This study contained four stages: discovery stage, training stage, validation stage I and validation stage II. All patients were from the Department of Critical Care Medicine, Nanjing Drum Tower …
(A) Schematic diagram of screening species-specific DNA tags. (B) Genomic distribution of species-specific DNA tags in 10 bacteria. (C) Genomic proportion of species-specific DNA tags in 10 bacteria.
(A) SSBD workflow for clinical validation stages. (B) Cas12a and Cas12a-after-PCR detection of different concentrations and reaction times including 30 min (left) and 60 min (right). Blue bars …
The reaction condition test of Cas12a detection.
The cross-validation of 10 selected bacteria using SSBD.
(A) Cross-tables for 5 of 10 bacteria by both SSBD and CCT in the validation stage I. (B) Cross-tables for 5 of 10 bacteria by both SSBD and CCT in the validation stage II. (C) Antibiotics coverage …
(A) Statistics of pathogenic infection status of BALF samples in the two validation stages. (B) Verification from NGS results for 6 samples identified as polymicrobial infection by SSBD but not CCT …
(A) Optimizing the algorithm of sequence alignment. Abbreviations: SA, sequence alignment; N, number of double sequence alignment; n, number of sequences. (B) Schematic map of screening …
10 targeted bacteria were indicated with the box.
Epidemic data of pathogens in the ICU of Nanjing Drum Tower Hospital in 2017.
(A) SSBD results of purified and unpurified DNA. NC, namely the fluorescence values of PCR products of using DEPC-H2O as input. Each group had three repeats. Error bars indicated mean ± SEM of …
The test of SSBD with or without DNA purification.
The test of SSBD with different incubation times.
The validation of SSBD with clinical strains.
(A) Judgment process of antibiotics coverage. (B) The raw results of antibiotics coverage in two groups. Exp meant the experimental group, and Con meant the control group.
Classification of antibiotic coverage for each test in two groups.
Numbers and fractions of different strength levels among all false-positive samples of each bacteria species in the validation stage I (A) and II (B). Strength could be seen roughly as bacterial …
Experimental group (n=22) | Control group(n=24) | p value | |
---|---|---|---|
Women | 9 (40.9%) | 11 (45.8%) | 0.774 |
Men | 13 (59.1%) | 13 (54.2%) | 0.774 |
Age, years (SD) | 58 (17.4) | 68 (9.5) | 0.015* |
Patients' numbers of chronic comorbidities | |||
Hypertension | 9 (40.9%) | 17 (70.8%) | 0.073 |
Coronary artery disease | 1 (4.5%) | 3 (12.5%) | 0.609 |
Chronic pulmonary disease | 2 (9.1%) | 4 (16.7%) | 0.667 |
Chronic kidney disease | 2 (9.1%) | 6 (25.0%) | 0.247 |
Diabetes | 5 (22.7%) | 12 (50.0%) | 0.072 |
Malignancy | 0 (0.0%) | 2 (8.3%) | 0.490 |
Stroke | 3 (13.6%) | 8 (33.3%) | 0.171 |
Immunodeficiency/immune suppressive therapy | 5 (22.7%) | 3 (12.5%) | 0.451 |
Recent surgery | 4 (18.2%) | 3 (12.5%) | 0.694 |
Hemodynamic support (using vasoactive drugs) | 7 (31.8%) | 7 (29.2%) | 1.000 |
Norepinephrine ≤0.1 μg/(kg•min) | 2 | 3 | |
Norepinephrine >0.1 μg/(kg•min) | 1 | 1 | |
Dopamine ≤5 μg/(kg•min) | 3 | 2 | |
Dopamine >5 μg/(kg•min) | 0 | 1 | |
Dobutamine ≤5 μg/(kg•min) | 1 | 0 | |
Dobutamine >5 μg/(kg•min) | 0 | 0 | |
Status at randomization (D1) | |||
Temperature, °C | 38.4 (0.6) | 38.3 (0.7) | 0.345 |
Coma | 6 (27.3%) | 6 (25.0%) | 1.000 |
Systolic blood pressure, mmHg | 112.2 (19.3) | 121.6 (17.8) | 0.057 |
Invasive mechanical ventilation | 20 (90.9%) | 24 (100.0%) | 0.223 |
Renal replacement therapy | 0 (0.0%) | 2 (8.3%) | 0.493 |
SOFA score | 6.3 (0.7) | 6.0 (0.5) | 0.935 |
APACHE II score | 17.3 (1.6) | 18.9 (1.5) | 0.422 |
Albumin, g/L | 32.1 (5.1) | 31.0 (3.7) | 0.442 |
Globulin, g/L | 21.8 (3.9) | 23.1 (5.9) | 0.489 |
Absolute lymphocyte count, 109 /L | 0.9 (0.7) | 0.7 (0.3) | 0.909 |
White blood cells, 109 /L | 11.0 (5.7) | 12.7 (6.3) | 0.210 |
CRP, mg/L | 94.7 (101.2) | 108.3 (84.0) | 0.424 |
SOFA score and APACHE II score are mean (SEM), other data are mean (SD), n (%). Mean (SEM/SD) is compared using Mann-Whitney test, and n (%) is compared using Fisher’s exact test. * indicated p-value <0.05.
