Background
Materials and methods
Bacterial isolates
Isolate | Collection date(mm/dd/yy) | Sex | Age(y) | Ward | Source | Antibiotic exposure | Clinical diagnosis | outcome |
---|---|---|---|---|---|---|---|---|
S.epidermidis-1 | 02-18-22 | M | 67 | RICU | pf | BIA, LVX, TGC | Severe pneumonia | death |
S.epidermidis-2 | 11-28-20 | F | 74 | neurosurgery | sf | CAZ, VAN | Postoperative recurrence of meningioma | Discharge |
S.epidermidis-3 | 07-06-21 | M | 63 | ICU | bl | ATM, LNZ, VAN | Sepsis | Discharge |
S.epidermidis-4 | 04-05-22 | F | 48 | ICU | bl | SCF,TEC | Cerebral hemorrhage | death |
S.epidermidis-5 | 03-18-22 | M | 76 | RICU | pf | LNZ, BIA, DOX, LVX, TGC | Sepsis | Discharge |
S.epidermidis-6 | 07-14-22 | M | 59 | ICU | bl | SCF, VAN | Sepsis | Discharge |
S.epidermidis-7 | 07-30-22 | F | 54 | ICU | bl | SCF | Malignant tumor of esophagus | Discharge |
S.epidermidis-8 | 07-16-22 | M | 53 | ICU | bl | MEM | Multiple organ failure | death |
S.cohnii-9 | 01-13-21 | F | 45 | ICU | bl | LNZ,TEC, BIA | Pulmonary malignant tumor | Discharge |
S.cohnii-10 | 07-29-22 | M | 69 | RICU | bl | CXM | Pericarditis | Discharge |
S.cohnii-11 | 08-16-22 | F | 28 | ICU | bl | CAZ, MOX | Pneumonia | Discharge |
S.cohnii-12 | 07-28-22 | M | 68 | ICU | bl | SCF, BIA, LNZ, IPM | Cirrhosis | Discharge |
S.cohnii-13 | 06-20-21 | M | 52 | ICU | bl | CXM,CNX | Malignant tumor of the right ureter | Discharge |
S.cohnii-14 | 03-21-23 | M | 14 | EICU | bl | SCF, LNZ | Drug poisoning | Discharge |
S.hominis-15 | 11-30-20 | F | 62 | ICU | bl | CNX | Gastrointestinal hemorrhage | death |
S.hominis-16 | 01-13-21 | M | 61 | AICU | bl | SCF, LNZ | liver transplantation | Discharge |
S.hominis-17 | 04-23-21 | M | 68 | RICU | bl | CXM, SCF, IPM, TEC | Malignant neoplasm of rectum | Discharge |
S.hominis-18 | 05-26-21 | F | 60 | RICU | bl | BIA, IPM, SCF, TGC, TEC | Septic shock | death |
S.hominis-19 | 04-09-21 | M | 53 | RICU | bl | IPM, TEC | Septic shock | death |
S.hominis-20 | 08-14-22 | M | 88 | emergency surgery | bl | SCF | Gastric perforation | Discharge |
S.hominis-21 | 08-13-22 | F | 70 | ICU | bl | BIA, SCF, VAN | Lumbar spinal stenosis | Discharge |
S.hominis-22 | 02-17-23 | M | 76 | EICU | bl | SCF | Pneumonia | Discharge |
S.hominis-23 | 03-15-23 | M | 76 | AICU | bl | LVX, TZP, IPM, TEC, MEM | Malignant neoplasm of rectum | Discharge |
S. capitis-24 | 12-31-19 | M | 37 | ICU | bl | CXM, TZP, LNZ, TGC | Acute disseminated encephalomyelitis | Discharge |
S. capitis-25 | 01-17-20 | M | 64 | ICU | bl | TZP,TGC, GEN, CAZ, MEM, LNZ | Cerebral hemorrhage | Discharge |
S. capitis-26 | 10-31-20 | F | 75 | ICU | bl | TZP | Cerebral infarction | death |
S. capitis-27 | 04-21-20 | M | 41 | ICU | bl | MOX, LNZ, TZP, LVX | Cerebral hemorrhage | Discharge |
S. capitis-28 | 03-26-21 | M | 48 | RICU | bl | MOX, LNZ, BIA | Cerebral hemorrhage | Discharge |
S. capitis-29 | 02-16-21 | M | 65 | Respiratory | ab | IPM, MEM, LNZ | Primary hepatocellular carcinoma | Discharge |
S. capitis-30 | 01-12-21 | M | 62 | ICU | bl | MOX, BIA | Cardiac arrest | death |
S. capitis-31 | 11-14-20 | M | 57 | RICU | bl | BIA, LNZ | Severe pneumonia | Discharge |
