Background
Methods
Bacterial isolates and testing of antibiotic resistance
Characterization of resistance genes
Conjugation experiments
Detection of hypermucoviscocity phenotyping and virulence associated genes
Multilocus sequence typing, allelic diversity, and population structure analysis
Results
Isolate | ST | Sampling Date | Speciman | Carbapenemase gene | ESBLs | Other β-Lactamase | Plasmid Replicon |
---|---|---|---|---|---|---|---|
RD- 51 | 37 | 27-Oct-11 | Blood | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 52 | 974 | 22-Oct-11 | wound | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | FIIK, FII, L/M |
RD- 53 | 29 | 8-Aug-11 | Rectal | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FIIK, L/M |
RD- 54 | 37 | 9-May-11 | Abd. Drain | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 56 | 37 | 31-Jul-11 | Sputum | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 57 | 694 | 4-Sep-11 | Urine | Negative | CTX-M 15 | SHV-1 | FIIK, L.M |
RD- 58 | 199 | 9-Sep-11 | Wound | Negative | CTX-M 14 | TEM-1, SHV-1 | L/M |
RD- 59 | 709 | 5-Sep-11 | Blood | OXA-48 | ND | SHV-11 | L/M |
RD- 60 | 340 | 28-May-11 | Trachea | Negative | CTX-M 15 | SHV-11 | FII, FIIK |
RD- 61 | 37 | 24-Sep-11 | Wound | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 62 | 709 | 9-Jan-11 | Blood | OXA-48 | CTX-M 14 | SHV-11 | L/M |
RD- 63 | 37 | 28-Jan-11 | Sputum | Negative | CTX-M 15 | TEM-1, SHV-11 | FIIK |
RD- 64 | 15 | 9-Jan-11 | Trachea | Negative | CTX-M 15 | SHV-1 | FII, L/M, IncN |
RD- 66 | 199 | 13-Oct-11 | Wound | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M |
RD- 67 | 348 | 7-Feb-11 | Rectal | OXA-48 | ND | TEM-1, SHV-11 | FIIK, L/M |
RD- 68 | 199 | 27-Jul-11 | Rectal | OXA-48 | ND | TEM-1, SHV-1 | L/M |
RD- 69 | 974 | 8-Jan-11 | Urine | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | FIIK, L/M |
RD- 70 | 48 | 26-Mar-11 | Trachea | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FIIK |
RD- 71 | 29 | 10-Jun-11 | Wound | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | L/M |
RD- 72 | 37 | 2-Feb-11 | Blood | OXA-48 | ND | TEM-1, SHV-11 | L/M, FIIK |
RD- 73 | 199 | 21-Mar-11 | Wound | OXA-48 | CTX-M 14 | TEM-1, SHV-11 | L/M, FIIK |
RD- 74 | 111 | 24-Mar-11 | Wound | OXA-48 | CTX-M 14 | TEM-1, SHV-11 | IncN |
RD- 75 | 199 | 30-Mar-11 | Trachea | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK, IncN |
RD- 76 | 37 | 8-Feb-11 | Trachea | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 78 | 152 | 14-Oct-11 | Rectal | OXA-48 + NDM-1 | CTX-M 15 | TEM-1, SHV-1 | Negative |
RD- 79 | 37 | 31-Oct-11 | Trachea | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 80 | 199 | 13-Nov-11 | Wound | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK |
RD- 82 | 37 | 24-Nov-11 | Trachea | OXA-48 | ND | TEM-1, SHV-11 | L/M, FIIK |
RD- 83 | 348 | 28-Nov-11 | Rectal | OXA-48 + NDM-1 | CTX-M 15 | TEM-1, SHV-1 | FIIK, L/M |
RD- 84 | 340 | 3-May-12 | Trachea | Negative | CTX-M 15 | SHV-11 | FII, FIB, FIA, FIIK |
RD- 85 | 340 | 9-Nov-12 | Urine | OXA-48 | CTX-M 15 | SHV-11 | FIIK |
RD- 86 | 152 | 16-Feb-12 | Urine | NDM-1 | CTX-M 15 | TEM-1, SHV-1 | FIA |
RD- 87 | 17 | 6-Nov-12 | Trachea | OXA-48 | CTX-M 15 | SHV-11 | FIIK, L/M |
