Genome Sequences of Livestock-Associated Methicillin-Resistant Staphylococcus aureus spa Type t899 Strains Belonging to Three Different Sequence Types (ST398, ST9, and ST4034)

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is an emerging MRSA lineage rapidly evolving in the community. In this report, we present the draft genome sequences of nine LA-MRSA strains.

Staphylococcus aureus protein A (spa) typing has a remarkable predictive power over clonal relatedness (5,6). In most instances, a single spa type is strictly associated with a specific multilocus sequence type (MLST). However, some exceptions do exist, such as spa type t899, which is reported in multiple sequence types, namely, ST398 and ST9. In this report, we present the draft genome sequences of nine LA-MRSA strains, all belonging to spa type t899 but clustering in three different sequence types, ST398 (3), ST9 (5), and ST4034 (1) ( Table 1).
Isolates were obtained from meat samples collected in retail markets and from a nasal swab sample from a dialysis patient that was taken during hospital screening in the Czech Republic. The meat from which the samples were drawn was produced in different countries and sold in the Czech Republic. The samples were primarily enriched in buffered peptone water and cultured on Baird-Parker agar. Presumptive S. aureus colonies were transferred to blood agar and confirmed using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (7). All MRSA isolates were identified using PCR detection of the S. aureus-specific fragment SA442 and the mecA gene (8). MLST (https://cge.cbs.dtu.dk/services/MLST) (9) and spa typing (https://www.spaserver.ridom.de) (10) were performed prior to the whole-genome sequence run.
Total genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen, Valencia, CA) from pure culture colonies cultivated on Columbia sheep blood agar (Bio-Rad Laboratories, Temse, Belgium). Whole-genome sequencing was performed with a MiSeq sequencing platform (Illumina, San Diego, CA). Library preparation was performed with the Nextera XT DNA sample preparation kit (Illumina). The libraries were then sequenced using a 250-bp paired-end protocol (MiSeq reagent kit v.3, Illumina) according to the manufacturer's instructions. Data analysis was performed using an in-house instance of the Galaxy workflow management system (11). Sequencing yielded a total of 9,573,010 reads with 35-to 251-bp read lengths. Raw reads were quality checked with FastQC v.0.65, and low-quality reads were trimmed using Trimmomatic v.0.36.4 (12). Subsequently, assemblies were generated using the SPAdes v.1.3.1 algorithm (13). Contigs Ն200 bp long were retained in the assembly. The genome sizes ranged from 2,730,307 to 2,922,579 bp. The average GC content and the N 50 value were 32.8% and 61,574 bp, respectively. Final assemblies consisted of 64 to 303 contigs with an average coverage of 88.64ϫ (Table 1). Annotation was carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (https://www.ncbi.nlm .nih.gov/genome/annotation_prok/) (14).
Data availability. The genome sequences reported here have been deposited at DDBJ/ENA/GenBank under the accession numbers QYAQ00000000 to QYAY00000000. The versions described in this paper are the first versions, QYAQ01000000 to QYAY01000000 (Table 1). Raw sequences are available under the SRA study accession number SRP161670.

ACKNOWLEDGMENTS
We thank the service Transversal Activities in Applied Genomics from Sciensano for the paired-end sequencing reactions and for the development and maintenance of the in-house instance of the Galaxy workflow management system. This study was supported by projects of the Ministry of Agriculture of the Czech Republic, NAZV KUS QJ1510216, and project LO1218 from MEYS of the Czech Republic under the NPU I program. Funding sources did not affect the design of this study, data collection, data analysis, decisions on publication, or preparation of the manuscript.