Name | Sequence (5' ->3') | Target | Product length (bp) |
---|---|---|---|
pGL3-amplify-F | GAAGATGGAACCGCTGGAGA | pGL3 | 597 |
pGL3-amplify-R | GCAGGCAGTTCTATGAGGCA | ||
Aba-amplify-F | CACAGCGTTTAACCCATGCC | A. baumannii | 564 |
Aba-amplify-R | TATCGCCACCTGCACAGAAG | ||
Eco-amplify-F | GTTCCTGACTATCTGGCGGG | E. coli | 371 |
Eco-amplify-R | GCTTCCTGACTCCAGACACC | ||
Kpn-amplify-F | CATGGGCATATCGACGGTCA | K. pneumoniae | 740 |
Kpn-amplify-R | CCTGCAACATAGGCCAGTGA | ||
Sau-amplify-F | AGGTGCAGTAGACGCATAGC | S. aureus | 563 |
Sau-amplify-R | CATTCGCTGCGCCAATACAA | ||
Pae-amplify-F | TCTCTCTATCACGCCGGTCA | P. aeruginosa | 467 |
Pae-amplify-R | TCGCATCGAGGTATTCCAGC | ||
Sep-amplify-F | CACGCATGGCACTAGGTACA | S. epidermidis | 383 |
Sep-amplify-R | CGAAAAAGAGTTGTCCTTGTTGA | ||
Sca-amplify-F | GGTTCAGTCATCCCCACGTT | S. capitis | 591 |
Sca-amplify-R | CAGCTGCGACAACTGCTTAC | ||
Efa-amplify-F | CGGCAAGTTTGGAAGCAGAC | E. faecalis | 627 |
Efa-amplify-R | CAGCGCCTAGTCCTTGTGAT | ||
Efm-amplify-F | ATCGGAAATCGGTGTGGCTT | E. faecium | 507 |
Efm-amplify-R | TCAAATGCATCCCTGTGCCT | ||
Sma-amplify-F | CGCCTCCCGTTTACAGATTA | S. maltophilia | 356 |
Sma-amplify-R | TCGGCTCCACCACATACAC |
Name | Sequence (5′->3′) | Target |
---|---|---|
T7-Forward | TAATACGACTCACTATAGGT | |
LbcrRNA-Reverse-PGL3 | ATGTGACGAACGTGTACATCGACTATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | PGL3 |
LbcrRNA-Reverse-Aba | TTCAAGTAATTCTTCTTTACATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | A. baumannii |
LbcrRNA-Reverse-Eco | CTTGCCATCATAGCGACCGTATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | E. coli |
LbcrRNA-Reverse-Kpn | AAGATGGCGATTACCGCAGTATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | K. pneumoniae |
LbcrRNA-Reverse-Sau | CCTCAGCAAGTTCACGTTGTATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | S. aureus |
LbcrRNA-Reverse-Pae | CTCCTCATGTGTGTTTACAAATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | P. aeruginosa |
LbcrRNA-Reverse-Sep | TCTCTAATTGATGAATATTAATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | S. epidermidis |
LbcrRNA-Reverse-Sca | TATTGATTAATAAGGTGATTATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | S. capitis |
LbcrRNA-Reverse-Efa | TCAGCTGTGTTATTTGGTGCATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | E. faecalis |
LbcrRNA-Reverse-Efm | TGTATATAAGTTCAGGTAGTATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | E. faecium |
LbcrRNA-Reverse-Sma | CCTGGTCGCAGGTGTCATGCATCTACACTTAGTAGAAATTACCTATAGTGAGTCGTATTA | S. maltophilia |
Sample ID | SSBD Results | CCT Results | NGS Results |
---|---|---|---|
A01 | S. aureus (I) | N | S. aureus |
A02 | A. baumannii (III) | A. baumannii | |
A03 | A. baumannii (III) S. aureus (I) | A. baumannii S. aureus | A. baumannii S. aureus |
A04 | A. baumannii (III) K. pneumoniae (II) S. maltophilia (II) | N | |
