Identification

Identification & Serotyping of suspected Escherichia coli.

Isolate from urine, stool, blood, environmental, food, other.

Isolate provided on appropriate culture medium with visible growth. Samples can also be submitted under frozen conditions provided they are shipped in appropriate media to survive transport.

Send as growth on appropriate culture medium or in appropriate transport medium. Frozen samples should be shipped on dry ice or other method to ensure they remain frozen. Culture vessel should be leak-proof or sealed appropriately.

Shipping of specimens shall be done by a TDG certified individual in accordance with TDG regulations. For additional information regarding classification of specimens for the purposes of shipping, consult either Part 2 Appendix 3 of the TDG Regulations or section 3.6.2 of the IATA Dangerous Goods Regulations as applicable.

Gastroenteritis, septicemia, infection, other.

Completed Enteric Diseases requisition form.

N/A

Molecular Identification:
(Primary) In silico serotype prediction (ECTyper)*
(Alternative) Other whole genome sequencing based methodologies may be applied (Not accredited to ISO/IEC 17025 at this time)

Phenotypic Identification:
(Secondary) Biotyping-biochemical substrate utilization assays
(Secondary) Serotyping* - Serum agglutination assay

*Note: The Primary method for E.coli sent for Identification is whole genome sequencing and in silico serotype prediction (ECTyper). If the isolate has already been sequenced, please provide the IRIDA Next sample number and ensure that the Traditional Serotyping test is selected on the Division of Enteric Diseases requisition form.

For clinical diagnostic or outbreak samples*: 28 calendar days

For surveillance or research samples*: 3 months

*Please indicate on requisition if identification is for i) clinical diagnostic or outbreak OR ii) surveillance or research application. Turnaround times for routine isolates may be extended during major foodborne outbreak activities or due to limited availability of resources.

Please note that for poor or slower growing organisms reporting of results may be delayed beyond listed turnaround times.

1. Bessonov K, Laing C, Robertson J, Yong I, Ziebell K, Gannon VPJ, Nichani A, Arya G, Nash JHE, Christianson S. ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data. Microb Genom. 2021 Dec;7(12):000728. doi: 10.1099/mgen.0.000728. PMID: 34860150; PMCID: PMC8767331.
2. Murray, P.R., Baron, E.J., Jorgensen, J.H., Pfaller, M.A., Yolken, R.H., Manual of Clinical Microbiology. 2003. ASM Press. Washington, DC. USA
3. Gross RJ, Rowe B. The serotyping of Escherichia coli In: Sussman M, ed. The Virulence of Escherichia coli: Reviews and Methods. London: Society for General Microbiology, Academic Press, 1985:345-63