S. capitis-32 | 04-01-22 | F | 73 | ICU | cs | IPM, TZP | Atrial fibrillation | Discharge |
S. capitis-33 | 02-18-22 | M | 76 | RICU | bl | LNZ, BIA, LVX, TGC | Sepsis | Discharge |
S. capitis-34 | 02-22-22 | M | 10 | ICU | bl | MEM, POL | Cerebral hemorrhage | death |
S. capitis-35 | 10-17-22 | M | 72 | ICU | bl | TZP | Cerebral hemorrhage | Discharge |
S. capitis-36 | 03-11-23 | F | 68 | ICU | cs | LNZ | Subarachnoid hemorrhage | Discharge |
S. haemolyticus-37 | 02-12-23 | M | 88 | RICU | bl | BIA | Severe pneumonia | Discharge |
Antimicrobial susceptibility testing
Genomic DNA extraction and whole-genome sequencing
Molecular detection of resistance genes and mutations
Results
Antimicrobial susceptibility
Isolate | MIC(µg/mL) | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LNZ | PEN | OXA | CHL | CLI | ERY | Inducible Clindamycin Resistance | GEN | SXT | CIP | LVX | RIF | TCY | TGC | VAN | TEC | |
S.epidermidis-1 | > 128 | 2 | >=8 | >=32 | >=4 | 0.5 | neg | >=32 | 1/19 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 1 | 0.5 |
S.epidermidis-2 | > 128 | 1 | >=8 | >=32 | >=4 | 0.5 | neg | >=32 | 4/76 | >=4 | >=8 | <= 0.5 | <=2 | 0.12 | 1 | 2 |
S.epidermidis-3 | > 128 | 0.25 | >=8 | >=32 | >=4 | 0.5 | neg | >=32 | 1/19 | >=4 | >=8 | 4 | <=2 | 0.25 | 1 | 4 |
S.epidermidis-4 | > 128 | 0.25 | >=8 | >=32 | >=4 | 0.5 | neg | >=32 | 1/19 | >=4 | >=8 | >=8 | <=2 | 0.12 | 1 | 4 |
S.epidermidis-5 | > 128 | 0.25 | >=8 | >=32 | >=4 | 0.5 | neg | 16 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 1 | 2 |
S.epidermidis-6 | > 128 | 2 | >=8 | >=32 | >=4 | 0.5 | neg | 16 | 1/19 | >=4 | >=8 | 2 | <=2 | 0.25 | 1 | 2 |
S.epidermidis-7 | 8 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | 4/76 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 1 | 1 |
S.epidermidis-8 | > 128 | 0.25 | >=8 | >=32 | >=4 | 0.5 | neg | 16 | 1/19 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 1 | 4 |
S.cohnii-9 | 64 | 2 | >=8 | >=32 | >=4 | >=8 | pos | 8 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | >=32 | 0.25 | 1 | 2 |
S.cohnii-10 | 8 | 2 | >=8 | 8 | >=4 | >=8 | pos | 4 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 1 | 2 |
S.cohnii-11 | 32 | 2 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 1 | 2 |
S.cohnii-12 | 128 | 4 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | >=32 | 0.25 | 1 | 2 |
S.cohnii-13 | 128 | 2 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | >=32 | 0.25 | 1 | 1 |
S.cohnii-14 | 128 | >=16 | >=8 | >=32 | >=4 | <=0.25 | neg | 4 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | >=32 | 0.25 | 1 | 0.5 |
S.hominis-15 | 16 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | >=8/152 | >=4 | >=8 | >=8 | >=32 | 0.25 | 0.5 | 0.5 |
S.hominis-16 | 32 | 4 | >=8 | >=32 | 1 | 1 | neg | 4 | 4/76 | 2 | 2 | <= 0.5 | <=2 | 0.12 | 1 | 8 |
S.hominis-17 | 16 | 0.25 | 4 | >=32 | 1 | 0.5 | neg | 4 | 4/76 | 2 | 2 | <= 0.5 | <=2 | 0.25 | 0.5 | 4 |
S.hominis-18 | 32 | 1 | >=8 | >=32 | 1 | 0.5 | neg | <=2 | 4/76 | 2 | 2 | <= 0.5 | <=2 | 0.12 | 1 | 8 |
S.hominis-19 | 16 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | 16 | >=8/152 | >=4 | >=8 | <= 0.5 | <=2 | 0.12 | 0.5 | 0.25 |