A05 | A. baumannii (III) K. pneumoniae (III) P. aeruginosa (III) | K. pneumoniae P. aeruginosa | |
A06 | A. baumannii (III) | A. baumannii | |
A07 | S. maltophilia (II) | S. maltophilia | |
A08 | A. baumannii (III) | A. baumannii | |
A09 | A. baumannii (II) S. aureus (I) | A. baumannii | |
A10 | A. baumannii (III) K. pneumoniae (III) P. aeruginosa (I) | A. baumannii K. pneumoniae | |
A11 | A. baumannii (III) K. pneumoniae (I) | A. baumannii | |
A12 | N | N | |
A13 | A. baumannii (II) | A. baumannii | |
A14 | N | N | |
A15 | K. pneumoniae (III) | K. pneumoniae | |
A16 | K. pneumoniae (III) P. aeruginosa (III) | K. pneumoniae | |
A17 | N | N | |
A18 | K. pneumoniae (I) P. aeruginosa (III) | K. pneumoniae P. aeruginosa | |
A19 | P. aeruginosa (I) | P. aeruginosa | |
A20 | E. faecium (III) S. capitis (II) | N | E. faecium S. capitis |
A21 | A. baumannii (III) K. pneumoniae (III) S. aureus (I) | A. baumannii S. aureus | |
A22 | A. baumannii (III) S. epidermidis (III) | A. baumannii | |
A23 | N | N | |
A24 | A. baumannii (III) | A. baumannii | |
A25 | N | N | N |
A26 | P. aeruginosa (III) | P. aeruginosa | |
A27 | A. baumannii (III) S. epidermidis (III) | A. baumannii | A. baumannii S. epidermidis |
A28 | A. baumannii (II) P. aeruginosa (III) | A. baumannii | |
A29 | S. epidermidis (I) S. maltophilia (I) | N | |
A30 | A. baumannii (III) S. aureus (III) S. epidermidis (I) | A. baumannii | |
A31 | K. pneumoniae (I) P. aeruginosa (I) S. epidermidis (I) | N | K. pneumoniae |
A32 | P. aeruginosa (I) S. epidermidis (I) | N | |
A33 | S. aureus (I) S. maltophilia (II) | S. aureus | |
A34 | N | N | A. baumannii |
A35 | A. baumannii (III) | A. baumannii | |
A36 | A. baumannii (III) S. maltophilia (I) | A. baumannii | |
A37 | A. baumannii (III) S. epidermidis (III) | A. baumannii | |
A38 | A. baumannii (III) | A. baumannii | |
A39 | A. baumannii (III) | A. baumannii | |
A40 | N | N | |
A41 | N | N | |
A42 | A. baumannii (I) | N | |
A43 | A. baumannii (III) | A. baumannii | |
A44 | A. baumannii (III) | A. baumannii | A. baumannii |
A45 | A. baumannii (III) K. pneumoniae (II) | A. baumannii | |
A46 | A. baumannii (III) | A. baumannii | |
A47 | A. baumannii (I) | A. baumannii | |
A48 | A. baumannii (III) | A. baumannii | |
A49 | A. baumannii (III) S. aureus (III) S. maltophilia (III) | A. baumannii S. aureus | A. baumannii S. aureus S. maltophilia |
A50 | S. epidermidis (III) | N | |
A51 | N | N | |
A52 | N | N | |
A53 | K. pneumoniae (III) | K. pneumoniae | |
A54 | N | N | |
A55 | A. baumannii (III) E. coli (II) K. pneumoniae (III) S. maltophilia (III) | A. baumannii | |
A56 | S. epidermidis (III) E. faecalis (I) | N | |
A57 | N | N | |
A58 | P. aeruginosa (III) | N | |
A59 | S. maltophilia (I) | S. maltophilia | S. aureus S. maltophilia |
A60 | A. baumannii (I) P. aeruginosa (III) | A. baumannii P. aeruginosa | |
