| 1. |
- Eriksson, Lorraine, 1990-, et al.
(författare)
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Difference in virulence between Neisseria meningitidis serogroups W and Y in transgenic mice
- 2020
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Ingår i: BMC Microbiology. - : BioMed Central. - 1471-2180. ; 20:1
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Neisseria meningitidis serogroups W and Y are the most common serogroups causing invasive meningococcal disease in Sweden. The majority of cases are caused by the serogroup W UK 2013 strain of clonal complex (cc) 11, and subtype 1 of the serogroup Y, YI strain of cc23. In this study, virulence factors of several lineages within cc11 and cc23 were investigated in transgenic BALB/c mice expressing human transferrin. Transgenic mice were infected intraperitoneally with serogroup W and Y isolates. Levels of bacteria and the proinflammatory cytokine CXCL1 were determined in blood collected 3 h and 24 h post-infection. Apoptosis was investigated in immune cells from peritoneal washes of infected mice. Adhesion and induction of apoptosis in human epithelial cells were also scored.RESULTS: The levels of bacteraemia, CXCL1, and apoptosis were higher in serogroup W infected mice than in serogroup Y infected mice. Serogroup W isolates also induced higher levels of apoptosis and adhesion in human epithelial cells. No significant differences were observed between different lineages within cc11 and cc23.CONCLUSIONS: N. meningitidis Serogroup W displayed a higher virulence in vivo in transgenic mice, compared to serogroup Y. This was reflected by higher bacteremia, proinflammatory activity, and ability to induce apoptosis in mouse immune cells and human epithelial cells.
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| 2. |
- Eriksson, Lorraine, 1990-
(författare)
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Exploring genomic and phenotypic differences in Neisseria meningitidis : understanding carriage and invasive disease
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Neisseria meningitidis can colonise the nasopharynx in humans and is also the cause of invasive meningococcal disease (IMD), which often presents as septicaemia and meningitis with high mortality rates. Invasive disease is often associated with specific capsular serogroups and clonal complexes (CC). In Sweden, serogroups Y and W have had a high incidence in recent years, but were previously considered rare causes of IMD, suggesting a change in the virulence potential of these serogroups. Currently, no specific genes exist that can reliably predict whether an N. meningitidis isolate will result in invasive disease or remain in the carriage state. Genetically similar isolates can be found during carriage and IMD, and it is more common for the carriage isolates to lack a capsule. The aim of this thesis was to investigate how genetic and phenotypic differences in N. meningitidis, can affect the virulence and the transition from a carriage state to invasive disease.The results indicate that the increase of serogroup W in Sweden is due to a specific lineage of CC11. This CC is rarely found among carriers and is considered highly virulent. Infections in transgenic mice with serogroup W CC11 isolates showed a greater virulence compared to serogroup Y isolates from other CCs. Although both serogroups are common causes of IMD in Sweden, they differ in virulence in transgenic mice. A genome-wide association study comparing carriage and invasive isolates, revealed that there were genetic variants in genes associated with virulence between these isolates. Among these variants were pilE/pilS, which are involved in the type IV pili. Comparison of pilE gene expression between carriage and invasive isolates showed no significant difference between these isolates. However, a difference in the class of the PilE protein was found between invasive and carriage isolates. Further research is needed to understand the impact of these genetic variations on the transition from carriage to invasive disease, also considering how factors in the human host and the environment that may contribute to the development of invasive disease.
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| 3. |
- Eriksson, Lorraine, 1990-, et al.
(författare)
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Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis
- 2023
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Ingår i: Microbial Genomics. - : Microbiology Society. - 2057-5858. ; 9:10
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Tidskriftsartikel (refereegranskat)abstract
- Neisseria meningitidis can be a human commensal in the upper respiratory tract but is also capable of causing invasive diseases such as meningococcal meningitis and septicaemia. No specific genetic markers have been detected to distinguish carriage from disease isolates. The aim here was to find genetic traits that could be linked to phenotypic outcomes associated with carriage versus invasive N. meningitidis disease through a bacterial genome-wide association study (GWAS). In this study, invasive N. meningitidis isolates collected in Sweden (n=103) and carriage isolates collected at Örebro University, Sweden (n=213) 2018-2019 were analysed. The GWAS analysis, treeWAS, was applied to single-nucleotide polymorphisms (SNPs), genes and k-mers. One gene and one non-synonymous SNP were associated with invasive disease and seven genes and one non-synonymous SNP were associated with carriage isolates. The gene associated with invasive disease encodes a phage transposase (NEIS1048), and the associated invasive SNP glmU S373C encodes the enzyme N-acetylglucosamine 1-phosphate (GlcNAC 1-P) uridyltransferase. Of the genes associated with carriage isolates, a gene variant of porB encoding PorB class 3, the genes pilE/pilS and tspB have known functions. The SNP associated with carriage was fkbp D33N, encoding a FK506-binding protein (FKBP). K-mers from PilS, tbpB and tspB were found to be associated with carriage, while k-mers from mtrD and tbpA were associated with invasiveness. In the genes fkbp, glmU, PilC and pilE, k-mers were found that were associated with both carriage and invasive isolates, indicating that specific variations within these genes could play a role in invasiveness. The data presented here highlight genetic traits that are significantly associated with invasive or carriage N. meningitidis across the species population. These traits could prove essential to our understanding of the pathogenicity of N. meningitidis and could help to identify future vaccine targets.
