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Tsang RSW, Shuel M, Ahmad T, Hayden K, Knox N, Van Domselaar G, Hoang L, Tyrrell GJ, Minion J, Van Caeseele P, Kus JV, Ulanova M, Lefebvre B, Haldane D, Garceau R, German G, Zahariadis G, Hanley B, Kandola K, Patterson M. Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada. Can J Microbiol 2019; 66:99-110. [PMID: 31661630 DOI: 10.1139/cjm-2019-0406] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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.
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Affiliation(s)
- Raymond S W Tsang
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Michelle Shuel
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Tauqeer Ahmad
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Kristy Hayden
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Natalie Knox
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gary Van Domselaar
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Linda Hoang
- BC Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada
| | | | - Jessica Minion
- Roy Romanow Provincial Laboratory, Regina, Saskatchewan, Canada
| | | | - Julianne V Kus
- Public Health Ontario, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Marina Ulanova
- Northern Ontario School of Medicine, Thunder Bay, Ontario, Canada
| | - Brigitte Lefebvre
- Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - David Haldane
- Nova Scotia Health Authority, Halifax, Nova Scotia, Canada.,Dalhousie University, Halifax, Nova Scotia, Canada
| | - Richard Garceau
- Communicable Disease Control Unit, Department of Health, Government of New Brunswick, Fredericton, New Brunswick, Canada
| | - Greg German
- Department of Health, Government of Prince Edward Island, Charlottetown, Prince Edward Island, Canada
| | - George Zahariadis
- Provincial Public Health Laboratory, Eastern Health Microbiology Services, St. John's, Newfoundland and Labrador, Canada.,Department of Laboratory Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada
| | - Brendan Hanley
- Department of Health and Social Services, Government of Yukon, Whitehorse, Yukon, Canada
| | - Kami Kandola
- Department of Health and Social Services, Government of Northwest Territories, Yellowknife, Northwest Territories, Canada
| | - Michael Patterson
- Department of Health, Government of Nunavut, Iqaluit, Nunavut, Canada
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