LOCUS       NZ_CP083879             6278 bp    DNA     circular CON 05-NOV-2023
DEFINITION  Escherichia coli strain NDM4 plasmid unnamed2, complete sequence.
ACCESSION   NZ_CP083879
VERSION     NZ_CP083879.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN21398205
            Assembly: GCF_020149605.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6278)
  AUTHORS   Simner,P., Mostafa,H., Bergman,Y., Ante,M., Tekle,T., Adebayo,A.,
            Beisken,S., Dzintars,K. and Tamma,P.D.
  TITLE     Progressive Development of Cefiderocol Resistance in Escherichia
            coli During Therapy Is Associated with Increased blaNDM-5 Copy
            Number and Gene Expression
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6278)
  AUTHORS   Simner,P., Mostafa,H., Bergman,Y., Ante,M., Tekle,T., Adebayo,A.,
            Beisken,S., Dzintars,K. and Tamma,P.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-SEP-2021) BioIT, Ares-Genetics, Karl-Farkas-Gasse 18,
            Vienna 1180, Austria
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2021
            Assembly Method                   :: Canu v. JAN-2021
            Assembly Name                     :: Isolate4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 330x
            Sequencing Technology :: Oxford Nanopore MiniION + Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/05/2023 02:01:27
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,793
            CDSs (total)                      :: 4,670
            Genes (coding)                    :: 4,388
            CDSs (with protein)               :: 4,388
            Genes (RNA)                       :: 123
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 282
            CDSs (without protein)            :: 282
            Pseudo Genes (ambiguous residues) :: 0 of 282
            Pseudo Genes (frameshifted)       :: 126 of 282
            Pseudo Genes (incomplete)         :: 161 of 282
            Pseudo Genes (internal stop)      :: 48 of 282
            Pseudo Genes (multiple problems)  :: 53 of 282
            Pseudo Genes (short protein)      :: 4 of 282
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP083879.1.
            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..6278
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="NDM4"
                     /isolation_source="Pelvic abcsess"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="USA: Baltimore"
                     /lat_lon="39.296 N 76.591 W"
                     /collection_date="2020"
                     /collected_by="Johns Hopkins University"
                     /genotype="ST167"
     gene            1..390
                     /locus_tag="LCE22_RS23790"
                     /old_locus_tag="LCE22_23790"
     CDS             1..390
                     /locus_tag="LCE22_RS23790"
                     /old_locus_tag="LCE22_23790"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            434..>838
                     /locus_tag="LCE22_RS23795"
                     /old_locus_tag="LCE22_23795"
                     /pseudo=""
     CDS             434..>838
                     /locus_tag="LCE22_RS23795"
                     /old_locus_tag="LCE22_23795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(943..1777)
                     /locus_tag="LCE22_RS23800"
                     /old_locus_tag="LCE22_23800"
                     /pseudo=""
     CDS             complement(943..1777)
                     /locus_tag="LCE22_RS23800"
                     /old_locus_tag="LCE22_23800"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="APH(6)-I family aminoglycoside
                     O-phosphotransferase"
                     /name="APH(6)-I family aminoglycoside O-phosphotransferase"
     gene            complement(1777..2535)
                     /locus_tag="LCE22_RS23805"
                     /old_locus_tag="LCE22_23805"
     CDS             complement(1777..2535)
                     /locus_tag="LCE22_RS23805"
