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Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing

Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent qualit...

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Autores principales: Kumar, Abhishek, Skrahina, Volha, Atta, Joshua, Boettcher, Veronika, Hanig, Nicola, Rolfs, Arndt, Oprea, Gabriela, Ameziane, Najim
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9941560/
https://www.ncbi.nlm.nih.gov/pubmed/36824435
http://dx.doi.org/10.3389/fgene.2023.1081424
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author Kumar, Abhishek
Skrahina, Volha
Atta, Joshua
Boettcher, Veronika
Hanig, Nicola
Rolfs, Arndt
Oprea, Gabriela
Ameziane, Najim
author_facet Kumar, Abhishek
Skrahina, Volha
Atta, Joshua
Boettcher, Veronika
Hanig, Nicola
Rolfs, Arndt
Oprea, Gabriela
Ameziane, Najim
author_sort Kumar, Abhishek
collection PubMed
description Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent quality of human DNA that can be isolated from such samples, we observed the presence of non-human DNA sequences at varying percentages. We investigated the proportion of non-human mapped reads (NHMR) sequenced from buccal swabs and saliva, the type of microbial genomes from which they were derived, and impact on molecular classification. Read sequences that did not map to the human reference genome were aligned to complete reference microbial reference sequences from the National Center for Biotechnology Information’s (NCBI) RefSeq database using Kraken2. Out of 765 analyzed samples over 80% demonstrated more than 5% NHMRs. The majority of NHMRs were from bacterial genomes (average 69%, buccal swabs and 54% saliva), while the proportion of viruses was low, averaging 0.32% (buccal swabs) and 0.07% (saliva). We identified more than 30 different bacterial families of which Streptococcus mitis and Rothia mucilaginosa were the most common species. Importantly, the level of contamination did not impact the diagnostic yield.
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spelling pubmed-99415602023-02-22 Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing Kumar, Abhishek Skrahina, Volha Atta, Joshua Boettcher, Veronika Hanig, Nicola Rolfs, Arndt Oprea, Gabriela Ameziane, Najim Front Genet Genetics Biological material from the oral cavity is an excellent source of samples for genetic diagnostics. This is because collection is quick, easy-to-access, and non-invasive. We have set-up clinical whole genome sequence testing for patients with suspected hereditary disease. Beside the excellent quality of human DNA that can be isolated from such samples, we observed the presence of non-human DNA sequences at varying percentages. We investigated the proportion of non-human mapped reads (NHMR) sequenced from buccal swabs and saliva, the type of microbial genomes from which they were derived, and impact on molecular classification. Read sequences that did not map to the human reference genome were aligned to complete reference microbial reference sequences from the National Center for Biotechnology Information’s (NCBI) RefSeq database using Kraken2. Out of 765 analyzed samples over 80% demonstrated more than 5% NHMRs. The majority of NHMRs were from bacterial genomes (average 69%, buccal swabs and 54% saliva), while the proportion of viruses was low, averaging 0.32% (buccal swabs) and 0.07% (saliva). We identified more than 30 different bacterial families of which Streptococcus mitis and Rothia mucilaginosa were the most common species. Importantly, the level of contamination did not impact the diagnostic yield. Frontiers Media S.A. 2023-02-07 /pmc/articles/PMC9941560/ /pubmed/36824435 http://dx.doi.org/10.3389/fgene.2023.1081424 Text en Copyright © 2023 Kumar, Skrahina, Atta, Boettcher, Hanig, Rolfs, Oprea and Ameziane. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Kumar, Abhishek
Skrahina, Volha
Atta, Joshua
Boettcher, Veronika
Hanig, Nicola
Rolfs, Arndt
Oprea, Gabriela
Ameziane, Najim
Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
title Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
title_full Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
title_fullStr Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
title_full_unstemmed Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
title_short Microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
title_sort microbial contamination and composition of oral samples subjected to clinical whole genome sequencing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9941560/
https://www.ncbi.nlm.nih.gov/pubmed/36824435
http://dx.doi.org/10.3389/fgene.2023.1081424
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