RD- 88 | 152 | 3-Jan-12 | Wound | NDM-1 | CTX-M 15 | TEM-1, SHV-1 | FIB |
RD- 89 | 298 | 6-Oct-12 | Urine | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FIIK, L/M, IncN |
RD- 90 | 37 | 6-May-12 | Blood | OXA-48 | ND | TEM-1, SHV-11 | L/M, FIIK |
RD- 92 | 199 | 22-Jul-12 | Rectal | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK |
RD- 93 | 199 | 22-Jan-12 | Trachea | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK, IncN |
RD- 94 | 152 | 15-Apr-12 | Trachea | NDM-1 | CTX-M 15 | TEM-1, SHV-1 | FIB, FIA |
RD- 95 | 340 | 16-Mar-12 | Blood | Negative | CTX-M 15 | SHV 11 | FIIK |
RD- 96 | 16 | 16-Jul-12 | Trachea | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FII, FIIK, FIA |
RD- 97 | 48 | 1-Dec-12 | Trachea | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | FIIK |
RD- 99 | 48 | 12-Jan-12 | Rectal | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | FIB, FIIK, L/M |
RD- 100 | 37 | 2-Jul-12 | Urine | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 102 | 37 | 1-Sep-12 | TIP | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 103 | 199 | 7-May-12 | Rectal | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | L/M, FIIK |
RD- 104 | 37 | 25-Jul-12 | Wound | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 105 | 152 | 29-Jan-12 | Blood | OXA-48 + NDM-1 | CTX-M 15 | TEM-1, SHV-1 | L/M, IncN |
RD- 106 | 152 | 27-Jul-12 | Blood | NDM-1 | CTX-M 15 | TEM-1, SHV-1 | IncN |
RD- 107 | 29 | 22-Oct-12 | Trachea | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FIIK, L/M, IncN |
RD- 108 | 199 | 14-Aug-12 | Wound | OXA-48 + NDM-1 | CTX-M 15 | TEM-1, SHV-1 | L/M, FIIK |
RD- 109 | 199 | 16-Feb-12 | Urine | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK |
RD- 111 | 152 | 26-Mar-12 | Urine | NDM-1 | CTX-M 15 | TEM-1, SHV-1 | Negative |
RD- 112 | 15 | 28-Oct-12 | Wound | OXA-48 | CTX-M 15 | SHV-1 | FIIK, L/M |
RD- 113 | 199 | 4-Oct-12 | Trachea | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK |
RD- 114 | 16 | 18-Nov-12 | Trachea | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FII, FIIK, FIA |
RD- 116 | 48 | 7-Jun-12 | Rectal | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | FIIK |
RD- 117 | 16 | 8-Jun-12 | Urine | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FII, FIIK, L/M, FIA |
RD- 118 | 152 | 7-Aug-12 | Trachea | OXA-48 + NDM-1 | CTX-M 15 | TEM-1, SHV-1 | L/M, FIB |
RD- 119 | 709 | 3-Dec-12 | Wound | OXA-48 | CTX-M 14 | SHV-11 | L/M |
RD- 120 | 48 | 11-Mar-12 | Rectal | OXA-48 | CTX-M 15 | TEM-1, SHV-1 | FIB, FIA |
RD- 121 | 15 | 6-Nov-12 | Rectal | Negative | CTX-M 15 | TEM-1, SHV-1 | FIIK |
RD- 122 | 11 | 17-Nov-12 | Urine | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | FIIK, IncI1, L/M |
RD- 123 | 353 | 17-Nov-12 | Rectal | OXA-48 | CTX-M 15 | TEM-1, SHV-11 | L/M, FIIK |
RD- 124 | 152 | 17-Sep-12 | Urine | OXA-48 + NDM-1 | CTX-M 15 | TEM-1, SHV-1 | Negative |
RD- 125 | 199 | 11-Aug-12 | Wound | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK, IncN |
RD- 126 | 199 | 25-Jun-12 | Trachea | OXA-48 | CTX-M 14 | TEM-1, SHV-1 | L/M, FIIK |
RD- 127 | 152 | 12-May-12 | Trachea | NDM-1 | ND | TEM-1, SHV-1 | Negative |
RD- 128 | 1045 | 12-Nov-12 | Urine | NDM-1 | ND | TEM-1, SHV-11 | FIIK |
