Complete Genome Sequence of a Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolate from the United States.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) may be the largest MRSA reservoir outside the hospital setting. One concern with LA-MRSA is the acquisition of novel mobile genetic elements by these isolates. Here, we report the complete genome sequence of a swine LA-MRSA sequence type 5 isolate from the United States.

GENOME ANNOUNCEMENT

Methicillin-resistant Staphylococcus aureus (MRSA) has circulated primarily in hospitals since the 1960s (1). More recently, MRSA has been isolated outside the hospital setting (community-acquired MRSA) and from livestock (livestock-associated MRSA [LA-MRSA]) (2, 3). Outside of the United States, LA-MRSA isolates are primarily sequence type 398 (ST398) and ST9 in Europe and Asia, respectively (4, 5). LA-MRSA in the United States also contains MRSA ST5 isolates (6). These isolates have raised concerns because, unlike ST398 and ST9, which are considered livestock adapted, ST5 isolates are a widespread and successful hospital-acquired MRSA (HA-MRSA) lineage (2). The pathogenicity of ST5 isolates is thought to be associated with the capacity and ease with which they acquire mobile genetic elements (7).

Here, we report the generation of whole-genome sequence data for one swine-associated LA-MRSA ST5 isolate (ISU935) obtained from a study conducted at Iowa State University (6). ISU935 was isolated from a healthy pig in a high-density swine operation. The isolate was grown in Trypticase soy broth (BD Biosciences, Sparks, MD), and the High Pure template preparation kit (Roche Applied Science, Indianapolis, IN) was used to extract total genomic DNA from the sample.

Both PacBio and Illumina MiSeq platforms were used to generate whole-genome sequence data. The PacBio library was prepared utilizing the PacBio 10-kb insert library preparation protocol found online (http://www.pacb.com/wp-content/uploads/2015/09/Procedure-Checklist-10-kb-Template-Preparation-and-Sequencing.pdf). The library was sequenced with a PacBio RSII platform on a single-molecule real-time (SMRT) cell. A MiSeq indexed library was created using the Nextera XT DNA sample preparation and index kits (Illumina, San Diego, CA). The library was sequenced with a MiSeq v2 500-cycle reagent kit, generating 2- × 250-bp paired-end reads on the Illumina MiSeq platform (Illumina, San Diego, CA).

PacBio SmrtAnalysis v. 2.3.0 and CANU v. 1.3 software were used to generate the whole-genome assembly. ISU935 had an average PacBio coverage of 449×. After assembly, the PacBio data were trimmed to remove overlapping sequences and oriented with dnaA as the start of the genome. The Broad Institute’s Pilon v. 1.18 was used to polish and error correct the ISU935 genome using Illumina data with an average coverage of 18×.

Accession number(s).

The whole-genome sequence for ISU935 was deposited in DDBJ/ENA/GenBank with the accession number CP017090.