Table 2.
Examples of the potential impact of clinical shotgun metagenomics (2019–2022) on infectious disease diagnosis.
| Study details | Type of the study (n = subjects) | Samples and target population | Sequencing platform | Main findings |
|---|---|---|---|---|
| Respiratory infections | ||||
| Chen H. et al. (2020) | Prospective, observational study (n = 93) | Bronchoalveolar lavage fluid from patients with lower respiratory tract infections | Illumina Nextseq 550 | The detection rate of mNGS for causative pathogen of lower respiratory infection was significantly higher (65% vs. 20%) than traditional culture method. |
| Li et al. (2020) | Prospective study (n = 121) | Lung biopsies from patients with peripheral pulmonary lesions and lung infection | BGISEQ-50 | The percentage of mNGS-positive samples in radial endobronchial ultrasound (R-EBUS)-guided transbronchial lung biopsy (TBLB) was 78.8% that was significantly greater than TBLB (60.0%). |
| Zhou et al. (2021) | Multi-center, prospective, observational study (n = 159) | Bronchoalveolar lavage fluid from patients with pulmonary infections | Illumina NextSeq 550 | mNGS detected more organisms (117 vs. 72) when compared with standard methods including bacteria (89 vs. 54), viruses (10 vs. 3), and fungi (18 vs. 15). Importantly, the bacteria known to cause pneumonia was detected only by mNGS that included Haemophilus influenzae, Legionella pneumoniae, Mycobacterium avium, Mycobacteroides abscessus, Chlamydia psittaci, and Actinomyces species. mNGS also led to the treatment modification for 59 patients. |
| Azar et al. (2021) | Prospective, observational study, (n = 30) | Bronchoalveolar lavage fluid from immunocompromised adults with pneumonia | Illumina NextSeq500 or NextSeq550 | A combination of mNGS and conventional testing improved the diagnostic rate of pneumonia from 35% to 58%. |
| Chen S. et al. (2021) | Single center, retrospective, observation study (n = 408) | Blood, sputum, urine and bronchoalveolar lavage fluid from COVID-19 patients | BGISEQ-50 | mNGS showed positive detection rate of 92.3% in bronchoalveolar lavage and 66.7% in sputum. Overall, mNGS results were comparable with conventional culture. |
| Chen Y. et al. (2021) | Retrospective study (n = 90) | Bronchoalveolar lavage fluid, transbronchial brushing from patients with focal pulmonary infections | Illumina Nextseq 550 | The analysis of patients with focal pulmonary infections revealed sensitivity of mNGS in bronchoalveolar lavage fluid, transbrochial brushing group, and pathological specimen was 50%, 66.7%, and 90%, respectively. |
| Deng et al. (2022) | Retrospective, observational study (n = 103) | Bronchoalveolar lavage fluid from children with pneumonia | Illumina NextSeq CN500 sequencer | Out of 52 monomicrobial and 44 polymicrobial cases, mNGS detected 48 and 29 cases, respectively. Overall, the pathogen detection rate of mNGS was higher than conventional detection methods. |
| Zhang et al. (2022) | Retrospective, observational study (n = 47) | Bronchoalveolar lavage fluid from patients with lower respiratory tract infections | MGISEQ-2000 | As compared to conventional culturing, mNGS increased the detection rate for causative pathogens of lower respiratory tract infections with a diagnostic sensitivity of 80% and specificity of 35.13%. |
| Xu et al. (2022) | Retrospective, observational study (n = 35) | Alveolar lavage fluid or venous blood from patients with severe psittacosis pneumonia | DA8600 | mNGS detected DNA of chlamydia psittaci in alveolar lavage fluid of 30 patients and blood of 5 patients. |
| Pollock et al. (2021) | Single-center, proof-of-concept study (n = 30) | Plasma samples from patients with pulmonary tuberculosis | Illumina NextSeq 550 | Mycobacterium tuberculosis cell-free DNA was detected from the plasma of 50% of pediatric and 60% of adult patients. Furthermore, it was also detected in an additional 25% of pediatric and 40% of adult patients when the relaxed research use statistical threshold was applied. |
| Mu et al. (2021) | Single-center, prospective study (n = 292) | Bronchoalveolar lavage fluid and sputum from patients with different kinds of lower respiratory tract infections | Nanopore | Compared with conventional testing, mNGS showed 96.6% sensitivity and 80% specificity and detected pathogens in 63 out of 161 culture-negative cases. Furthermore, mNGS proposed antibiotic de-escalation for 34 patients. |
| Li et al. (2022) | Single-center, prospective study (n = 138) | Bronchoalveolar lavage fluid from patients with pulmonary infections | Illumina Miniseq | mNGS improved diagnosis by detecting more pathogens such as bacteria (53 vs. 27) and viruses (16 vs. 1) than conventional methods. Importantly, mNGS led to the treatment modification for 34 out of 138 patients. |
| Guo et al. (2022) | Single-center, retrospective study (n = 121) | Bronchoalveolar lavage fluid from children with community-acquired pneumonia | Illumina Novaseq | The causative pathogens of pneumonia were only detected by mNGS. These organisms included Streptococcus pneumoniae, Mycoplasma pneumoniae, Haemophilus influenza, Human bocavirus 1, and Mycobacterium tuberculosis. Moreover, mNGS identified 50% of human bocavirus-infected cases which were co-infected with other bacteria of respiratory origin. |
| Bloodstream infections | ||||
| Hogan et al. (2021) | Multicenter, retrospective study (n = 82) | Plasma samples from patients with suspicion of several infections | Illumina | The positivity rate for Karius-based mNGS was 61.0%. Of which 50% of cases were detected with monomicrobial infections and 50% of them were infected with 2 or more organisms. Overall, Karius-based mNGS showed a positive impact on 7.3% of cases, a negative impact on 3.7% of cases, and showed no impact on 86.6% of cases. |
