, targeting a total of 26 pathogens using the FilmArray® ME panel (BioFire, bioMerieux, Salt Lake City, UT), the MeningoFinder® 2SMART (PathoFinder, Maastricht, The Netherlands), and an in-house PCR test for dengue virus (DENV), Japanese encephalitis virus (JEV), and Nipah virus (NiV). The etiology could be determined in 23%. The bacteria detected were Haemophilus influenzae (n = 5), Streptococcus pneumoniae (n = 4), and Neisseria meningitidis (n = 1). The most common virus was enterovirus detected in eight samples, all during the monsoon season. Other viruses detected were cytomegalovirus (n = 6), varicella zoster virus (n = 5), Epstein-Barr virus (n = 3), herpes simplex virus (HSV) type 1 (HSV-1) (n = 3), HSV-2 (n = 3), human herpes virus (HHV) type 6 (HHV-6) (n = 3), and HHV-7 (n = 2). Cryptococcus neoformans/gatti was found in four samples. None of the samples were positive for DENV, JEV, or NiV. Of the patients, 67% had been exposed to antibiotics before lumbar puncture. In conclusion, the etiology could not be found in 77% of the samples, indicating that the commercial PCR panels used are not suitable in this setting. Future studies on the etiology of CNS infections in Nepal could include metagenomic techniques.
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| 6. |
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| 7. |
- Thulin Hedberg, Sara, 1980-, et al.
(författare)
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Droplet digital PCR for absolute quantification of proviral load of human T-cell lymphotropic virus (HTLV) types 1 and 2
- 2018
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Ingår i: Journal of Virological Methods. - : Elsevier. - 0166-0934 .- 1879-0984. ; 260, s. 70-74
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Human T-lymphotrophic virus (HTLV) types 1 and 2 cause lifelong infection whereby most infected individuals are asymptomatic whilst a minority develop infection-related disease. These latter patients invariably have been found to have high proviral load (PVL). Therefore, infected patients are monitored by determining the proportion of lymphocytes that are infected with HTLV-1/2. An increase in PVL has been shown to represent an increasing risk of developing HTLV-associated diseases. Monitoring of PVL requires a reliable and sensitive method. In this study assays based on droplet digital PCR (ddPCR) were established and evaluated for detection and quantification of HTLV-1/2.OBJECTIVES: To develop two parallel assays to detect the tax genes and determine the PVL of HTLV-1 and -2.STUDY DESIGN: Sixty-seven clinical samples from patients infected with HTLV-1 or HTLV-2 were analysed. The samples had previously been analysed with a qPCR and a comparison between ddPCR and qPCR was performed. The specificity of the assays were determined by analyzing samples from 20 healthy blood donors.RESULTS: The ddPCR was a stable and sensitive method for detection and quantification of HTLV-1 and -2. When comparing the qPCR and ddPCR the correlation was high (Pearsons correlation coefficient 0.96). The variability of the ddPCR was very low with intra-assay coefficient of variation (CV) of 0.97-3.3% (HTLV-1) and 1.7-8.2% (HTLV-2) and inter-assay CV of 1.8-6.1% (HTLV-1) and 1.2-12.9% (HTLV-2).CONCLUSIONS: The ddPCR reliably quantified HTLV DNA in clinical samples and could be a useful tool for monitoring of PVLs in HTLV-infected individuals.
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| 8. |
- Thulin Hedberg, Sara, et al.
