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- Title
Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada.
- Authors
Tsang, Raymond S.W.; Shuel, Michelle; Ahmad, Tauqeer; Hayden, Kristy; Knox, Natalie; Van Domselaar, Gary; Hoang, Linda; Tyrrell, Gregory J.; Minion, Jessica; Van Caeseele, Paul; Kus, Julianne V.; Ulanova, Marina; Lefebvre, Brigitte; Haldane, David; Garceau, Richard; German, Greg; Zahariadis, George; Hanley, Brendan; Kandola, Kami; Patterson, Michael
- Abstract
This study examined the phylogenetic structure of serotype a Haemophilus influenzae (Hia) isolates recovered from patients in Canada. Hia isolates from 490 separate patients and an American Type Culture Collection (ATCC) strain were analyzed by multilocus sequence typing (MLST), with 18 different sequence types (STs) identified. Most (85.7%) Hia patient isolates were typed as ST-23 and another 12.7% belonged to 14 different STs with 6, 5, or 4 MLST gene loci related to ST-23 (ST-23 complex). Core genome single-nucleotide variation phylogeny (SNVPhyl) on whole genome sequence (WGS) data of 121 Hia patient isolates representing all identified STs and the ATCC strain revealed 2 phylogenetic populations, with all the ST-23 complex isolates within 1 population. The other phylogenetic population contained only the ATCC strain and 3 patient isolates. Concatenated hitABC sequences retrieved from WGS data and analyzed by MEGA (Molecular Evolutionary Genetic Analysis) alignment confirmed the phylogeny obtained by SNVPhyl. The sodC gene was found only in isolates in the minor phylogenetic population. The 2 phylogenetic populations of the Canadian Hia isolates are similar to the 2 clonal divisions described for serotype b H. influenzae. Combining MLST, core SNVPhyl, and hitABC gene sequence alignment showed that most (99.4%) Canadian Hia patient isolates belonged to 1 major phylogenetic population.
- Subjects
CANADA; HAEMOPHILUS diseases; HAEMOPHILUS influenzae; NUCLEOTIDE sequencing; SEQUENCE alignment; EXOMES; PHYLOGENY
- Publication
Canadian Journal of Microbiology, 2020, Vol 66, Issue 2, p99
- ISSN
0008-4166
- Publication type
Article
- DOI
10.1139/cjm-2019-0406