LOCUS       NZ_CP096534             2361 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Staphylococcus aureus strain RIVM_M083782 plasmid pM083782_2,
            complete sequence.
ACCESSION   NZ_CP096534
VERSION     NZ_CP096534.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN27760540
            Assembly: GCF_026547075.1
KEYWORDS    RefSeq.
SOURCE      Staphylococcus aureus
  ORGANISM  Staphylococcus aureus
            Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
            Staphylococcus.
REFERENCE   1  (bases 1 to 2361)
  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 2361)
  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_026547075.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 05:04:57
            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)                     :: 2,947
            CDSs (total)                      :: 2,865
            Genes (coding)                    :: 2,768
            CDSs (with protein)               :: 2,768
            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)              :: 97
            CDSs (without protein)            :: 97
            Pseudo Genes (ambiguous residues) :: 0 of 97
            Pseudo Genes (frameshifted)       :: 44 of 97
            Pseudo Genes (incomplete)         :: 46 of 97
            Pseudo Genes (internal stop)      :: 29 of 97
            Pseudo Genes (multiple problems)  :: 19 of 97
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP096534.1.
            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..2361
                     /organism="Staphylococcus aureus"
                     /mol_type="genomic DNA"
                     /strain="RIVM_M083782"
                     /isolation_source="Urinairy tract"
                     /host="Homo sapiens"
                     /db_xref="taxon:1280"
                     /plasmid="pM083782_2"
                     /geo_loc_name="Netherlands"
                     /lat_lon="52.13 N 5.29 E"
                     /collection_date="2020-02-17"
                     /collected_by="RIVM"
                     /genotype="GG0398 (CC398)"
     gene            complement(520..1443)
                     /locus_tag="M1F48_RS14710"
                     /old_locus_tag="M1F48_14690"
     CDS             complement(520..1443)
                     /locus_tag="M1F48_RS14710"
                     /old_locus_tag="M1F48_14690"
                     /function="essential for plasmid replication"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002501032.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_011428876.1"
                     /translation="MDKYTEKKRRNQVFQKFIKRHVGENQMTLVRECNTFLSFVTDKSL
                     EKNKLYKANSCKNRFCPVCAWRKARKDALGLSLMMQYVQKEHEKEFIFLTLTTPNVSKN
                     KLENEIKHYNQSFRRLSNRTKFKKVVKGYVRKLEITYNKERDDYNPHFHVLIAVNKSYF
                     KDTKSYISQKEWLNLWRDVTGMPEITQVHVEKVKANNDKELYEMAKYSGKDSDYLSNQK
                     VFDAYYRSLKGKQVLVYSGLFKEARKLLKNGDLDYLKEIDPTEYIYQIFYIWKQKEYLA
                     SELYDLTEQEKRELNHQMIDEIEEET"
                     /name="protein rep"
     gene            1709..2194
                     /gene="lnu(A)"
                     /locus_tag="M1F48_RS14715"
                     /old_locus_tag="M1F48_14695"
     ARG             1710..2191
                     /name="lnu(A)"
                     /gene="lnu(A)"
                     /gene_name="lincosamide nucleotidyltransferase Lnu(A)"
                     /tool="amrfinderplus"
