| Species . | Sequencer . | Core Genes . | Soft-Core Genes . | Shell Genes . | Cloud Genes . | Total Genes, No. . |
|---|---|---|---|---|---|---|
| Enterococcus faecium | Illumina | 1706 (27.5) | 288 (4.6) | 1425 (22.9) | 2795 (45.0) | 6214 |
| ONT | 1529 (8.5) | 387 (2.1) | 3339 (18.5) | 12 793 (70.9) | 18 048 | |
| Hybrid | 1696 (11.82) | 300 (2.09) | 2018 (14.06) | 10 337 (72.03) | 14 351 | |
| Staphylococcus aureus | Illumina | 2117 (27.1) | 55 (0.7) | 842 (10.8) | 4802 (61.4) | 7816 |
| ONT | 2039 (27.5) | 90 (1.2) | 1013 (13.7) | 4278 (57.7) | 7420 | |
| Hybrid | 2115 (36.47) | 45 (0.78) | 884 (15.24) | 2755 (47.51) | 5799 | |
| Klebsiella pneumoniae | Illumina | 978 (2.6) | 3097 (8.1) | 2139 (5.6) | 31 974 (83.7) | 38 188 |
| ONT | 1888 (2.3) | 1548 (1.9) | 7702 (9.3) | 72 109 (86.6) | 83 247 | |
| Hybrid | 3201 (7.24) | 944 (2.14) | 2287 (5.17) | 37 764 (85.45) | 44 196 | |
| Acinetobacter baumannii | Illumina | 1904 (11.7) | 763 (4.7) | 1651 (10.2) | 11 925 (73.4) | 16 243 |
| ONT | 2038 (5.74) | 580 (1.63) | 2999 (8.45) | 29 859 (84.17) | 35 476 | |
| Hybrid | 2494 (13.9) | 290 (1.6) | 1675 (9.3) | 13 499 (75.2) | 17 958 | |
| Pseudomonas aeruginosa | Illumina | 53 (0.1) | 4981 (13.2) | 2177 (5.8) | 30 447 (80.9) | 37 658 |
| ONT | 150 (0.3) | 3953 (8.2) | 4331 (9.0) | 39 748 (82.5) | 48 182 | |
| Hybrid | 256 (0.77) | 4901 (14.75) | 2209 (6.65) | 25 859 (77.83) | 33 225 | |
| Enterobacter cloacae | Illumina | 1004 (2.8) | 1947 (5.5) | 2900 (8.2) | 29 676 (83.5) | 35 527 |
| ONT | 1719 (2.4) | 737 (1.0) | 5020 (7.1) | 62 938 (89.4) | 70 414 | |
| Hybrid | 2556 (6.4) | 621 (1.6) | 2767 (6.9) | 33 686 (85.0) | 39 630 |
| Species . | Sequencer . | Core Genes . | Soft-Core Genes . | Shell Genes . | Cloud Genes . | Total Genes, No. . |
|---|---|---|---|---|---|---|
| Enterococcus faecium | Illumina | 1706 (27.5) | 288 (4.6) | 1425 (22.9) | 2795 (45.0) | 6214 |
| ONT | 1529 (8.5) | 387 (2.1) | 3339 (18.5) | 12 793 (70.9) | 18 048 | |
| Hybrid | 1696 (11.82) | 300 (2.09) | 2018 (14.06) | 10 337 (72.03) | 14 351 | |
| Staphylococcus aureus | Illumina | 2117 (27.1) | 55 (0.7) | 842 (10.8) | 4802 (61.4) | 7816 |
| ONT | 2039 (27.5) | 90 (1.2) | 1013 (13.7) | 4278 (57.7) | 7420 | |
| Hybrid | 2115 (36.47) | 45 (0.78) | 884 (15.24) | 2755 (47.51) | 5799 | |
| Klebsiella pneumoniae | Illumina | 978 (2.6) | 3097 (8.1) | 2139 (5.6) | 31 974 (83.7) | 38 188 |
| ONT | 1888 (2.3) | 1548 (1.9) | 7702 (9.3) | 72 109 (86.6) | 83 247 | |
| Hybrid | 3201 (7.24) | 944 (2.14) | 2287 (5.17) | 37 764 (85.45) | 44 196 | |
| Acinetobacter baumannii | Illumina | 1904 (11.7) | 763 (4.7) | 1651 (10.2) | 11 925 (73.4) | 16 243 |
| ONT | 2038 (5.74) | 580 (1.63) | 2999 (8.45) | 29 859 (84.17) | 35 476 | |
| Hybrid | 2494 (13.9) | 290 (1.6) | 1675 (9.3) | 13 499 (75.2) | 17 958 | |
| Pseudomonas aeruginosa | Illumina | 53 (0.1) | 4981 (13.2) | 2177 (5.8) | 30 447 (80.9) | 37 658 |
| ONT | 150 (0.3) | 3953 (8.2) | 4331 (9.0) | 39 748 (82.5) | 48 182 | |
| Hybrid | 256 (0.77) | 4901 (14.75) | 2209 (6.65) | 25 859 (77.83) | 33 225 | |
| Enterobacter cloacae | Illumina | 1004 (2.8) | 1947 (5.5) | 2900 (8.2) | 29 676 (83.5) | 35 527 |
| ONT | 1719 (2.4) | 737 (1.0) | 5020 (7.1) | 62 938 (89.4) | 70 414 | |
| Hybrid | 2556 (6.4) | 621 (1.6) | 2767 (6.9) | 33 686 (85.0) | 39 630 |
Data are presented as No. (%) unless otherwise indicated.
