LOCUS       NZ_CP096538             2407 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Staphylococcus aureus strain RIVM_M047916 plasmid pM047916_3,
            complete sequence.
ACCESSION   NZ_CP096538
VERSION     NZ_CP096538.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27760539
            Assembly: GCF_026547095.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2407)
  AUTHORS   Schouls,L.M., Veldman,K., Brouwer,M.S.M., Dierikx,C., Witteveen,S.,
            van Santen-Verheuvel,M., Hendrickx,A.P.A., Landman,F., Hengeveld,P.,
            Wullings,B., Rapallini,M., Wit,B. and van Duijkeren,E.
  CONSRTM   Dutch MRSA surveillance study group
  TITLE     cfr and fexA genes in methicillin-resistant Staphylococcus aureus
            from humans and livestock in the Netherlands
  JOURNAL   Commun Med (Lond) 2, 135 (2022)
   PUBMED   36317053
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2407)
  AUTHORS   Schouls,L.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-APR-2022) Infectious Diseases Research, Diagnostics
            and laboratory Surveillance, National Institute for Public Health
            and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven,
            Utrecht 3720 BA, Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v.0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 30x
            Sequencing Technology :: Illumina MiSeq and HiSeq 2500, Nanopore
            GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_026547095.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 04:51:55
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 2,880
            CDSs (total)                      :: 2,798
            Genes (coding)                    :: 2,710
            CDSs (with protein)               :: 2,710
            Genes (RNA)                       :: 82
            rRNAs                             :: 7, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 59
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 88
            CDSs (without protein)            :: 88
            Pseudo Genes (ambiguous residues) :: 0 of 88
            Pseudo Genes (frameshifted)       :: 41 of 88
            Pseudo Genes (incomplete)         :: 43 of 88
            Pseudo Genes (internal stop)      :: 25 of 88
            Pseudo Genes (multiple problems)  :: 18 of 88
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096538.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..2407
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM_M047916"
                     /isolation_source="Nose"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pM047916_3"
                     /geo_loc_name="Netherlands"
                     /lat_lon="52.13 N 5.29 E"
                     /collection_date="2019-06-18"
                     /collected_by="RIVM"
                     /genotype="GG0398 (CC398)"
     gene            1..735
                     /gene="erm(C)"
                     /locus_tag="M1F47_RS14375"
                     /old_locus_tag="M1F47_14360"
     ARG             2..732
                     /name="erm(C)"
                     /gene="erm(C)"
                     /gene_name="23S rRNA (adenine(2058)-N(6))-methyltransferase
                     Erm(C)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE/MACROLIDE/STREPTOGRAMIN"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1183..1659
                     /locus_tag="M1F47_RS14380"
                     /old_locus_tag="M1F47_14365"
     CDS             1183..1659
                     /locus_tag="M1F47_RS14380"
                     /old_locus_tag="M1F47_14365"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000664727.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000664727.1"
                     /translation="MKERYGTVYKGSQRLIDEESGEVIEVDKLYRKQTSGNFVKAYIVQ
                     LISMLDMIGGKKLKIVNYILDNVHLSNNTMIATTREIAKATGTSLQTVITTLKILEEGN
