MLST and serotyping 55989 in silico

1. 1. MLST

Multilocus sequence typing is a widely used method for characterizing the core genomes of a bacterial isolates. Seven conserved loci are sequenced and the sequences are compared against a database. Each allelic variant is assigned an identifier and the string of the seven identifiers is the 'sequence type' of the isolate.

For E.coli/Shigella the [MLST](http://mlst.ucc.ie/mlst/dbs/Ecoli/documents/primersColi_html) is most widely used.

E.coli isolate 55989 has been fully sequenced in high quality by Institute Pasteur/Genoscope and sequences where deposited in Genbank with accession numbers [CU928145.2](http://www.ncbi.nlm.nih.gov/nuccore/CU928145.2) and [CU928159.2](http://www.ncbi.nlm.nih.gov/nuccore/CU928159.2), but its MLST has never been determined or published. Since the complete chromosomal sequence is available, the MLST can be exactly derived from this sequnce.

Cork database MLST for isolate 55989:

• ADK-6 100.000 % CU928145.2[524518:525053]
• FUMC-6 100.000 % CU928145.2[1834827:1835295:r]
• GYRB-5 100.000 % CU928145.2[4254482:4254941:r]
• ICD-136 100.000 % CU928145.2[1305516:1306033]
• MDH-9 100.000 % CU928145.2[3733495:3733946:r]
• PURA-7 100.000 % CU928145.2[4850597:4851074]
• RECA-7 100.000 % CU928145.2[3033953:3034462:r]
• **ST678** 100.000 %

The prototype isolate for ST678 is '01-9591' summitted by Helge Karch from Münster. '01-9591' is also the prototype isolate for the clade [HUSEC041](http://www.ehec-hus.de/index.php?lang=en&pid=HUSEC&hid=43) in the [HUSEC](http://www.ehec-hus.org/).

A note has been sent to Mark Achtman and isolate 55989 will be added to the MLST database soon.

1. 1. Serotyping

The serotype of an bacterial isolate is a phenotypical property of the cell. In serotyping the reaction of several antibodies with a bacterial cell is tested. With E.coli, the standard antibodies used for serotyping react with certain sugar components of the cell wall and with the flagellum. The proteins for assembling the cell wall and formimg the flagellar are encoded in the genome. In general, deducing the serotyp from the genomic sequence is not a valid method to determine the serotype. However, since the serotype of isolate 55989 has never been determined or published, it is better than nothing.

The serotype can be tentatively assigned based on the chromosomal sequence. 55989 carries the genes wzx_O104 and wxy_O104 which are exclusively found in O104 isolates, and furthermore the variant H4 of the fliC gene. Thus the tentative serotype of 55989 is **O104:H4**.

1. 1. Sandbox

text  block    ------------ d