TABLE 4.
Diagnostic efficacy of 11 indicators in mNGS of eight pathogens.
| Pathogens | Different index | AUC | Cut-off value | Sensitivity | Specificity | PPV | NPV |
|---|---|---|---|---|---|---|---|
| A. baumannii | Raw reads | 0.920 | 187 | 0.844 | 0.905 | 0.443 | 0.985 |
| 10M normalize reads | 0.919 | 141 | 0.844 | 0.888 | 0.403 | 0.984 | |
| Double discard reads | 0.938 | 78 | 0.871 | 0.938 | 0.557 | 0.988 | |
| RPM | 0.939 | 11326.63 | 0.844 | 0.958 | 0.643 | 0.986 | |
| TPM | 0.929 | 1312.836 | 0.844 | 0.924 | 0.499 | 0.985 | |
| Coverage | 0.542 | 16.059 | 0.25 | 1 | 1.000 | 0.937 | |
| In Genus Rank | 0.836 | 1.5 | 0.935 | 0.741 | 0.244 | 0.992 | |
| Genus Rank Ratio | 0.942 | 0.236 | 0.938 | 0.896 | 0.447 | 0.994 | |
| King Genus Rank Ratio | 0.941 | 0.268 | 0.969 | 0.873 | 0.406 | 0.997 | |
| Genus Rank Ratio*in Genus Rank | 0.945 | 0.273 | 0.938 | 0.904 | 0.467 | 0.994 | |
| King Genus Rank Ratio*in Genus Rank | 0.944 | 0.267 | 0.938 | 0.918 | 0.506 | 0.994 | |
| K. pneumoniae | Raw reads | 0.978 | 296.5 | 0.886 | 0.971 | 0.687 | 0.992 |
| 10M normalize reads | 0.973 | 120.5 | 0.914 | 0.936 | 0.506 | 0.993 | |
| Double discard reads | 0.938 | 112.5 | 0.857 | 0.953 | 0.567 | 0.989 | |
| RPM | 0.915 | 1571.132 | 0.914 | 0.809 | 0.256 | 0.992 | |
| TPM | 0.916 | 403.752 | 0.943 | 0.809 | 0.262 | 0.995 | |
| Coverage | 0.461 | 1.016 | 0.086 | 1 | 1.000 | 0.938 | |
| In Genus Rank | 0.728 | 1.5 | 0.943 | 0.514 | 0.122 | 0.992 | |
| Genus Rank Ratio | 0.931 | 0.169 | 0.886 | 0.953 | 0.575 | 0.991 | |
| King Genus Rank Ratio | 0.931 | 0.201 | 0.914 | 0.936 | 0.506 | 0.993 | |
| Genus Rank Ratio*in Genus Rank | 0.941 | 0.169 | 0.886 | 0.971 | 0.687 | 0.992 | |
| King Genus Rank Ratio*in Genus Rank | 0.941 | 0.201 | 0.914 | 0.955 | 0.593 | 0.994 | |
| S. pneumoniae | Raw reads | 0.921 | 577.5 | 0.818 | 0.872 | 0.239 | 0.990 |
| 10M normalize reads | 0.915 | 512 | 0.818 | 0.868 | 0.234 | 0.990 | |
| Double discard reads | 0.997 | 18.5 | 1.000 | 0.975 | 0.663 | 1.000 | |
| RPM | 0.984 | 10.923 | 1.000 | 0.890 | 0.309 | 1.000 | |
| TPM | 0.986 | 22.009 | 1.000 | 0.897 | 0.323 | 1.000 | |
| Coverage | 0.506 | 5.312 | 0.227 | 1.000 | 1.000 | 0.963 | |
| In Genus Rank | 0.973 | 3.5 | 1.000 | 0.913 | 0.361 | 1.000 | |
| Genus Rank Ratio | 0.795 | 0.049 | 0.818 | 0.729 | 0.129 | 0.988 | |
| King Genus Rank Ratio | 0.780 | 0.06 | 0.864 | 0.691 | 0.121 | 0.990 | |
| Genus Rank Ratio*in Genus Rank | 0.997 | 0.352 | 1.000 | 0.955 | 0.522 | 1.000 | |
| King Genus Rank Ratio*in Genus Rank | 0.997 | 0.305 | 1.000 | 0.962 | 0.564 | 1.000 | |
| S. aureus | Raw reads | 0.952 | 15.5 | 0.952 | 0.803 | 0.211 | 0.997 |
| 10M normalize reads | 0.947 | 115.5 | 0.762 | 0.979 | 0.667 | 0.987 | |
| Double discard reads | 0.961 | 31 | 0.810 | 0.974 | 0.633 | 0.989 | |
| RPM | 0.964 | 2132.809 | 0.905 | 0.942 | 0.463 | 0.994 | |
| TPM | 0.966 | 806.17 | 0.905 | 0.918 | 0.379 | 0.994 | |
| Coverage | 0.5 | 0.051 | 0.143 | 0.971 | 0.214 | 0.953 | |
| In Genus Rank | 0.896 | 1.5 | 0.905 | 0.823 | 0.220 | 0.994 | |
| Genus Rank Ratio | 0.892 | 0.342 | 0.952 | 0.700 | 0.149 | 0.996 | |
| King Genus Rank Ratio | 0.895 | 0.314 | 0.905 | 0.747 | 0.165 | 0.993 | |
| Genus Rank Ratio*in Genus Rank | 0.965 | 0.343 | 0.905 | 0.934 | 0.431 | 0.994 | |
