Whole-genome phylogenomic heterogeneity of Neisseria gonorrhoeae isolates with decreased cephalosporin susceptibility collected in Canada between 1989 and 2013.
A large-scale, whole-genome comparison of Canadian Neisseria gonorrhoeae isolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While some N. gonorrhoeae multiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaic penA alleles, followed in 2000/2001 with the penA mosaic X allele and then in 2007 with ST1407 strains with the penA mosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated with penA mosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.
Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada Walter.Demczuk@phac-aspc.gc.ca.
Walter
W
Demczuk
Alberta Health Services, Calgary, Alberta, Canada.
Tarah
T
Lynch
Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
Irene
I
Martin
Science Technology Cores and Services Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada, and Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
Gary
G
Van Domselaar
Science Technology Cores and Services Division, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada, and Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
Morag
M
Graham
Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
Amrita
A
Bharat
Public Health Ontario Laboratories, Toronto, Ontario, Canada.
Vanessa
V
Allen
British Columbia Public Health Microbiology and Reference Laboratory, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada.
Linda
L
Hoang
Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Québec, Canada.
Brigitte
B
Lefebvre
Provincial Laboratory for Public Health, Edmonton, Alberta, Canada.
Greg
G
Tyrrell
Saskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada.
Greg
G
Horsman
Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia, Canada.
David
D
Haldane
Dr. G.L. Dumont Hospital, Moncton, New Brunswick, Canada.
Richard
R
Garceau
Cadham Provincial Laboratory, Winnipeg, Manitoba, Canada.
John
J
Wylie
Centre for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa, Ontario, Canada.
Tom
T
Wong
Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
Michael R
MR
Mulvey
D000293:Adolescent; D000328:Adult; D000900:Anti-Bacterial Agents / Q000494:pharmacology; D002170:Canada / Q000453:epidemiology; D018550:Cephalosporin Resistance; D002648:Child; D002675:Child, Preschool; D005260:Female; D016680:Genome, Bacterial; D005838:Genotype; D006069:Gonorrhea / Q000453:epidemiology* / Q000266:history / Q000382:microbiology*; D049673:History, 20th Century; D049674:History, 21st Century; D006801:Humans; D007223:Infant; D008297:Male; D008826:Microbial Sensitivity Tests; D008875:Middle Aged; D058885:Multilocus Sequence Typing; D009344:Neisseria gonorrhoeae / Q000145:classification / Q000187:drug effects* / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D055815:Young Adult
D000900:Anti-Bacterial Agents