Table 1.
The analytical performance of mNGS in the diagnosis of respiratory tract infections.
| Study | Platform | Confirmatory tests | Samples | Sequencing | Sensitivity (%) | Specificity (%) | Concordance (%) | PPV (%) |
NPV (%) |
|---|---|---|---|---|---|---|---|---|---|
| Langelier C et al. [9] | Illumina HiSeq 4000 | Clinical microbiologic testing | 92 TA samples | RNA and DNA based mNGS | 100 | 87.5 | NA | NA | 100 (In the validation cohort) |
| Charalampous T et al. [3] | MinION | qPCR | 81 Respiratory samples (sputum, endotracheal secretions and ETAs) | DNA based mNGS | 96.6 | 41.7 | NA | NA | NA |
| Wang J et al. [7] | NA | Conventional tests (smear, culture, pathology, GM test, Xpert MTB) | 55 Pulmonary biopsy and BALFs | DNA based mNGS | 97.2 | 63.2 | 39.9 | 83.3 | 92.3 |
| van Rijn AL et al. [71] | Illumina NextSeq 500 | qPCR | 88 Nasopharyngeal samples | RNA and DNA based mNGS | 96 | 100 | NA | 82 | 100 |
| Li H et al. [5] | BGISEQ-500 | Culture | 20 Lung biopsy tissues | DNA based mNGS | Bacteria :100.0 Fungi: 57.1 |
Bacteria:76.5 Fungi :61.5 |
NA | Bacteria:42.9 Fungi:44.4 |
Bacteria:100 Fungi:72.7 |
| Huang J et al. [54] | BGISEQ-100 | Culture, microscopic examination | 240 Samples (lung tissue, BALF, and PSB) | DNA based mNGS | 88.3 | 81.16 | N | 92.07 | 73.68 |
| Shi CL et al. [13] | Illumina NextSeq CN500 | Xpert, culture, and AFS | 110 BALFs | DNA based mNGS | 47.92 | 98.39 | N | N | N |
| van Boheemen S et al. [19] | Illumina HiSeq 4000 and NextSeq 500 | qPCR | 19 Nasopharyngeal washings, 2 sputa, 2 BALF, 1 bronchial washing and 1 throat swab | RNA based mNGS | 83 | 94 | N | N | N |
| Li Y et al. [72] | BGISEQ-50 | Culture | 35 BALFs | DNA based mNGS | 88.89 | 74.07 | 77.78 | 53.33 | 95.24 |
| Smear and PCR | 77.78 | 70.00 | 73.68 | 70 | 77.78 |
Abbreviations: AFS, acid-fast stain; BALF, broncho-alveolar lavage fluid; NA, no accessible; NPV, negative predict value; PPV, positive predict value; PSB, protected specimen brushes; TA, tracheal aspirate.