Abbreviation: ONT, Oxford Nanopore Technologies.
| Species . | Sequencer . | Core Genes . | Soft-Core Genes . | Shell Genes . | Cloud Genes . | Total Genes, No. . |
|---|---|---|---|---|---|---|
| Enterococcus faecium | Illumina | 1706 (27.5) | 288 (4.6) | 1425 (22.9) | 2795 (45.0) | 6214 |
| ONT | 1529 (8.5) | 387 (2.1) | 3339 (18.5) | 12 793 (70.9) | 18 048 | |
| Hybrid | 1696 (11.82) | 300 (2.09) | 2018 (14.06) | 10 337 (72.03) | 14 351 | |
| Staphylococcus aureus | Illumina | 2117 (27.1) | 55 (0.7) | 842 (10.8) | 4802 (61.4) | 7816 |
| ONT | 2039 (27.5) | 90 (1.2) | 1013 (13.7) | 4278 (57.7) | 7420 | |
| Hybrid | 2115 (36.47) | 45 (0.78) | 884 (15.24) | 2755 (47.51) | 5799 | |
| Klebsiella pneumoniae | Illumina | 978 (2.6) | 3097 (8.1) | 2139 (5.6) | 31 974 (83.7) | 38 188 |
| ONT | 1888 (2.3) | 1548 (1.9) | 7702 (9.3) | 72 109 (86.6) | 83 247 | |
| Hybrid | 3201 (7.24) | 944 (2.14) | 2287 (5.17) | 37 764 (85.45) | 44 196 | |
| Acinetobacter baumannii | Illumina | 1904 (11.7) | 763 (4.7) | 1651 (10.2) | 11 925 (73.4) | 16 243 |
| ONT | 2038 (5.74) | 580 (1.63) | 2999 (8.45) | 29 859 (84.17) | 35 476 | |
| Hybrid | 2494 (13.9) | 290 (1.6) | 1675 (9.3) | 13 499 (75.2) | 17 958 | |
| Pseudomonas aeruginosa | Illumina | 53 (0.1) | 4981 (13.2) | 2177 (5.8) | 30 447 (80.9) | 37 658 |
| ONT | 150 (0.3) | 3953 (8.2) | 4331 (9.0) | 39 748 (82.5) | 48 182 | |
| Hybrid | 256 (0.77) | 4901 (14.75) | 2209 (6.65) | 25 859 (77.83) | 33 225 | |
| Enterobacter cloacae | Illumina | 1004 (2.8) | 1947 (5.5) | 2900 (8.2) | 29 676 (83.5) | 35 527 |
| ONT | 1719 (2.4) | 737 (1.0) | 5020 (7.1) | 62 938 (89.4) | 70 414 | |
| Hybrid | 2556 (6.4) | 621 (1.6) | 2767 (6.9) | 33 686 (85.0) | 39 630 |
| Species . | Sequencer . | Core Genes . | Soft-Core Genes . | Shell Genes . | Cloud Genes . | Total Genes, No. . |
|---|---|---|---|---|---|---|
| Enterococcus faecium | Illumina | 1706 (27.5) | 288 (4.6) | 1425 (22.9) | 2795 (45.0) | 6214 |
| ONT | 1529 (8.5) | 387 (2.1) | 3339 (18.5) | 12 793 (70.9) | 18 048 | |
| Hybrid | 1696 (11.82) | 300 (2.09) | 2018 (14.06) | 10 337 (72.03) | 14 351 | |
| Staphylococcus aureus | Illumina | 2117 (27.1) | 55 (0.7) | 842 (10.8) | 4802 (61.4) | 7816 |
| ONT | 2039 (27.5) | 90 (1.2) | 1013 (13.7) | 4278 (57.7) | 7420 | |
| Hybrid | 2115 (36.47) | 45 (0.78) | 884 (15.24) | 2755 (47.51) | 5799 | |
| Klebsiella pneumoniae | Illumina | 978 (2.6) | 3097 (8.1) | 2139 (5.6) | 31 974 (83.7) | 38 188 |
| ONT | 1888 (2.3) | 1548 (1.9) | 7702 (9.3) | 72 109 (86.6) | 83 247 | |
| Hybrid | 3201 (7.24) | 944 (2.14) | 2287 (5.17) | 37 764 (85.45) | 44 196 | |
| Acinetobacter baumannii | Illumina | 1904 (11.7) | 763 (4.7) | 1651 (10.2) | 11 925 (73.4) | 16 243 |
| ONT | 2038 (5.74) | 580 (1.63) | 2999 (8.45) | 29 859 (84.17) | 35 476 | |
| Hybrid | 2494 (13.9) | 290 (1.6) | 1675 (9.3) | 13 499 (75.2) | 17 958 | |
| Pseudomonas aeruginosa | Illumina | 53 (0.1) | 4981 (13.2) | 2177 (5.8) | 30 447 (80.9) | 37 658 |
| ONT | 150 (0.3) | 3953 (8.2) | 4331 (9.0) | 39 748 (82.5) | 48 182 | |
| Hybrid | 256 (0.77) | 4901 (14.75) | 2209 (6.65) | 25 859 (77.83) | 33 225 | |
| Enterobacter cloacae | Illumina | 1004 (2.8) | 1947 (5.5) | 2900 (8.2) | 29 676 (83.5) | 35 527 |
| ONT | 1719 (2.4) | 737 (1.0) | 5020 (7.1) | 62 938 (89.4) | 70 414 | |
| Hybrid | 2556 (6.4) | 621 (1.6) | 2767 (6.9) | 33 686 (85.0) | 39 630 |
Data are presented as No. (%) unless otherwise indicated.
Abbreviation: ONT, Oxford Nanopore Technologies.
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