Table 2.
Studies in Hospitalized COVID-19 Patients With Types of Microorganisms Reported, Rate of Antibiotic Use, and Time to Diagnosis of Secondary Pulmonary Infections
| Study | Top Five Bacterial Microorganisms From Respiratory Tract Culture | Fungal Microorganisms From Respiratory Tract Culture | Empirical Antibiotic Therapy (%) | Median Day to Secondary Pulmonary Infection Diagnosis From Admission |
|---|---|---|---|---|
| Observational Studies | ||||
| Alanio et al. [43] | NR | 100% Aspergillus fumigatus | NR | NR |
| Barrasa et al. [25] | 50% Pseudomonas aeruginosa, 16% Enterococcus faecium, 16% Haemophilus influenzae, 16% Methicillin-Resistant Staphylococcus aureus (MRSA) | NR | 87.5 | NR |
| Bartoletti et al. [14] | NR | 78.9% Aspergillus fumigatus, 15.8% Aspergillus niger, 5.3% Aspergillus flavus | NR | 4 (ICU) |
| Chang et al. [12] | 36% Klebsiella spp., 23% MSSA, 11% Escherichia coli, 11% Serratia spp., 11% Stenotrophomonas spp. | NR | NR | NR |
| Du et al. [56] | Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Staphylococcus species** | NR | NR | NR |
| Dupont et al. [69] | NR | 87.5% Aspergillus fumigatus, 6.3% Aspergillus flavus, 6.3% Aspergillus calidoustus | NR | 11 (ICU) |
| Fekkar et al. [17] | NR | 66.7% Aspergillus fumigatus, 22.2% Mucor spp., 11.1% Fusarium proliferatum | NR | 18 (ICU) |
| Feng et al. [32] | NR | NR | 67.1 | NR |
| Fu et al. [23] | 29% Pseudomonas aeruginosa, 29% Burkholderia cepacia, 14% Escherichia coli, 14% Extended-spectrum beta-lactamase (ESBL) Klebsiella pneumoniae, 14% Stenotrophomonas maltophilia | 100% Aspergillus fumigatus | NR | 12 |
| Gangneux et al. [70] | NR | 100% Aspergillus fumigatus | NR | NR |
| Garcia-Vidal et al. [22] | 33% multidrug-resistant (MDR) Pseudomonas aeruginosa, 25% ESBL Escherichia coli, 21% ESBL Klebsiella pneumoniae, 21% Staphylococcus aureus | 100% Aspergillus fumigatus | 61.9 | 11 |
| Helleberg et al. [71] | NR | 100% Aspergillus fumigatus | NR | 3 (ICU) |
| Huang et al. [30] | NR | NR | 100 | > 2 |
| Karmen-Tuohy et al. [58] | 29% Stenotrophomonas maltophilia, 29% Pseudomonas aeruginosa, 14% Escherichia coli, 14% Klebsiella pneumoniae, 14% Staphylococcus aureus | NR | NR | > 6 |
| Lamoth et al. [72] | NR | 100% Aspergillus fumigatus | 100 | 6 (ICU) |
| Machado et al. [35] | NR | 66.6% Aspergillus fumigatus, 16.7% Aspergillus citrinoterreus, 16.7% Aspergillus lentulus | 100 | 15 (ICU) |
| Nasir et al. [26] | 25% Pseudomonas aeruginosa, 25% Acinetobacter spp., 25% Stenotrophomonas maltophilia, 12.5% Klebsiella pneumoniae, 12.5% MRSA | 60% Aspergillus flavus, 20% Aspergillus fumigatus, 20% Aspergillus terreus | 77.7 | 7 |
| Roman-Montes et al. [73] | NR | 54.5% Aspergillus fumigatus, 27.3% Aspergillus spp., 9.1% Aspergillus flavus, 9.1% Aspergillus niger | NR | 9 |
| Rouze et al. [13] | 22.3% Pseudomonas aeruginosa, 18.8% Enterobacter spp., 11.5% Klebsiella spp., 9.4% MSSA, 8.4% Escherichia coli | NR | 93.2 | NR |
| Rutsaert et al. [15] | NR | 83% Aspergillus fumigatus, 17% Aspergillus Flavus | NR | 6 |