A61 | A. baumannii (II) | A. baumannii | |
A62 | K. pneumoniae (II) S. maltophilia (III) | K. pneumoniae S. maltophilia | |
A63 | A. baumannii (III) | A. baumannii | |
A64 | A. baumannii (III) | A. baumannii | |
A65 | A. baumannii (III) P. aeruginosa (I) S. maltophilia (II) | A. baumannii P. aeruginosa | |
A66 | K. pneumoniae (II) | K. pneumoniae | |
A67 | S. aureus (III) | S. aureus | |
A68 | A. baumannii (III) P. aeruginosa (III) | A. baumannii | |
A69 | A. baumannii (I) P. aeruginosa (III) | A. baumannii | P. aeruginosa |
A70 | A. baumannii (I) | A. baumannii | |
A71 | N | N | |
A72 | A. baumannii (III) S. maltophilia (I) | A. baumannii | |
A73 | A. baumannii (III) K. pneumoniae (III) P. aeruginosa (III) | A. baumannii P. aeruginosa | |
A74 | A. baumannii (III) | A. baumannii | |
A75 | A. baumannii (III) P. aeruginosa (III) | A. baumannii | |
A76 | A. baumannii (I) P. aeruginosa (III) S. maltophilia (I) | P. aeruginosa | |
A77 | S. epidermidis (I) | N |
Sample ID | SSBD Results | CCT Results | NGS Results |
---|---|---|---|
A01 | S. aureus (I) | N | S. aureus |
A03 | A. baumannii (III) S. aureus (I) | A. baumannii S. aureus | A. baumannii S. aureus |
A20 | E. faecium (III) S. capitis (II) | N | E. faecium S. capitis |
A25 | N | N | N |
A27 | A. baumannii (III) S. epidermidis (III) | A. baumannii | A. baumannii S. epidermidis |
A31 | K. pneumoniae (I) P. aeruginosa (I) S. epidermidis (I) | N | K. pneumoniae |
A34 | N | N | A. baumannii |
A44 | A. baumannii (III) | A. baumannii | A. baumannii |
A49 | A. baumannii (III) S. aureus (III) S. maltophilia (III) | A. baumannii S. aureus | A. baumannii S. aureus S. maltophilia |
A59 | S. maltophilia (I) | S. maltophilia | S. maltophilia S. aureus |
A69 | A. baumannii (I) P. aeruginosa (III) | A. baumannii | P. aeruginosa |
Patient ID | Sample ID | Test No. | SSBD Results | CCT Results | NGS Results |
---|---|---|---|---|---|
Exp. | |||||
B01 | B01-1 | Test 1 | N | N | |
B01-2 | Test 2 | N | N | N | |
B01-3 | Test 3 | A. baumannii (III) | A. baumannii | ||
B03 | B03-1 | Test 1 | N | N | N |
B03-2 | Test 2 | A. baumannii (III) | A. baumannii | ||
B05 | B05-1 | Test 1 | A. baumannii (III) S. maltophilia (II) | A. baumannii | A. baumannii S. maltophilia |
B05-2 | Test 2 | A. baumannii (III) S. maltophilia (I) | A. baumannii | ||
B05-3 | Test 3 | A. baumannii (III) S. maltophilia (I) | |||
B07 | B07-1 | Test 1 | P. aeruginosa (III) | P. aeruginosa | P. aeruginosa |
B07-2 | Test 2 | P. aeruginosa (III) | P. aeruginosa | ||
B07-3 | Test 3 | P. aeruginosa (III) | P. aeruginosa | ||
B09 | B09-1 | Test 1 | A. baumannii (III) S. aureus (III) S. capitis (III) S. maltophilia (III) | A. baumannii | |
B11 | B11-1 | Test 1 | A. baumannii (III) P. aeruginosa (III) S. maltophilia (II) | A. baumannii | A. baumannii P. aeruginosa S. maltophilia |