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| 4. |
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| 5. |
- 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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| 6. |
- Stenmark, Bianca, 1987-, et al.
(författare)
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Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease
- 2020
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif CACNNNNNTAC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.
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| 7. |
- Stenmark, Bianca, 1987-, et al.
(författare)
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Complete genome and methylome comparison of two Neisseria meningitidis serogroup Y subtypes
- 2017
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Ingår i: 2nd ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines. - Washington, DC : American Society for Microbiology. ; , s. 32-33
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Background: A significant increase in invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (MenY) strains 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%. cgMLST 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]. The aim was to compare the complete genome and methylome 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 strain were sequenced using SMRT sequencing on a PacBio®RS II. 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 the Restriction Enzyme Database REBASE (rebase.neb.com).Results: Genomic comparison of the two MenY subtypes revealed that these possessed highly similar genomes, only two genes encoding hypothetical proteins were present in subtype 2 but absent in subtype 1. There were 99 genes with allelic differences and non-synonymous differences were found in genes implicated in adhesion, lipooligosaccharides (LOS) production, pilin production and iron acquisition. The genome-wide analysis of the methylome identified three modified motifs: GATC, GGNNCC and CACNNNNNTAC, the latter was only found in isolates belonging to subtype 2 and a trans-posase was found inserted in the candidate enzyme: a type I restriction system specificity protein (NEIS2535). In general, modifications were found in both cytosine and adenine bases although the latter, 6mA, was the most frequent modification in all isolates and more predominant among subtype 2. Many inactive restriction modification systems were present; however, in order to reveal more active sys-tems, further analysis on 5mC is needed.Conclusion: Our preliminary results indicate that there is a difference in methylation motifs as well as positional distribution of modifications between the two MenY subtypes. Since no differences were found in the presence of genes potentially involved in pathogenicity between the two subtypes, and it has been previously established that there was rather a tendency of a milder clinical picture among IMD caused by subtype 1 [2], the emergence of subtype 1 was most probably due to increased transmission or that the human population was more immunologically naïve to this subtype.References: 1. Törös B et al. J Clin Microbiol 2015, 53(7):2154-2162. 2. Säll O et al.Epidemiol Infect 2017, 145(10):2137-2143.
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| 8. |
- Stenmark, Bianca, 1987-, et al.
(författare)
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Genome-wide methylome analysis of two strains belonging to the hypervirulent Neisseria meningitidis serogroup W ST-11 clonal complex
- 2021
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- A rising incidence of meningococcal serogroup W disease has been evident in many countries worldwide. Serogroup W isolates belonging to the sequence type (ST)-11 clonal complex have been associated with atypical symptoms and increased case fatality rates. The continued expansion of this clonal complex in the later part of the 2010s has been largely due to a shift from the so-called original UK strain to the 2013 strain. Here we used single-molecule real-time (SMRT) sequencing to determine the methylomes of the two major serogroup W strains belonging to ST-11 clonal complex. Five methylated motifs were identified in this study, and three of the motifs, namely 5'-GATC-3', 5'-GAAGG-3', 5'-GCGCGC-3', were found in all 13 isolates investigated. The results showed no strain-specific motifs or difference in active restriction modification systems between the two strains. Two phase variable methylases were identified and the enrichment or depletion of the methylation motifs generated by these methylases varied between the two strains. Results from this work give further insight into the low diversity of methylomes in highly related strains and encourage further research to decipher the role of regions with under- or overrepresented methylation motifs.
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| 9. |
- 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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| 10. |
- 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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