Table 2.
Proportion of pathogens identified from autopsy samples
| Pathogen group | Frequency | %/group | %/total |
|---|---|---|---|
| Mycobacteria | |||
| Mycobacterium tuberculosis complex | 929 | 98.2 | 39.8 |
| Non-tuberculous mycobacteria | 17 | 1.8 | 0.73 |
| 946 | 40.6 | ||
| Fungi | |||
| Cryptococcus spp | 654 | 76.4 | 28.0 |
| Pneumocystis jirovecii | 167 | 19.5 | 7.16 |
| Histoplasma spp | 16 | 1.9 | 0.69 |
| Aspergillus spp | 15 | 1.8 | 0.64 |
| Candida spp | 4 | 0.5 | 0.17 |
| 856 | 36.7 | ||
| Viruses | |||
| Cytomegalovirus | 172 | 74.5 | 7.37 |
| Varicella-zoster virus | 15 | 6.5 | 0.64 |
| Herpes simplex virus | 10 | 4.3 | 0.43 |
| Human papillomavirus | 8 | 3.5 | 0.34 |
| Respiratory syncytial virus | 8 | 3.5 | 0.34 |
| Influenza A virus | 5 | 2.2 | 0.21 |
| Measles | 5 | 2.2 | 0.21 |
| Adenovirus | 3 | 1.3 | 0.13 |
| Hepatitis B virus | 3 | 1.3 | 0.13 |
| Severe acute respiratory syndrome coronavirus 2 | 1 | 0.4 | 0.04 |
| Human herpesvirus 8 | 1 | 0.4 | 0.04 |
| 231 | 9.9 | ||
| Parasites | |||
| Toxoplasma gondii | 173 | 83 | 7.42 |
| Cryptosporidium spp | 17 | 8 | 0.73 |
| Strongyloides stercoralis | 11 | 5 | 0.47 |
| Plasmodium falciparum | 7 | 3 | 0.30 |
| 208 | 8.9 | ||
| Bacteria | |||
| Nocardia spp | 23 | 25 | 0.99 |
| Klebsiella pneumoniae | 22 | 24 | 0.94 |
| Streptococcus pneumoniae | 12 | 13 | 0.51 |
| Unspecified | 11 | 12 | 0.47 |
| Enterobacter spp | 4 | 4 | 0.17 |
| Acinetobacter spp | 4 | 4 | 0.17 |
| Salmonella spp | 3 | 3 | 0.13 |
| Clostridia spp | 3 | 3 | 0.13 |
| Staphylococcus aureus | 3 | 3 | 0.13 |
| Escherichia coli | 2 | 2 | 0.09 |
| Haemophilus influenzae | 1 | 1 | 0.04 |
| Pseudomonas spp | 1 | 1 | 0.04 |
| Mycoplasma hominis | 1 | 1 | 0.04 |
| Streptococcus dysagalactiae | 1 | 1 | 0.04 |
| Proteus mirabilis | 1 | 1 | 0.04 |
| 92 | 3.9 | ||
| Grand total | 2333 | 100% |