Modules for Escherichia species#

--preset escherichia

These modules will be run if the enterobacterales__species module confirms the input assembly as a member of the Escherichia genus.

E. coli MLST#

-m escherichia__mlst_achtman, escherichia__mlst_pasteur

Genomes identified as belonging to the Escherichia genus are subjected to MLST using two 7-locus schemes.

The Pasteur scheme is described at the Escherichia coli Database at Pasteur Institute. Please see here for more details.

The Achtman scheme is hosted at Enterobase.

The genes included in each scheme are noted in the Outputs table below.

A copy of the MLST alleles and ST definitions used in each module is stored in the /data directory of the module.

E. coli MLST parameters#

--escherichia_mlst_achtman_min_identity

Minimum alignment percent identity for Escherchia-Achtman MLST (default: 90.0)

--escherichia_mlst_achtman_min_coverage

Minimum alignment percent coverage for Escherchia-Achtman MLST (default: 80.0)

--escherichia_mlst_achtman_required_exact_matches

At least this many exact matches are required to call an ST (default: 3)

--escherichia_mlst_pasteur_min_identity

Minimum alignment percent identity for Escherchia-Pasteur MLST (default: 90.0)

--escherichia_mlst_pasteur_min_coverage

Minimum alignment percent coverage for Escherchia-Pasteur MLST (default: 80.0)

--escherichia_mlst_pasteur_required_exact_matches

At least this many exact matches are required to call an ST (default: 4)

E. coli MLST outputs#

Output of the Pasteur E. coli MLST module is the following columns:

ST

sequence type

dinB, icdA, pabB, polB, putP, trpA, trpB, uidA

allele number

Output of the Achtman E. coli MLST module is the following columns:

ST

sequence type

adk, fumC, gyrB, icd, mdh, purA, recA

allele number

  • Kleborate makes an effort to report the closest matching ST if a precise match is not found.

  • Imprecise allele matches are indicated with a *.

  • Imprecise ST calls are indicated with -nLV, where n indicates the number of loci that disagree with the ST reported. So 258-1LV indicates a single-locus variant (SLV) of ST258, i.e. 6/7 loci match ST258.