Genome Sequences of Eight Shiga Toxin-Producing Escherichia coli Strains Isolated from a Produce-Growing Region in California

Abstract

Produce contaminated with Shiga toxin-producing Escherichia coli (STEC) is a continuing source of foodborne illness in the United States. This report documents the complete genome sequences of eight STEC strains isolated from livestock and water samples taken from a major agricultural region for leafy greens in California.

Complete Genome Sequence of Pantoea agglomerans ASB05 Using Illumina and PacBio Sequencing

“…P. agglomerans strain ASB05 was primarily sequenced via the Pacific Biosciences (PacBio, Menlo Park, CA) RS II platform and produced sequences that were compared and confirmed with sequences generated with the Illumina (San Diego, CA) MiSeq platform. Both sequencing methods were performed by following the standard library construction protocol described previously by Parker et al ( 9 ). For the PacBio platform, the SMRTbell library was prepared from 10 μg of bacterial genomic DNA fragmented using G-tube (Covaris, Woburn, MA) following the standard PacBio 20-kb library preparation procedure ( 10 ) but with 1× AMPure bead (PacBio) cleanup and an extra DNA repair step after BluePippin size selection with a 0.75% DF Marker S1 high-pass 6- to 10-kb vs3 cassette (Sage Science, Beverly, MA).…”

Complete Genome Sequences of Three Shiga Toxin-Producing Escherichia coli O111:H8 Strains Exhibiting an Aggregation Phenotype

“…A single colony for each STEC O111 strain was grown overnight on LB agar plates at 37°C, and genomic DNA was extracted using a sucrose-Tris method, followed by phenol-chloroform cleanup, as described previously (12). Sequencing was performed using a Pacific Biosciences RS II platform (Menlo Park, CA), with 20-kb SMRTbell libraries, and assembled using PacBio HGAP version 3.0 in the SMRT Analysis package (version 2.3.0), as described previously (13). Additionally, sequencing was performed on a MiSeq platform (Illumina, Inc., San Diego, CA) with an LTP library preparation kit (Kapa Biosystems, Wilmington, MA), a MiSeq reagent kit version 2 (Illumina, Inc.), and 2 × 250-bp cycles, as described previously (13).…”

“…Sequencing was performed using a Pacific Biosciences RS II platform (Menlo Park, CA), with 20-kb SMRTbell libraries, and assembled using PacBio HGAP version 3.0 in the SMRT Analysis package (version 2.3.0), as described previously (13). Additionally, sequencing was performed on a MiSeq platform (Illumina, Inc., San Diego, CA) with an LTP library preparation kit (Kapa Biosystems, Wilmington, MA), a MiSeq reagent kit version 2 (Illumina, Inc.), and 2 × 250-bp cycles, as described previously (13). A final base call validation of the PacBio contigs was performed using Illumina MiSeq reads trimmed using a quality score threshold of 20 or higher (≥Q20) and the reference assembler within Geneious (version 11.1; Biomatters, Ltd., Auckland, New Zealand).…”

Complete Genome Sequence of Lactococcus lactis subsp . lactis Strain 14B4, Which Inhibits the Growth of Salmonella enterica Serotype Poona In Vitro

“… L. lactis strain 14B4 was isolated by washing almond drupes in phosphate-buffered saline for 1 h at 25°C with shaking (200 rpm), followed by plating onto de Man, Rogosa, and Sharpe (MRS) agar that was incubated anaerobically for 24 h at 37°C. For DNA extraction, a single colony was transferred to 100 ml of tryptic soy broth (Oxoid, Basingstoke, Hampshire, England) and incubated at 37°C for 24 h. Genomic DNA was extracted using sucrose-Tris with phenol-chloroform cleanup extractions as described previously ( 3 ).…”

“…Sequencing was carried out using a Pacific Biosciences (PacBio) RS II sequencer using standard protocols as described previously ( 3 ). For Illumina sequencing, DNA was sheared at 30 lb/in 2 for 40 s, and 700- to 770-bp fragments were selected and libraries were constructed using standard protocols ( 3 ). Sequencing was performed using a 2 × 250-bp MiSeq paired-end reagent kit version 2 on a MiSeq instrument (Illumina, San Diego, CA) following the manufacturer’s protocol.…”