ABSTRACT
Methicillin-resistant Staphylococcus aureus (MRSA) can be a commensal or pathogen in humans. Pathogenicity and disease are related to the acquisition of mobile genetic elements encoding virulence and antimicrobial resistance genes. Here, we report draft genome sequences for 50 clinical MRSA isolates from humans with MRSA-related disease.
GENOME ANNOUNCEMENT
Methicillin-resistant Staphylococcus aureus (MRSA) was first isolated in 1961 (1). MRSA rapidly became widespread in the hospital setting and remained contained there until the late 1990s, when isolates began infecting patients with no known risk factors for hospital-acquired MRSA (HA-MRSA) (2). This subset of MRSA isolates was termed community-acquired MRSA (CA-MRSA). The third group of isolates are acquired by contact with livestock species and are called livestock-associated MRSA (LA-MRSA). Specific lineages of S. aureus predominate within each subset, and these lineages are defined by their multilocus sequence type (ST). S. aureus lineages are defined by differing characteristics that allow them to possess distinct niches. The ST5 lineage, specifically, is a widespread and successful lineage of HA-MRSA (3). This is primarily attributed to the capacity of this lineage to acquire mobile genetic elements encoding virulence factors and antimicrobial resistance genes (3).
Here, we report the generation of 50 draft genome sequences from MRSA ST5 isolates obtained from the hospital at the University of California, Irvine (4). Isolates sequenced, listed in Table 1, were from patients who had MRSA-related disease and no known livestock exposure. Minimal patient history was available, including source information, making HA- and CA-MRSA indistinguishable. The isolates were grown in trypticase soy broth (BD Biosciences, Sparks, MD), and the High Pure Template preparation kit (Roche Applied Science, Indianapolis, IN) was used to isolate total genomic DNA.
TABLE 1 .
Assembled draft genome sequences obtained from this project
| Isolate name | Avg coverage | No. of contigs | GenBank accession no. |
|---|---|---|---|
| UCI 1 | 73.13 | 89 | LKYS00000000 |
| UCI 2 | 51.15 | 162 | LKYT00000000 |
| UCI 4 | 69.93 | 137 | LKYV00000000 |
| UCI 5 | 83.47 | 105 | LKYW00000000 |
| UCI 6 | 59.19 | 111 | LKYX00000000 |
| UCI 7 | 51.04 | 158 | LKYY00000000 |
| UCI 8 | 53.59 | 120 | LKYZ00000000 |
| UCI 10 | 50.26 | 125 | LKZB00000000 |
| UCI 12 | 61.68 | 167 | LKZD00000000 |
| UCI 13 | 46.01 | 144 | LKZE00000000 |
| UCI 14 | 43.15 | 183 | LKZF00000000 |
| UCI 15 | 46.20 | 123 | LKZG00000000 |
| UCI 16 | 83.09 | 117 | LKZH00000000 |
| UCI 17 | 83.32 | 140 | LKZI00000000 |
| UCI 18 | 55.44 | 205 | LKZJ00000000 |
| UCI 20 | 55.04 | 201 | LKZL00000000 |
| UCI 22 | 59.19 | 148 | LKZN00000000 |
| UCI 23 | 38.77 | 311 | LKZO00000000 |
| UCI 25 | 80.63 | 125 | LKZQ00000000 |
| UCI 26 | 71.95 | 114 | LKZR00000000 |
| UCI 28 | 48.98 | 145 | LKZT00000000 |
| UCI 29 | 65.78 | 247 | LKZU00000000 |
| UCI 30 | 66.07 | 148 | LKZV00000000 |
| UCI 31 | 56.88 | 219 | LKZW00000000 |
| UCI 32 | 43.65 | 269 | LKZX00000000 |
| UCI 33 | 43.35 | 242 | LKZY00000000 |
| UCI 34 | 49.12 | 224 | LKZZ00000000 |
| UCI 35 | 46.42 | 111 | LLAA00000000 |
| UCI 36 | 46.00 | 246 | LLAB00000000 |
| UCI 37 | 37.53 | 264 | LLAC00000000 |
| UCI 38 | 53.12 | 227 | LLAD00000000 |
| UCI 39 | 83.79 | 107 | LLAE00000000 |
| UCI 40 | 44.79 | 171 | LLAF00000000 |