                     /old_locus_tag="LCE22_23805"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006576439.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="APH(3'') family aminoglycoside
                     O-phosphotransferase"
                     /protein_id="WP_001145207.1"
                     /translation="MPVRGGESGDFVFRRGDGHAFAKIAPASRRGELAGERDRLIWLKG
                     RGVACPEVINWQEEQEGACLVITAIPGVPAADLSGADLLKAWPSMGQQLGAVHSLSVDQ
                     CPFERRLSRMFGRAVDVVSRNAVNPDFLPDEDKSTPQLDLLARVERELPVRLDQERTDM
                     VVCHGDPCMPNFMVDPKTLQCTGLIDLGRLGTADRYADLALMIANAEENWAAPDEAERA
                     FAVLFNVLGIEAPDRERLAFYLRLDPLTWG"
                     /name="APH(3'') family aminoglycoside O-phosphotransferase"
     gene            complement(2640..3449)
                     /gene="sul2"
                     /locus_tag="LCE22_RS23810"
                     /old_locus_tag="LCE22_23810"
                     /pseudo=""
     ARG             complement(3319..3449)
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide resistant sul"
                     /tool="rgi"
                     /drug_class="sulfonamide antibiotic"
                     /identity="100.0"
                     /coverage="15.87"
     gene            complement(<3473..3556)
                     /locus_tag="LCE22_RS23815"
                     /old_locus_tag="LCE22_23815"
                     /pseudo=""
     CDS             complement(<3473..3556)
                     /locus_tag="LCE22_RS23815"
                     /old_locus_tag="LCE22_23815"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001043267.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="sulfonamide-resistant dihydropteroate synthase
                     Sul1"
                     /name="sulfonamide-resistant dihydropteroate synthase Sul1"
     gene            complement(4015..4176)
                     /locus_tag="LCE22_RS24015"
     CDS             complement(4015..4176)
                     /locus_tag="LCE22_RS24015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_318010574.1"
                     /translation="MYARTPVQSDRCALSGNYQLESNPERHDKTPLAAAISNRSAREDR
                     LRGLEVEA"
                     /name="replication initiation protein"
     gene            4733..4882
                     /locus_tag="LCE22_RS23820"
                     /old_locus_tag="LCE22_23820"
     CDS             4733..4882
                     /locus_tag="LCE22_RS23820"
                     /old_locus_tag="LCE22_23820"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     gene            complement(5623..6062)
                     /locus_tag="LCE22_RS23825"
                     /old_locus_tag="LCE22_23825"
                     /pseudo=""
     CDS             complement(5623..6062)
                     /locus_tag="LCE22_RS23825"
                     /old_locus_tag="LCE22_23825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005119689.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="entry exclusion protein 1"
                     /name="entry exclusion protein 1"
     ARG             complement(1781..2562)
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="97.75"
     ARG             complement(1021..1301)
                     /name="APH(6)-Id"
                     /gene="APH(6)-Id"
                     /gene_name="APH(6)"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="100.0"
                     /coverage="33.45"
     ARG             complement(1778..2535)
                     /name="APH(3'')-Ib"
                     /gene="APH(3'')-Ib"
                     /gene_name="APH(3'')"
                     /tool="rgi"
                     /drug_class="aminoglycoside antibiotic"
                     /identity="99.21"
                     /coverage="94.38"
     Typing          4525..4698
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          complement(4007..4601)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.805"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atgagtacag agttaaatag cggtactgtc ggtggttttg gtcacatggg accaaatgac