(författare)
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Invasive meningococcal disease in Sweden 2016
- 2017
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Ingår i: 14th Congress of the EMGM, European Meningococcal and Haemophilus Disease Society. - Prague : The European Meningococcal and Haemophilus Disease Society EMGM. - 9788090666238 ; , s. 69-69
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Invasive meningococcal disease (IMD) is notifiable in Sweden. The reporting system comprises of mandatory notification of cases and mandatory laboratory notification of samples to the Public Health Agency of Sweden, Stockholm. All samples are sent to the National Reference Laboratory for Pathogenic Neisseria, Örebro for further typing and surveillance.In 2016, 62 cases of IMD (incidence 0.6/100 000 population) were reported in Sweden. Among the patients 58 % were females and 42 % males, aged from 1 month to95 years with mean age of 42 years. The incidence was highest, as in previous years, in the age group 15-19 years (2.1/100 000 population) followed by elderly ≥80 years (1.8/100 000 population) and infants ≤1 year (1.7/100 000 population). The case fatality rate increased in 2016 to 12.9 % compared with 7.5 % in 2015, eight people died from the disease (MenW, n=3; MenY, n=2; MenB, n=2 and MenC n=1). None of the IMD cases in 2016 had any epidemiological linkage.All 62 cases of IMD were laboratory confirmed: 54 were culture-confirmed, three PCR-confirmed and in five cases further typing data are missing because no samples were sent to the National Reference Laboratory for Pathogenic Neisseria. The serogroup distribution was MenW (n=18, 31.5 %), MenY (n=18, 31.5 %), MenB (n=10, 17.5 %), MenC (n=10, 17.5 %) and one non-groupable isolate. The W:P1.5,2:F1-1:ST11 (cc11) (n=15) were predominant among the culture-confirmed meningococci during 2016 followed by Y:P1.5-2,10-1:F4-1:ST23 (cc23) (n=7) och Y:P1.5-1,2-2:F5-8:ST23 (cc23) (n=6). Antibiotic susceptibility testing was performed with Gradient test (Etest, BioMerieux). Decreased susceptibility to penicillin was seen in 30 % of the isolates (MIC >0,064 mg/L) of which one was resistant (MIC=0.5 mg/L). One of the isolates with decreased susceptibility to penicillin was also resistant to ciprofloxacin (MIC=0.125 mg/L). All other isolates were susceptible to cefotaxime, chloramphenicol, ciprofloxacin, rifampicin and meropenem. No β-lactamase producing isolates has so far been found in Sweden.To conclude, the incidence of IMD continues to be relatively low in Sweden, however, a shift in the serogroup distribution of N. meningitidisin Sweden is ongoing; the previously dominating disease-causing MenB and MenC have been replaced, first by MenY which emerged in 2009 and since 2015 also by MenW. MenW has gone from only causing invasive disease in a few, 0-6 cases per year from 1990 onwards, to now being the dominating serogroup together with MenY in Sweden 2016.
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| 9. |
- Törös, Bianca, 1987-, et al.
(författare)
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Genome-based characterization of emergent invasive Neisseria meningitidis serogroup Y isolates in Sweden from 1995 to 2012
- 2015
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Ingår i: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 53:7, s. 2154-2162
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Tidskriftsartikel (refereegranskat)abstract
- Invasive meningococcal disease (IMD) caused by Neisseria meningitidis serogroup Y has increased in Europe, especially in Scandinavia. In Sweden, serogroup Y is now the dominating serogroup, and in 2012, the serogroup Y disease incidence was 0.46/100,000 population. We previously showed that a strain type belonging to sequence type 23 was responsible for the increased prevalence of this serogroup in Sweden. The objective of this study was to investigate the serogroup Y emergence by whole-genome sequencing and compare the meningococcal population structure of Swedish invasive serogroup Y strains to those of other countries with different IMD incidence. Whole-genome sequencing was performed on invasive serogroup Y isolates from 1995 to 2012 in Sweden (n = 186). These isolates were compared to a collection of serogroup Y isolates from England, Wales, and Northern Ireland from 2010 to 2012 (n = 143), which had relatively low serogroup Y incidence, and two isolates obtained in 1999 in the United States, where serogroup Y remains one of the major causes of IMD. The meningococcal population structures were similar in the investigated regions; however, different strain types were prevalent in each geographic region. A number of genes known or hypothesized to have an impact on meningococcal virulence were shown to be associated with different strain types and subtypes. The reasons for the IMD increase are multifactorial and are influenced by increased virulence, host adaptive immunity, and transmission. Future genome-wide association studies are needed to reveal additional genes associated with serogroup Y meningococcal disease, and this work would benefit from a complete serogroup Y meningococcal reference genome.
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