Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts
The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microb...
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doaj-8292cde0c6cc47ba94c84545fcd193ff2021-04-27T23:06:43ZengMDPI AGMicroorganisms2076-26072021-04-01993793710.3390/microorganisms9050937Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean SproutsMilada Solcova0Katerina Demnerova1Sabina Purkrtova2Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 16628 Prague 6, Czech RepublicDepartment of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 16628 Prague 6, Czech RepublicDepartment of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technicka 3, 16628 Prague 6, Czech RepublicThe aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. The species diversity obtained by NS and by cultivation methods with MALDI-TOF MS identification was comparable. In both samples, before and after cultivation (30 °C, 48 h), the dominant part of bacteriome formed <i>Gammaproteobacteria</i> (<i>Enterobacteriaceae, Erwiniaceae, Pseudomonadaceae, Moraxellaceae</i>) and then <i>Firmicutes</i> (<i>Streptococcaceae</i>). The diversity and abundance of single ARGs groups were comparable for both samples despite bacteriome differences. More than 50% of the detected ARGs alignments were mutations conferring resistance to aminoglycosides (16S rRNA), resistance to fluoroquinolones (<i>gyr</i>A, <i>gyr</i>B, <i>par</i>C, <i>par</i>D) and elfamycin (EF-Tu). ARGs encoding efflux pumps formed more than 30% of the detected alignments. Beta-lactamases were represented by many variants, but were less abundant.https://www.mdpi.com/2076-2607/9/5/937spread of antibiotic resistanceantibiotic resistance genesfood chainfood safetynanopore sequencingMinION |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Milada Solcova Katerina Demnerova Sabina Purkrtova |
spellingShingle |
Milada Solcova Katerina Demnerova Sabina Purkrtova Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts Microorganisms spread of antibiotic resistance antibiotic resistance genes food chain food safety nanopore sequencing MinION |
author_facet |
Milada Solcova Katerina Demnerova Sabina Purkrtova |
author_sort |
Milada Solcova |
title |
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts |
title_short |
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts |
title_full |
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts |
title_fullStr |
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts |
title_full_unstemmed |
Application of Nanopore Sequencing (MinION) for the Analysis of Bacteriome and Resistome of Bean Sprouts |
title_sort |
application of nanopore sequencing (minion) for the analysis of bacteriome and resistome of bean sprouts |
publisher |
MDPI AG |
series |
Microorganisms |
issn |
2076-2607 |
publishDate |
2021-04-01 |
description |
The aspiration these days is to apply rapid methods for parallel analysis of bacteriome and resistome of food samples to increase food safety and prevent antibiotic resistance genes (ARGs) spreading. In this work, we used nanopore sequencing (NS) to determine the diversity and dynamics of the microbiome and resistome in two types of bean sprouts. We proved that NS provided an easy, quick, and reliable way to identify the microbiome and resistome of a food sample also. The species diversity obtained by NS and by cultivation methods with MALDI-TOF MS identification was comparable. In both samples, before and after cultivation (30 °C, 48 h), the dominant part of bacteriome formed <i>Gammaproteobacteria</i> (<i>Enterobacteriaceae, Erwiniaceae, Pseudomonadaceae, Moraxellaceae</i>) and then <i>Firmicutes</i> (<i>Streptococcaceae</i>). The diversity and abundance of single ARGs groups were comparable for both samples despite bacteriome differences. More than 50% of the detected ARGs alignments were mutations conferring resistance to aminoglycosides (16S rRNA), resistance to fluoroquinolones (<i>gyr</i>A, <i>gyr</i>B, <i>par</i>C, <i>par</i>D) and elfamycin (EF-Tu). ARGs encoding efflux pumps formed more than 30% of the detected alignments. Beta-lactamases were represented by many variants, but were less abundant. |
topic |
spread of antibiotic resistance antibiotic resistance genes food chain food safety nanopore sequencing MinION |
url |
https://www.mdpi.com/2076-2607/9/5/937 |
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