Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii
Abstract
1. Introduction
2. Investigated Loci and Typing Schemes
2.1. Nuclear rRNA Gene Cluster
2.2. Mitochondrial Genes
2.3. Nuclear Genes
3. Amplification Rate and Variation of Target Loci
4. Case Study: Assessing the Ability to Discriminate between Clinical Isolates
5. Discussion
6. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Schemes (Included Loci) and Reference | Country | Total # of Samples | # of Samples Sequenced | # of Sequence Types | Genetic Locus | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5.8S | 18S | 23S | 26S | ITS1 | ITS2 | ITS1/2 | msg | mt26S | β-TUB | TS | arom/EPSP | mtSSU | DHPS | UCS | Kex1 | CYB | SOD | DHRF | TRR1 | |||||
Scheme 1 (5.8S, 18S, 26S, ITS1, ITS2) | ||||||||||||||||||||||||
[6] | USA | 15 | 15 | 6 | 1 | 1 | 1 | 2 | 3 | NG | ||||||||||||||
[7] | GBR | 24 | 24 | NG | 1 | 1 | 1 | 5 | 7 | NG | ||||||||||||||
Scheme 2 (ITS1, ITS2, msg, mt26S) | ||||||||||||||||||||||||
[8] | USA | 15 | 15 | NG | NG | NG | NG | NG | ||||||||||||||||
[38] | IND | 180 | 29 | NG | NG | NG | NG | NG | ||||||||||||||||
Scheme 3 (26S, β-TUB, ITS1, mt26S) | ||||||||||||||||||||||||
[9] | CHE | 11 | 11 | NG | 3 | 3 | 3 | 2 | ||||||||||||||||
[20] | EUR | 212 | 212 | 6 | 6 | 3 | 4 | 3 | ||||||||||||||||
[19] | EUR | 91 | 91 | 28 | NG | NG | NG | NG | ||||||||||||||||
[33] | DEU | 7 | 7 | 2 | NG | NG | NG | NG | ||||||||||||||||
[42] | DEU | 20 | 14 | NG | 2 | 4 | 4 | 1 | ||||||||||||||||
[43] | CHE | 19 | 7 | 1(+) | 2 | 4 | 3 | 2 | ||||||||||||||||
[50] | DE | 18 | 18 | NG | 2 | 3 | 3 | 2 | ||||||||||||||||
[53] | GBR | 670 | 31 | NG | NA | 5 | 4 | NA | ||||||||||||||||
[54] | FRA | 13 | 10 | 3 | 2 | 2 | 3 | 1 | ||||||||||||||||
Scheme 4 (ITS1, ITS2, mt26S) | ||||||||||||||||||||||||
[10] | USA | 15 | 15 | 6 | 4 | 3 | 7 | 4 | ||||||||||||||||
[11] | SWE, FRA | 7 | 7 | NG | 4 | 4 | NG | 3 | ||||||||||||||||
[48] | GBR | 27 | 27 | NG | NG | NG | 2 | 3 | ||||||||||||||||
Scheme 5 (5.8S, ITS1, ITS2, mt26S, TS) | ||||||||||||||||||||||||
[12] | FRA, ITA | 20 | 18 | NG | 6 | 3 | 3 | 10 | 4 | 1 | ||||||||||||||
Scheme 6 (arom, ITS1, ITS2, mt26S, mtSSU) | ||||||||||||||||||||||||
[13] | NLD | 6 | 6 | NG | NG | NG | 9 | 3 | 1 | 2 | ||||||||||||||
Scheme 7 (ITS1, ITS2) | ||||||||||||||||||||||||
[14] | GLO | 207 | 207 | NG | 15 | 14 | NG | |||||||||||||||||
[18] | JPN | 24 | 24 | NG | 11 | 11 | NG | |||||||||||||||||
[31] | ZAF | 20 | 20 | NG | 11 | 13 | NG | |||||||||||||||||
[49] | SWE | 64 | 64 | 12 | 10 | 12 | NG | |||||||||||||||||
Scheme 8 (DHPS, ITS1, ITS2, mt26S) | ||||||||||||||||||||||||
[15] | FRA | 14 | 14 | NG | NG | NG | NG | NG | NG | |||||||||||||||
[39] | PRT, ESP | 108 | ✕ | NG | 12 | 10 | NG | 4 | 4 | |||||||||||||||
[44] | AUS | 68 | 68 | NG | 8 | 9 | 16 | 2 | 2 | |||||||||||||||
Scheme 9 (DHFR, DHPS) | ||||||||||||||||||||||||
[16] | USA | 37 | 37 | NG | 4 | 2 | ||||||||||||||||||
[32] | FRA | 33 | 33 | NG | 3 | 2 | ||||||||||||||||||
[40] | THA | 29 | 18 | NG | 3 | 3 | ||||||||||||||||||
