TY - JOUR
T1 - Comparative pangenome analysis of capsulated Haemophilus influenzae serotype f highlights their high genomic stability
AU - Gonzalez-Diaz, Aida
AU - Carrera-Salinas, Anna
AU - Pinto, Miguel
AU - Cubero, Meritxell
AU - van der Ende, Arie
AU - Langereis, Jeroen D.
AU - Domínguez, M. Ángeles
AU - Ardanuy, Carmen
AU - Bajanca-Lavado, Paula
AU - Marti, Sara
N1 - Funding Information: This study was funded by Instituto de Salud Carlos III (ISCIII) through the Projects from the Fondo de Investigaciones Sanitarias “PI16/00977” to SM, and CIBER de Enfermedades Respiratorias (CIBERES–CB06/06/0037), co-funded by the European Regional Development Fund/European Social Fund (ERDF/ESF, “Investing in your future”), and CERCA Programme/Generalitat de Catalunya for institutional support. Bioinformatic analysis was supported by an Amazon Web Services (AWS) research grant to SM. AC was supported by FPU grant “FPU16/02202” (Formación de Profesorado Universitario, Ministerio de Educación, Spain), and SM was supported by Miguel Servet contract “CP19/00096” (ISCIII). Funding Information: We would like to thank the staff of the Microbiology Laboratory of Bellvitge University Hospital who contributed daily to this project. Publisher Copyright: © 2022, The Author(s).
PY - 2022/12/1
Y1 - 2022/12/1
N2 - Haemophilus influenzae is an opportunistic pathogen adapted to the human respiratory tract. Non-typeable H. influenzae are highly heterogeneous, but few studies have analysed the genomic variability of capsulated strains. This study aims to examine the genetic diversity of 37 serotype f isolates from the Netherlands, Portugal, and Spain, and to compare all capsulated genomes available on public databases. Serotype f isolates belonged to CC124 and shared few single nucleotide polymorphisms (SNPs) (n = 10,999), but a high core genome (> 80%). Three main clades were identified by the presence of 75, 60 and 41 exclusive genes for each clade, respectively. Multi-locus sequence type analysis of all capsulated genomes revealed a reduced number of clonal complexes associated with each serotype. Pangenome analysis showed a large pool of genes (n = 6360), many of which were accessory genome (n = 5323). Phylogenetic analysis revealed that serotypes a, b, and f had greater diversity. The total number of SNPs in serotype f was significantly lower than in serotypes a, b, and e (p < 0.0001), indicating low variability within the serotype f clonal complexes. Capsulated H. influenzae are genetically homogeneous, with few lineages in each serotype. Serotype f has high genetic stability regardless of time and country of isolation.
AB - Haemophilus influenzae is an opportunistic pathogen adapted to the human respiratory tract. Non-typeable H. influenzae are highly heterogeneous, but few studies have analysed the genomic variability of capsulated strains. This study aims to examine the genetic diversity of 37 serotype f isolates from the Netherlands, Portugal, and Spain, and to compare all capsulated genomes available on public databases. Serotype f isolates belonged to CC124 and shared few single nucleotide polymorphisms (SNPs) (n = 10,999), but a high core genome (> 80%). Three main clades were identified by the presence of 75, 60 and 41 exclusive genes for each clade, respectively. Multi-locus sequence type analysis of all capsulated genomes revealed a reduced number of clonal complexes associated with each serotype. Pangenome analysis showed a large pool of genes (n = 6360), many of which were accessory genome (n = 5323). Phylogenetic analysis revealed that serotypes a, b, and f had greater diversity. The total number of SNPs in serotype f was significantly lower than in serotypes a, b, and e (p < 0.0001), indicating low variability within the serotype f clonal complexes. Capsulated H. influenzae are genetically homogeneous, with few lineages in each serotype. Serotype f has high genetic stability regardless of time and country of isolation.
UR - http://www.scopus.com/inward/record.url?scp=85125351000&partnerID=8YFLogxK
U2 - https://doi.org/10.1038/s41598-022-07185-5
DO - https://doi.org/10.1038/s41598-022-07185-5
M3 - Article
C2 - 35210526
SN - 2045-2322
VL - 12
JO - Scientific reports
JF - Scientific reports
IS - 1
M1 - 3189
ER -