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Copy number analysis of German outbreak strain E. Coli EHEC O104:H4

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gklambauer edited this page Jun 21, 2011 · 65 revisions

Copy number analysis of German outbreak strain E. Coli EHEC O104:H4 (TY-2482, LB226692) by comparing it to strain K12 DH10B at Ion Torrent sequencing data

Günter Klambauer, Martin Heusel, Djork-Arné Clevert and Sepp Hochreiter

We estimated the DNA copy numbers of the 2011 German outbreak strain E. coli O104:H4 from BGI TY-2482 (ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/) and LB226692 from Life Tech on Ion Torrent sequencing data. The O104:H4 copy numbers are given in relation to the copy numbers of the E. coli strain K12 DH10B (from http://www.edgebio.com/services/iontorrent.php, download instructions at the bottom). As reference genomes, to which the sequencing reads are mapped, we used E. coli strains DH10B, 55989, and O157:H7. Including the sequencing data from K12 strain in our analysis allowed us to separate technical / biological variations from true copy numbers. For copy number estimation, we used our probabilistic model cn.MOPS (http://www.bioinf.jku.at/software/cnmops/cnmops.html) which has been designed for estimating copy numbers in next generation sequencing data. cn.MOPS decomposes read count variations into variation caused by DNA copy numbers and random/noisy variations. See http://www.bioinf.jku.at/research/ehec/ehec.html for more information on our analysis.

Major results concerning the O104:H4 genome:

  • Shiga toxin stx2 is amplified (2 copies) in O104:H4 (red arrows in Fig. 1)

  • Tellurite gene cluster ter are present in O104:H4 (green arrows in Fig. 1)

  • Intimin gene eae is missing in O104:H4 (light blue arrow in Fig. 1)

  • β-lactamases ampC, ampD, ampE, ampG, and ampH are present in O104:H4

  • A large copy number 2 region from 610kbp to 705kbp (DH10B as reference) or 675kbp to 770kbp (O157:H7 as reference) has been detected in DH10B

Plasmids that were top ranked by cn.MOPS' call:

  • plasmid pKL1 (cn.MOPS call of 1.6) containing one gene repA which controls the plasmid copy number

  • plasmid pO26-S1 (cn.MOPS call of 1.36) found in the Shiga-toxin producing E. coli strain O26

  • plasmid pEC_Bactec (cn.MOPS call of 1.02) containing genes TEM-1 (common plasmid encoded beta-lactamase) and CTX-M-15 (extended-spectrum beta-lactamase gene)

  • plasmid pMG828-1 (cn.MOPS call of 0.71) containing one gene encoding a replication protein

  • plasmid 55989p (cn.MOPS call of 0.71) containing the genes aatA (ABC-transporter protein gene) and aggR (master regulator gene of Vir-plasmid genes)

  • plasmid pAPEC-O1-R (cn.MOPS call of 0.35) carrying an antibiotic resistance gene cluster

  • plasmid pO86A1 (cn.MOPS call of 0.2) containing the gene aatA (ABC-transporter protein gene)

Figure 1: Copy numbers variable regions of O104:H4 compared to DH10B if mapped to O157:H7. Red arrows: Shiga toxin stx2 is amplified in O104:H4; Green arrows: tellurite gene cluster ter are present in O104:H4; Light blue arrow: intimin gene eae is missing in O104:H4; Violet arrow: a large copy number 2 region from 675kbp to 770kbp detected in DH10B. Figure as SVG.

Copy number table of the outbreak strain O104:H4 and DH10B using reference O157:H7 (http://www.bioinf.jku.at/research/ehec/integerCNTable_ref_O157.txt, http://www.bioinf.jku.at/research/ehec/integerCNTable_ref_O157.xls).

Copy number table of the outbreak strain O104:H4 and DH10B using reference 55989 (http://www.bioinf.jku.at/research/ehec/integerCNTable_ref_55989.txt, http://www.bioinf.jku.at/research/ehec/integerCNTable_ref_55989.xls).

Copy number table of the outbreak strain O104:H4 and DH10B using reference K12 DH10B (http://www.bioinf.jku.at/research/ehec/integerCNTable_ref_K12.txt, http://www.bioinf.jku.at/research/ehec/integerCNTable_ref_K12.xls).

Our results reconfirm findings of the Robert-Koch-Institute (see summary ftp://ftp.genomics.org.cn/pub/Ecoli_TY-2482/2011vs2001_v2.xls) that the outbreak strain E. coli O104:H4 is:

  • Shiga toxin 2 (stx2) positive

  • intimin negative

The Shiga toxin stx2 is characteristic for O104:H4 as a manuscript of "Bundesinstitut für Risikobewertung" states (http://www.bfr.bund.de/cm/349/enterohaemorrhagic_escherichia_coli_o104_h4.pdf).

That Shiga toxin is produced by O104:H4 was reported in a NatureNews article (http://www.nature.com/news/2011/110609/full/news.2011.360.html) from June 9th by Marian Turner who writes “The bacterium in this outbreak, currently recognised as strain O104:H4, makes Shiga toxin, which is responsible for the severe diarrhoea and kidney damage in patients whose E. coli infections develop into haemolytic uremic syndrome (HUS).”

Our finding that tellurium resistance genes are present in O104:H4 has also been reported in NatureNews (http://www.nature.com/news/2011/110602/full/news.2011.345.html) at June 2nd by Marian Turner who writes “In addition to the antibiotic-resistance genes, the bacteria contain a gene for resistance to the mineral tellurite (tellurium dioxide)”.

In the same article Marian Turner writes “One telltale sign is that the strain does not contain the eae gene, which codes for a protein called intimin, an adhesion protein that allows the bacteria to attach to cells in the gut” which we also confirmed.

Our findings concerning β-lactamases are of interest as they tend to make bacteria resistant to common antibiotics.

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