B11-2 | Test 2 | A. baumannii (III) S. aureus (I) S. maltophilia (III) | |||
B11-3 | Test 3 | P. aeruginosa (III) | N | ||
B13 | B13-1 | Test 1 | S. epidermidis (I) | N | N |
B13-2 | Test 2 | K. pneumoniae (I) | K. pneumoniae | ||
B15 | B15-1 | Test 1 | A. baumannii (I) E. coli (I) K. pneumoniae (II) | N | |
B15-2 | Test 2 | K. pneumoniae (I) E. faecium (I) | |||
B15-3 | Test 3 | E. faecium (III) | |||
B17 | B17-1 | Test 1 | A. baumannii (III) | ||
B17-2 | Test 2 | A. baumannii (III) K. pneumoniae (III) | |||
B17-3 | Test 3 | A. baumannii (I) K. pneumoniae (I) E. faecalis (I) | A. baumannii | ||
B19 | B19-1 | Test 1 | A. baumannii (III) P. aeruginosa (I) S. maltophilia (II) | A. baumannii | |
B19-2 | Test 2 | A. baumannii (III) P. aeruginosa (III) S. maltophilia (III) | A. baumannii S. maltophilia | ||
B19-3 | Test 3 | K. pneumoniae (III) P. aeruginosa (III) S. maltophilia (III) | K. pneumoniae S. maltophilia | ||
B21 | B21-1 | Test 1 | P. aeruginosa (III) S. aureus (III) S. maltophilia (III) | S. aureus S. maltophilia | |
B21-2 | Test 2 | P. aeruginosa (III) S. aureus (III) S. maltophilia (III) | S. maltophilia | ||
B21-3 | Test 3 | S. aureus (I) S. maltophilia (II) | N | ||
B23 | B23-1 | Test 1 | S. capitis (I) S. maltophilia (III) | S. maltophilia | |
B23-2 | Test 2 | S. maltophilia (III) | S. maltophilia | ||
B25 | B25-1 | Test 1 | A. baumannii (II) | A. baumannii | |
B25-2 | Test 2 | A. baumannii (III) | |||
B25-3 | Test 3 | A. baumannii (III) | A. baumannii | ||
B27 | B27-1 | Test 1 | S. maltophilia (I) | N | N |
B27-2 | Test 2 | A. baumannii (III) | |||
B29 | B29-1 | Test 1 | K. pneumoniae (III) | K. pneumoniae | K. pneumoniae |
B29-2 | Test 2 | K. pneumoniae (III) | |||
B31 | B31-1 | Test 1 | A. baumannii (III) S. capitis (III) | A. baumannii | A. baumannii S. capitis |
B31-2 | Test 2 | A. baumannii (III) | |||
B31-3 | Test 3 | A. baumannii (I) | N | ||
B33 | B33-1 | Test 1 | N | N | |
B33-2 | Test 2 | A. baumannii (I) S. epidermidis (II) | N | ||
B33-3 | Test 3 | N | N | ||
B35 | B35-1 | Test 1 | A. baumannii (III) | A. baumannii | A. baumannii |
B35-2 | Test 2 | A. baumannii (III) | A. baumannii | ||
B35-3 | Test 3 | A. baumannii (III) | A. baumannii | ||
B37 | B37-1 | Test 1 | N | N | A. baumannii |
B37-2 | Test 2 | P. aeruginosa (I) | |||
B39 | B39-1 | Test 1 | N | P. aeruginosa | |
B39-2 | Test 2 | A. baumannii (I) E. coli (I) K. pneumoniae (III) P. aeruginosa (III) | K. pneumoniae P. aeruginosa | ||
B39-3 | Test 3 | K. pneumoniae (I) P. aeruginosa (III) | |||
B41 | B41-1 | Test 1 | N | N | N |
B41-2 | Test 2 | N | |||
B43 | B43-1 | Test 1 | N | N | |
B43-2 | Test 2 | A. baumannii (I) S. epidermidis (I) | |||
B43-3 | Test 3 | A. baumannii (II) | A. baumannii | ||
Con. | |||||
C02 | Test 1 | A. baumannii | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C04 | Test 1 | N | |||
