Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates

Cerqueira, Gustavo M., McBride, Alan J.A., Hartskeerl, Rudy A., Ahmed, Nyiaz, Dellagostin, Odir A., Eslabão, Marcus R., and Nascimento, Ana L.T. (2010) Bioinformatics describes novel Loci for high resolution discrimination of leptospira isolates. PLoS ONE, 5. e15335. pp. 1-7.

[img]
Preview
PDF (Published Version) - Published Version
Available under License Creative Commons Attribution.

Download (270kB) | Preview
View at Publisher Website: http://dx.doi.org/10.1371/journal.pone.0...
 
56


Abstract

Background: Leptospirosis is one of the most widespread zoonoses in the world and with over 260 pathogenic serovars there is an urgent need for a molecular system of classification. The development of multilocus sequence typing (MLST) schemes for Leptospira spp. is addressing this issue. The aim of this study was to identify loci with potential to enhance Leptospira strain discrimination by sequencing-based methods.

Methodology and Principal Findings: We used bioinformatics to evaluate pre-existing loci with the potential to increase the discrimination of outbreak strains. Previously deposited sequence data were evaluated by phylogenetic analyses using either single or concatenated sequences. We identified and evaluated the applicability of the ligB, secY, rpoB and lipL41 loci, individually and in combination, to discriminate between 38 pathogenic Leptospira strains and to cluster them according to the species they belonged to. Pairwise identity among the loci ranged from 82.0-92.0%, while interspecies identity was 97.7-98.5%. Using the ligB-secY-rpoB-lipL41 superlocus it was possible to discriminate 34/38 strains, which belong to six pathogenic Leptospira species. In addition, the sequences were concatenated with the superloci from 16 sequence types from a previous MLST scheme employed to study the association of a leptospiral clone with an outbreak of human leptospirosis in Thailand. Their use enhanced the discriminative power of the existing scheme. The lipL41 and rpoB loci raised the resolution from 81.0-100%, but the enhanced scheme still remains limited to the L. interrogans and L. kirschneri species.

Conclusions: As the first aim of our study, the ligB-secY-rpoB-lipL41 superlocus demonstrated a satisfactory level of discrimination among the strains evaluated. Second, the inclusion of the rpoB and lipL41 loci to a MLST scheme provided high resolution for discrimination of strains within L. interrogans and L. kirschneri and might be useful in future epidemiological studies.

Item ID: 37417
Item Type: Article (Research - C1)
ISSN: 1932-6203
Additional Information:

© 2010 Cerqueira, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Date Deposited: 25 Feb 2015 03:20
FoR Codes: 06 BIOLOGICAL SCIENCES > 0601 Biochemistry and Cell Biology > 060102 Bioinformatics @ 40%
06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060502 Infectious Agents @ 30%
06 BIOLOGICAL SCIENCES > 0605 Microbiology > 060503 Microbial Genetics @ 30%
SEO Codes: 97 EXPANDING KNOWLEDGE > 970106 Expanding Knowledge in the Biological Sciences @ 100%
Downloads: Total: 56
Last 12 Months: 22
More Statistics

Actions (Repository Staff Only)

Item Control Page Item Control Page