IntiminTyper

What does it do?

Use IntiminTyper to assign subtypes to intimin (eae) genes in Escherichia coli sequence assemblies.

IntiminTyper uses Phylotyper, developed at the Public Health Agency of Canada, to compare an intimin allele with known subtypes and predict the closest subtype when an exact match is unavailable.

How do I use it?

Subject

In the Subject field, enter:

intimin_typer

Spelling matters, but matching is not case-sensitive.

Description

Enter one E. coli assembly SEQID per line:

2026-SEQ-0001
2026-SEQ-0002

Assemblies that are not E. coli can be included without causing the request to fail, but they are not expected to produce IntiminTyper results.

Attachments

No attachment is required. IntiminTyper retrieves the assembly associated with each requested SEQID.

Optional parameters

The supplied documentation does not identify optional parameters for the Redmine IntiminTyper automator.

Example

See issue 16512 for an example IntiminTyper request.

Interpreting results

IntiminTyper uploads:

intimin_predictions.tsv

The report identifies the predicted intimin subtype for each sample with a result. It distinguishes between:

  • an exact match to a known allele; and
  • a subtype prediction based on similarity to known alleles.

When the subtype is predicted rather than matched exactly, the report also provides a probability representing the model's confidence in that prediction.

Interpret an exact allele match more strongly than a similarity-based prediction. For predicted subtypes, review the reported probability and supporting biological context before drawing conclusions.

A requested SEQID may be absent from the report when it is not E. coli, does not contain a detectable eae gene, or could not otherwise produce a subtype result.

How long does it take?

IntiminTyper generally takes approximately 30 seconds per sample. Total runtime depends on sample count and service workload.

What can go wrong?

A requested SEQID is unavailable

Symptom: The requested sample does not appear in the final report.

Likely cause: IntiminTyper could not locate the assembly associated with the requested SEQID.

What to do: Verify the SEQID and confirm that its assembly is available.

A requested sample produces no subtype

Symptom: The SEQID is absent from intimin_predictions.tsv or has no usable subtype result.

Likely cause: The assembly may not be E. coli, may not contain a detectable eae gene, or may have insufficient sequence evidence for typing.

What to do: Confirm the organism, review assembly quality, and verify whether the sample is expected to carry eae.

A predicted subtype has low confidence

Symptom: The result is similarity-based and has a low reported probability.

Likely cause: The detected allele differs from known reference alleles or the available sequence is incomplete.

What to do: Treat the subtype as provisional and review the allele sequence, probability, and supporting evidence.

  • ECTyper — predicts O- and H-antigen serotypes for E. coli assemblies.
  • MLST — determines an E. coli sequence type using a selected Achtman or Pasteur scheme.
  • PrimerFinder — performs in silico PCR against assemblies using VTyper or attached custom primers.