Draft Genome Sequences of Five Novel Polyketide Synthetase-Containing Mouse Escherichia coli Strains.

We report herein the draft genomes of five novel Escherichia coli strains isolated from surveillance and experimental mice housed at MIT and the Whitehead Institute and describe their genomic characteristics in context with the polyketide synthetase (PKS)-containing pathogenic E. coli strains NC101, IHE3034, and A192PP.

GENOME ANNOUNCEMENT

Escherichia coli is typically considered a harmless commensal bacteria colonizing the mammalian intestine. However, infection by numerous strains from the B2 phylogroup can cause septicemia/bacteremia, urinary tract infection, and meningitis and are increasingly being linked to inflammatory bowel disease and colorectal tumors in humans (1–3). These strains commonly harbor an ~54-kb polyketide synthetase (PKS) pathogenicity island that produces a genotoxin called colibactin (4, 5). Recently, colibactin expression by the mouse commensal E. coli strain NC101 was shown to potentiate colitis-associated colorectal cancer in IL-10−/− mice (2). Furthermore, aside from causing double-strand DNA breaks, colibactin facilitates intestinal colonization and systemic translocation that causes septicemia and meningitis (6). Thus, the virulence and oncogenic modalities of colibactin-producing E. coli strains in experimental mice may represent a potential confounder of results, especially in models of inflammatory disease and cancer.

In this report, we announce the draft genomes of five novel B2-phylotype E. coli strains isolated from the feces of two asymptomatic surveillance mice, the uterine fluid of a transgenic mouse, and from the blood of two experimental immunocompromised mice with sepsis housed under specific-pathogen-free conditions. We previously found all these strains except A4 were PCR-positive for the PKS genes clbA and clbQ and caused megalocytosis and γ-H2AX-detectable DNA damage in HeLa cells in vitro, suggesting colibactin activity by these organisms ([7]; our unpublished data). We briefly describe the features of these novel E. coli genomes in context to the previously sequenced genomes of NC101 and the PKS-containing septicemia- and meningitis-causing strains IHE3034 and A192PP (4, 6).

Genomes were sequenced using PacBio RSII and resulting sequencing data were assembled into two to five contigs using RS_HGAP_Assembly.3 from the SMRT Portal 2.3. Contigs were annotated using the RAST tool kit (RASTtk) (8). Novel strains have genomic sizes, G+C content, protein-coding sequences, and RNAs comparable to those of the genomes of NC101 (GenBank: NZ_AEFA00000000.1), IHE3034 (GenBank: NC_017628.1), and A192PP (GenBank: NZ_CVOH00000000.1) (Table 1). All novel genomes except A4 contained complete PKS islands, with all genes having ≥99% sequence identity and coverage as well as identical synteny to those from NC101, IHE3034, and A192PP.

TABLE 1 

Genomic characteristics of novel mouse E. coli strains

Strain	GenBank accession no.	Origin of mouse isolates	Genome size (bp)	No. of contigs	Fold coverage	G+C content (%)	No. of protein-coding sequences	No. of RNA sequences
E. coli 1409150006 (MIT A2)	MBNU00000000	Feces	5,292,961	3	114.7	50.5	5,203	108
E. coli 1409160003 (MIT A4)	MBNV00000000	Feces	5,066,411	4	166.4	50.5	5,003	114
E. coli 1408270010 (MIT A21)	MBNW00000000	Uterine fluid	5,318,023	5	129.9	50.5	5,280	108
E. coli 1512290008 (Whitehead Institute 0008)	MBNX00000000	Blood	5,289,663	3	147.7	50.5	5,203	108
E. coli 1512290026 (Whitehead Institute 0026)	MBNY00000000	Blood	5,005,444	2	140.6	50.6	4,876	108

PATRIC’s proteome comparison service was used to determine the number of homologous genes between NC101, IHE3034, and A192PP as references versus the novel E. coli strains (9). NC101 and the novel PKS-containing strains shared >4,780 proteins (>97%) as homologs, whereas between NC101 and A4, 4,732 proteins (~89%) were homologous. All novel E. coli strain shared considerably less homologs to IHE3034 (4,386 to 4,525 proteins; ~87 to 90%) and A192PP (4,472 to 4,624; ~80 to 83%).

Aside from PKS, the virulence factors enterobactin siderophore receptor protein, s-fimbriae minor subunit, glutamate decarboxylase, per-activated serine protease autotransporter enterotoxin, and bor protein precursor were identified in NC101 and the novel PKS-containing strains using VirulenceFinder 1.5 (10). A4 also contained glutamate decarboxylase, per-activated serine protease autotransporter enterotoxin, and bor protein precursor as well as serine protease autotransporters of Enterobacteriaceae.

Together, these genomic data suggest that the novel PKS-containing strains are more similar to NC101 than IHE3034 and A192PP. Future studies will investigate the pathogenic and carcinogenic potential of these and other PKS-containing E. coli strains in mice under differing experimental protocols.

Accession number(s).

The genome sequences have been submitted to GenBank under the accession numbers listed in Table 1.