Overnight I received an email from Scott Weissman at the Seattle Children’s Hospital. He has done some analysis of the IncI, blaCTX-M bearing plasmid from the outbreak strain using the plasmid MLST database. Here’s what he did:
To facilitate comparisons to other plasmids, I analyzed the LB226692 contigs in order to identify a plasmid Sequence Type (pST) for this outbreak strain’s IncI1 plasmid carrying CTX-M-15 and TEM-1. I extracted fragments for the 5 MLST loci (as described at http://pubmlst.org/plasmid/primers/incI1.shtml) from the GenBank contigs, and obtained allele assignments as follows: repI 3 | ardA 4 | trbA 6| sogS 3 | pilL 3, which corresponds to pST31. (I should note that the extracted sequence for trbA contained a 1-nt “insertion” relative to reference allele 6, which I assume to be sequencing artifact, although a novel allele cannot be excluded – given the indel occurrence within a poly-T tract of 4 T’s).
The database contains 15 plasmid entries for IncI1 pST31 (see below), including pEC_Bactec (described by Smet et al, PLoS One, 2011;5:e11202). All of these entries carry the CTX-M-15 and TEM-1 enzymes, so there are no headlines here.
I would note, however, that this CTX-M-15 plasmid is distinct from the IncF-family plasmids that have been globally distributed by E. coli ST131 (eg, pC15a-1a, as described by Boyd et al, AAC 2004;48:3758-64) and detected subsequently in multiple Klebsiella pneumoniae clones (see Oteo et al, JAC, 2009;64:524-528).
IncI pST31 entries in the IncI pMLST database
To supplement this I had a quick look at the latest BGI assembly of TY2482, the other outbreak strain that has been sequenced. I found the same results, but this time with a precise trbA allele 6 (i.e. Scott was right in guessing this is an error in the Ion Torrent data at a homopolymeric tract).
Re the table above, the paper describing the 2004 Shigella sonnei plasmid is here, I’m not sure if the others are published.
This is what the eBURST diagram looks like for the data in the IncI plasmid MLST database…the German outbreak sequence type, pST31, is pointed out with a red arrow.
eBurst diagram for IncI plasmid MLST
The pMLST sequences from TY2482 (BGI assembly 2, June 6) are:
>repI1-3 GAGAGATGGCATGTACGGGCAGTAAGTCAGAAGACTGAAGATGCTCCGGAAGCCATAAAA GGAAAACCCCCACTATCTTTCTTACGAACTTGGCGGAACGACGAA >ardA-4 AATACAACTGTGGAAGCATCGCCGGACGCTGGTTTGACCTGACCACGTTTGATGATGAGC GCGACTTTTTCGCCGCCTGCCGTGCTCTTCACCAGGATGAAGCCGATCCTGAACTGATGT TTCAGGATTATGAGGGATTCCCGGGGAATATGGCCTCTGAATGCCATATCAACTGGGCCT GGGTTGAAGGCTTCCGCCTGGCACGGGATGAAGGCTGCGAAGAGGCTTATCGTCTCTGGG TGGAGGATACCGGTGAGACGGATTTTGACACCTTCCGCGATGCCTGGTGGGGCGAGGCTG ACAGTGAGGAGGCTTTTGCGGTTGAGTTCGCCAGTGATACCGG >trbA-6 GCAACCCGCCGCTCAGGCCGTTTGCCACCATGAAAGAGTTTTTCCGGATCACCATCTGCC AGTACTGGGGCGATAGCAGGGGACAACGAGGCAAAGATGTGTGGCAGTCGGGTAATATCT ACAGGTCTGCGGGTGAAACGGCTTTGTCCCGGGTGTTGATACCATTCCCATAAACACCAG AGTGTCACAGGTAAAAGATACATCCACAGAATACCTATGGTCTGCTCCATGACGTTAATC CACTGGCTATAGCTTATGTTGGCGGCGTTGTTACCGGTCATGGCAAGCAGGTTGTATCGT GGTGCTGCATAGTTATGAAATGGTCCCCAGTCGACCAGTCCCCATAAGGTATGAAGAATC AGGCAGCTGGCGTAAACCACTTCCGGCAAGAATAACCATATGACGAATAGCAGCAGGATA AGAAGGACACCAACAGCGCCCCATATCTGCATAGGATCTTCTGCGACAGGCTGTCGATTG TAAGA >sogS-3 GTCGTCGTGGTTTCCGCTGAGGGCGTGGGATCACTGTTCTCATGCGCCTGTGAATCCGTT TTTTTACGCGTAAAAAGGCCACGCGCTTTGTCGAGAAACGATGAAGTATTATCAGAAGGT GATGTGCTCTGAACAGGTTGCTGCGGAGTGGGTTCATCCCGGACAGCCGGTTCTATAGTG GCTGTTGTGGCCTGAAGTTCTGACTCATCTGCCTGAACGTGGCCTGTGTCCGGTTGCGAC GGCATATCACTGTT >pilL-3 TTGATGCCATGCTTTCGCATTTTGTTTCTTCTGCCCACTTAATAATGTTTTCCCTTAATG TAGTGCCTGCCGGCGCACGCCACTCTTTACCCTGAGATACCGGTTTGACAGGTGTCCCGG TCATGAGTGGGATAGACTTGACTGTAGAGCCGGTCGGAGTCGGGATTGCTGCGGGCGTAG ACGGAGATACGCTGTTTCCCCTGAATGGGTTTCGTGGTTTGTTCTGGCTATTTGCTGTCG TTGAAGACTCCGGGGAAGTGGATGTGGTTACCATGG
BacPathGenomics 
We did pMLST analysis for the O104:H4 outbreak strain by conventional PCR and sequencing and could confirm your results – ST31 for the IncI1 plasmid (TEM-1 + CTX-M-15). Many thanks to Alessandra Carattoli for the pMLST protocol.
kind regards, Yvonne Pfeifer. (Robert Koch Instiute, Germany)