Fig. 1
Genotypes of Pneumocystis jirovecii detected at eight genetic loci_
| Patient No. | HIV1/2 anti-body | Genotypes at 8 loci | |||||||
|---|---|---|---|---|---|---|---|---|---|
| ITS | sod | dhfr | dhps | cyb | mtLSU rRNA | β-Tub | 26S rRNA | ||
| SX_0001 | +/− | ITS2 + ITS59 | sod1 | dhfr312 | WT | cyb7 | mt3 | β-Tub1 + β-Tub2 | 26S2 |
| SX_0002 | +/− | ITS4 | sod1 | dhfr312 | WT | cyb2 | mt3 | β-Tub2 | 26S2 |
| SX_0003 | −/− | ITS10 + ITS16 | sod1 + sod2 | dhfr312 | WT | cyb1 + cyb8 | mt1 + mt 2 | β-Tub1 + β-Tub2 | 26S3 + 26S4 |
Nucleotide polymorphic sites and number of plasmid clones sequenced at eight distinct loci of Pneumocystis jirovecii_
| Locus | Genotypesa | Locationb | No. of plasmid clones sequenced | ||
|---|---|---|---|---|---|
| SX_0001 | SX_0002 | SX_0003 | |||
| ITS | ITS 4 | KC470776 | 0 | 12 | 0 |
| ITS 10 | JQ365725 | 0 | 0 | 4 | |
| ITS 16 | AB469817 | 0 | 0 | 8 | |
| ITS 22 | KC470795 | 6 | 0 | 0 | |
| ITS 59 | MK300661 | 10 | 0 | 0 | |
| sod | sod 1 | 110C/215T | 11 | 13 | 8 |
| sod 2 | 110T/215C | 0 | 0 | 2 | |
| dhps | dhps WT | 165A (55Thr) / 171C (57Pro) | 12 | 12 | 12 |
| dhps | dhfr312 | 312C (117Gly) | 12 | 11 | 11 |
| cyb | cyb 1 | 279C/348A/516C/547C/566C/838C | 0 | 0 | 6 |
| cyb 2 | 279C/348A/516C/547C/566C/838T | 0 | 8 | 0 | |
| cyb 7 | 279C/348A/516C/547C/566T/838C | 9 | 0 | 0 | |
| cyb 8 | 279T/348A/516C/547C/566C/838C | 0 | 0 | 3 | |
| mt LSU rRNA | mt1 | 85C/248C | 0 | 0 | 2 |
| mt2 | 85A/248C | 0 | 0 | 8 | |
| mt3 | 85T/248C | 10 | 10 | 0 | |
| β-Tub | β-Tub 1 | 86G/281A | 8 | 0 | 6 |
| β-Tub 2 | 86G/281G | 4 | 12 | 5 | |
| 26S rRNA | 26S 2 | 86T/290A | 12 | 11 | 0 |
| 26S 3 | 86C/290A | 0 | 0 | 5 | |
| 26S 4 | 86A/290A | 0 | 0 | 6 | |
Multi-locus sequence type (MLST) profiles of P_ jirovecii from PCP patients in this study in comparison with known P_ jirovecii MLST profiles in Fungal MLST Database_
| MLST types* | β-Tub | cyb | 26S rRNA | sod | Patient no. |
|---|---|---|---|---|---|
| 3 | 1 | 1 | 4 | 2 | SX_0003 |
| 8 | 2 | 8 | 4 | 1 | SX_0003 |
| 13 | 1 | 1 | 4 | 1 | SX_0003 |
| 15 | 1 | 8 | 4 | 1 | SX_0003 |
| 19 | 1 | 8 | 3 | 2 | SX_0003 |
| 21 | 2 | 1 | 3 | 1 | SX_0003 |
| 22 | 2 | 1 | 3 | 2 | SX_0003 |
| 23 | 2 | 1 | 4 | 1 | SX_0003 |
| 35 | 2 | 7 | 2 | 1 | SX_0001 |
| 51 | 1 | 7 | 2 | 1 | SX_0001 |
| 52 | 2 | 2 | 2 | 1 | SX_0002 |
| NA | 1 | 1 | 3 | 2 | SX_0003 |
| NA | 2 | 8 | 3 | 1 | SX_0003 |
| NA | 2 | 8 | 3 | 2 | SX_0003 |
| NA | 2 | 1 | 4 | 2 | SX_0003 |
| NA | 2 | 8 | 4 | 2 | SX_0003 |
| NA | 1 | 1 | 3 | 1 | SX_0003 |
| NA | 1 | 8 | 3 | 1 | SX_0003 |
| NA | 1 | 8 | 4 | 2 | SX_0003 |
PCR primers used in this study_
| Genes (reference) | Primer names and sequences (5′-3′) | Size of nested PCR products (bp) |
|---|---|---|
| ITS (Lee et al. 1998) | 1724F 5′-AAGTTGATCAAATTTGGTC-3′ | 578 |
| sod (Esteves et al. 2010b) | MnSOD_Fw 5′-GGGTTTAATTAGTCTTTTTAGGCAC-3′ | 560 |
| dhfr (Lane et al. 1997) | FR208 5′-GCAGAAAGTAGGTACATTATTACGAGA-3′ | 798 |
| dhps (Ma et al. 1999) | DHPS1 5′-CAAATTAGCGTATCGAATGACC-3′ | 278 |
| cyb (Esteves et al. 2010a) | CytbFw 5′-CCCAGAATTCTCGTTTGGTCTATT-3′ | 590 |
| mtLSU rRNA (Wakefield 1996) | pAZ102_E 5′-GATGGCTGTTTCCAAGCCCA-3′ | 252 |
| β-Tub (Pasic et al. 2020) | Pneumo | 303 |
| 26S rRNA (Pasic et al. 2020) | PneumoLSU_F 5′-TCAGGTCGAACTGGTGTACG-3′ | 297 |
Clinical characteristics of patients with Pneumocystis jirovecii pneumonia_
| Clinical information | Patient No. | ||
|---|---|---|---|
| SX_0001 | SX_0002 | SX_0003 | |
| Age (years) | 65 | 51 | 65 |
| Sex | Male | Male | Male |
| Underlying conditions | NAa | Hepatic cysts | ILD |
| Thoracic HRCT findings | GGO d + | GGO + | GGO + |
| HIV 1/2 antibody | +/– | +/– | –/– |
| CD4 T-lymphocyte count (cells/µl) | 232 | 176 | NA |
| Serum parameters | |||
| 1,3-β-D-glucan, normal < 10 pg/ml | > 600 | NA | > 600 |
| Lactate dehydrogenase, normal 120–250 U/l | 432 | 699 | 9,734 |
| C-reactive protein, normal 0–6 mg/l | 73.63 | 129.17 | 340.00 |
| Procalcitonin, normal 0–0.05 ng/ml | 0.975 | 0.161 | 11.26 |
| Partial pressure of oxygen, normal 80–110 mmHg | 80 | 65 | 59.70 |
| Erythrocyte sedimentation rate, normal 0–15 mm/h | 61.10 | 60.80 | 47.30 |
| Concurrent infection | – | – | C.n. and B.c.b |
| Anti-PCP therapya | – | – | – |
| HAART before PCP | – | – | – |
| Clinical outcomes | survived | survived | died |