                     IIKRKTGVLMLNPELLMRGDDQKQKYLLLEFGNFEQEANEKQENALSDYYSFKD"
                     /name="replication/maintenance protein RepL"
     ARG             2..735
                     /name="ErmC"
                     /gene="ErmC"
                     /gene_name="Erm 23S ribosomal RNA methyltransferase"
                     /tool="rgi"
                     /drug_class="macrolide antibiotic; lincosamide antibiotic;
                     streptogramin antibiotic; streptogramin A antibiotic;
                     streptogramin B antibiotic"
                     /identity="99.59"
                     /coverage="100.0"
     Typing          1184..1669
                     /name="rep_cluster_1947"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.591"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaacgaga aaaatataaa acacagtcaa aactttatta cttcaaaaca taatatagat
       61 aaaataatga caaatataag attaaatgaa catgataata tctttgaaat cggctcagga
      121 aaagggcatt ttacccttga attagtacag aggtgtaatt tcgtaactgc cattgaaata
      181 gaccataaat tatgcaaaac tacagaaaat aaacttgttg atcacgataa tttccaagtt
      241 ttaaacaagg atatattgca gtttaaattt cctaaaaacc aatcctataa aatatttggt
      301 aatatacctt ataacataag tacggatata atacgcaaaa ttgtttttga tagtatagct
      361 gatgagattt atttaatcgt ggaatacggg tttgctaaaa gattattaaa tacaaaacgc
      421 tcattggcat tatttttaat ggcagaagtt gatatttcta tattaagtat ggttccaaga
      481 gaatattttc atcctaaacc taaagtgaat agctcactta tcagattaaa tagaaaaaaa
      541 tcaagaatat cacacaaaga taaacagaag tataattatt tcgttatgaa atgggttaac
      601 aaagaataca agaaaatatt tacaaaaaat caatttaaca attccttaaa acatgcagga
      661 attgacgatt taaacaatat tagctttgaa caattcttat ctcttttcaa tagctataaa
      721 ttatttaata agtaagttaa gggatgcata aactgcatcc cttaacttgt ttttcgtgta
      781 cctatttttt gtgaatcgat tatgtctttt gcgcattcac ttcttttcta tataaatatg
      841 agcgaagcga ataagcgtcg gaaaagcagc aaaaagtttc ctttttgctg ttggagcatg
      901 ggggttcagg gggtgcagta tctgacgtca atgccgagcg aaagcgagcc gaagggtagc
      961 atttacgtta gataaccccc tgatatgctc cgacgcttta tatagaaaag aagattcaac
     1021 taggtaaaat cttaatatag gttgagatga taaggtttat aaggaatttg tttgttctaa
     1081 tttttcactc attttgttct aatttctttt aacaaatgtt cttttttttt tagaacagtt
     1141 atgatatagt tagaatagtt taaaataagg agtgagaaaa agatgaaaga aagatatgga
     1201 acagtctata aaggctctca gaggctcata gacgaagaaa gtggagaagt catagaggta
     1261 gacaagttat accgtaaaca aacgtctggt aacttcgtaa aggcatatat agtgcaatta
     1321 ataagtatgt tagatatgat tggcggaaaa aaacttaaaa tcgttaacta tatcctagat
     1381 aatgtccact taagtaacaa tacaatgata gctacaacaa gagaaatagc aaaagctaca
     1441 ggaacaagtc tacaaacagt aataacaaca cttaaaatct tagaagaagg aaatattata
     1501 aaaagaaaaa ctggagtatt aatgttaaac cctgaactac taatgagagg cgacgaccaa
     1561 aaacaaaaat acctcttact cgaatttggg aactttgagc aagaggcaaa tgaaaaacaa
     1621 gaaaatgcat tatctgatta ttattctttc aaggactagt ataacataaa atcgtctaca
     1681 aatagacaaa aaacctgcac gcttaatgta gatcaaaagc ttaacgcaaa tgaaatagat
     1741 tgacctccca ataacaccac gtagttattg ggaggtcaat ctatgaaatg cgattaagct
     1801 ttttctaatt cacataagcg tgcaggttta aagtacataa aaaatataat gaaaaaaagc
     1861 atcattatac taacgttata ccaacattat actctcatta tactaattgc ttattccaat
     1921 ttcctattgg ttggaaccaa caggcgttag tgtgttgttg agttggtact ttcatgggat
     1981 taatcccatg aaacccccaa ccaactcgcc aaagctttgg ctaacacaca cgccattcca
     2041 accaatagtt ttctcggcat aaagccatgc tctgacgctt aaatgcacta atgccttaaa
     2101 aaaacattaa agtataacac actagactta tttacttcgt aattaagtcg ttaaaccgtg
     2161 tgctctacga ccaaaagtat aaaaccttta agaactttct tttttcttgt aaaaaaagaa
     2221 actagataaa tctctcatat cttttattca ataatcgcat cagattgcag tataaattta
     2281 acgatcactc atcatgttca tatttatcag agctcgtgct ataattattc aaccaaacaa
     2341 aaaataagtg gttataatga atcgttaata agcaaaattc attataacca aattaaagag
     2401 ggttata
//