       61 ccctacaatg atggtcatag cggctctgga agttcgggag gtagttttaa cggtggtggt
      121 aatggtggcc atgataatag tagtggttca tcttatactg catcctttgg tctcatcact
      181 ggccgacacc cgataactgt cccaggtacg aagaatatta attctgtcga tctttctgct
      241 gtcattaata acattataca tcatgaaggt gcacgcaata acatgtacct agatactgcg
      301 aacaatgtaa gagtgggagt gacgggcact ggctggcaat gtctagcaac ggcaggcatt
      361 tcggctgagg gtaaaagaac tttccgctaa gcgatagact gtatgtaaac acagtattgc
      421 aaggacgcgg aacatgcctc atgtggcggc caggacggcc agccgggatc gggatactgg
      481 tcgttaccag agccaccgac ccgagcaaac ccttctctat cagatcgttg acgagtatta
      541 cccggcattc gctgcgctta tggcagagca gggaaaggaa ttgccgggct atgtgcaacg
      601 ggaatttgaa gaatttctcc aatgcgggcg gctggagcat ggctttctac gggttcgctg
      661 cgagtcttgc cacgccgagc acctggtcgc tttcagctgt aagcgtcgcg gtttctgccc
      721 gagctgtggg gcgcggcgga tggccgaaag tgccgccttg ctggttgatg aagtactgcc
      781 tgaacaaccc atgcgtcagt gggtgttgag cttcccgttt cagctgcgtt tcctgtttgg
      841 ggtcgtttgc gggaaggggc ggaatcctac gctaaggctt tggccagcga tattctccgg
      901 tgagattgat gtgttcccag gataggagaa gtcgcttgat atctagtatg acgtctgtcg
      961 cacctgcttg atcgcggccg cgatagctag atcgcgttgc tcctcttctc catccgcgtt
     1021 caagctgcgg aaaggcaccc ataagcgtac gcctggtcga gcaggcgacg cggatcgacg
     1081 tccagcgcac gagagaatgc gtccgccatc tgtgcaatgc gtctaggatc gagacaaagg
     1141 tcgtctctgt cagccggatc gtagaacata ttggcggcgc caaagcccac ttcaccgacc
     1201 agaccgacgg gatctatcac cagccagccg cgactggaga acatgatgtt ttcatgatgc
     1261 agatcgccat gtagcccacg cagttccgag gcattgctca tcatttgatc ggctataatc
     1321 gccgcgtgga cgtagtcagt ttgacaacct gcgttttgat catcgcgcgc ccgctgaaac
     1381 aaagctgcaa agcgatcccg gatcgggaga agggcagaag gcagggttcc tcagatgcgg
     1441 catacagctt cgccattagt tccgctgcaa tttcggtcgc ctggtagtcg ccgtgctcgg
     1501 caacgatgtg agagagcatt cgctccccgg catattcgag caacatcaga ttgttctcac
     1561 gaccgagcaa ccggactgct cccctcccat tgcgccatac cagatagtcg gccccgcgca
     1621 gttcatcagc aatgtcttct ataggtttca atcccttgac gattgcagga gtcccgtctg
     1681 gcaatgaaac tttccaaacg aggctggaaa aggtgtccgc aatgagaaca ggttgcgaaa
     1741 cgtgccaatg agcaggaaaa acaggcggca tgaacatcaa ccccaagtca gagggtccaa
     1801 tcgcagatag aaggcaaggc gttcgcggtc gggggcttcg atccccaata cattgaatag
     1861 gacagcgaag gcgcgctctg cttcatctgg cgctgcccag ttctcttcgg cgttagcaat
     1921 catgagtgcc aaatcggcat agcgatctgc tgttccgagc cgcccaaggt cgatcagacc
     1981 cgtgcattga agagttttag ggtccaccat gaagttcggc atgcagggat caccatggca
     2041 aacaaccata tcggtgcgct cttggtcgag ccgcaccggt agctctcgtt cgacacgagc
     2101 caaaagatcg agctgcggcg tactcttgtc ctcgtccggt aagaagtcgg gattgacggc
     2161 attgcgggac accacatcaa cggcgcgtcc gaacattcgc gacagcctgc gctcaaacgg
     2221 acattgatca accgataggc tgtgaacagc gccaagttgc tgccccattg acggccacgc
     2281 tttgagcaaa tccgctccag acagatcagc cgccggtact cccggaattg ccgttatcac
     2341 caagcatgca ccctcctgtt cctcctgcca gttgatgacc tcggggcaag ccacacctcg
     2401 acctttgagc caaatgaggc ggtcacgctc tccagcgagc tcaccgcggc gggaagcagg
     2461 tgcgattttc gcgaaggcat gcccgtcacc acgtcgaaaa acaaaatcac cagattctcc
     2521 gcctctgaca ggcaaccagt cagaatgcga ttcaccaaaa aaatattagt tcgattcaat
     2581 ggaggttcct tcagttttct gatgaagcgc gaatatagag aaatatcccg aatgtgcagt
     2641 taacgaattc ttgcggtttc tttcagcgcc gccaataccg ccagcccgtc gcgcaagggg
     2701 cgcggctcgt gtgtgcggat gaagtcagct ccacctgcgg cggcggcaag ctctgcagcg
     2761 agtgtcgcgg ccccgacatc cccggaccac ggcctgtgag cgcgcgcaga aaggatttgc
     2821 gcgaaacaga cagaagcacc ggcaaatcga agcgcagccg caattcatcg aaccgcgcca
     2881 gcaccgagag cgaggtttcg ggagcagccc cagaaaaacc ccatgccggg atcaaggaca
     2941 aggcggttgc gtttgatacc ggcacccgtc agccgcgatg cgcgcgtcaa aaacgccgca
     3001 atgtgatcca tgatgtcgcc agcgggttgc ctcgcgccga tctgcctgcc cgtcttgcac
     3061 cgaatgcata acgacgagtt tggcagatga tttcgccaat tgcggataga acgcagcgtc