| UCI 41 | 50.09 | 175 | LLAG00000000 |
| UCI 42 | 54.66 | 160 | LLAH00000000 |
| UCI 44 | 60.57 | 140 | LLAJ00000000 |
| UCI 47 | 65.17 | 191 | LLAM00000000 |
| UCI 49 | 57.85 | 237 | LLAO00000000 |
| UCI 50 | 50.05 | 174 | LLAP00000000 |
| UCI 51 | 41.44 | 184 | LLAQ00000000 |
| UCI 53 | 69.80 | 97 | LLAS00000000 |
| UCI 54 | 49.38 | 138 | LLAT00000000 |
| UCI 55 | 80.91 | 156 | LLAU00000000 |
| UCI 57 | 80.99 | 87 | LLAW00000000 |
| UCI 58 | 79.17 | 112 | LLAX00000000 |
| UCI 59 | 82.31 | 132 | LLAY00000000 |
| UCI 60 | 49.91 | 231 | LLAZ00000000 |
| UCI 61 | 66.52 | 178 | LLBA00000000 |
| UCI 62 | 61.44 | 131 | LLBB00000000 |
| UCI 63 | 54.37 | 96 | LLBC00000000 |
Draft genome sequences were produced using the Illumina MiSeq platform. Indexed libraries were produced with the Nextera XT DNA sample preparation and index kit (Illumina, San Diego, CA). Sequencing employed the MiSeq v2 500 Cycle reagent kit (Illumina) and generated 2 × 250-bp paired-end reads.
Sequence reads were assembled into draft genomes using MIRA v4.0.2 (http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html). The average coverage for each isolate is listed in Table 1. For retention in the assembly, the contigs were required to be >1,500 bp and have a coverage with at least two-thirds the average coverage of the genome. When repetitive elements were identified during assembly, the contig was required to be >2,000 bp to be included in the assembly.
Accession number(s).
The assembled draft genome sequences obtained from this project were deposited into DDBJ/ENA/GenBank with the accession numbers listed in Table 1.
ACKNOWLEDGMENTS
Funding for this research was provided by the USDA Agricultural Research Service and the National Pork Board. S.J.H. is supported by the Veterinary Diagnostic Laboratory at Iowa State University.
Funding sources did not impact study design, data collection, data analysis, decisions on publication, or preparation of the manuscript. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture.
Footnotes
Citation Hau SJ, Bayles DO, Alt DP, Nicholson TL. 2017. Draft genome sequences of 50 methicillin-resistant Staphylococcus aureus sequence type 5 isolates obtained from a U.S. hospital. Genome Announc 5:e01083-17. https://doi.org/10.1128/genomeA.01083-17.
REFERENCES
- 1.Jevons M. 1961. “Celbenin”-resistant staphylococci. Br Med J 1:124–125. [Google Scholar]
- 2.Pantosti A. 2012. Methicillin-resistant Staphylococcus aureus associated with animals and its relevance to human health. Front Microbiol 3:127. doi: 10.3389/fmicb.2012.00127. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Monecke S, Coombs G, Shore AC, Coleman DC, Akpaka P, Borg M, Chow H, Ip M, Jatzwauk L, Jonas D, Kadlec K, Kearns A, Laurent F, O’Brien FG, Pearson J, Ruppelt A, Schwarz S, Scicluna E, Slickers P, Tan HL, Weber S, Ehricht R. 2011. A field guide to pandemic, epidemic and sporadic clones of methicillin-resistant Staphylococcus aureus. PLoS One 6:e17936. doi: 10.1371/journal.pone.0017936. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Hudson LO, Murphy CR, Spratt BG, Enright MC, Elkins K, Nguyen C, Terpstra L, Gombosev A, Kim D, Hannah P, Mikhail L, Alexander R, Moore DF, Huang SS. 2013. Diversity of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from inpatients of 30 hospitals in Orange County, California. PLoS One 8:e62117. doi: 10.1371/journal.pone.0062117. [DOI] [PMC free article] [PubMed] [Google Scholar]