[71] | USA | 13 | 13 | NG | 2 | 2 | ||||||||||||||||||
[70] | COL | 98 | 45 | NG | 4 | 2 | ||||||||||||||||||
Scheme 10 (DHPS, mt26S) | ||||||||||||||||||||||||
[17] | USA | 324 | 191 | 14 | 4 | 4 | ||||||||||||||||||
[26] | ESP | 255 | 79 | NG | 4 | 4 | ||||||||||||||||||
[34] | ESP | 50 | 12 | NG | 4 | 1 | ||||||||||||||||||
[35] | USA | 442 | ❋ | NG | 4 | 4 | ||||||||||||||||||
[45] | ESP | 60 | 19 | NG | 3 | 1 | ||||||||||||||||||
[51] | ITA | 67 | ⚑ | NG | 4 | 3 | ||||||||||||||||||
Scheme 11 (26S, β-TUB, DHPS, ITS1, mt26S) | ||||||||||||||||||||||||
[21] | USA | 22 | 22 | 10 | 2 | 5 | 4 | 2 | 3 | |||||||||||||||
Scheme 12 (26S, β-TUB, ITS1, ITS2, mt26S) | ||||||||||||||||||||||||
[22] | ITA | 25 | 18 | 15 | 4 | 6 | 6 | 4 | 3 | |||||||||||||||
Scheme 13 (DHPS, ITS1, ITS2) | ||||||||||||||||||||||||
[23] | USA | 57 | 37 | NG | 6 | 7 | NG | 3 | ||||||||||||||||
[27] | PRT | 43 | 43 | NG | 15 | 14 | 17 | 2 | ||||||||||||||||
[36] | ITA | 261 | 174 | NG | NG | NG | 9 | 3 | ||||||||||||||||
Scheme 14 (CYB, DHFR, DHPS) | ||||||||||||||||||||||||
[24] | JPN | 34 | 34 | NG | 4 | 2 | 1 | |||||||||||||||||
Scheme 15 (DHPS, ITS1, ITS2, mtSSU) | ||||||||||||||||||||||||
[25] | GBR | 2 | 2 | NG | NG | NG | 2 | 1 | 1 | |||||||||||||||
Scheme 16 (DHPS, mt26S, mtSSU) | ||||||||||||||||||||||||
[28] | GBR, ZWE | 51 | 30 | NG | 3 | 4 | 2 | |||||||||||||||||
Scheme 17 (DHPS, mtSSU, mt26S, SOD) | ||||||||||||||||||||||||
[29] | GBR | 16 | 16 | NG | NG | NG | NG | NG | ||||||||||||||||
[30] | NG | 76 | 76 | 15 | 4 | 4 | 4 | 4 | ||||||||||||||||
Scheme 18 (DHFR, DHPS, ITS1, ITS2) | ||||||||||||||||||||||||
[37] | PRT | 68 | 68 | NG | NG | NG | 19 | 4 | 4 | |||||||||||||||
Scheme 19 (UCS, Kex1) | ||||||||||||||||||||||||
[39] | PRT | 87 | 35 | NG | 4 | 4 | ||||||||||||||||||
Scheme 20 (CYB, DHFR, DHPS, mt26S, SOD) | ||||||||||||||||||||||||
[46] | PRT | 102 | 78 | NG | 9 | 6 | 3 | 6 | 6 | |||||||||||||||
Scheme 21 (β-TUB, CYB, DHFR, DHPS, mt26S, TRR1, TS, SOD) | ||||||||||||||||||||||||
[47] | PRT | 70 | ► | 48 | 5 | 3 | ⌘ | 3 | 7 | 4 | 3 | ⌘ | ||||||||||||
Scheme 22 (β-TUB, DHPS, ITS1/2, mt26S) | ||||||||||||||||||||||||
[3] | AUS | 11 | 11 | 2 | 4 | 2 | 2 | 1 | ||||||||||||||||
[55] | AUS | 48 | 48 | 4 | 2 | 2 | 1 | 1 | ||||||||||||||||
[57] | AUS | 7 | 7 | NG | NG | NG | NG | NG | ||||||||||||||||
Scheme 23 (mt26S, mtSSU) | ||||||||||||||||||||||||
[52] | FRA, CUB, ESP | 75 | 75 | NG | 5 | 3 | ||||||||||||||||||
Scheme 24 (26S, β-TUB, CYB, DHFR, DHPS, ITS1, mt26S, SOD) | ||||||||||||||||||||||||
[5] | FRA | 23 | 23 | NG | 7 | 9 | 4 | 2 | 1 | 7 | 3 | 3 | ||||||||||||
Scheme 25 (26S, ITS1, ITS2, mt26S) | ||||||||||||||||||||||||
[56] | DNK | 22 | 18 | 3 | NG | NG | NG | NG | NG | |||||||||||||||
Scheme 26 (CYB, ITS1, mt26S, SOD) | ||||||||||||||||||||||||
[58] | FRA | 37 | 32 | NG | NG | NG | NG | NG | ||||||||||||||||
Scheme 27 (β-TUB, CYB, DHFR, mt26S, SOD) | ||||||||||||||||||||||||
[59] | BEL | 20 | 20 ^ | NG | NA | 4 | 2 | 4 | 2 | 2 | ||||||||||||||
