Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada-Reference-Cited by-同舟云学术

Whole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada

Published:2020-02 Issue:2 Volume:66 Page:99-110
ISSN:0008-4166
Container-title:Canadian Journal of Microbiology
language:en
Short-container-title:Can. J. Microbiol.

Author:

Tsang Raymond S.W.¹,Shuel Michelle¹,Ahmad Tauqeer¹,Hayden Kristy¹,Knox Natalie¹²,Van Domselaar Gary¹²,Hoang Linda³,Tyrrell Gregory J.⁴,Minion Jessica⁵,Van Caeseele Paul⁶,Kus Julianne V.⁷⁸,Ulanova Marina⁹,Lefebvre Brigitte¹⁰,Haldane David¹¹¹²,Garceau Richard¹³,German Greg¹⁴,Zahariadis George¹⁵¹⁶,Hanley Brendan¹⁷,Kandola Kami¹⁸,Patterson Michael¹⁹

Affiliation:

1. National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.

2. Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Manitoba, Canada.

3. BC Public Health Microbiology and Reference Laboratory, Vancouver, British Columbia, Canada.

4. Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.

5. Roy Romanow Provincial Laboratory, Regina, Saskatchewan, Canada.

6. Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada.

7. Public Health Ontario, Toronto, Ontario, Canada.

8. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.

9. Northern Ontario School of Medicine, Thunder Bay, Ontario, Canada.

10. Laboratoire de santé publique du Québec, Institut national de santé publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada.

11. Nova Scotia Health Authority, Halifax, Nova Scotia, Canada.

12. Dalhousie University, Halifax, Nova Scotia, Canada.

13. Communicable Disease Control Unit, Department of Health, Government of New Brunswick, Fredericton, New Brunswick, Canada.

14. Department of Health, Government of Prince Edward Island, Charlottetown, Prince Edward Island, Canada.

15. Provincial Public Health Laboratory, Eastern Health Microbiology Services, St. John’s, Newfoundland and Labrador, Canada.

16. Department of Laboratory Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada.

17. Department of Health and Social Services, Government of Yukon, Whitehorse, Yukon, Canada.

18. Department of Health and Social Services, Government of Northwest Territories, Yellowknife, Northwest Territories, Canada.

19. Department of Health, Government of Nunavut, Iqaluit, Nunavut, Canada.

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.

Publisher

Canadian Science Publishing

Subject

Genetics,Molecular Biology,Applied Microbiology and Biotechnology,General Medicine,Immunology,Microbiology

Link

http://www.nrcresearchpress.com/doi/pdf/10.1139/cjm-2019-0406

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