Test 2 | N | ||||
Test 3 | N | ||||
C06 | Test 1 | N | |||
Test 2 | A. baumannii | ||||
C08 | Test 1 | E. coli | |||
Test 2 | E. coli | ||||
Test 3 | K. pneumoniae | ||||
C10 | Test 1 | N | |||
Test 2 | N | ||||
Test 3 | A. baumannii | ||||
C12 | Test 1 | N | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C14 | Test 1 | A. baumannii | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C16 | Test 1 | N | |||
Test 2 | N | ||||
C18 | Test 1 | A. baumannii | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C20 | Test 1 | N | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C22 | Test 1 | N | |||
Test 2 | N | ||||
Test 3 | A. baumannii | ||||
C24 | Test 1 | N | |||
Test 2 | N | ||||
C26 | Test 1 | A. baumannii | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C28 | Test 1 | S. aureus | |||
Test 2 | N | ||||
Test 3 | A. baumannii | ||||
C30 | Test 1 | N | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C32 | Test 1 | N | |||
Test 2 | K. pneumoniae | ||||
Test 3 | A. baumannii K. pneumoniae | ||||
C34 | Test 1 | N | |||
C36 | Test 1 | S. aureus | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C38 | Test 1 | A. baumannii | |||
Test 2 | A. baumannii | ||||
Test 3 | A. baumannii | ||||
C40 | Test 1 | P. aeruginosa | |||
Test 2 | P. aeruginosa | ||||
C42 | Test 1 | N | |||
Test 2 | N | ||||
C44 | Test 1 | S. aureus | |||
Test 2 | A. baumannii | ||||
C46 | Test 1 | N | |||
Test 2 | N | ||||
Test 3 | A. baumannii | ||||
C48 | Test 1 | A. baumannii | |||
Test 2 | A. baumannii |
Patient ID | Sample ID | Test No. | SSBD Results | CCT Results | NGS Results |
---|---|---|---|---|---|
B01 | B01-2 | Test 2 | N | N | N |
B03 | B03-1 | Test 1 | N | N | N |
B05 | B05-1 | Test 1 | A. baumannii (III) S. maltophilia (II) | A. baumannii | A. baumannii S. maltophilia |
B07 | B07-1 | Test 1 | P. aeruginosa (III) | P. aeruginosa | P. aeruginosa |
B11 | B11-1 | Test 1 | A. baumannii (III) P. aeruginosa (III) S. maltophilia (II) | A. baumannii | A. baumannii P. aeruginosa S. maltophilia |
B13 | B13-1 | Test 1 | S. epidermidis (I) | N | N |
B27 | B27-1 | Test 1 | S. maltophilia (I) | N | N |
B29 | B29-1 | Test 1 | K. pneumoniae (III) | K. pneumoniae | K. pneumoniae |
B31 | B31-1 | Test 1 | A. baumannii (III) S. capitis (III) | A. baumannii | A. baumannii S. capitis |
B35 | B35-1 | Test 1 | A. baumannii (III) | A. baumannii | A. baumannii |
B37 | B37-1 | Test 1 | N | N | A. baumannii |
B41 | B41-1 | Test 1 | N | N | N |
Empirical antibiotic therapy | |
---|---|
Experimental group | |
B01 | Piperacillin -tazobactam |
B03 | Biapenem |
B05 | Biapenem, Teicoplanin and Tigecycline |
B07 | Biapenem |
B09 | Biapenem and vancomycin |
B11 | Cefoperazone-sulbactam and Tigecycline |
B13 | Piperacillin-Tazobactam, trimethoprim-sulfamethoxazole and Teicoplanin |