| Blauwkamp et al. (2019) | Prospective study (n = 350) | Plasma samples from patients with clinical suspicion of sepsis | Illumina NextSeq 500 | In contrast to culture, mNGS identified much more bacteria. 62 out of 166 samples were negative by traditional testing but sequencing identified these microorganisms in cell-free DNA. |
| Kalantar et al. (2022) | Prospective study (n = 221) | Blood and plasma from critically ill patients | Illumina Novaseq 6000 | The pathogen detection in plasma by mNGS and traditional testing varied by organism. For example, mNGS showed 100% sensitivity for Staphylococcus aureus and Escherichia coli. However, mNGS missed the detection of Streptococcus pyogenes. Furthermore, the findings suggest that detection of a pathogen alone is not sufficient for sepsis diagnosis, instead when combined with hosts transcriptional profiling it may provide promising diagnostic utility. |
| Wang et al. (2022) | Retrospective, observational study (n = 435) | Blood, tissues, urine, sputum and different types of body fluids from patients with clinical suspicion of infections | Illumina NextSeq CN500 sequencer | The overall sensitivity of mNGS results were significantly higher than traditional methods. However, there was no difference in specificity of two methods. The sensitivity of mNGS for bronchoalveolar lavage fluid was 72.6% that was higher than blood that showed mNGS sensitivity of 39.3%. |
| Liu et al. (2021) | Prospective study (n = 24) | Blood samples from patients with hematological malignancies and sepsis | MGISEQ-200 | The pathogen detection rate of mNGS was comparable with conventional testing for 9 out of 24 patients. However, for 10 patients, mNGS identified additional pathogens as compared to traditional methods most of the identified pathogens were viruses. |
| Jing et al. (2021) | Retrospective study (n = 209) | Blood samples from patients with suspected bloodstream infections | Illumina NextSeq 550 | mNGS of plasma improved the clinical sensitivity (87.1%) and specificity (80.2%) as compared to conventional testing. |
| Fu et al. (2022) | Single center, retrospective study (n = 175) | Blood samples from patients with fever of unknown origin | BGISEQ-2000 | mNGS increased the detection rate of new organisms in patients with fever of unknown origin by 22.9 and 19.79% than culture and standard detection methods, respectively. Specifically, it improved the detection rate of bloodstream infections by 38 and 32% respectively, as compared to culture and conventional testing. |
| Central nervous system infections | ||||
| Wilson et al. (2019) | Multicenter, prospective study (n = 204) | Severely ill pediatric and adult patients admitted to the intensive care unit | Illumina Hiseq | mNGS improved diagnosis over traditional methods of neurologic infections by identifying 22% (13 out of 58) of unique pathogens that were missed by clinical testing. The identification of these pathogens led to the treatment modification of 50% (7 out of 13) of these patients. |
| Miller et al. (2019) | Development and prospective study (n = 115) | CSF samples from patients with meningitis and/or encephalitis and patients with suspected neurological infections | Illumina Hiseq and Illumina MiSeq | For 95 samples, mNGS revealed 73% sensitivity and 99% specificity as compared to conventional testing. Moreover, for 20 CSF samples collected from pediatric patients 92% sensitivity and 96% specificity was observed relative to microbiological testing of CSF. |
| Hasan et al. (2020) | Retrospective study (n = 83) | Hospitalized children with suspected CNS infections | Illumina Miseq | In contrast to conventional methods, mNGS showed 100% diagnostic accuracy, 95% sensitivity, and 96% specificity for cerebrospinal fluid samples for hospitalized patients. |
| Morsli et al. (2022b) | Prospective and proof-of-concept study (n = 52) | Patients with community-acquired meningitis | MinION | Out of 52 subjects enrolled, 47 patients showed positive results on CSF samples via routine diagnostics and MinION sequencer. However, in addition to pathogen detection MinION sequencer provided additional information about genotype and antibiotic susceptibility of pathogens. |
| Haston et al. (2020) | Prospective study (n = 20) | Children with encephalitis of unidentified etiology | Illumina Miseq or NextSeq 500 | mNGS detected sequence reads of pathogens such as Mycoplasma bovis, Neisseria meningitidis, parvovirus B19, and Balamuthia mandrillaris in 6 out of 20 patients. Furthermore, mNGS also detected some nonpathogenic organisms such as Cladophialophora species, human bocavirus, and tobacco mosaic virus. The patients with detectable pathogens via mNGS presented immune-mediated phenomena than patients for whom mNGS did not make any diagnosis. |
| Chen et al. (2021b) | Retrospective study (n = 88) | Patients suspected of encephalitis and meningitis | BGISEQ-50 and MGISEQ-2000 | mNGS of cerebrospinal fluid detected pathogens in 56.81% (50 out of 88) of patients. The outcomes of mNGS helped in the treatment modification for 23.9% of patients and provided confidence in the continuation of original treatment for 34.1% of patients. |
We used predefined filters to refine PubMed search on “classical article,” “clinical study,” “observational study,” “randomized controlled trial,” and “validation study” from 2019 to 2023. We included only retrospective or prospective clinical studies focusing on hospitalized patients using shotgun metagenomics. We have used the keys words “metagenomics AND respiratory infections” for respiratory diseases. Similarly, “metagenomics AND blood infections” and “metagenomics AND central nervous system infections” for blood stream infections and central nervous system infections, respectively. We also search these same terms in google scholar search and added clinical studies and studies focusing on hospitalized patients using shotgun metagenomics not found in PubMed.