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Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities
Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9176274/ https://www.ncbi.nlm.nih.gov/pubmed/35298369 http://dx.doi.org/10.1099/mgen.0.000788 |
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author | Ghaly, Timothy M. Penesyan, Anahit Pritchard, Alexander Qi, Qin Rajabal, Vaheesan Tetu, Sasha G. Gillings, Michael R. |
author_facet | Ghaly, Timothy M. Penesyan, Anahit Pritchard, Alexander Qi, Qin Rajabal, Vaheesan Tetu, Sasha G. Gillings, Michael R. |
author_sort | Ghaly, Timothy M. |
collection | PubMed |
description | Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants; investigating the functional diversity of integron-carrying bacteria; and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their amplification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the amplification, sequence processing, and validation of gene cassette amplicons from complex communities. We describe two different PCR assays that either amplify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the performance of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent amplicons from genuine integrons. Using a diverse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per sample and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single sample. In particular, we show that class one integrons are collecting and concentrating resistance genes out of the broader diversity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome sample. |
format | Online Article Text |
id | pubmed-9176274 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-91762742022-06-09 Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities Ghaly, Timothy M. Penesyan, Anahit Pritchard, Alexander Qi, Qin Rajabal, Vaheesan Tetu, Sasha G. Gillings, Michael R. Microb Genom Methods Integrons are microbial genetic elements that can integrate mobile gene cassettes. They are mostly known for spreading antibiotic resistance cassettes among human pathogens. However, beyond clinical settings, gene cassettes encode an extraordinarily diverse range of functions important for bacterial adaptation. The recovery and sequencing of cassettes has promising applications, including: surveillance of clinically important genes, particularly antibiotic resistance determinants; investigating the functional diversity of integron-carrying bacteria; and novel enzyme discovery. Although gene cassettes can be directly recovered using PCR, there are no standardised methods for their amplification and, importantly, for validating sequences as genuine integron gene cassettes. Here, we present reproducible methods for the amplification, sequence processing, and validation of gene cassette amplicons from complex communities. We describe two different PCR assays that either amplify cassettes together with integron integrases, or gene cassettes together within cassette arrays. We compare the performance of Nanopore and Illumina sequencing, and present bioinformatic pipelines that filter sequences to ensure that they represent amplicons from genuine integrons. Using a diverse set of environmental DNAs, we show that our approach can consistently recover thousands of unique cassettes per sample and up to hundreds of different integron integrases. Recovered cassettes confer a wide range of functions, including antibiotic resistance, with as many as 300 resistance cassettes found in a single sample. In particular, we show that class one integrons are collecting and concentrating resistance genes out of the broader diversity of cassette functions. The methods described here can be applied to any environmental or clinical microbiome sample. Microbiology Society 2022-03-17 /pmc/articles/PMC9176274/ /pubmed/35298369 http://dx.doi.org/10.1099/mgen.0.000788 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution. |
spellingShingle | Methods Ghaly, Timothy M. Penesyan, Anahit Pritchard, Alexander Qi, Qin Rajabal, Vaheesan Tetu, Sasha G. Gillings, Michael R. Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
title | Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
title_full | Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
title_fullStr | Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
title_full_unstemmed | Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
title_short | Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
title_sort | methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities |
topic | Methods |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9176274/ https://www.ncbi.nlm.nih.gov/pubmed/35298369 http://dx.doi.org/10.1099/mgen.0.000788 |
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