Draft Genome Sequence of Escherichia coli ARS-CC7049, a Sequence Type 38 Strain Isolated from Dry Cow Feces on a Commercial Dairy Operation.

Escherichia coli is a diverse species of commensal and pathogenic strains, of which some can cause extraintestinal infections, such as sequence type 38 (ST38) strains. Here, we report the genome sequence of E. coli ARS-CC7049, an ST38 strain that was isolated from a composite fecal sample on a dairy farm.

ANNOUNCEMENT

Annually there are approximately 8 to 10 million diagnosed urinary tract infections (UTI) in the United States. Most of these infections are caused by a relatively small number of extraintestinal pathogenic Escherichia coli (ExPEC) sequence types (STs), with ST38 being one of the leading disease-causing ExPEC STs globally (1). In a larger study conducted between 2013 and 2015, E. coli was isolated from composite fecal samples collected from preweaned and postweaned calves and dry and lactating dairy cows on 80 commercial dairy operations in Pennsylvania (2). Here, we present the genome sequence of an E. coli ST38 isolate collected from dry cow feces in 2015.

Six fecal samples were collected from the floor of a dry cow pen on a commercial dairy farm in Pennsylvania and combined (approximately 120 g of combined feces). The sample was transported on ice to the laboratory, and approximately 5 g was homogenized in 45 mL of buffered peptone water which was subsequently streaked onto CHROMagar EC agar (Paris, France). Colonies were confirmed as E. coli after incubation for 24 h at 37°C on Simmons citrate agar (BD Diagnostics), MacConkey agar (Remel, Lenexa, KS), MacConkey sorbitol agar, and Luria-Bertani agar. DNA was extracted from a purified colony grown overnight in Luria-Bertani broth using a QIAcube with a QIAmp DNA mini kit (Qiagen, Hilden, Germany). Paired-end libraries (2 × 150 bp) were constructed using the Nextera XT library prep kit (Illumina, La Jolla, CA), which were then sequenced using a high-output v 1.0 flow cell on a NextSeq 500 platform (Illumina). Sequence data were demultiplexed using the BCL2FastQ program, and PhiX reads were removed using DeconSeq (PhiX NCBI accession NC_001422) (3). Reads were further trimmed using Trimmomatic v 0.35 (LEADING:20 TRAILING:20 SLIDINGWINDOW4:20 MINLEN:36) (4) and assessed using FastQC v 0.11.6. The genome sequence was assembled de novo using SPAdes v 3.8.0 with the –careful option (5). Genome quality was assessed using QUAST (6).

The E. coli ARS-CC7049 genome was assembled into 135 contigs with a genome size of 4,877,373 bp and a GC content of 50.7%. The total number of reads was 1,705,268, the coverage was 45×, and the N50 value was 141,319 bp. Curated sequencing reads and the assembled genome were analyzed using the Center for Genomic Epidemiology Web server with parameters set to default (http://www.genomicepidemiology.org/services/). Using the MLST 2.0 program, the isolate was identified as ST38 of the ST38 Cplx within phylotype D (7). Using ResFinder 4.1, antimicrobial resistance genes or resistance-conferring single nucleotide polymorphisms (SNPs) were not identified among the reads or the assembled genome (8). No sequences with plasmid replicons were identified among the reads or the assembled genome using PlasmidFinder (9). In the assembled genome, kps genes of the K1 capsule and the chu heme uptake genes (chuA, eilA, gad, iss, kpsE, ompT, and terC) were identified, indicating the presence of some virulence factors known to play a role in extraintestinal pathogenic E. coli infections (10).

Data availability.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number JAIQGV000000000 and BioProject number PRJNA761377. The version described in this paper is the first version, JAIQGV000000000.1. The raw sequence data are available in the Sequence Read Archive under the accession number SRR15793117.