| Segrelles-Calvo et al. [74] | NR | 42.8% Aspergillus fumigatus, 28.6% Aspergillus flavus, 28.6% Aspergillus niger | NR | NR |
| Torrego et al. [11] | 39% Pseudomonas aeruginosa, 11% Enterobacter cloacae, 11% Enterococcus faecalis, 11% Klebsiella aerogenes, 11% Staphylococcus aureus | NR | NR | < 21 |
| Van Arkel et al. [75] | NR | 100% Aspergillus fumigatus | NR | 12 |
| Van Biesen et al. [16] | NR | 71.4% Aspergillus fumigatus, 14.3% Aspergillus flavus, 14.3% Aspergillus terreus | NR | 5 (ICU) |
| Wang et al. [57] | NR | NR | NR | NR |
| White et al. [34] | NR | 91.6% Aspergillus fumigatus, 8.4% Aspergillus versicolor | 98.0 | 8 (ICU) |
| Yang et al. [24] | 25% ESBL Klebsiella pneumoniae, 25% Carbapenem-resistant Klebsiella pneumoniae, 25% MDR Pseudomonas aeruginosa, 25% Serratia marcescens | 50% Aspergillus fumigatus, 50% Aspergillus flavus | 94.2 | NR |
| Zhou et al. [31] | NR | NR | 94.8 | 17 |
| Case Series/Reports | Top Five Bacterial Microorganisms From Respiratory Tract Culture | Fungal Microorganisms From Respiratory Tract Culture | Antibiotic/ Antifungal Therapy* (%) |
Median Day to Secondary Pulmonary Infection Diagnosis From Admission |
|---|---|---|---|---|
| Abdalla et al. [76] | NR | 50% Aspergillus niger, 50% Aspergillus terreus | 100 | 12 (ICU) |
| Blanco et al. [19] | NR | 100% Pneumocystis jirovecii | 60.0 | 12 |
| Falces-Romero et al. [77] | NR | 87.5% Aspergillus fumigatus, 12.5% A. nidulans | 80.0 | 17.1 |
| Koehler et al. [78] | NR | 100% Aspergillus fumigatus | NR | NR |
| Lahmer et al. [79] | NR | 100% Aspergillus fumigatus | NR | 5.5 (ICU) |
| Lescure et al. [80] | 100% Acinetobacter baumannii | 100% Aspergillus fumigatus | NR | NR |
| Sharifipour et al. [81] | 89.4% Acinetobacter baumannii, 5.3% MSSA, 5.3% MRSA | NR | NR | NR |
| Antinori et al. [82] | NR | 100% Aspergillus fumigatus | 100 | 9 |
| Blaize et al. [83] | NR | 100% Aspergillus fumigatus | 100 | 4 |
| Duployez et al. [84] | 100% Panton-Valentine Leukocidin (PVL) Methicillin-Sensitive Staphylococcus aureus (MSSA) | N/A | 100 | 5 |
| Fernandez et al. [85] | 100% Enterococcus faecalis, Acinetobacter baumannii | 100% Aspergillus fumigatus | 100 | 10 |
| Ghelfenstein et al. [86] | NR | 100% Aspergillus fumigatus | 100 | 6 |
| Kelly et al. [21] | NR | 100% Pneumocystis jirovecii | 100 | 10 |
| Mang et al. [20] | NR | 100% Pneumocystis jirovecii | 100 | 20 |
| Meijer et al. [87] | NR | 100% Aspergillus fumigatus | 100 | 6 |
| Menon et al. [18] | NR | 100% Pneumocystis jirovecii | NR | NR |
| Mohamed et al. [47] | Klebsiella Varicola | 100% Aspergillus fumigatus | 100 | 7 |
| Nasri et al. [88] | NR | 100% Aspergillus spp. | 100 | 9 |
| Prattes et al. [89] | NR | 100% Aspergillus fumigatus | 100 | 3 (ICU) |
| Schein et al. [90] | NR | 100% Aspergillus spp. | 100 | 16 |
| Sharma et al. [91] | NR | 100% Aspergillus fumigatus | 100 | 16 |
*Among those with secondary infections
**Percentage frequency of bacterial or fungal microorganisms not reported
NR not reported, Spp. Species