Draft Genomic Sequences of Nine Extraintestinal Pathogenic Escherichia coli Isolates from Retail Chicken Skin.

Extraintestinal pathogenic Escherichia coli strains were isolated from retail chicken skin. Here, we report the draft genomic sequences for these nine E. coli isolates, which are currently being used in agricultural and food safety research.

ANNOUNCEMENT

Extraintestinal pathogenic Escherichia coli (ExPEC) isolates, often multidrug resistant, are associated with urinary tract infections, ulcerative colitis, meningitis, and sepsis, which affect over 11 million people in the United States annually (1–3). Also, ExPEC is associated with similar veterinary diseases in addition to avian colibacillosis (4). ExPEC commonly contaminates poultry meat and other foods (5–8). Isolates from food that contain the appropriate virulence factors cause disease in animal model systems (9, 10). Control of ExPEC in food and agricultural production could reduce the incidence of ExPEC-related disease in both humans and animals. Toward this end, nine ExPEC strains recovered from retail chicken skin are currently being used for agricultural and food safety research (11).

Stock cultures were streaked onto Trypticase soy agar plates and incubated for 24 h at 37°C. Genomic DNA was extracted from single colonies using the DNeasy blood and tissue kit (Qiagen, Hilden, Germany) and quantified in a Qubit 3.0 fluorimeter (Life Technologies, Carlsbad, CA, USA). The genomic DNA library was prepared using the Nextera DNA flex library prep kit (Illumina, San Diego, CA, USA). Libraries were analyzed for concentration, pooled, and denatured for loading onto a flow cell for cluster generation. Denatured libraries (1.8 pM) were sequenced on an Illumina MiniSeq platform using the 2 × 150-bp paired-end protocol with 50× coverage. Illumina reads were assembled de novo using SPAdes version 3.9.0. Virulence factors, antibiotic resistance genes, genome size, N50 values, multilocus sequence type (MLST), noncoding RNAs (ncRNAs), rRNAs, tRNAs, genes, and coding sequences (CDSs) were determined using the Illumina Bacterial Analysis Pipeline version 1.0.4 and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 4.3. The accession numbers and assembly metrics are listed in Table 1.

TABLE 1

Accession numbers and assembly and annotation metrics of nine draft whole-genome sequences

Strain	Serotype	GenBank accession no.	BioProject no.	Genome size (bp)	% G+C content	No. of contigs	N50 (bp)	No. of genes	No. of CDSs	No. of tRNAs	No. of rRNAs	No. of ncRNAs	No. of pseudogenes
B7S3	O1:H7	PNYG00000000	PRJNA429000	5,235,670	50.41	3222	91,992	6,158	6,056	82	9	11	428
B7S10	O24:H4	PNYH00000000	PRJNA429009	5,178,520	50.69	320	91,992	6,164	6,060	85	9	10	427
B7S19	O120:H4	QEMS00000000	PRJNA454292	4,903,012	50.5	339	91,992	6,178	6,076	82	10	10	429
B8S18	O2:H6	PPHQ00000000	PRJNA430921	5,495,366	50.59	244	200,704	5,780	5,693	77	2	8	346
B8S56	O120:H4	QEMT00000000	PRJNA454295	5,271,935	50.3	352	80,290	6,108	6,005	78	15	10	460
B8S59	O11:H25	QEMU00000000	PRJNA454299	5,417,305	50.47	209	156,178	5,771	5,679	76	10	6	228
B9S20	O11:H25	QEMP00000000	PRJNA454260	5,459,244	50.41	214	156,178	5,816	5,718	82	10	6	233
B9S22	O11:H25	QEMQ00000000	PRJNA454275	5,462,443	50.41	229	162,858	5,836	5,736	82	12	6	232
B9S24	O1:H45	QEMR00000000	PRJNA454280	5,441,656	50.15	206	162,858	5,816	5,716	81	13	6	228

Genomics data are now considered an integral part of risk assessment for food safety and environmental microbiology (http://www.fsis.usda.gov/wps/wcm/connect/d79eaa29-c53a-451e-ba1c-36a76a6c6434/Microbial_Risk_Assessment_Guideline_2012-001.pdf?MOD=AJPERES ). These genomic data will be useful for understanding ExPEC pathogenesis and helping to elucidate its role in human and veterinary diseases.

Data availability.

The whole-genome shotgun projects reported here have been deposited in DDBJ/ENA/GenBank under the accession numbers and BioProject numbers listed in Table 1. The versions described in this paper are the first versions.