From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms
<b>Background.</b> The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world’s second largest producer of salmon, aquacult...
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MDPI AG
2025-01-01
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| Series: | Antibiotics |
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| author | Javiera Ortiz-Severín Iñaki Hojas Felipe Redin Ervin Serón Jorge Santana Alejandro Maass Verónica Cambiazo |
| author_facet | Javiera Ortiz-Severín Iñaki Hojas Felipe Redin Ervin Serón Jorge Santana Alejandro Maass Verónica Cambiazo |
| author_sort | Javiera Ortiz-Severín |
| collection | DOAJ |
| description | <b>Background.</b> The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world’s second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. <b>Methods.</b> Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover <i>floR</i> gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. <b>Results.</b> Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The <i>floR</i> gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference <i>floR</i>. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the <i>floR</i> sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. <b>Conclusions.</b> This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms. |
| format | Article |
| id | doaj-art-c0e87aadf5554ae89f87784f31b54568 |
| institution | DOAJ |
| issn | 2079-6382 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj-art-c0e87aadf5554ae89f87784f31b545682025-08-20T02:44:52ZengMDPI AGAntibiotics2079-63822025-01-0114212210.3390/antibiotics14020122From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon FarmsJaviera Ortiz-Severín0Iñaki Hojas1Felipe Redin2Ervin Serón3Jorge Santana4Alejandro Maass5Verónica Cambiazo6Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830490, ChileCentro de Modelamiento Matemático, Universidad de Chile and UMI-CNRS 2807, Santiago 8370415, ChileLaboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830490, ChileEtecma EIRL, Puerto Montt 5500001, ChileEtecma EIRL, Puerto Montt 5500001, ChileCentro de Modelamiento Matemático, Universidad de Chile and UMI-CNRS 2807, Santiago 8370415, ChileLaboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago 7830490, Chile<b>Background.</b> The increase in antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is related to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world’s second largest producer of salmon, aquaculture is considered the main source of antibiotics in coastal waters. In this work, we aimed to characterize the genetic and phenotypic profiles of antibiotic resistance in bacterial communities from salmon farms. <b>Methods.</b> Bacterial metagenomes from an intensive aquaculture zone in southern Chile were sequenced, and the composition, abundance and sequence of antibiotic resistance genes (ARGs) were analyzed using assembled and raw read data. Total DNA from bacterial communities was used as a template to recover <i>floR</i> gene variants, which were tested by heterologous expression and functional characterization of phenicol resistance. <b>Results.</b> Prediction of ARGs in salmon farm metagenomes using more permissive parameters yielded significantly more results than the default Resistance Gene Identifier (RGI) software. ARGs grouped into drug classes showed similar abundance profiles to global ocean bacteria. The <i>floR</i> gene was the most abundant phenicol-resistance gene with the lowest gene counts, showing a conserved sequence although with variations from the reference <i>floR</i>. These differences were recovered by RGI prediction and, in greater depth, by mapping reads to the <i>floR</i> sequence using SNP base-calling. These variants were analyzed by heterologous expression, revealing the co-existence of high- and low-resistance sequences in the environmental bacteria. <b>Conclusions.</b> This study highlights the importance of combining metagenomic and phenotypic approaches to study the genetic variability in and evolution of antibiotic-resistant bacteria associated with salmon farms.https://www.mdpi.com/2079-6382/14/2/122salmon aquaculturemarine bacterial communitiesmetagenomicsflorfenicolantibiotic resistance<i>floR</i> gene |
| spellingShingle | Javiera Ortiz-Severín Iñaki Hojas Felipe Redin Ervin Serón Jorge Santana Alejandro Maass Verónica Cambiazo From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms Antibiotics salmon aquaculture marine bacterial communities metagenomics florfenicol antibiotic resistance <i>floR</i> gene |
| title | From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms |
| title_full | From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms |
| title_fullStr | From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms |
| title_full_unstemmed | From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms |
| title_short | From Metagenomes to Functional Expression of Resistance: <i>floR</i> Gene Diversity in Bacteria from Salmon Farms |
| title_sort | from metagenomes to functional expression of resistance i flor i gene diversity in bacteria from salmon farms |
| topic | salmon aquaculture marine bacterial communities metagenomics florfenicol antibiotic resistance <i>floR</i> gene |
| url | https://www.mdpi.com/2079-6382/14/2/122 |
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