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. 2015 Jul 30;3(4):e00852-15. doi: 10.1128/genomeA.00852-15

Draft Genome Sequences of Human-Pathogenic Escherichia coli O26:H11 Strains Carrying the stx2 Gene Only and Circulating in France

Sabine Delannoy a,, Patricia Mariani-Kurkdjian b,c,d, Stephane Bonacorsi b,c,d, Sandrine Liguori b, Sarah A Ison e, Patrick Fach a
PMCID: PMC4520904  PMID: 26227606

Abstract

Shiga toxin-producing Escherichia coli (STEC) O26:H11 is one of the most frequent pathogens associated with diarrhea and hemolytic-uremic syndrome (HUS). In this report, we present the draft genome sequences of seven strains of STEC O26:H11 carrying the stx2a or stx2d gene only and isolated in France from HUS patients.

GENOME ANNOUNCEMENT

Among Shiga toxin-producing Escherichia coli (STEC) isolates, serotype O26:H11 is the second most frequently associated with severe human diseases worldwide, after O157:H7 (1, 2). Strains of STEC O26:H11 usually harbor the stx1a gene only or in combination with stx2a. However, in the 1990s, a new clonal subgroup of STEC O26 emerged that carries the stx2a gene alone (3). This new clone, first described in Germany, has spread over Europe and has recently been described on the American continent (4, 5).

In a previous study (6), we analyzed 23 STEC O26 strains carrying the stx2 gene only, which were isolated in France between 2010 and 2013 from hemolytic-uremic syndrome (HUS) patients. Although most of the strains appeared to correspond to this new clone, 12 of them exhibited significantly different characteristics.

In order to investigate more thoroughly the genetic relationship between the different clones, we sequenced seven of these strains covering the different combination observed between sequence types (ST), stx gene subtype, and virulence gene profile.

Genomic DNA was extracted from an overnight culture in tryptic soy broth (TSB) medium using the DNeasy blood and tissue kit (Qiagen), with an additional RNase A (Roche) treatment. Libraries were prepared using the Nextera XT kit (Illumina). Whole-genome sequencing was performed using an Illumina MiSeq platform (Illumina), according to the manufacturer’s instructions. Two MiSeq runs were carried out, one with paired-end 150-nucleotide (nt) reads on MiSeq V2 microchemistry and another with paired-end 300-nt reads on V3 chemistry. The raw reads were trimmed (minimum length, 35 bp; quality score, 0.03) and assembled in CLC Genomics Workbench 7.5.1 by de novo assembly (minimum contig length, 1,000 bp), producing 192 to 223 contigs (Table 1). The median read depth of the assemblies ranged from 38× for 34827 and 34870 to 84× for 36708, with an N50 between 65 kbp and 114 kbp (Table 1). The sequences were annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) at http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html.

TABLE 1 .

NCBI accession numbers and assembly metrics of the O26:H11 E. coli draft genomes

Isolate ST stx subtype No. of contigs Genome size (bp) N50 (bp) Median read depth (×) No. of coding sequences (per PGAAP) NCBI accession no.
36084 ST21 stx2a 205 5,235,007 96,218 45 5,209 LDXI00000000
36708 ST29 stx2a 192 5,526,827 114,644 84 5,579 LDXG00000000
34827 ST29 stx2a 223 5,604,044 73,150 38 5,674 LDXF00000000
34870 ST29 stx2a 196 5,498,010 65,024 38 5,524 LDXE00000000
36348 ST29 stx2d 208 5,570,467 94,008 71 5,573 LDXD00000000
36293 ST29 stx2d 207 5,458,923 75,621 45 5,460 LDXC00000000
36493 ST29 stx2d 204 5,422,929 78,448 47 5,389 LDXB00000000

The average size of the genomes in this study is 5.47 Mb, with 5.23 Mb being the smallest genome size (isolate 36084, Table 1) and 5.60 Mb the largest genome size (isolate 34827, Table 1). On average, 5,487 coding sequences were identified in the genomes (Table 1). BLAST analysis of the stx genes confirmed the previously identified subtypes (Table 1).

A detailed report on further analyses of the draft genome sequences will be released in a future publication.

Nucleotide sequence accession numbers.

The annotated draft whole-genome sequences of these O26:H11 strains were deposited in DDBJ/ENA/GenBank under the accession numbers LDXB00000000 to LDXG00000000 and LDXI00000000 (Table 1). The versions described in this paper are the first versions, LDXB01000000 to LDXG01000000 and LDXI01000000.

ACKNOWLEDGMENT

This project was partly funded by the French Joint ministerial program of R&D against CBRNE risks (grant C17609-2).

Footnotes

Citation Delannoy S, Mariani-Kurkdjian P, Bonacorsi S, Liguori S, Ison SA, Fach P. 2015. Draft genome sequences of human-pathogenic Escherichia coli O26:H11 strains carrying the stx2 gene only and circulating in France. Genome Announc 3(4):e00852-15. doi:10.1128/genomeA.00852-15.

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