Here, we present the draft genome sequences of 14 strains of 4 species of the genus Macrococcus. These strains were isolated from bovine milk and tongue samples obtained during a screening program.
ABSTRACT
Here, we present the draft genome sequences of 14 strains of 4 species of the genus Macrococcus. These strains were isolated from bovine milk and tongue samples obtained during a screening program.
ANNOUNCEMENT
Fourteen strains belonging to four members of the Macrococcus genus, namely, 3 Macrococcus caseolyticus strains (DPC 6291, DPC 7170, and DPC 7171), 7 Macrococcus canis strains (DPC 7158, DPC 7160, DPC 7162, DPC 7163, DPC 7165, DPC 7168, and DPC 7169), 3 Macrococcus goetzii strains (DPC 7159, DPC 7164, and DPC 7166), and 1 Macrococcus bohemicus strain (DPC 7215), were isolated from bovine milk and tongue by utilizing a ctaC PCR, as described previously (1). Recently emerging information regarding multidrug resistance and putative virulence genes present in species belonging to this genus prompted us to perform whole-genome sequencing (WGS) to investigate the presence of such genes in these Macrococcus strains (2–4).
The genomic DNA was isolated from overnight cultures grown at 37°C in tryptic soy broth (TSB; Becton, Dickinson and Company, Berkshire, England) using the UltraClean microbial DNA isolation kit (Mo Bio Laboratories, Cambridge, UK) as per the included protocol. Genomic libraries were prepared with a Nextera XT DNA library preparation kit (Illumina, Inc., San Diego, CA, USA). The 2 × 250-bp paired read sequencing was performed on an Illumina HiSeq 2500 platform (MicrobesNG, University of Birmingham, UK). Reads were adapter trimmed using Trimmomatic version 0.30, with a sliding window quality cutoff of Q15 (5). De novo assembly was performed on each sample using SPAdes version 3.7 with the program’s default parameters (6). Detection of acquired antimicrobial resistance genes in the assembled genomes was analyzed using ResFinder version 3.4 and Resistance Gene Identifier (RGI) version 4.2.2 to search against the Comprehensive Antibiotic Resistance Database (CARD). Virulence genes were identified using VirulenceFinder version 2.0, PathogenFinder version 1.1, and the Virulence Factors Database (VFDB) (7–10). The genome sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (11). The final draft genomes were estimated using CheckM (12) to be ≥96% complete with <2.5% contamination.
All sequenced genomes illustrated the presence of putative virulence factors, namely, hemolysin III (hlyIII), aureolysin (aur), and capsule (cap) genes. An RGI search of the homology models in CARD identified a total of 86 different antibiotic resistance genes, most of which are predicted to confer resistance to fluoroquinolone (n = 19), macrolides (n = 26), and tetracycline (n = 24). The sequencing and assembly statistics of the draft genome sequences of the above-mentioned Macrococcus strains are shown in Table 1. The sequencing data contribute to the pool of available Macrococcus genomes and enable further generation of information regarding the presence of antibiotic resistance determinants and other virulence factors present in Macrococcus species.
TABLE 1.
Genome characteristics of the Macrococcus strains used in this study
| Organism | SRA accession no. | GenBank accession no. | Draft genome size (bp) | G+C content (%) | No. of contigs | Coverage (×) | N50 (bp) |
|---|---|---|---|---|---|---|---|
| M. caseolyticus DPC 6291 | SRR8868656 | SDQM00000000 | 2,171,480 | 36.68 | 74 | 70 | 229,924 |
| M. canis DPC 7158 | SRR8868660 | SDQI00000000 | 2,179,466 | 36.75 | 69 | 197 | 578,934 |
| M. goetzii DPC 7159 | SRR8868665 | SDGN00000000 | 2,530,812 | 34.06 | 93 | 184 | 275,573 |
| M. canis DPC 7160 | SRR8868666 | SDQF00000000 | 2,148,516 | 36.58 | 37 | 136 | 413,516 |
| M. canis DPC 7162 | SRR8868667 | SDQG00000000 | 2,139,904 | 36.62 | 44 | 107 | 353,259 |
| M. canis DPC 7163 | SRR8868668 | SDQH00000000 | 2,167,812 | 36.63 | 79 | 147 | 417,178 |
| M. goetzii DPC 7164 | SRR8868659 | SDGO00000000 | 2,563,253 | 34.07 | 61 | 137 | 458,326 |
| M. canis DPC 7165 | SRR8868658 | SDGP00000000 | 2,165,327 | 36.68 | 72 | 158 | 1,280,134 |
| M. goetzii DPC 7166 | SRR8868662 | SDGQ00000000 | 2,591,067 | 34.16 | 95 | 202 | 466,093 |
| M. canis DPC 7168 | SRR8868661 | SDGR00000000 | 2,134,151 | 36.68 | 41 | 95 | 397,880 |
| M. canis DPC 7169 | SRR8868664 | SDGS00000000 | 2,160,199 | 36.56 | 89 | 264 | 1,113,524 |
| M. caseolyticus DPC 7170 | SRR8868655 | SDQK00000000 | 2,106,646 | 36.77 | 67 | 48 | 147,285 |
| M. caseolyticus DPC 7171 | SRR8868657 | SDQJ00000000 | 2,110,528 | 36.77 | 99 | 231 | 108,839 |
| M. bohemicus DPC 7215 | SRR8868663 | SELR00000000 | 2,555,877 | 33.98 | 55 | 160 | 234,144 |
Data availability.
The draft WGS data were deposited into NCBI GenBank and the Sequence Read Archive (SRA) under the BioProject no. PRJNA515496. The accession numbers are listed in Table 1.
ACKNOWLEDGMENTS
This research was funded by Teagasc (reference no. 6697) and the Teagasc Walsh Fellowship Programme (reference no. 2015055).
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Associated Data
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Data Availability Statement
The draft WGS data were deposited into NCBI GenBank and the Sequence Read Archive (SRA) under the BioProject no. PRJNA515496. The accession numbers are listed in Table 1.