Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources

Leptospirosis is currently emerging globally as reflected by the increase in the number of Leptospira infections. The scope of research on identification of individual Leptospira species through a rapid assay in local setting is still lacking. This study attempts to determine the Leptospira speci...

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Main Author:	Zulkifli, Nurul Farhana
Format:	Thesis
Language:	English
Published:	2019
Subjects:	Leptospirosis
Online Access:	http://psasir.upm.edu.my/id/eprint/84213/1/FPSK%20%28m%29%202019%2038%20UPM%20ir.pdf
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id	my-upm-ir.84213
record_format	uketd_dc
spelling	my-upm-ir.842132022-01-04T02:33:26Z Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources 2019-01 Zulkifli, Nurul Farhana Leptospirosis is currently emerging globally as reflected by the increase in the number of Leptospira infections. The scope of research on identification of individual Leptospira species through a rapid assay in local setting is still lacking. This study attempts to determine the Leptospira species distribution in clinical and environmental samples using molecular approach. The blood for clinical samples (n=64) were collected from patients whom have been suspected with leptospirosis, and the environmental samples (n=105) consisting of soils and waters were collected from areas with potential sources of Leptospira transmission. All samples were directly extracted for DNA and subjected to PCR using three sets of established primers; 16S rRNA, rpoB, and lipL32. Positive samples were further analysed on their DNA sequences and also through phylogenetic analysis. Six clinical samples were amplified for 16S rRNA gene and four clinical samples showed an amplification of rpoB gene that was highly matched to pathogenic Leptospira spp. in GenBank. Out of 13 positive results amplified for 16S rRNA from environmental samples, only five were detected to have been contaminated by Leptospira spp. while the others showed a higher number of contamination by different species of bacteria. The BLAST similarity results for clinical samples targeting lipL32 showed that only one out of 64 samples was highly matched to pathogenic Leptospira spp. in GenBank. The phylogenetic trees constructed shows that the positive clinical samples were clustered into group with pathogenic Leptospira spp. while the environmental samples showed a clustering into uncultured Leptospira. Overall, this study showed the ability of the molecular approach in combination with PCR in determine Leptospira species directly on both clinical and environmental samples. Although the number of positive samples were low, but the tendency of the species to appear in limited positive samples may infer the species as the likely agents in causing leptospirosis at this study setting. Leptospirosis 2019-01 Thesis http://psasir.upm.edu.my/id/eprint/84213/ http://psasir.upm.edu.my/id/eprint/84213/1/FPSK%20%28m%29%202019%2038%20UPM%20ir.pdf text en public masters Universiti Putra Malaysia Leptospirosis Mohd Desa, Mohd Nasir
institution	Universiti Putra Malaysia
collection	PSAS Institutional Repository
language	English
advisor	Mohd Desa, Mohd Nasir
topic	Leptospirosis
spellingShingle	Leptospirosis Zulkifli, Nurul Farhana Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources
description	Leptospirosis is currently emerging globally as reflected by the increase in the number of Leptospira infections. The scope of research on identification of individual Leptospira species through a rapid assay in local setting is still lacking. This study attempts to determine the Leptospira species distribution in clinical and environmental samples using molecular approach. The blood for clinical samples (n=64) were collected from patients whom have been suspected with leptospirosis, and the environmental samples (n=105) consisting of soils and waters were collected from areas with potential sources of Leptospira transmission. All samples were directly extracted for DNA and subjected to PCR using three sets of established primers; 16S rRNA, rpoB, and lipL32. Positive samples were further analysed on their DNA sequences and also through phylogenetic analysis. Six clinical samples were amplified for 16S rRNA gene and four clinical samples showed an amplification of rpoB gene that was highly matched to pathogenic Leptospira spp. in GenBank. Out of 13 positive results amplified for 16S rRNA from environmental samples, only five were detected to have been contaminated by Leptospira spp. while the others showed a higher number of contamination by different species of bacteria. The BLAST similarity results for clinical samples targeting lipL32 showed that only one out of 64 samples was highly matched to pathogenic Leptospira spp. in GenBank. The phylogenetic trees constructed shows that the positive clinical samples were clustered into group with pathogenic Leptospira spp. while the environmental samples showed a clustering into uncultured Leptospira. Overall, this study showed the ability of the molecular approach in combination with PCR in determine Leptospira species directly on both clinical and environmental samples. Although the number of positive samples were low, but the tendency of the species to appear in limited positive samples may infer the species as the likely agents in causing leptospirosis at this study setting.
format	Thesis
qualification_level	Master's degree
author	Zulkifli, Nurul Farhana
author_facet	Zulkifli, Nurul Farhana
author_sort	Zulkifli, Nurul Farhana
title	Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources
title_short	Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources
title_full	Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources
title_fullStr	Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources
title_full_unstemmed	Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources
title_sort	detection of leptospira species targeting 16s rrna, rpob, and lipl32 gene from clinical and environmental sources
granting_institution	Universiti Putra Malaysia
publishDate	2019
url	http://psasir.upm.edu.my/id/eprint/84213/1/FPSK%20%28m%29%202019%2038%20UPM%20ir.pdf
_version_	1747813450183081984

Detection of Leptospira species targeting 16S rRNA, rpoB, and lipL32 gene from clinical and environmental sources

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