Table 1.
Clinical studies related to dynamic respiratory microbiota in patients with invasive MV based on NGS analysis of respiratory tract samples
| Study design | Duration | Region (country) | Patients groups/numbers | Age (years) | Antibiotics | Samples from | Targets | Sequencing platform | Conclusion regarding to microbiota change during invasive MV | Study |
|---|---|---|---|---|---|---|---|---|---|---|
| NA | NA | America (USA) | Invasive MV patients (15) | ≥ 18 | Yes for all patients | Oropharynx and trachea | 16S rRNA | MiSeq (Illumina) | Diminished bacterial diversity in the two kinds of samples from patients with invasive MV | Kelly et al. [22] |
| Post hoc analysis | Sep. 2008–Sep. 2010 | Europe (mainly Spain) | Invasive MV with VAP (11); Invasive MV without VAP (18) | ≥ 18 | Yes for all patients | Trachea | 16S rRNA | 454 GS FLX + (Roche) | Diminished bacterial diversity in invasive MV patients | Zakharkina et al. [23] |
| Prospective | Dec. 2015–Nov. 2016 | Europe (Switzerland) | Invasive MV with VAP (5); Invasive MV without VAP (5) | ≥ 18 | Yes for 8 patients | Oropharynx and trachea | 16S rRNA | MiSeq (Illumina) | No significant change | Sommerstein et al. [24] |
| Prospective case control | Oct. 2012–Mar. 2014 | Europe (Switzerland) | Invasive MV with VAP (18); Invasive MV without VAP (36) | ≥ 18 | Yes for virtually all patients | Oropharynx and trachea | 16S rRNA | MiSeq (Illumina) | Diminished bacterial diversity in invasive MV patients | Emonet et al. [25] |
| Prospective | Jul. 2017–Aug. 2018 | Asia (Korea) | Invasive MV with pneumonia (41); Invasive MV without pneumonia (19) | ≥ 18 | Yes for most patients | Trachea | 16S rRNA | MiSeq (Illumina) | Diminished bacterial diversity in invasive MV patients with pneumonia; No relevant result reported in invasive MV patients without pneumonia | Woo et al. [26] |
| Prospective | Aug. 2014–Aug. 2018 | America (USA) | Invasive MV with oral suctioning intervention (9); invasive MV without oral suctioning intervention (7) | ≥ 18 | Yes for most patients (14/16) | Oropharynx and trachea | 16S rRNA | MiSeq (Illumina) | Diminished bacterial diversity in invasive MV patients | Sole et al. [27] |
| Prospective | As of Jul. 2020 | America (USA) | Invasive MV COVID-19 with VAP (16); Invasive MV COVID-19 without VAP (17) | ≥ 18 | Yes for all patients | Trachea | Total RNA with human cytosolic and mitochondrial ribosomal RNA depleted | NovaSeq 6000 (Illumina) | Diminished bacterial diversity in invasive MV COVID-19 patients | Tsitsiklis et al. [28] |
| Post hoc analysis | November 2015-November 2016 | Germany | 30 patients in two groups were enrolled in the study: 15 patients with sepsis-induced ARDS following major abdominal surgery and 15 patients undergoing esophageal resection (serving as controls) | ≥ 18 | Yes for all patients | Bronchoalveolar lavage (BAL) | 16S rRNA | MiSeq (Illumina) | Decreased alpha diversity was associated with increased duration of mechanical ventilation (= 0.48, P = 0.009) and diversity. Patients with ARDS had lower alpha diversity in BAL compared to controls (Shannon index 3 (2; 3.6) versus 1 (0.5; 1.5); P = 0.007) | Schmitt et al. 2020 |
NA: not available; ARDS acute respiratory distress syndrome