| King Genus Rank Ratio*in Genus Rank | 0.966 | 0.361 | 0.905 | 0.932 | 0.424 | 0.994 | |
| H. influenzae | Raw reads | 0.923 | 324.5 | 0.724 | 0.960 | 0.676 | 0.968 |
| 10M normalize reads | 0.936 | 97.5 | 0.828 | 0.865 | 0.414 | 0.978 | |
| Double discard reads | 0.983 | 19.5 | 1.000 | 0.892 | 0.516 | 1.000 | |
| RPM | 0.992 | 3646.02 | 1.000 | 0.948 | 0.689 | 1.000 | |
| TPM | 0.986 | 2062.13 | 1.000 | 0.905 | 0.548 | 1.000 | |
| Coverage | 0.709 | 0.055 | 0.621 | 0.786 | 0.250 | 0.947 | |
| In Genus Rank | 0.900 | 1.5 | 1.000 | 0.801 | 0.366 | 1.000 | |
| Genus Rank Ratio | 0.938 | 0.137 | 0.862 | 0.893 | 0.481 | 0.983 | |
| King Genus Rank Ratio | 0.936 | 0.12 | 0.828 | 0.925 | 0.560 | 0.979 | |
| Genus Rank Ratio*in Genus Rank | 0.992 | 0.3 | 0.966 | 0.948 | 0.681 | 0.996 | |
| King Genus Rank Ratio*in Genus Rank | 0.992 | 0.268 | 0.966 | 0.972 | 0.799 | 0.996 | |
| S. maltophilia | Raw reads | 0.974 | 175.5 | 0.909 | 0.952 | 0.636 | 0.991 |
| 10M normalize reads | 0.969 | 139.5 | 0.909 | 0.950 | 0.627 | 0.991 | |
| Double discard reads | 0.981 | 120 | 0.909 | 0.966 | 0.712 | 0.991 | |
| RPM | 0.987 | 4996.882 | 1.000 | 0.919 | 0.533 | 1.000 | |
| TPM | 0.966 | 661.789 | 0.939 | 0.863 | 0.388 | 0.994 | |
| Coverage | 0.41 | 0.206 | 0.061 | 0.994 | 0.484 | 0.920 | |
| In Genus Rank | 0.773 | 51 | 1.000 | 0.579 | 0.180 | 1.000 | |
| Genus Rank Ratio | 0.988 | 0.232 | 0.970 | 0.936 | 0.584 | 0.997 | |
| King Genus Rank Ratio | 0.988 | 0.274 | 1.000 | 0.927 | 0.559 | 1.000 | |
| Genus Rank Ratio*in Genus Rank | 0.985 | 0.309 | 1.000 | 0.882 | 0.439 | 1.000 | |
| King Genus Rank Ratio*in Genus Rank | 0.985 | 0.275 | 0.970 | 0.927 | 0.551 | 0.997 | |
| P. aeruginosa | Raw reads | 0.974 | 293.5 | 0.939 | 0.894 | 0.455 | 0.994 |
| 10M normalize reads | 0.968 | 242.5 | 0.939 | 0.891 | 0.448 | 0.994 | |
| Double discard reads | 0.984 | 86.5 | 0.970 | 0.905 | 0.490 | 0.997 | |
| RPM | 0.943 | 24694.8 | 0.818 | 0.949 | 0.602 | 0.982 | |
| TPM | 0.945 | 3300.692 | 0.848 | 0.911 | 0.473 | 0.985 | |
| Coverage | 0.553 | 0.084 | 0.364 | 0.966 | 0.502 | 0.942 | |
| In Genus Rank | 0.758 | 1.5 | 1.000 | 0.516 | 0.163 | 1.000 | |
| Genus Rank Ratio | 0.937 | 0.159 | 0.909 | 0.814 | 0.315 | 0.990 | |
| King Genus Rank Ratio | 0.928 | 0.202 | 0.939 | 0.743 | 0.256 | 0.992 | |
| Genus Rank Ratio*in Genus Rank | 0.962 | 0.224 | 1.000 | 0.806 | 0.327 | 1.000 | |
| King Genus Rank Ratio*in Genus Rank | 0.955 | 0.269 | 1.000 | 0.774 | 0.294 | 1.000 | |
| A. fumigatus | Raw reads | 0.992 | 34.5 | 1.000 | 0.964 | 0.588 | 1.000 |
| 10M normalize reads | 0.991 | 29.5 | 1.000 | 0.960 | 0.563 | 1.000 | |
| Double discard reads | 0.992 | 29.5 | 1.000 | 0.968 | 0.616 | 1.000 | |
| RPM | 0.969 | 566.965 | 1.000 | 0.857 | 0.265 | 1.000 | |
| TPM | 0.984 | 93.432 | 1.000 | 0.924 | 0.404 | 1.000 | |
| Coverage | 0.601 | 0.023 | 0.222 | 0.998 | 0.851 | 0.961 | |
| In Genus Rank | 0.818 | 2.5 | 1.000 | 0.616 | 0.118 | 1.000 | |
| Genus Rank Ratio | 0.981 | 0.304 | 1.000 | 0.926 | 0.410 | 1.000 | |
| King Genus Rank Ratio | 0.905 | 0.348 | 0.815 | 0.905 | 0.306 | 0.990 | |
| Genus Rank Ratio*in Genus Rank | 0.989 | 0.303 | 1.000 | 0.971 | 0.639 | 1.000 | |
| King Genus Rank Ratio*in Genus Rank | 0.964 | 0.709 | 0.963 | 0.869 | 0.274 | 0.998 |