| Literature DB >> 27288706 |
Ibrahim Abbasi1, Oscar D Kirstein2, Asrat Hailu3, Alon Warburg4.
Abstract
Visceral leishmaniasis (VL), one of the most important neglected tropical diseases, is caused by Leishmania donovani eukaryotic protozoan parasite of the genus Leishmania, the disease is prevalent mainly in the Indian sub-continent, East Africa and Brazil. VL can be diagnosed by PCR amplifying ITS1 and/or kDNA genes. The current study involved the optimization of Loop-mediated isothermal amplification (LAMP) for the detection of Leishmania DNA in human blood or tissue samples. Three LAMP systems were developed; in two of those the primers were designed based on shared regions of the ITS1 gene among different Leishmania species, while the primers for the third LAMP system were derived from a newly identified repeated region in the Leishmania genome. The LAMP tests were shown to be sufficiently sensitive to detect 0.1pg of DNA from most Leishmania species. The green nucleic acid stain SYTO16, was used here for the first time to allow real-time monitoring of LAMP amplification. The advantage of real time-LAMP using SYTO 16 over end-point LAMP product detection is discussed. The efficacy of the real time-LAMP tests for detecting Leishmania DNA in dried blood samples from volunteers living in endemic areas, was compared with that of qRT-kDNA PCR.Entities:
Keywords: Isothermal loop-mediated amplification; Leishmania donovani; Real time LAMP; SYTO16; Visceral leishmaniasis
Mesh:
Substances:
Year: 2016 PMID: 27288706 PMCID: PMC4987123 DOI: 10.1016/j.actatropica.2016.06.009
Source DB: PubMed Journal: Acta Trop ISSN: 0001-706X Impact factor: 3.112
DNA sequences of the primers designed for the three LAMP systems. Two targeting the ITS1 gene (See Fig. 1) and one targeting the L. donovanirepeat DNA region.
| LAMP System | Primer Name | Primer sequence |
|---|---|---|
| LITS-LAMP1 | LITSF3.1 | TTTCCCACATACACAGCAAA |
| LITSB3.3 | GCGGCGTGTTGTTTTTTG | |
| LITSFIP1 | CGCCAAAAACCGAAACGCCTTTTCAGTAAAAAAAGGCCGATCG | |
| LITSBIP3 | CGCAAACGGCGCATGGGAGAAGCTTTTCTGAGAATATGGCATGCACG | |
| LITS-LAMP2 | LITSF3.2 | GTGGATAACGGCTCACATAA |
| LITSB33 | GCGGCGTGTTGTTTTTTG | |
| LITSFIP2 | CTGCAATTGATACCACTTATCGCACTTTTACTTGGCTTCCTATTTCGTTG | |
| LITSBIP3 | CGCAAACGGCGCATGGGAGAAGCTTTTCTGAGAATATGGCATGCACG | |
| L151-LAMP | L151F3 | GATGAGAAGCTCACGGAG |
| L151B3 | ATCCTCCTCCTCGTCTTC | |
| L151FIP | CGGGTACGTGAGTCCGTATTTTGTCTGCCAGTCAACAAGA | |
| L151BIP | GAAGCTCATGATCGAGAAGGAGTTTTTTCGTCTGATGCGTTGCT |
Fig. 1DNA sequence of the L. donovaniITS1 gene, showing the location of the LAMP primers on the sequences shared by different Leishmania species.
Fig. 2Agarose gel electrophoresis analysis and SYBR Green I end point detection of LITS-LAMP1 (A,B), and LITS-LAMP2 (C,D). The analysis shows LAMP DNA amplification products of different concentrations amplified from different amounts of L. donovani template DNA, (1) 0.1 ng, (2) 0.01 ng, (3) 1 pg, (4) 0.1 pg. And the amplification of 1 ng template DNA of each of the following Leishmania species: (5) L. major, (6) L. aethiopica, (7) L. tropica, (8) L. infantum chagasi. (9) and (10) No DNA [control], (11–16) Select blood samples obtained by finger prick from volunteers in North Ethiopia. (M) DNA size marker.
Fig. 3Monitoring of LAMP amplification from different Leishmania DNA control samples and from DNA extracted finger pricks samples. The analysis shows the DNA amplification detection in real time by measuring the increasing fluorescence of DNA binding to SYTO-16 dye.
Parasite concentrations (per ml) in finger prick blood of volunteers from northern Ethiopia estimated by qRT-kDNA PCR. Results are compared with the corresponding results obtained by the different LAMP assays. Positive LAMP results are designated by the take-off time in mins (see materials and methods).
| Sample number | History of VL | Parasite/ml | Estimated take-off time of LAMP amplification (min) | ||
|---|---|---|---|---|---|
| LITS- LAMP1 | LITS- LAMP2 | L151 LAMP | |||
| 1 | + | 0 | – | – | 61 |
| 2 | – | 0 | – | – | – |
| 3 | – | 0 | – | – | – |
| 4 | – | 0 | – | – | – |
| 5 | – | 0 | – | – | – |
| 6 | + | 0 | – | – | 67 |
| 7 | – | 0 | – | – | – |
| 8 | – | 0 | – | – | – |
| 9 | – | 0 | – | – | – |
| 10 | – | 0 | – | – | – |
| 11 | + | 18 | 69 | 57 | – |
| 12 | – | 0 | – | – | – |
| 13 | – | 0 | – | – | – |
| 14 | – | 0 | – | – | – |
| 15 | – | 0 | – | – | – |
| 16 | + | 0 | – | – | – |
| 17 | – | 0 | – | – | – |
| 18 | – | 0 | – | – | – |
| 19 | – | 0 | – | – | – |
| 20 | – | 3 | – | – | – |
| 21 | + | 11 | – | 78 | 63 |
| 22 | – | 595 | 59 | 54 | 52 |
| 23 | – | 0 | – | – | 86 |
| 24 | – | 59 | – | 85 | 65 |
| 25 | – | 0 | – | – | – |
| 26 | + | 0 | – | – | – |
| 27 | – | 0 | – | 72 | 86 |
| 28 | – | 0 | – | 62 | 65 |
| 29 | – | 0 | – | 48 | – |
| 30 | – | 0 | – | 48 | 103 |
| 31 | + | 0 | – | 41 | 34 |
| 32 | – | 0 | – | 57 | – |
| 33 | – | 0 | – | 47 | – |
| 34 | – | 9 | – | – | – |
| 35 | – | 0 | – | – | – |
| 36 | + | 2 | 75 | 41 | 34 |
| 37 | – | 0 | – | 59 | – |
| 38 | – | 1 | – | 43 | – |
| 39 | – | 0 | – | – | – |
| 40 | + | 0 | 56 | 44 | 58 |
| 41 | – | 0 | 60 | 54 | – |
| 42 | – | 23 | – | 42 | 52 |
| 43 | – | 0 | 60 | 53 | – |
| 44 | – | 0 | – | 45 | – |
A four by four matrix depicting the relationships between the different LAMP systems and the qRT-kDNA PCR results among the 44 individuals tested. Total numbers detected by each system are in the shaded cells. Note higher sensitivity of the LITS LAMP2 system compared with the PCR as well as the other two LAMP systems.