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. 2020 Sep 30;10:16154. doi: 10.1038/s41598-020-73123-y

Table 5.

Genome features, acquired antimicrobial resistance genes, putative prophages, copper tolerance, virulence genes, and CRISPR-associated (cas) genes identified in whole genome sequences of phage susceptible A. baumannii.

Strain ID/Genome characteristics AB003 AB053 AB089 AB135 AB140 AB229 AB329
Hospital/year isolated HE/2006 HA/2013 HA/2013 HB/2014 HB/2014 HB/2014 HD/2015
Specimens Sputum Sputum Sputum Pus Sputum Urine Sputum
Phage susceptibility (9/17) (2/17) (3/17) (3/17) (4/17) (3/17) (6/17)
Genome features
Number of assembled contigs 57 142 174 99 77 333 256
Average genome size (bp) 4,050,570 4,108,360 3,897,375 4,036,789 3,990,813 4,070,648 3,943,615
GC content (%) 38.8 38.9 39.0 38.9 39.8 39.1 39.0
Number of CDSs 3,965 4,059 3,808 3,955 3,875 4,134 3,923
Number of RNAs 70 69 70 72 73 68 68
MLST/Rep type ST1/R34 ST129/R15 ST2/R4 ST2/R4 ST2/R4 ST2/R4 ST98/R4
Acquired antimicrobial resistance genes
Sulfonamide resistance ND sul1, sul1 sul2 sul2 ND sul2 sul2
Tetracycline resistance ND tet(B) tet(B) tet(B) tet(B) tet(B) tet(B)
Beta-lactam resistance blaADC-25, blaOXA-23, blaOXA-69, blaTEM-181 blaADC-25, blaOXA-23, blaOXA-66 blaADC-25, blaOXA-23, blaOXA-66, blaTEM-1D blaADC-25, blaOXA-23, blaOXA-66, blaTEM-1D blaADC-25, blaCARB-16/49/5, blaOXA-23, blaOXA-66, blaTEM-1D blaADC-25, blaOXA-23, blaOXA-66, blaTEM-1D blaADC-25, blaOXA-23, blaOXA-66, blaTEM-1D
Aminoglycoside resistance aph(3′)-IIa aac(6′)-Ib3, aadA1, ant(2′')-Ia, aph(3′')-Ib, aph(3′)-Ia, aph(6)-Id, armA aph(3′')-Ib, aph(3′)-Ia, aph(6)-Id, armA aph(3′')-Ib, aph(3′)-Ia, aph(6)-Id, armA aph(3′')-Ib, aph(3′)-VIa, aph(6)-Id, armA aph(3′')-Ib, aph(3′)-Ia, aph(6)-Id, armA aph(3′')-Ib, aph(3′)-Ia, aph(6)-Id, armA
Macrolide resistance ND mph(E), msr(E) mph(E), msr(E) mph(E), msr(E) mph(E), msr(E) mph(E), msr(E) mph(E), msr(E)
Phenicol resistance ND catB8 ND ND ND ND ND
Virulence genes
Iron acquisition entE, zur entE, zur entE, zur entE, zur entE, zur entE, zur entE, zur
Biofilm formation ompA, adeRS, csuE, gacS, csuCD, bfmS ompA, adeRS, gacS, bfmS ompA, adeRS, csuE, gacS, csuCD, bap, bfmS ompA, adeRS, csuE, gacS, csuCD, bap, bfmS ompA, csuE, gacS, csuCD, bap, bfmS ompA, adeRS, csuE, gacS, csuCD, bap, bfmS ompA, adeRS, csuE, gacS, csuCD, bfmS
Type V, VI and IV secretion systems hcp, traU, traC ata, hcp ata, hcp ata, hcp, traU, traC ata, hcp, traU, traC ata, hcp, traU, traC ata, hcp, traU, traC
Other systems ostA, ompF, rstA ostA, ompF, rstA ostA, ompF, rstA ostA, ompF, rstA ostA, ompF, rstA ostA, ompF, rstA ostA, ompF, rstA
Copper tolerance (genotype/phenotype) copRS+/tolerance copRS+/tolerance copRS−/susceptible copRS−/susceptible copRS−/susceptible copRS−/susceptible copRS−/susceptible
Number of prophages (complete/incomplete) 9 (1/8) 8 (1/7) 4 (0/4) 10 (0/10) 5 (0/5) 8 (0/8) 6 (0/6)
Plasmid replicon typing (GR) GR2, GR6 GR1, GR2, pRAY GR2 GR2, GR6 GR2, GR6 GR2, GR6 GR2
CRISPR-associated (cas) genes CAS-TypeI (cas6, cas3-cas2, cas1) Negative Negative Negative Negative Negative CAS-TypeI (cas3)
Accession no/Bioproject PRJEB32181 JABCNM000000000 JABCNJ000000000 JABCNK000000000 JABCNI000000000 JABCNL000000000 JABCNH000000000
Reference Thummeepak et al.35 This study This study This study This study This study This study

ND not detected.