                     /drug_class="LINCOSAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     ARG             1710..2194
                     /name="lnuA"
                     /gene="lnuA"
                     /gene_name="lincosamide nucleotidyltransferase (LNU)"
                     /tool="rgi"
                     /drug_class="lincosamide antibiotic"
                     /identity="93.79"
                     /coverage="100.0"
     Typing          complement(521..1443)
                     /name="rep_cluster_1230"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tataatttaa ttaacgttct gttttgtttt cactgttcac ttccaaaaat aaaaaaagcc
       61 accaaatttt attggtggct ttttttattt tgttaaatct taaatgccct taattttaat
      121 tctaaagggg tattttaaag ttttaagtgt aaatcatata gttttatacc taaaaacata
      181 cataagctct taaaacgcaa atatgagcca aataaaagca tgttataaca ctacattttt
      241 attaaccaaa acgatacaac ttaactacat ttaaatcgta aatcacttgt aagctttttg
      301 taccttaaat gtagcctttt ctgtatttac tcttagcttg tagaaatcgg acacgttcaa
      361 caattttaaa atcaacctaa tatcgttgta acttatcagt attagtttca atactgccca
      421 tctacatgca aattaatttg catacatttt ttatagttcc cacagaggca ggcgaccata
      481 tatttaacaa taaaaaagtg tcagtctaag accaacactt tatgtttctt cttcaatttc
      541 atcaatcatt tgatgattta attctctttt ttcttgttct gttaaatcat acaattcact
      601 cgctaaatat tctttttgtt tccaaatata aaaaatttga tagatatatt cagttggatc
      661 aatctctttt aaataatcta aatcgccatt ttttaataac tttctcgcct ctttaaataa
      721 tcccgaatac actaatacct gcttaccttt taaagaacga taatacgcgt cgaatacttt
      781 ttgattactt aaataatcac tatctttacc agaatattta gccatttcat aaagttcttt
      841 gtcattatta gccttaactt tctcgacatg aacttgtgta atttctggca ttcccgtcac
      901 atctcgccat aaattcaacc attctttttg gctaatataa gatttagtat ctttgaaata
      961 agatttgtta accgcaatta aaacgtgaaa atgtgggtta taatcatccc gctctttgtt
     1021 gtatgtaatt tctaattttc ttacataacc cttaacaacc tttttaaatt ttgttcgatt
     1081 acttaatcgt ctaaatgatt gattataatg cttaatctca ttttctaatt tatttttaga
     1141 cacattaggc gtcgttaaag ttaaaaatat aaattctttt tcatgttctt tttgtacata
     1201 ctgcatcatc aaagataaac ccaacgcatc ttttctcgct ttacgccatg cacaaaccgg
     1261 acaaaaacga tttttacatg aatttgcttt atataattta tttttttcta acgacttatc
     1321 tgtcacaaaa gacaaaaagg tattacattc ccgtaccaat gtcatttgat tttcccccac
     1381 atgtcgcttt ataaatttct gaaatacttg atttcttcgt ttcttctcag tatacttatc
     1441 catgttatat aacttaaaaa acaacttagt tttcacaaac tatgacaata aaaaaagttg
     1501 ctttttctcc tttctcataa tgtttttaga ctagacacct aaaacactac atgagtatgc
     1561 taaaaaaagc aacttttttt gtgtttcaac ccagatatac caacacttta agggtaacta
     1621 ttctactctg taatagttac ccttattatc aagacaagaa gaaactcgtt ttcaactcgt
     1681 ttcaaattcc taaattagga gggataaaat gaaaattaat aatgtaacag aaaaggattt
     1741 attttatatt ttagacttat ttgaaaaaat ggaagtaact tattggttag atggaggttg
     1801 gggtgtagat gtattaactg gaaaacaaca aagagaacac agagatatag atatagattt
     1861 tgacgcccaa cacactcaaa aagttataca aaaattagaa gatataggat ataaaataga
     1921 agttgattgg atgccttcac gcatggaact taaacataaa aaatatggat atttagatat
     1981 tcatcccata aatttaaatg atgatggttc cattactcaa gcaaatccag aaggtggcaa
     2041 ttacgttttt caaaatgaat ggttttcaga aactaattat aaaggtcgaa aaataccatg
     2101 tatttcaaaa gaagctcagc ttctttttca ttctggttat gacttaacag aaaaagacca
     2161 ttttgatata aaaaatttaa aatcaataac ataattgctt tattccaatt gctttattga
     2221 cgttgagcct cggaaccctt aacaatccca aaacttgtcg aatggtcggc ttaatagctc
     2281 acgctatgcc gacattcgtc tacaagttta gttaagggtt cttctcaacg atcaataaat
     2341 tttctcggca taaaagcgtg t
//