B15 | Imipenem-cilastatin and Linezolid |
B17 | Biapenem |
B19 | Biapenem |
B21 | Ceftazidine-avibatam |
B23 | Imipenem-Cilastatin |
B25 | Imipenem-Cilastatin and Linezolid |
B27 | Piperacillin-Tazobactam and trimethoprim-sulfamethoxazole |
B29 | Imipenem-Cilastatin |
B31 | Imipenem-Cilastatin and Teicoplanin |
B33 | Piperacillin-tazobactam |
B35 | Moxifloxacin and Piperacillin -tazobactam |
B37 | Biapenem, trimethoprim-sulfamethoxazole and Linezolid |
B39 | Piperacillin-tazobactam |
B41 | Piperacillin-tazobactam |
B43 | Meropenem and Linezolid |
Control group | |
C02 | Meropenem and vancomycin |
C04 | Biapenem and vancomycin |
C06 | Piperacillin-tazobactam |
C08 | Imipenem-Cilastatin |
C10 | Cefoperazone-sulbactam |
C12 | Moxifloxacin |
C14 | Biapenem and Linezolid |
C16 | Cefoperazone-sulbactam |
C18 | Moxifloxacin |
C20 | Piperacillin-tazobactam |
C22 | Piperacillin-tazobactam and vancomycin |
C24 | Cefoperazone-sulbactam, Linezolid and trimethoprim-sulfamethoxazole |
C26 | Cefoperazone-sulbactam and Moxifloxacin |
C28 | Piperacillin-tazobactam |
C30 | Piperacillin-tazobactam |
C32 | Piperacillin-tazobactam and Moxifloxacin |
C34 | Meropenem |
C36 | Cefoperazone-sulbactam |
C38 | Piperacillin-tazobactam |
C40 | Imipenem-Cilastatin |
C42 | Cefoperazone-sulbactam |
C44 | Piperacillin-tazobactam |
C46 | Cefoperazone-sulbactam |
C48 | Piperacillin-tazobactam and Linezolid |
Experimental group (n=22) | Control group(n=24) | p | |
---|---|---|---|
Number of patients who have clinical indexes improved | |||
Day 3 vs. Day 1 | |||
Temperature, °C | 15 (68.2%) | 9 (37.5%) | 0.045* |
WBC, 109 /L | 15 (68.2%) | 12 (50.0%) | 0.211 |
PCT, ng/mL | 18 (81.8%) | 19 (82.6%) | 0.945 |
Day 7 vs. Day 1 | |||
Temperature, °C | 13 (72.2%) | 12 (54.5%) | 0.332 |
WBC, 109 /L | 16 (84.2%) | 11 (50.0%) | 0.021* |
PCT, ng/mL | 13 (68.4%) | 19 (86.4%) | 0.166 |
Day 10 vs. Day 1 | |||
Temperature, °C | 13 (82.6%) | 12 (70.6%) | 0.688 |
WBC, 109 /L | 9 (56.3%) | 8 (47.1%) | 0.598 |
PCT, ng/mL | 12 (75.0%) | 15 (88.2%) | 0.325 |
Number of patients undergoing effective treatment | |||
Day 3 | 13 (59.1%) | 11 (45.8%) | 0.395 |
Day 7 | 16 (84.2%) | 11 (50.0%) | 0.046* |
Day 10 | 13 (81.3%) | 10 (58.8%) | 0.259 |
Clinical endpoint outcomes | |||
Hospital stay duration, days | 21 (13.7) | 23.5 (17.2) | 0.987 |
28 days mortality | 8 (36.4%) | 8 (33.3%) | 1.000 |
Mechanical ventilation from randomization to 28th day, days | 11.3 (7.7) | 11.5 (7.7) | 0.970 |
Shock from randomization to 28th day, days | 3.1 (4.3) | 2.3 (3.6) | 0.456 |
Numbers of antibiotic-associated diarrhea | 0 (0.0%) | 2 (8.3%) | 0.490 |
For those data are n (%), all p values are calculated using Fisher’s exact tests. For those data are mean (SD), all p values are calculated using Mann-Whitney tests. * indicated P-value <0.05.
