Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives

European Food Safety Authority (EFSA); Silvia Peluso; Margarita Aguilera-Gómez; Valeria Bortolaia; Francesco Catania; Pier Sandro Cocconcelli; Lieve Herman; Simon Moxon; Laurence Vernis; Giovanni Iacono; Simone Lunardi; Elisa Pettenati; Arianna Gallo; Jaime Aguilera

doi:10.2903/sp.efsa.2024.EN-8931

Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives

European Food Safety Authority (EFSA), Silvia Peluso, Margarita Aguilera-Gómez, Valeria Bortolaia, Francesco Catania, Pier Sandro Cocconcelli, Lieve Herman, Simon Moxon, Laurence Vernis, Giovanni Iacono, Simone Lunardi, Elisa Pettenati, Arianna Gallo, Jaime Aguilera

School of Biological Sciences

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Abstract

A key step in the characterisation of bacterial strains used in the food and feed chain is the identification of antimicrobial resistance (AMR) genes in their genomes. The presence of acquired AMR genes influences important aspects of the risk assessment, such as the applicability of the qualified presumption of safety (QPS) approach, which can have a direct impact on the data requirements. Aiming to implement the EFSA approach to discriminate between ‘intrinsic’ and ‘acquired’ AMR genes, a bioinformatics pipeline was developed and applied to the species of the genus Bacillus that are most frequently subjects of applications for regulated products submitted to EFSA. The results are presented as a catalogue of genes indicating their abundance and distribution among complete and confirmed genomes publicly available for each species. The results of this work are aimed to support the evaluation of AMR genes in a consistent and harmonised way.

Original language	English
Journal	EFSA Journal
Volume	21
Issue number	7
Early online date	18 Jul 2024
DOIs	https://doi.org/10.2903/sp.efsa.2024.EN-8931
Publication status	Published - Jul 2024

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European Food Safety Authority (EFSA), Peluso, S., Aguilera-Gómez, M., Bortolaia, V., Catania, F., Cocconcelli, P. S., Herman, L., Moxon, S., Vernis, L., Iacono, G., Lunardi, S., Pettenati, E., Gallo, A., & Aguilera, J. (2024). Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives. EFSA Journal, 21(7). https://doi.org/10.2903/sp.efsa.2024.EN-8931

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title = "Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives",

abstract = "A key step in the characterisation of bacterial strains used in the food and feed chain is the identification of antimicrobial resistance (AMR) genes in their genomes. The presence of acquired AMR genes influences important aspects of the risk assessment, such as the applicability of the qualified presumption of safety (QPS) approach, which can have a direct impact on the data requirements. Aiming to implement the EFSA approach to discriminate between {\textquoteleft}intrinsic{\textquoteright} and {\textquoteleft}acquired{\textquoteright} AMR genes, a bioinformatics pipeline was developed and applied to the species of the genus Bacillus that are most frequently subjects of applications for regulated products submitted to EFSA. The results are presented as a catalogue of genes indicating their abundance and distribution among complete and confirmed genomes publicly available for each species. The results of this work are aimed to support the evaluation of AMR genes in a consistent and harmonised way.",

author = "{European Food Safety Authority (EFSA)} and Silvia Peluso and Margarita Aguilera-G{\'o}mez and Valeria Bortolaia and Francesco Catania and Cocconcelli, {Pier Sandro} and Lieve Herman and Simon Moxon and Laurence Vernis and Giovanni Iacono and Simone Lunardi and Elisa Pettenati and Arianna Gallo and Jaime Aguilera",

year = "2024",

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European Food Safety Authority (EFSA), Peluso, S, Aguilera-Gómez, M, Bortolaia, V, Catania, F, Cocconcelli, PS, Herman, L, Moxon, S, Vernis, L, Iacono, G, Lunardi, S, Pettenati, E, Gallo, A & Aguilera, J 2024, 'Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives', EFSA Journal, vol. 21, no. 7. https://doi.org/10.2903/sp.efsa.2024.EN-8931

TY - JOUR

T1 - Catalogue of antimicrobial resistance genes in species of Bacillus used to produce food enzymes and feed additives

AU - European Food Safety Authority (EFSA)

AU - Peluso, Silvia

AU - Aguilera-Gómez, Margarita

AU - Bortolaia, Valeria

AU - Catania, Francesco

AU - Cocconcelli, Pier Sandro

AU - Herman, Lieve

AU - Moxon, Simon

AU - Vernis, Laurence

AU - Iacono, Giovanni

AU - Lunardi, Simone

AU - Pettenati, Elisa

AU - Gallo, Arianna

AU - Aguilera, Jaime

PY - 2024/7

Y1 - 2024/7

N2 - A key step in the characterisation of bacterial strains used in the food and feed chain is the identification of antimicrobial resistance (AMR) genes in their genomes. The presence of acquired AMR genes influences important aspects of the risk assessment, such as the applicability of the qualified presumption of safety (QPS) approach, which can have a direct impact on the data requirements. Aiming to implement the EFSA approach to discriminate between ‘intrinsic’ and ‘acquired’ AMR genes, a bioinformatics pipeline was developed and applied to the species of the genus Bacillus that are most frequently subjects of applications for regulated products submitted to EFSA. The results are presented as a catalogue of genes indicating their abundance and distribution among complete and confirmed genomes publicly available for each species. The results of this work are aimed to support the evaluation of AMR genes in a consistent and harmonised way.

AB - A key step in the characterisation of bacterial strains used in the food and feed chain is the identification of antimicrobial resistance (AMR) genes in their genomes. The presence of acquired AMR genes influences important aspects of the risk assessment, such as the applicability of the qualified presumption of safety (QPS) approach, which can have a direct impact on the data requirements. Aiming to implement the EFSA approach to discriminate between ‘intrinsic’ and ‘acquired’ AMR genes, a bioinformatics pipeline was developed and applied to the species of the genus Bacillus that are most frequently subjects of applications for regulated products submitted to EFSA. The results are presented as a catalogue of genes indicating their abundance and distribution among complete and confirmed genomes publicly available for each species. The results of this work are aimed to support the evaluation of AMR genes in a consistent and harmonised way.

U2 - 10.2903/sp.efsa.2024.EN-8931

DO - 10.2903/sp.efsa.2024.EN-8931

M3 - Comment/debate

VL - 21

JO - EFSA Journal

JF - EFSA Journal

SN - 1831-4732

IS - 7

ER -