S.hominis-20 | 16 | >=16 | >=8 | 16 | >=4 | >=8 | pos | 8 | 4/76 | >=4 | >=8 | <= 0.5 | <=2 | 0.12 | 1 | 0.25 |
S.hominis-21 | 8 | >=16 | >=8 | >=32 | >=4 | >=8 | neg | 8 | <=0.5/9.5 | 2 | 1 | <= 0.5 | <=2 | 0.12 | 0.5 | < 0.125 |
S.hominis-22 | 8 | >=16 | >=8 | >=32 | >=4 | 4 | neg | >=32 | <=0.5/9.5 | >=4 | 4 | <= 0.5 | <=2 | 0.12 | 0.5 | < 0.125 |
S.hominis-23 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | 8 | <=0.5/9.5 | >=4 | >=8 | 1 | >=32 | 0.25 | 2 | 1 |
S. capitis-24 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | <=2 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 0.5 | 0.25 |
S. capitis-25 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | <=2 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | <=2 | 0.25 | 0.5 | 0.25 |
S. capitis-26 | 32 | >=16 | >=8 | >=32 | 1 | >=8 | pos | <=2 | 1/19 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 0.5 | 0.25 |
S. capitis-27 | 32 | >=16 | >=8 | >=32 | 1 | >=8 | pos | >16 | 1/19 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 0.5 | 0.25 |
S. capitis-28 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | <=2 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 1 | 0.25 |
S. capitis-29 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | <=2 | <=0.5/9.5 | >=4 | >=8 | 1 | <=2 | 0.25 | 1 | 0.25 |
S. capitis-30 | 32 | >=16 | >=8 | >=32 | 1 | >=8 | pos | >=32 | 2/38 | >=4 | >=8 | 2 | 4 | 0.25 | 0.5 | 0.25 |
S. capitis-31 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | 4 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | 4 | 0.5 | 0.5 | 0.25 |
S. capitis-32 | 32 | >=16 | >=8 | >=32 | 1 | >=8 | pos | >=32 | >=8/152 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 1 | 0.25 |
S. capitis-33 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | <=2 | 1/19 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 0.5 | 0.25 |
S. capitis-34 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | <=2 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 0.5 | 0.25 |
S. capitis-35 | 32 | >=16 | >=8 | >=32 | 1 | >=8 | pos | >=32 | 1/19 | >=4 | >=8 | <= 0.5 | 4 | 0.25 | 0.5 | 0.25 |
S. capitis-36 | 32 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | <=0.5/9.5 | >=4 | >=8 | <= 0.5 | 4 | 0.5 | 1 | 0.25 |
S. haemolyticus-37 | > 128 | >=16 | >=8 | >=32 | >=4 | >=8 | pos | >=32 | >=8/152 | >=4 | >=8 | >=8 | <=2 | 0.12 | 1 | 2 |
Molecular characteristics and the mechanisms of linezolid resistance
Isolate | MLST | cfr gene | 23S rRNA mutations | Ribosomal protein mutation | Other resistance genes | ||
---|---|---|---|---|---|---|---|
L3 | L4 | L22 | |||||
S.epidermidis-1 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, fusB, fosB, msr(A),mph(C) |
S.epidermidis-2 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, fusB, qacA, mecA, blaZ, fosB, msr(A), mph(C) |
S.epidermidis-3 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, fosB, fusB, msr(A), mph(C) |
S.epidermidis-4 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, fosB, fusB, msr(A), mph(C) |
S.epidermidis-5 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, fosB, fusB, msr(A), mph(C) |
S.epidermidis-6 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, fosB, fusB, msr(A), mph(C) |
