Draft Genome Sequence of Escherichia coli MS499, Isolated from the Infected Uterus of a Postpartum Cow with Metritis.

Specific Escherichia coli strains associated with bovine postpartum uterine infection have recently been described. Many recognized virulence factors are absent in these strains; therefore, to define a prototypic strain, we report here the genome sequence of E. coli isolate MS499 from a cow with the postpartum disease metritis.

GENOME ANNOUNCEMENT

Escherichia coli is a diverse species, and several of its pathotypes are well-characterized, including extraintestinal pathogenic E. coli (ExPEC). ExPEC infections of the udder and uterus of cattle have been of increasing significance, and E. coli is a cause of postpartum uterine disease (metritis) in cattle (1–3) and was recently proposed as a novel pathotype termed intrauterine E. coli or endometrial pathogenic E. coli (EnPEC) (2, 4). To date, genomic characterization of E. coli has focused on phylogenetic grouping, genotyping, and pathotyping based on the detection of defined virulence-associated factors. Among metritis isolates, phylogroup B1 strains have predominated (>65%), and these lack many virulence-associated factors typical of other E. coli pathotypes. Thus, we undertook genome sequencing of an EnPEC strain to define a prototype for this pathotype.

E. coli MS499 isolated from the uterus of an animal with metritis was previously confirmed as phylogroup B1 and possessed only fyuA of 17 fitness- and virulence-associated genes (4). The isolate was cultured on LB agar plates, and genomic DNA was prepared using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s instructions. Sequencing was carried out using 454 GS-FLX and Illumina GA IIx 120-bp paired-end sequencing. The reads were assembled using Velvet (5) and the Celera assembler with the best overlap graph (CABOG) (6), and gaps were closed using unmapped 454 and Illumina reads. The assembled 447 contigs totaled 4,883,598 bp, with a G+C content of 50.7%. The assembled contigs were subjected to preliminary annotation using the RAST resource (release 70) (7) and subsequently using the NCBI annotation tool. The genome was predicted to encode 4,708 proteins. Several contigs assembled into a large plasmid showing high similarity to plasmids that confer functions in host colonization, persistence, and pathogenicity in Salmonella enterica serovar Kentucky and avian pathogenic E. coli (APEC) (8).

Frequently, E. coli strains of phylogroup B1 are considered nonpathogenic or poorly pathogenic (9) though strain MS499 contains many pathogenicity-associated determinants, including multiple fimbriae, iron acquisition systems, and autotransporter proteins (type 5 secretion system [T5SS]), as well as flagella. Putative toxins were absent, with the exception of an ortholog of the hylF hemolysin. Like many EnPEC isolates, E. coli MS499 is resistant to β-lactams (4), and a gene encoding a TEM-1 family β-lactamase was present.

E. coli MS499 from bovine metritis has many of the characteristics typifying ExPEC, i.e., elements that may contribute to pathogenicity, fitness, and resistance, and this initial genome sequence supports the previous proposal of EnPEC as a novel E. coli pathotype. This first reported genome sequence for EnPEC provides a resource for further defining this novel E. coli pathotype and forms the basis for systematic studies. Comparative genomic analyses are under way and will be reported separately in order to further define this E. coli pathotype.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JDRV00000000. The version described in this paper is version JDRV01000000.