     3121 tggaaaaccg cgaatatcat tgagataggc cacaccacgc gacaaggcat aggcttgcgt
     3181 cgcgggttga taactgtcga gcgagacggg aatgccatct gccttgagcg cgtccagcac
     3241 cggcgcgata cgcgcgattt ctgtgtcgga cgaaacaggc gcggcgtcgg gattgctgga
     3301 tgccggaccg aggtcgatca catctgcccc tcggccatca gcttacgcgc ctgcgcaatg
     3361 gctgcgtctg gcgccagata ccggcctcca tcggagaaac tgtccgaggt tatgttgacg
     3421 atgccgaaaa tgatgagcga tttattcatg ggggcttcta taataataat aatcctggcg
     3481 ccagataccg gcctccatcg gagaaactgt ccgaggttat gttgacgatg ccgaaaatga
     3541 tgagcgattt attcatgggg gcttctataa taataataat cgagcatgag tctcatacgg
     3601 atgctcgggt cgaaagggaa tccccaggcg agtaacctgt ttgcggtgat ccgtttcatg
     3661 atgatgtatc tgtagcattt tggaaataaa tatatcatct ctcaataagt agatatattt
     3721 atcttttttg cttctttggt gctgcaagtc accaatacga gggaaacctg ttacggagcg
     3781 gtttaaccgt aatcaacagt gactggtgtc atgttcggaa gattaattga tagtaatcta
     3841 caaaggatct tcttgagatc cttttcaatg aatcgtaatc tcttgctctg taaacgaaaa
     3901 aaccgcctgg gaggcggttt gttcgaaggt taagtcagtt ggggaactgc ttaacccggt
     3961 aacaaggttc acgagaccgc cattaccaaa actgttcttt cagtgtagcc gcagtcaggc
     4021 ctctacttca agacctctta atctatcttc tcgtgcactc ctgttactaa tggctgctgc
     4081 cagtggcgtt ttgtcgtgtc tttccgggtt ggactcaagt tgatagttac cggacaaggc
     4141 gcagcggtcg gactgaacgg gggttcgtgc atacagtcca gcttggagcg aactgccttc
     4201 acggaactga gtgtcaggcg tggaatgaga aaccgcggcc ataacagcgg aatgacaccg
     4261 gtaaaccgaa aggcaggaac aggagaggga gctaccaggg gaaacgcctg ggatctttat
     4321 agtcctgtcg ggtttcgcca ccactgattt gagcgtcaga ttttgcgatg cttgtcaggg
     4381 ggcggagcct atggaaaaac ggcttcgccg tggccttatc tcttctttgc taagtgtctt
     4441 cctggtatct tccaggaaat ttccgtcccc gtccgtaagc cggtaccgct cgccgcagcc
     4501 gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga atatctcctg tatcgcatat
     4561 tctgctgacg cgccggtgct gccttttttc tcctgccaca tgaagcactt cactgatttt
     4621 cgcaatcgtg gcaacatagt aagccagtat acactccgct agcgctacat gactggttca
     4681 gggctgcgcc ccgaaacccg ctaacaacct ctcagctact ggatatcacc ccatgccatc
     4741 tgaatatgat gaacaactgg attcgactga tacgcagctt cccggcgaat atgacctttt
     4801 tgatttaatg gcgcaggtta ctgaagagaa cctgcatgcc cctgtggatt ttgggtcgcc
     4861 tgtcggccgg gaagcgttat agctttttcg cttgcccgcg tacgtggtaa tactccggta
     4921 ttacctttta tttctttatt ttcatgtaat tacagtggat ttttaatacc cgggtattac
     4981 tcgtgaaaac gaaatattcc ttttttcttt taattcatgc agttgcgatg aaaatcgcgg
     5041 ctgcgttagg tgtatgacca ttttgaggtt gaaaaataat caaccatggc gggtgattta
     5101 cgcaggttaa gggagatcgt gacaaaaaaa gcgttcctca ctgtatcgtt catgcctgca
     5161 tgaacgggtt attcttcctg actacagaat tacatcgctc cttcagttca tacatcagtt
     5221 ttacatcact tatacatcac ttttacatca ttccttcagc tcatacgtca ctttcatcct
     5281 ctgtgccatt tgtacatcac cccttcctga acgtgctgac agcgggtttt ccggctgcgc
     5341 cggcaacgct tcacggccac gcaataaatt gcgtccccgt tcaccgtttt cggatgggaa
     5401 gaacgccgga aacaggactt accccggctg aatggtgtga atttccgcgc tatgcacttg
     5461 tgcgcatact catgcatgcc gtaaaaacag agcctgcgcg tttctggcgg gttttcgggt
     5521 ggtttgttgc ctgttttacc ggtttcccgt cagaaacgcc ctgagggcgt ctgagatggt
     5581 gcacgcaacg aatgttatgg taaatcagag tcacctgcac tgttactctg aaccggagcg
     5641 aaacagccgc gaccagaatc cccgcttttt tcctgtgcca gcgcgtcagc cagacggcta
     5701 atttcggcct gtagttgttc cctctcctca tttcgcaggc ggttttctgc ttcccgcgcc
     5761 atcttgtctt caagcattag ggtaacagtc tgctgcagag cgtccagttt ctgctgaatg
     5821 acgtctagct gagcattttc cgcctggcta acgacagatt tggagtgtcc ctccttgtgc
     5881 ctttttggtg tctcagaagt gcgcagctcg ccataggccc gaatcagttc actggtctcg
     5941 aactcccggc gatcattttt tcctgtgcga tagctgacaa ggcctttagc catgtcacga
     6001 tataattgcg agcgcgactt tcctgttaat ttcagtgtct cttgaactgt gtgccatgcc
     6061 ataaaagtga cagtgtctcc tgtgtgtacc gtattgtaac agcagaacat attactgttt
     6121 taacacaaaa ggtctgaggc tgcccgtgag gcgtgaaaaa tacacaaaaa cctgttgacg
     6181 gtgtggtttt gacgggcgta gtatttcgaa tactgtatat aaacacattg ttataaatac
     6241 agtttttgct gtttttaaaa gtcaaagagg ataatttt
//