S.epidermidis-7 | ST2 | + | − | L101V | − | − | mecA, blaZ, aac(6')-aph(2''), qacA, fosB, erm(T), mupA, |
S.epidermidis-8 | ST22 | − | T2504A C2534T | L101V, G152D, D159Y | N158S | − | mecA, blaZ, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, fosB, fusB, msr(A),mph(C) |
S.cohnii-9 | N/D | + | − | S158Y, D159Y | − | − | mecA, qacA, fosB, erm(C), mupA, tet(K), dfrG |
S.cohnii-10 | N/D | − | − | S158Y, D159Y | − | − | mecA, aac(6')-aph(2''), qacA, fosB, erm(C), mupA |
S.cohnii-11 | N/D | + | − | − | − | − | mecA, aac(6')-aph(2''), qacA, erm(C), mupA, dfrG, |
S.cohnii-12 | N/D | + | − | S158Y, D159Y | − | − | mecA, aac(6')-aph(2''), qacA, fosB, erm(C), mupA, tet(K) |
S.cohnii-13 | N/D | + | − | S158Y, D159Y | − | − | mecA, aac(6')-aph(2''), qacA, erm(C), mupA, tet(K), dfrG |
S.cohnii-14 | N/D | + | − | S158Y, D159Y | − | − | mecA, aac(6')-aph(2''),qacA, fosB, fexA, mupA, tet(K), dfrG |
S.hominis-15 | ST2 | + | − | − | − | − | mecA, blaZ, aadD, aac(6')-aph(2''), bleO, qacA, fosB, fusC, erm(C), mecA, blaZ, mupA, tet(K), dfrG |
S.hominis-16 | ST1 | − | G2576T | − | − | − | mecA, blaZ, aadD, aac(6')-aph(2''), bleO, qacA, lnu(A), mupA |
S.hominis-17 | ST1 | − | G2576T | − | − | − | mecA, blaZ, aadD, aac(6')-aph(2''), bleO, qacA, lnu(A), mupA |
S.hominis-18 | ST1 | − | G2576T | − | − | − | mecA, blaZ, aadD, aac(6')-aph(2''), bleO, qacA, lnu(A), mupA, |
S.hominis-19 | ST1 | + | − | − | − | − | mecA, blaZ, aac(6')-aph(2''), qacA, fusC, erm(C), mupA |
S.hominis-20 | ST1 | + | − | − | − | − | mecA, blaZ, aac(6')-aph(2''), qacA, erm(C), lnu(A), mupA |
S.hominis-21 | ST85 | + | − | − | T124I | − | mecA, aadD, aac(6')-aph(2''), bleO, qacA, qacB, msr(A), lnu(A) |
S.hominis-22 | ST85 | + | − | − | − | − | mecA, aac(6')-aph(2''), qacA, erm(C), mupA |
S.hominis-23 | ST2 | + | − | V154L,M156T | − | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(6)-Ia, aph(3')-III, qacA, msr(A), lsa(B), mph(C), mupA, tet(K) |
S. capitis-24 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-25 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-26 | N/D | − | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-27 | N/D | − | G2576T C2104T | − | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-28 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-29 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, fosB, erm(A) |
S. capitis-30 | N/D | + | G2576T C2104T | V154L | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-31 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-32 | N/D | − | G2576T C2104T | − | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, fusB, erm(A) |
S. capitis-33 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-34 | N/D | + | G2576T C2104T | M156T | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, erm(A) |
S. capitis-35 | N/D | − | G2576T C2104T | − | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, fusB, erm(A) |
S. capitis-36 | N/D | − | G2576T C2104T | − | I188S | − | mecA, blaZ, aadD, aac(6')-aph(2''), ant(9)-Ia, bleO, qacA, fusB, erm(A) |
S. haemolyticus-37 | ST1 | + | − | R138V | − | − | mecA, aadD, aac(6')-aph(2''), msr(A), lsa(B), mph(C), vga(A)LC, mupA |