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- 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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| 2. |
- 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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