Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018
BackgroundStreptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized.MethodsWe carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream...
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Frontiers Media S.A.
2023-04-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1171913/full |
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| author | Alba Kaci Christine M. Jonassen Christine M. Jonassen Steinar Skrede Steinar Skrede Audun Sivertsen The Norwegian Study Group on Streptococcus dysgalactiae Martin Steinbakk Oddvar Oppegaard Oddvar Oppegaard Aasmund Fostervold Aleksandra Jakovljev Annette Onken Åshild Marvik Nilsen Einar Fredrik Müller Ghantous Milad Chedid Gunnar Skov Simonsen Kyriakos Zaragkoulias Reidar Hjetland Roar Magne Baevre-Jensen Sandra Åsheim Ståle Tofteland Tine Smedsund Dons Truls Michael Leegaard |
| author_facet | Alba Kaci Christine M. Jonassen Christine M. Jonassen Steinar Skrede Steinar Skrede Audun Sivertsen The Norwegian Study Group on Streptococcus dysgalactiae Martin Steinbakk Oddvar Oppegaard Oddvar Oppegaard Aasmund Fostervold Aleksandra Jakovljev Annette Onken Åshild Marvik Nilsen Einar Fredrik Müller Ghantous Milad Chedid Gunnar Skov Simonsen Kyriakos Zaragkoulias Reidar Hjetland Roar Magne Baevre-Jensen Sandra Åsheim Ståle Tofteland Tine Smedsund Dons Truls Michael Leegaard |
| author_sort | Alba Kaci |
| collection | DOAJ |
| description | BackgroundStreptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized.MethodsWe carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE.ResultsThe phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling.ConclusionRecombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages. The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics. |
| first_indexed | 2024-03-13T00:50:09Z |
| format | Article |
| id | doaj.art-36e327a7b53e4465ab284b05a555d4b3 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-13T00:50:09Z |
| publishDate | 2023-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj.art-36e327a7b53e4465ab284b05a555d4b32023-07-07T19:06:09ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-04-011410.3389/fmicb.2023.11719131171913Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018Alba Kaci0Christine M. Jonassen1Christine M. Jonassen2Steinar Skrede3Steinar Skrede4Audun Sivertsen5The Norwegian Study Group on Streptococcus dysgalactiaeMartin Steinbakk6Oddvar Oppegaard7Oddvar Oppegaard8Aasmund FostervoldAleksandra JakovljevAnnette OnkenÅshild MarvikNilsen EinarFredrik MüllerGhantous Milad ChedidGunnar Skov SimonsenKyriakos ZaragkouliasReidar HjetlandRoar Magne Baevre-JensenSandra ÅsheimStåle ToftelandTine Smedsund DonsTruls Michael LeegaardCenter for Laboratory Medicine, Østfold Hospital Trust, Grålum, NorwayCenter for Laboratory Medicine, Østfold Hospital Trust, Grålum, NorwayDepartment of Virology, Norwegian Institute of Public Health, Oslo, NorwayDepartment of Clinical Science, University of Bergen, Bergen, NorwayDepartment of Medicine, Haukeland University Hospital, Bergen, NorwayDepartment of Microbiology, Haukeland University Hospital, Bergen, NorwayCenter for Laboratory Medicine, Østfold Hospital Trust, Grålum, NorwayDepartment of Clinical Science, University of Bergen, Bergen, NorwayDepartment of Medicine, Haukeland University Hospital, Bergen, NorwayBackgroundStreptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized.MethodsWe carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE.ResultsThe phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling.ConclusionRecombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages. The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1171913/fullwhole genome sequencing (WGS)SDSEsurveillance studiesgenomicshorizontal genetic transfer |
| spellingShingle | Alba Kaci Christine M. Jonassen Christine M. Jonassen Steinar Skrede Steinar Skrede Audun Sivertsen The Norwegian Study Group on Streptococcus dysgalactiae Martin Steinbakk Oddvar Oppegaard Oddvar Oppegaard Aasmund Fostervold Aleksandra Jakovljev Annette Onken Åshild Marvik Nilsen Einar Fredrik Müller Ghantous Milad Chedid Gunnar Skov Simonsen Kyriakos Zaragkoulias Reidar Hjetland Roar Magne Baevre-Jensen Sandra Åsheim Ståle Tofteland Tine Smedsund Dons Truls Michael Leegaard Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018 Frontiers in Microbiology whole genome sequencing (WGS) SDSE surveillance studies genomics horizontal genetic transfer |
| title | Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018 |
| title_full | Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018 |
| title_fullStr | Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018 |
| title_full_unstemmed | Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018 |
| title_short | Genomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018 |
| title_sort | genomic epidemiology of streptococcus dysgalactiae subsp equisimilis strains causing invasive disease in norway during 2018 |
| topic | whole genome sequencing (WGS) SDSE surveillance studies genomics horizontal genetic transfer |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1171913/full |
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