RD- 129 | 152 | 14-Dec-12 | Urine | NDM-1 | CTX-M 15 | TEM-1, SHV-1 | FIB |
RD- 130 | 152 | 25-Nov-12 | Rectal | NDM-1 | ND | TEM-1, SHV-1 | FIB, FIA, IncN |
Isolates and their minimum inhibitory concentrations
Genes of resistance and their clonal distributions
Plasmid profile
Virulence genes and hypermucoviscocity phenotyping
Conjugation experiments
Isolate | Resistance gene(s)/ Plasmid replicon(s) | |
---|---|---|
Clone | Transconjugant | |
RD-99 | CTX-M-15, OXA-48/ L/M, FIIK | CTX-M-15, OXA-48/ L/M, FIIK |
RD-76 | CTX-M-15, OXA-48/ L/M, FIIK | CTX-M-15, OXA-48/ L/M, FIIK |
RD-75 | CTX-M-14, OXA-48/ L/M, FIIK, IncN1 | OXA-48/ L/M, FIIK |
RD-62 | CTX-M-14, OXA-48/ L/M | OXA-48/ L/M |
RD-123 | CTX-M-15, OXA-48/ L/M, FIIK | CTX-M-15, OXA-48/ FIIK |
RD-122 | CTX-M-15, OXA-48/ L/M, FIIK, IncN1 | CTX-M-15, − / FIIK |
RD-114 | CTX-M-15, OXA-48/ FIIK, FII | CTX-M-15, OXA-48/ FIIK, FII |
RD-112 | CTX-M-15, OXA-48/ L/M, FIIK | CTX-M-15, OXA-48/ L/M, FIIK |
RD-118 | CTX-M-15, OXA-48, NDM-1/ L/M, FIB | CTX-M-15, OXA-48, NDM-1/ L/M |
RD-127 | CTX-M-15, NDM-1/ - | CTX-M-15, NDM-1/ - |
RD-129 | CTX-M-15, NDM-1/ FIB | CTX-M-15, NDM-1/ - |
RD-64 | CTX-M-15, OXA-48/ L/M, FII, IncN1 | CTX-M-15 / L/M, FII |
Multilocus sequence typing, clonal distribution, and genetic diversity
Locus | Length (bp) | No. alleles present | No. Polymorphic sites (%) | No. Synonymous mutations | No. Non-synonymous mutations | # SNPs | Ts | Tv | Ks | Ka | Ka/Ks | Diversity Index (π) |
---|---|---|---|---|---|---|---|---|---|---|---|---|
gapA
| 450 | 4 | 4 (0.89) | 4 | 0 | 32 | 26 | 6 | 0.0060 | NANa | – | 0.00161126 |
InfB
| 318 | 5 | 4 (1.25) | 4 | 0 | 69 | 69 | 0 | 0.0160 | NAN | – | 0.00393538 |
mdh
| 477 | 5 | 7 (1.47) | 6 | 1 | 35 | 33 | 2 | 0.0050 | 0.0000 | 0.0000 | 0.0014328 |
pgi
| 432 | 3 | 2 (0.46) | 2 | 0 | 9 | 0 | 9 | 0.0020 | NAN | – | 0.00055167 |
phoE
| 420 | 8 | 8 (1.90) | 8 | 0 | 77 | 73 | 4 | 0.0230 | NAN | – | 0.00533477 |
rpoB
| 501 | 2 | 1 (0.20) | 0 | 1 | 22 | 22 | 0 | NAN | 0.0010 | – | 0.00083368 |
tonB
| 414 | 10 | 13 (3.14) | 7 | 6 | 192 | 103 | 89 | 0.0160 | 0.0060 | 0.3750 | 0.0089006 |
Concatenated | 3012 | 0 | 39 (1.29) | 31 | 8 | 436 | 326 | 110 | 0.0090 | 0.0010 | 0.1100 | 0.00304244 |
Discussion
Clonality and resistance profile
Plasmid typing
Virulence factors
Clonality and genetic diversity
Sequence Type | n (% of total) | Clonal Group | Allelic Profile |
---|---|---|---|
37 | 14 (18.4%) | CG37 | 2–9–2-1-13–1-16 |
974 | 2 (2.6%) | 4–9–2-1-13–1-16 | |
353 | 1(1.3%) | 3–9–47-1-13–1-16 | |
340 | 5 (6.6%) | CG258 | 3–3–1-1-1-1-18 |
11 | 1(1.3%) | 3–3–1-1-1-1-4 | |
16 | 4 (5.3%) | CG17 | 2–1–2-1-4-4-4 |
17 | 1(1.3%) | 2–1–1-1-4-4-4 | |
15 | 3 (3.9%) | CG14 | 1–1–1-1-1-1-1 |
709 | 3 (3.9%) | 1–1–1-1-1-1-4 | |
348 | 2 (2.6%) | Singleton | 2–1–20-1-12-1-16 |
298 | 1(1.3%) | Singleton | 4–1–2-1-1-1-7 |
111 | 1(1.3%) | Singleton | 4–1–5-1-17-1-42 |
1045 | 1(1.3%) | Singleton | 2–1–1-1-1-1-42 |
649 | 1(1.3%) | Singleton | 2–1–1-5-4-1-1 |
199 | 15 (19.5%) | Singleton | 4–34–1-1-21–1-35 |
152 | 12 (15.8%) | Singleton | 2–3–2-1-1-4-56 |
48 | 5 (6.6%) | Singleton | 2–5–2-2-7-1-10 |
29 | 4 (5.3%) | Singleton | 2–3–2-2-6-4-4 |