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Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding

Leptospirosis is a zoonotic disease of global importance. The breadth of Leptospira diversity associated with both human and animal disease poses major logistical challenges to the use of classical diagnostic techniques, and increasingly molecular diagnostic tools are used for their detection. In Ne...

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Autores principales: Wilkinson, David A., Edwards, Matthew, Benschop, Jackie, Nisa, Shahista
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8480790/
https://www.ncbi.nlm.nih.gov/pubmed/34587213
http://dx.doi.org/10.1371/journal.pone.0257971
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author Wilkinson, David A.
Edwards, Matthew
Benschop, Jackie
Nisa, Shahista
author_facet Wilkinson, David A.
Edwards, Matthew
Benschop, Jackie
Nisa, Shahista
author_sort Wilkinson, David A.
collection PubMed
description Leptospirosis is a zoonotic disease of global importance. The breadth of Leptospira diversity associated with both human and animal disease poses major logistical challenges to the use of classical diagnostic techniques, and increasingly molecular diagnostic tools are used for their detection. In New Zealand, this has resulted in an increase in positive cases reported nationally that have not been attributed to the infecting serovar or genomospecies. In this study, we used data from all pathogenic Leptospira genomes to identify a partial region of the glmU gene as a suitable locus for the discrimination of the infecting species and serovars of New Zealand-endemic Leptospira. This method can be used in culture and culture-independent scenarios making it flexible for diagnostics in humans, animals, and environmental samples. We explored the use of this locus as a molecular barcoding tool via the Oxford Nanopore Technology (ONT) sequencing platform MinION. Sequences obtained by this method allowed specific identification of Leptospira species in mixed and enriched environmental cultures, however read error inherent in the MinION sequencing system reduced the accuracy of strain/variant identification. Using this approach to characterise Leptospira in enriched environmental cultures, we detected the likely presence of Leptospira genomospecies that have not been reported in New Zealand to date. This included a strain of L. borgpetersenii that has recently been identified in dairy cattle and sequences similar to those of L. mayottensis. L. tipperaryensis, L. dzianensis and L. alstonii.
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spelling pubmed-84807902021-09-30 Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding Wilkinson, David A. Edwards, Matthew Benschop, Jackie Nisa, Shahista PLoS One Research Article Leptospirosis is a zoonotic disease of global importance. The breadth of Leptospira diversity associated with both human and animal disease poses major logistical challenges to the use of classical diagnostic techniques, and increasingly molecular diagnostic tools are used for their detection. In New Zealand, this has resulted in an increase in positive cases reported nationally that have not been attributed to the infecting serovar or genomospecies. In this study, we used data from all pathogenic Leptospira genomes to identify a partial region of the glmU gene as a suitable locus for the discrimination of the infecting species and serovars of New Zealand-endemic Leptospira. This method can be used in culture and culture-independent scenarios making it flexible for diagnostics in humans, animals, and environmental samples. We explored the use of this locus as a molecular barcoding tool via the Oxford Nanopore Technology (ONT) sequencing platform MinION. Sequences obtained by this method allowed specific identification of Leptospira species in mixed and enriched environmental cultures, however read error inherent in the MinION sequencing system reduced the accuracy of strain/variant identification. Using this approach to characterise Leptospira in enriched environmental cultures, we detected the likely presence of Leptospira genomospecies that have not been reported in New Zealand to date. This included a strain of L. borgpetersenii that has recently been identified in dairy cattle and sequences similar to those of L. mayottensis. L. tipperaryensis, L. dzianensis and L. alstonii. Public Library of Science 2021-09-29 /pmc/articles/PMC8480790/ /pubmed/34587213 http://dx.doi.org/10.1371/journal.pone.0257971 Text en © 2021 Wilkinson et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Wilkinson, David A.
Edwards, Matthew
Benschop, Jackie
Nisa, Shahista
Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding
title Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding
title_full Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding
title_fullStr Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding
title_full_unstemmed Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding
title_short Identification of pathogenic Leptospira species and serovars in New Zealand using metabarcoding
title_sort identification of pathogenic leptospira species and serovars in new zealand using metabarcoding
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8480790/
https://www.ncbi.nlm.nih.gov/pubmed/34587213
http://dx.doi.org/10.1371/journal.pone.0257971
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