Table 2. Results of next-generation multilocus sequence typing for the 3 targeted loci of Pneumocystis jirovecii strains in a study of a P. jirovecii pneumonia outbreak at a university hospital in France, 2014–2015*.
| Patient |
mtLSU
|
CYTB
|
SOD
|
Final major genotype | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| No. reads | No. haplotypes | Major haplotype | No. reads | No. haplotypes | Major haplotype | No. reads | No. haplotypes | Major haplotype | ||||
| T1 | 1,413 | 1 | B | 531 | 1 | 1 | 946 | 1 | A | B1a | ||
| T2 | 1,062 | 1 | C | 1,361 | 1 | 2 | 2,506 | 1 | A | C2a | ||
| T3 | 638 | 4 | N | 84 | 1 | 3 | 491 | 1 | B | N3b | ||
| T4 | 87 | 1 | C | 215 | 1 | 2 | 204 | 1 | A | C2a | ||
| T5 | 460 | 1 | C | 1,030 | 1 | 2 | 337 | 1 | A | C2a | ||
| T6 | 42 | 1 | E | 237 | 1 | 2 | 171 | 1 | A | E2a | ||
| T7 | 546 | 1 | C | 1,088 | 1 | 2 | 303 | 4 | B | C2b† | ||
| T8 | 606 | 2 | C | 1,136 | 2 | 2 | 808 | 1 | A | C2a | ||
| T9 | 194 | 1 | C | 160 | 1 | 2 | 8 | 1 | B | C2b | ||
| T10 | 415 | 1 | C | 1,360 | 1 | 2 | 898 | 1 | A | C2a | ||
| T11 | 420 | 3 | O | 370 | 2 | 1 | 298 | 3 | B | O1b | ||
| T12 | 658 | 9 | F | 809 | 4 | 3 | 781 | 1 | A | F3a | ||
| C1 | 318 | 3 | P | 1,046 | 1 | 3 | 1,268 | 1 | A | P3a | ||
| C2 | 422 | 8 | B | 339 | 4 | 3 | 364 | 2 | A | ND | ||
| C3 | 350 | 1 | I | 564 | 1 | 3 | 1,268 | 1 | B | I3b | ||
| C4 | 292 | 2 | N | 492 | 1 | 3 | 427 | 1 | B | N3b | ||
| C5 | 71 | 1 | B | 651 | 1 | 2 | 880 | 1 | B | B2b | ||
| C6 | 368 | 12 | P | 473 | 3 | 3 | 575 | 4 | B | ND | ||
| C7 | 153 | 2 | F | 103 | 2 | 3 | 54 | 4 | A | F3a | ||
| C8 | 383 | 5 | I | 697 | 2 | 3 | 653 | 4 | B | ND | ||
| C9 | 148 | 2 | F | 104 | 4 | 2 | 154 | 1 | a | F2a | ||
| C10 | 934 | 2 | F | 1,146 | 5 | 2 | 550 | 3 | a | F2a | ||
| C11 | 229 | 4 | B | 750 | 3 | 3 | 119 | 2 | b | B3b | ||
| C12 | 580 | 2 | G | 398 | 1 | 1 | 509 | 1 | a | G1a | ||
| C13 | 869 | 1 | F | 1,998 | 1 | 3 | 663 | 1 | a | F3a | ||
| C14 | 901 | 9 | B | 1,403 | 1 | 2 | 411 | 1 | b | B2b | ||
| C15 | 653 | 1 | N | 1,664 | 2 | 3 | 5 | 1 | a | N3a | ||
| C16 | 1,275 | 1 | F | 1,052 | 1 | 11 | 591 | 1 | a | F11a | ||
| C17 | 372 | 10 | P | 434 | 3 | 2 | 361 | 1 | b | ND | ||
| C18 | 296 | 1 | F | 271 | 1 | 3 | 15 | 3 | b | F3b | ||
| C19 | 948 | 2 | F | 795 | 4 | 1 | 494 | 1 | a | ND | ||
| C20 | 243 | 5 | A | 284 | 9 | 2 | 240 | 2 | b | ND | ||
*T1–T12 indicate the 12 solid organ transplant patients from the cluster; C1–C20 indicate the 20 control patients. Underlined genotypes were included for Hunter Index calculation. CYTB, cytochrome b; mtLSU, mitochondrial large subunit of ribosomal RNA; ND, undetermined genotypes when haplotypes could not be cross-linked (multiple variants in >1 locus without any clear predominance); SOD, superoxide dismutase. †Patient carrying the C2a genotype as a minor strain.