Draft Genome Sequences of 14 Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Isolates from Swine Farms in the United States

ABSTRACT

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is a bacterium carried by or obtained from swine and other livestock. The initial and predominant swine-associated LA-MRSA sequence type (ST) identified is ST398. Here, we present 14 draft genome sequences from LA-MRSA ST398 isolates found in the United States.

GENOME ANNOUNCEMENT

The isolation of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) from swine in 2004 raised public health concerns that swine may serve as the largest reservoir of MRSA outside the hospital setting. Initial surveillance in Europe revealed that the primary multilocus sequence type (ST) of European swine-associated LA-MRSA was ST398 (1), which has also been identified in North American swine (2–4). While ST398 is generally considered a livestock-adapted lineage (5, 6), there have been reports of colonization and infection of humans with LA-MRSA ST398 isolates (7, 8). To address the concerns surrounding LA-MRSA ST398, genetic studies have evaluated isolate relatedness and found that LA-MRSA ST398 is likely derived from a methicillin-sensitive ST398 lineage from humans (9). Detection of genetic changes and potential for human outbreaks with LA-MRSA ST398 isolates relies on continuing evaluation of genomic data from LA-MRSA field isolates.

Here, we provide draft genome sequences for 14 LA-MRSA ST398 isolates from a study conducted by Iowa State University that examined U.S. swine farms for the presence and prevalence of LA-MRSA (4). Isolates were obtained by swabbing the nares of healthy pigs or the environment within three high-density livestock operations. Farm and source information for each isolate is shown in Table 1. The isolates were grown in Trypticase soy broth (BD Biosciences, Sparks, MD, USA) and the High Pure template preparation kit (Roche Applied Science, Indianapolis, IN, USA) was used to extract total genomic DNA.

TABLE 1.

Isolate information and genome assembly characteristics

Isolate name	Isolate source	Farm no.	Avg coverage (×)	No. of contigs	GenBank accession no.
ISU 909	Environment	35	53.51	113	LKWK00000000
ISU 912	Pig	37	22.28	157	LKWL00000000
ISU 913	Environment	37	48.98	131	LKWM00000000
ISU 914	Environment	37	66.90	91	LKWN00000000
ISU 915	Pig	36	69.78	131	LKWO00000000
ISU 916	Pig	36	19.05	180	LKWP00000000
ISU 917	Pig	36	55.79	118	LKWQ00000000
ISU 918	Pig	36	34.41	113	LKWR00000000
ISU 919	Environment	36	21.71	140	LKWS00000000
ISU 920	Environment	36	55.34	177	LKWT00000000
ISU 922	Pig	36	36.63	105	LKWU00000000
ISU 924	Pig	36	41.26	71	LKWV00000000
ISU 925	Pig	36	37.02	116	LKWW00000000
ISU 927	Environment	35	38.79	109	LKWX00000000

The Illumina MiSeq platform (Illumina, San Diego, CA, USA) was used to generate draft genomic sequence data. Indexed libraries were generated using the Nextera XT DNA sample preparation and index kit (Illumina). Libraries were pooled and run on an Illumina MiSeq instrument with the MiSeq V2 500-cycle reagent kit (Illumina), generating 2 × 250-bp paired-end reads.

The sequence data were assembled using MIRA version 4.0.2 (http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html). The average coverage obtained for each isolate can be found in Table 1. To be retained in the assembly, contigs were required to be >1,500 bp in length and have a coverage of >66% of the average coverage for the genome. The assembly tool identified repetitive elements that were required to be >2,000 bp to remain in the assembly.

Accession number(s).

The assembled draft genome sequences generated in this study can be found in DDBJ/ENA/GenBank with the accession numbers listed in Table 1.