Scheme 28 (CYB, mt26S, SOD) | ||||||||||||||||||||||||
[60] | FRA | 24 | ◎ | 14 | 6 | 5 | 3 | |||||||||||||||||
[61] | FRA | 32 | 32 | 18 | 22 | 14 | 4 | |||||||||||||||||
[62] | FRA | 7 | 7 | NG | 4 | 3 | 2 | |||||||||||||||||
[63] | POL | 17 | ◉ | 8 | 13 | 6 | 2 | |||||||||||||||||
[66] | FRA | 192 | 35 | 17 | 11 | 5 | 2 | |||||||||||||||||
[67] | TUR | 31 | 26 | 6 | 4 | 5 | 3 | |||||||||||||||||
[68] | REU, GUF, FRA | 47 | 47 | 23 | 5 | 9 | 3 | |||||||||||||||||
Scheme 29 (23S, 26S, DHPS) | ||||||||||||||||||||||||
[64] | BRA | 30 | 30 | 5 | 3 | 2 | 1 | |||||||||||||||||
Scheme 30 (DHFR, DHPS, mt26S) | ||||||||||||||||||||||||
[65] | IND | 37 | 37 | 13 | 3 | 3 | 2 | |||||||||||||||||
Scheme31 (CYB, DHPS, mt26S, SOD) | ||||||||||||||||||||||||
[69] | POL | 72 | N/A | N/A | 3 | 1 | 3 | 2 |
Locus | Primer Name | Ref. | Nucleotide Sequence | Product Size (Base Pairs) | PCR Conditions |
---|---|---|---|---|---|
β-TUB | PneumoβTub_F | - | 5′-TCATTAGGTGGTGGAACGGG-3′ | 303 | 95 °C 3 min; 45 cycles: 94 °C 30 s, 60 °C 45 s, 72 °C 45 s; 72 °C 7 min |
PneumoβTub_R | 5′-ATCACCATATCCTGGATCCG-3′ | ||||
SOD | MnSODFw | 5 | 5′-GGGTTTAATTAGTCTTTTTAGGCAC-3′ | 602 | |
MnSODRw | 5′-CATGTTCCCACGCATCCTAT-3′ | ||||
CYB | CytbFw | 5 | 5′-CCCAGAATTCTCGTTTGGTCTATT-3′ | 579 | 95 °C 3 min; 45 cycles: 94 °C 30 s, 55 °C 45 s, 72 °C 45 s; 72 °C 7 min |
CytbRw | 5′-AAGAGGTCTAAAAGCAGAACCTCAA-3′ | ||||
mt26S | PneumoLSU_F | - | 5′-TCAGGTCGAACTGGTGTACG-3′ | 297 | |
PneumoLSU_R | 5′-TGTTCCAAGCCCACTTCTT-3′ |
Strain Number | Country of Origin | Date of Sample | β-TUB | CYB | mt26S | SOD | Sequence Type |
---|---|---|---|---|---|---|---|
HVH21 | Spain | Jan 2015 | 2 | 1 | 3 | 1 | ST21 |
HVH22 | Spain | Jan 2015 | 2 | 1 | 3 | 1 | ST21 |
Case 63 | Australia | Dec 2016 | 1 | 3 | 1 | 4 | ST42 |
Case 71 | New Zealand | May 2017 | 4 | 2 | 2 | 4 | ST44 |
1794 | Chile | Feb 2011 | 2 | 5 | 4 | 1 | ST7 |
2165 | Chile | Oct 2014 | 2 | 2 | 4 | 5 | ST2 |
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Pasic, L.; Goterris, L.; Guerrero-Murillo, M.; Irinyi, L.; Kan, A.; Ponce, C.A.; Vargas, S.L.; Martin-Gomez, M.T.; Meyer, W. Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii. J. Fungi 2020, 6, 259. https://doi.org/10.3390/jof6040259
Pasic L, Goterris L, Guerrero-Murillo M, Irinyi L, Kan A, Ponce CA, Vargas SL, Martin-Gomez MT, Meyer W. Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii. Journal of Fungi. 2020; 6(4):259. https://doi.org/10.3390/jof6040259
Chicago/Turabian StylePasic, Lana, Lidia Goterris, Mercedes Guerrero-Murillo, Laszlo Irinyi, Alex Kan, Carolina A. Ponce, Sergio L. Vargas, M. Teresa Martin-Gomez, and Wieland Meyer. 2020. "Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii" Journal of Fungi 6, no. 4: 259. https://doi.org/10.3390/jof6040259
APA StylePasic, L., Goterris, L., Guerrero-Murillo, M., Irinyi, L., Kan, A., Ponce, C. A., Vargas, S. L., Martin-Gomez, M. T., & Meyer, W. (2020). Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii. Journal of Fungi, 6(4), 259. https://doi.org/10.3390/jof6040259