Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes
Listeria monocytogenes is a Gram-positive bacterium that can be found in a broad range of environments, including soil, food, animals, and humans. L. monocytogenes can cause a foodborne disease manifesting as sepsis and meningo-encephalitis. To evaluate signals of selection within the core genome of...
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| Format: | Article |
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Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fmicb.2019.02702/full |
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| author | Bart Ferwerda Mylène M. Maury Mathijs C. Brouwer Lukas Hafner Arie van der Ende Arie van der Ende Stephen Bentley Marc Lecuit Marc Lecuit Diederik van de Beek |
| author_facet | Bart Ferwerda Mylène M. Maury Mathijs C. Brouwer Lukas Hafner Arie van der Ende Arie van der Ende Stephen Bentley Marc Lecuit Marc Lecuit Diederik van de Beek |
| author_sort | Bart Ferwerda |
| collection | DOAJ |
| description | Listeria monocytogenes is a Gram-positive bacterium that can be found in a broad range of environments, including soil, food, animals, and humans. L. monocytogenes can cause a foodborne disease manifesting as sepsis and meningo-encephalitis. To evaluate signals of selection within the core genome of neuroinvasive L. monocytogenes strains, we sequenced 122 L. monocytogenes strains from cerebrospinal fluid (CSF) of Dutch meningitis patients and performed a genome-wide analysis using Tajima’s D and ω (dN/dS). We also evaluated the residual variation intolerance score (RVIS), a computationally less demanding methodology, to identify loci under selection. Results show that the large genetic distance between the listerial lineages influences the Tajima’s D and ω (dN/dS) outcome. Within genetic lineages we detected signals of selection in 6 of 2327 loci (<1%), which were replicated in an external cohort of 105 listerial CSF isolates from France. Functions of identified loci under selection were within metabolism pathways (lmo2476, encoding aldose 1-epimerase), putative antimicrobial resistance mechanisms (lmo1855, encoding PBPD3), and virulence factors (lmo0549, internalin-like protein; lmo1482, encoding comEC). RVIS over the two genetic lineages showed signals of selection in internalin-like proteins loci potentially involved in pathogen-host interaction (lmo0549, lmo0610, and lmo1290). Our results show that RVIS can be used to detect bacterial loci under selection. |
| first_indexed | 2024-12-23T20:18:23Z |
| format | Article |
| id | doaj.art-3553d8c2557d4eea9d86322923e0e3b0 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-23T20:18:23Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-3553d8c2557d4eea9d86322923e0e3b02022-12-21T17:32:37ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2019-11-011010.3389/fmicb.2019.02702497808Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenesBart Ferwerda0Mylène M. Maury1Mathijs C. Brouwer2Lukas Hafner3Arie van der Ende4Arie van der Ende5Stephen Bentley6Marc Lecuit7Marc Lecuit8Diederik van de Beek9Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, NetherlandsInstitut Pasteur, Biology of Infection Unit, Inserm U1117 and National Reference Centre – WHO Collaborating Centre for Listeria, Paris, FranceDepartment of Neurology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, NetherlandsInstitut Pasteur, Biology of Infection Unit, Inserm U1117 and National Reference Centre – WHO Collaborating Centre for Listeria, Paris, FranceDepartment of Medical Microbiology, Amsterdam Infection and Immunity, Amsterdam UMC, University of Amsterdam, Amsterdam, NetherlandsNetherlands Reference Laboratory for Bacterial Meningitis, Amsterdam UMC/RIVM, University of Amsterdam, Amsterdam, NetherlandsParasites and Microbes, Wellcome Sanger Institute, Cambridge, United KingdomInstitut Pasteur, Biology of Infection Unit, Inserm U1117 and National Reference Centre – WHO Collaborating Centre for Listeria, Paris, FranceParis Descartes University, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Paris, FranceDepartment of Neurology, Amsterdam Neuroscience, Amsterdam UMC, University of Amsterdam, Amsterdam, NetherlandsListeria monocytogenes is a Gram-positive bacterium that can be found in a broad range of environments, including soil, food, animals, and humans. L. monocytogenes can cause a foodborne disease manifesting as sepsis and meningo-encephalitis. To evaluate signals of selection within the core genome of neuroinvasive L. monocytogenes strains, we sequenced 122 L. monocytogenes strains from cerebrospinal fluid (CSF) of Dutch meningitis patients and performed a genome-wide analysis using Tajima’s D and ω (dN/dS). We also evaluated the residual variation intolerance score (RVIS), a computationally less demanding methodology, to identify loci under selection. Results show that the large genetic distance between the listerial lineages influences the Tajima’s D and ω (dN/dS) outcome. Within genetic lineages we detected signals of selection in 6 of 2327 loci (<1%), which were replicated in an external cohort of 105 listerial CSF isolates from France. Functions of identified loci under selection were within metabolism pathways (lmo2476, encoding aldose 1-epimerase), putative antimicrobial resistance mechanisms (lmo1855, encoding PBPD3), and virulence factors (lmo0549, internalin-like protein; lmo1482, encoding comEC). RVIS over the two genetic lineages showed signals of selection in internalin-like proteins loci potentially involved in pathogen-host interaction (lmo0549, lmo0610, and lmo1290). Our results show that RVIS can be used to detect bacterial loci under selection.https://www.frontiersin.org/article/10.3389/fmicb.2019.02702/fullListeria monocytogenesneuroinvasiveselectionresidual variation intolerance scoregenetic variation |
| spellingShingle | Bart Ferwerda Mylène M. Maury Mathijs C. Brouwer Lukas Hafner Arie van der Ende Arie van der Ende Stephen Bentley Marc Lecuit Marc Lecuit Diederik van de Beek Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes Frontiers in Microbiology Listeria monocytogenes neuroinvasive selection residual variation intolerance score genetic variation |
| title | Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes |
| title_full | Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes |
| title_fullStr | Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes |
| title_full_unstemmed | Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes |
| title_short | Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes |
| title_sort | residual variation intolerance score detects loci under selection in neuroinvasive listeria monocytogenes |
| topic | Listeria monocytogenes neuroinvasive selection residual variation intolerance score genetic variation |
| url | https://www.frontiersin.org/article/10.3389/fmicb.2019.02702/full |
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