title: Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.
abstract: The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland Department of Infectious Diseases, Inselspital, Bern University Hospital and University of Bern, Switzerland markus.hilty@ifik.unibe.ch.
authors.forename: Markus
authors.initials: M
authors.lastname: Hilty
authors.affiliation: Interfaculty Bioinformatics Unit, University of Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Wüthrich
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Susannah J
authors.initials: SJ
authors.lastname: Salter
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland.
authors.forename: Hansjürg
authors.initials: H
authors.lastname: Engel
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland.
authors.forename: Samuel
authors.initials: S
authors.lastname: Campbell
authors.affiliation: Instituto de Tecnologia Química e Biológica, University of Lisbon, Portugal.
authors.forename: Raquel
authors.initials: R
authors.lastname: Sá-Leão
authors.affiliation: Instituto de Tecnologia Química e Biológica, University of Lisbon, Portugal Laboratory of Microbiology and Infectious Diseases, The Rockefeller University.
authors.forename: Hermínia
authors.initials: H
authors.lastname: de Lencastre
authors.affiliation: Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands.
authors.forename: Peter
authors.initials: P
authors.lastname: Hermans
authors.affiliation: National Medicines Institute, Warsaw, Poland.
authors.forename: Ewa
authors.initials: E
authors.lastname: Sadowy
authors.affiliation: Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, United Kingdom.
authors.forename: Paul
authors.initials: P
authors.lastname: Turner
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand.
authors.forename: Claire
authors.initials: C
authors.lastname: Chewapreecha
authors.affiliation: Clinical Microbiology Department, Queens Medical Centre, Nottingham, United Kingdom.
authors.forename: Mathew
authors.initials: M
authors.lastname: Diggle
authors.affiliation: Swiss Tropical and Public Health Institute, University of Basel, Switzerland.
authors.forename: Gerd
authors.initials: G
authors.lastname: Pluschke
authors.affiliation: Respiratory Diseases Branch, Centers for Disease Control and Prevention, Georgia, Atlanta.
authors.forename: Lesley
authors.initials: L
authors.lastname: McGee
authors.affiliation: Department of Microbiology, Medical Faculty, Hacettepe University, Ankara, Turkey.
authors.forename: Özgen Köseoğlu
authors.initials: ÖK
authors.lastname: Eser
authors.affiliation: Mt Sinai Hospital & Public Health Laboratories, Toronto, Ontario, Canada.
authors.forename: Donald E
authors.initials: DE
authors.lastname: Low
authors.affiliation: Menzies School of Health Research, Charles Darwin University, Australia.
authors.forename: Heidi
authors.initials: H
authors.lastname: Smith-Vaughan
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland.
authors.forename: Andrea
authors.initials: A
authors.lastname: Endimiani
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland.
authors.forename: Marianne
authors.initials: M
authors.lastname: Küffer
authors.affiliation: Centre for Integrative Genomics, University of Lausanne, Switzerland.
authors.forename: Mélanie
authors.initials: M
authors.lastname: Dupasquier
authors.affiliation: Centre for Integrative Genomics, University of Lausanne, Switzerland.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Beaudoing
authors.affiliation: Centre for Integrative Genomics, University of Lausanne, Switzerland.
authors.forename: Johann
authors.initials: J
authors.lastname: Weber
authors.affiliation: Interfaculty Bioinformatics Unit, University of Bern, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Rémy
authors.initials: R
authors.lastname: Bruggmann
authors.affiliation: Department of Epidemiology, Center for Communicable Disease Dynamics, Harvard School of Public Health.
authors.forename: William P
authors.initials: WP
authors.lastname: Hanage
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland.
authors.forename: Lucy J
authors.initials: LJ
authors.lastname: Hathaway
authors.affiliation: Institute for Infectious Diseases, University of Bern, Switzerland Department of Infectious Diseases, Inselspital, Bern University Hospital and University of Bern, Switzerland.
authors.forename: Kathrin
authors.initials: K
authors.lastname: Mühlemann
authors.affiliation: Wellcome Trust Sanger Institute, Hinxton, United Kingdom Department of Medicine, Addenbrookes Hospital, University of Cambridge, United Kingdom.
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Bentley
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D016667:Bacterial Capsules / Q000235:genetics*; D002460:Cell Line; D004251:DNA Transposable Elements; D004847:Epithelial Cells / Q000382:microbiology; D056426:Genetic Loci; D049810:Genetic Speciation; D016680:Genome, Bacterial; D006801:Humans; D010802:Phylogeny; D013296:Streptococcus pneumoniae / Q000187:drug effects / Q000235:genetics* / Q000302:isolation & purification / Q000472:pathogenicity; D047090:beta-Lactams / Q000494:pharmacology
chemical_list: D000900:Anti-Bacterial Agents; D004251:DNA Transposable Elements; D047090:beta-Lactams
keywords: antibiotic nonsusceptibility; comparative genomics; integrative conjugative elements; pneumococcal isolates; whole-genome sequencing