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 |
