Phenotypic H-Antigen Typing by Mass Spectrometry Combined with Genetic Typing of H Antigens, O Antigens, and Toxins by Whole-Genome Sequencing Enhances Identification of Escherichia coli Isolates.
Mass spectrometry-based phenotypic H-antigen typing (MS-H) combined with whole-genome-sequencing-based genetic identification of H antigens, O antigens, and toxins (WGS-HOT) was used to type 60 clinical Escherichia coli isolates, 43 of which were previously identified as nonmotile, H type undetermined, or O rough by serotyping or having shown discordant MS-H and serotyping results. Whole-genome sequencing confirmed that MS-H was able to provide more accurate data regarding H antigen expression than serotyping. Further, enhanced and more confident O antigen identification resulted from gene cluster based typing in combination with conventional typing based on the gene pair comprising wzx and wzy and that comprising wzm and wzt The O antigen was identified in 94.6% of the isolates when the two genetic O typing approaches (gene pair and gene cluster) were used in conjunction, in comparison to 78.6% when the gene pair database was used alone. In addition, 98.2% of the isolates showed the existence of genes for various toxins and/or virulence factors, among which verotoxins (Shiga toxin 1 and/or Shiga toxin 2) were 100% concordant with conventional PCR based testing results. With more applications of mass spectrometry and whole-genome sequencing in clinical microbiology laboratories, this combined phenotypic and genetic typing platform (MS-H plus WGS-HOT) should be ideal for pathogenic E. coli typing.
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Department of Human Anatomy and Cell Sciences, College of Medicine, University of Manitoba, Winnipeg, MB, Canada Keding.Cheng@phac-aspc.gc.ca Gehua.Wang@phac-aspc.gc.ca.
Keding
K
Cheng
Henan Center of Disease Control and Prevention, Zhengzhou, Henan Province, China.
Huixia
H
Chui
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Larissa
L
Domish
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Angela
A
Sloan
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Drexler
D
Hernandez
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Stuart
S
McCorrister
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Alyssia
A
Robinson
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Matthew
M
Walker
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Lorea A M
LA
Peterson
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Miles
M
Majcher
Newfoundland and Labrador Public Health Laboratory, St. John's, NL, Canada.
Sam
S
Ratnam
Nova Scotia Provincial Public Health Laboratory Network, Halifax, NS, Canada.
David J M
DJ
Haldane
Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.
Sadjia
S
Bekal
Cadham Provincial Laboratory, Winnipeg, MB, Canada.
John
J
Wylie
Provincial Laboratory for Public Health and Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, AB, Canada.
Linda
L
Chui
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Shaun
S
Tyler
Henan Center of Disease Control and Prevention, Zhengzhou, Henan Province, China.
Bianli
B
Xu
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
Aleisha
A
Reimer
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada.
Celine
C
Nadon
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Department of Medical Microbiology, College of Medicine, University of Manitoba, Winnipeg, MB, Canada.
J David
JD
Knox
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada Keding.Cheng@phac-aspc.gc.ca Gehua.Wang@phac-aspc.gc.ca.
Gehua
G
Wang
D000942:Antigens, Bacterial / Q000032:analysis* / Q000235:genetics; D001427:Bacterial Toxins / Q000235:genetics*; D015373:Bacterial Typing Techniques / Q000379:methods*; D004926:Escherichia coli / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D004927:Escherichia coli Infections / Q000175:diagnosis; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D019081:O Antigens / Q000235:genetics*
D000942:Antigens, Bacterial; D001427:Bacterial Toxins; C022863:H antigen; D019081:O Antigens