Publication: Comparison of two multilocus sequence based genotyping schemes for Leptospira species.
Accepted Date
2011-09-13
Issued Date
2011-11
Copyright Date
2011
Resource Type
Language
eng
ISSN
1935-2735 (electronic)
1935-2727 (printed)
1935-2727 (printed)
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Mahidol University
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PubMed Central
Bibliographic Citation
Ahmed A, Thaipadungpanit J, Boonsilp S, Wuthiekanun V, Nalam K, Spratt BG, et al. Comparison of two multilocus sequence based genotyping schemes for Leptospira species. PLoS Negl Trop Dis. 2011 Nov;5(11):e1374.
Suggested Citation
Ahmed, Ahmed, Janjira Thaipadungpanit, จันทร์จิรา ไทยผดุงพานิช, Siriphan Boonsilp, ศิริพรรณ บุญศิลป์, Vanaporn Wuthiekanun, วรรณพร วุฒิเอกอนันต์, Nalam, Kishore, Spratt, Brian G., Aanensen, David M., Smythe, Lee D., Ahmed, Niyaz, Feil, Edward J., Hartskeer, Rudy A., Peacock, Sharon J. Comparison of two multilocus sequence based genotyping schemes for Leptospira species.. Ahmed A, Thaipadungpanit J, Boonsilp S, Wuthiekanun V, Nalam K, Spratt BG, et al. Comparison of two multilocus sequence based genotyping schemes for Leptospira species. PLoS Negl Trop Dis. 2011 Nov;5(11):e1374.. doi:10.1371/journal.pntd.0001374. Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/800
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Title
Comparison of two multilocus sequence based genotyping schemes for Leptospira species.
Corresponding Author(s)
Other Contributor(s)
Mahidol University. Faculty of Tropical Medicine. Department of Microbiology and Immunology.
Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.
Mahidol Univeristy. Faculty of Medicine Siriraj Hospital. Medical Proteomics Unit, Office for Research and Development.
Mahidol University. Faculty of Tropical Medicine. Mahidol-Oxford Tropical Medicine Research Unit.
Mahidol Univeristy. Faculty of Medicine Siriraj Hospital. Medical Proteomics Unit, Office for Research and Development.
Abstract
BACKGROUND: Several sequence based genotyping schemes have been developed for
Leptospira spp. The objective of this study was to genotype a collection of
clinical and reference isolates using the two most commonly used schemes and
compare and contrast the results.
METHODS AND FINDINGS: A total of 48 isolates consisting of L. interrogans
(n = 40) and L. kirschneri (n = 8) were typed by the 7 locus MLST scheme
described by Thaipadungpanit et al., and the 6 locus genotyping scheme described
by Ahmed et al., (termed 7L and 6L, respectively). Two L. interrogans isolates
were not typed using 6L because of a deletion of three nucleotides in lipL32. The
remaining 46 isolates were resolved into 21 sequence types (STs) by 7L, and 30
genotypes by 6L. Overall nucleotide diversity (based on concatenated sequence)
was 3.6% and 2.3% for 7L and 6L, respectively. The D value (discriminatory
ability) of 7L and 6L were comparable, i.e. 92.0 (95% CI 87.5-96.5) vs. 93.5 (95%
CI 88.6-98.4). The dN/dS ratios calculated for each locus indicated that none
were under positive selection. Neighbor joining trees were reconstructed based on
the concatenated sequences for each scheme. Both trees showed two distinct groups
corresponding to L. interrogans and L. kirschneri, and both identified two clones
containing 10 and 7 clinical isolates, respectively. There were six instances in
which 6L split single STs as defined by 7L into closely related clusters. We
noted two discrepancies between the trees in which the genetic relatedness
between two pairs of strains were more closely related by 7L than by 6L.
CONCLUSIONS: This genetic analysis indicates that the two schemes are comparable.
We discuss their practical advantages and disadvantages.