Sample ID | Bacteria detected by SSBD grow in CCT tests | Bacteria detected by SSBD could not grow in CCT tests | Probable relations among bacteria |
---|---|---|---|
A05 | K. pneumoniae (III) P. aeruginosa (III) | A. baumannii (III) | K. pneumoniae + P. aeruginosa > A. baumannii |
A09 | A. baumannii (II) | S. aureus (I) | Strength: II > I |
A10 | A. baumannii (III) K. pneumoniae (III) | P. aeruginosa (I) | Strength: III + III > I |
A11 | A. baumannii (III) | K. pneumoniae (I) | Strength: III > I |
A16 | K. pneumoniae (III) | P. aeruginosa (III) | K. pneumoniae > P. aeruginosa |
A21 | A. baumannii (III) S. aureus (I) | K. pneumoniae (III) | Strength: III + I > III |
A22 | A. baumannii (III) | S. epidermidis (III) | A. baumannii > S. epidermidis |
A27 | A. baumannii (III) | S. epidermidis (III) | A. baumannii > S. epidermidis |
A28 | A. baumannii (II) | P. aeruginosa (III) | A. baumannii > P. aeruginosa |
A30 | A. baumannii (III) | S. aureus (III) S. epidermidis (I) | A. baumannii > S. aureus + S. epidermidis |
A33 | S. aureus (I) | S. maltophilia (II) | S. aureus > S. maltophilia |
A36 | A. baumannii (III) | S. maltophilia (I) | A. baumannii > S. maltophilia |
A37 | A. baumannii (III) | S. epidermidis (III) | A. baumannii > S. epidermidis |
A45 | A. baumannii (III) | K. pneumoniae (II) | A. baumannii > K. pneumoniae |
A49 | A. baumannii (III) S. aureus (III) | S. maltophilia (III) | A. baumannii + S. aureus > S. maltophilia |
A55 | A. baumannii (III) | E. coli (II) K. pneumoniae (III) S. maltophilia (III) | A. baumannii > E. coli. coli + K. pneumoniae + S. maltophilia |
A65 | A. baumannii (III) P. aeruginosa (I) | S. maltophilia (II) | Strength: III + I > II |
A68 | A. baumannii (III) | P. aeruginosa (III) | A. baumannii > P. aeruginosa |
A69 | A. baumannii (I) | P. aeruginosa (III) | A. baumannii > P. aeruginosa |
A72 | A. baumannii (III) | S. maltophilia (I) | A. baumannii > S. maltophilia |
A73 | A. baumannii (III) P. aeruginosa (III) | K. pneumoniae (III) | A. baumannii + P. aeruginosa > K. pneumoniae |
A75 | A. baumannii (III) | P. aeruginosa (III) | A. baumannii > P. aeruginosa |
A76 | P. aeruginosa (III) | A. baumannii (I) S. maltophilia (I) | Strength: III > I + I |
B05-1 | A. baumannii (III) | S. maltophilia (II) | A. baumannii > S. maltophilia |
B05-2 | A. baumannii (III) | S. maltophilia (I) | A. baumannii > S. maltophilia |
B09-1 | A. baumannii (III) | S. aureus (III) S. capitis (III) S. maltophilia (III) | A. baumannii > S. aureus + S. capitis + S. maltophilia |
B11-1 | A. baumannii (III) | P. aeruginosa (III) S. maltophilia (II) | A. baumannii > P. aeruginosa + S. maltophilia |
B17-3 | A. baumannii (I) | K. pneumoniae (I) E. faecalis (I) | A. baumannii > K. pneumoniae +E. faecalis |
B19-1 | A. baumannii (III) | P. aeruginosa (I) S. maltophilia (II) | Strength: III >I + II |
B19-2 | A. baumannii (III), S. maltophilia (III) | P. aeruginosa (III) | A. baumannii + S. maltophilia > P. aeruginosa |
B19-3 | K. pneumoniae (III), S. maltophilia (III) | P. aeruginosa (III) | K. pneumoniae + S. maltophilia > P. aeruginosa |
B21-1 | S. aureus (III) S. maltophilia (III) | P. aeruginosa (III) | S. maltophilia + S. aureus > P. aeruginosa |
B21-2 | S. maltophilia (III) | S. aureu (III), P. aeruginosa (III) | S. maltophilia > S. aureus + P. aeruginosa |
B23-1 | S. maltophilia (III) | S. capitis (I) | Strength: III > I |
B31-1 | A. baumannii (III) | S. capitis (III) | A. baumannii > S. capitis |
B39-2 | K. pneumoniae (III) P. aeruginosa (III) | A. baumannii (I) E. coli (I) | Strength: III + III > I+I |
CCT | SSBD | NGS | ||
---|---|---|---|---|
Turnover time | 2–5 days | Less than 4 hours | 2–3 days | |
Cost | Low | Low | High | |
Detection target | Culturable bacteria | Selected targets | All microorganisms in the sample | |
Quantification | Semi | Relative | Semi | |
Instrument requirement | Low | Low | High |
Epidemic data of pathogens in the ICU of Nanjing Drum Tower Hospital in 2017.
The test of SSBD with or without DNA purification.
The test of SSBD with different incubation times.
The validation of SSBD with clinical strains.
Classification of antibiotic coverage for each test in two groups.