Cargando…
An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota
Naja atra is a major venomous snake found in Taiwan. The bite of this snake causes extensive wound necrosis or necrotizing soft tissue infection. Conventional microbial culture-based techniques may fail to identify potential human pathogens and render antibiotics ineffective in the management of wou...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8078740/ https://www.ncbi.nlm.nih.gov/pubmed/33857127 http://dx.doi.org/10.1371/journal.pntd.0009331 |
_version_ | 1783685096308473856 |
---|---|
author | Mao, Yan-Chiao Chuang, Han-Ni Shih, Chien-Hung Hsieh, Han-Hsueh Jiang, Yu-Han Chiang, Liao-Chun Lin, Wen-Loung Hsiao, Tzu-Hung Liu, Po-Yu |
author_facet | Mao, Yan-Chiao Chuang, Han-Ni Shih, Chien-Hung Hsieh, Han-Hsueh Jiang, Yu-Han Chiang, Liao-Chun Lin, Wen-Loung Hsiao, Tzu-Hung Liu, Po-Yu |
author_sort | Mao, Yan-Chiao |
collection | PubMed |
description | Naja atra is a major venomous snake found in Taiwan. The bite of this snake causes extensive wound necrosis or necrotizing soft tissue infection. Conventional microbial culture-based techniques may fail to identify potential human pathogens and render antibiotics ineffective in the management of wound infection. Therefore, we evaluated 16S Sanger sequencing and next-generation sequencing (NGS) to identify bacterial species in the oropharynx of N. atra. Using conventional microbial culture methods and the VITEK 2 system, we isolated nine species from snakebite wounds. On the basis of the 16S Sanger sequencing of bacterial clones from agar plates, we identified 18 bacterial species in the oropharynx of N. atra, including Morganella morganii, Proteus vulgaris, and Proteus mirabilis, which were also present in the infected bite wound. Using NGS of 16S metagenomics, we uncovered more than 286 bacterial species in the oropharynx of N. atra. In addition, the bacterial species identified using 16S Sanger sequencing accounted for only 2% of those identified through NGS of 16S metagenomics. The bacterial microbiota of the oropharynx of N. atra were modeled better using NGS of 16S metagenomics compared to microbial culture-based techniques. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri were also identified in the NGS of 16S metagenomics. Understanding the bacterial microbiota that are native to the oropharynx of N. atra, in addition to the bite wound, may have additional therapeutic implications regarding empiric antibiotic selection for managing N. atra bites. |
format | Online Article Text |
id | pubmed-8078740 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-80787402021-05-05 An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota Mao, Yan-Chiao Chuang, Han-Ni Shih, Chien-Hung Hsieh, Han-Hsueh Jiang, Yu-Han Chiang, Liao-Chun Lin, Wen-Loung Hsiao, Tzu-Hung Liu, Po-Yu PLoS Negl Trop Dis Research Article Naja atra is a major venomous snake found in Taiwan. The bite of this snake causes extensive wound necrosis or necrotizing soft tissue infection. Conventional microbial culture-based techniques may fail to identify potential human pathogens and render antibiotics ineffective in the management of wound infection. Therefore, we evaluated 16S Sanger sequencing and next-generation sequencing (NGS) to identify bacterial species in the oropharynx of N. atra. Using conventional microbial culture methods and the VITEK 2 system, we isolated nine species from snakebite wounds. On the basis of the 16S Sanger sequencing of bacterial clones from agar plates, we identified 18 bacterial species in the oropharynx of N. atra, including Morganella morganii, Proteus vulgaris, and Proteus mirabilis, which were also present in the infected bite wound. Using NGS of 16S metagenomics, we uncovered more than 286 bacterial species in the oropharynx of N. atra. In addition, the bacterial species identified using 16S Sanger sequencing accounted for only 2% of those identified through NGS of 16S metagenomics. The bacterial microbiota of the oropharynx of N. atra were modeled better using NGS of 16S metagenomics compared to microbial culture-based techniques. Stenotrophomonas maltophilia, Acinetobacter baumannii, and Proteus penneri were also identified in the NGS of 16S metagenomics. Understanding the bacterial microbiota that are native to the oropharynx of N. atra, in addition to the bite wound, may have additional therapeutic implications regarding empiric antibiotic selection for managing N. atra bites. Public Library of Science 2021-04-15 /pmc/articles/PMC8078740/ /pubmed/33857127 http://dx.doi.org/10.1371/journal.pntd.0009331 Text en © 2021 Mao 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 Mao, Yan-Chiao Chuang, Han-Ni Shih, Chien-Hung Hsieh, Han-Hsueh Jiang, Yu-Han Chiang, Liao-Chun Lin, Wen-Loung Hsiao, Tzu-Hung Liu, Po-Yu An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota |
title | An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota |
title_full | An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota |
title_fullStr | An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota |
title_full_unstemmed | An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota |
title_short | An investigation of conventional microbial culture for the Naja atra bite wound, and the comparison between culture-based 16S Sanger sequencing and 16S metagenomics of the snake oropharyngeal bacterial microbiota |
title_sort | investigation of conventional microbial culture for the naja atra bite wound, and the comparison between culture-based 16s sanger sequencing and 16s metagenomics of the snake oropharyngeal bacterial microbiota |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8078740/ https://www.ncbi.nlm.nih.gov/pubmed/33857127 http://dx.doi.org/10.1371/journal.pntd.0009331 |
work_keys_str_mv | AT maoyanchiao aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT chuanghanni aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT shihchienhung aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT hsiehhanhsueh aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT jiangyuhan aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT chiangliaochun aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT linwenloung aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT hsiaotzuhung aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT liupoyu aninvestigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT maoyanchiao investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT chuanghanni investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT shihchienhung investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT hsiehhanhsueh investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT jiangyuhan investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT chiangliaochun investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT linwenloung investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT hsiaotzuhung investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota AT liupoyu investigationofconventionalmicrobialcultureforthenajaatrabitewoundandthecomparisonbetweenculturebased16ssangersequencingand16smetagenomicsofthesnakeoropharyngealbacterialmicrobiota |