Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles

Yuda Disastra; Thidathip Wongsurawat; Piroon Jenjaroenpun; David Hampson; Ratchnida Kamwa; Nuvee Prapasarakul

doi:10.1371/journal.pone.0332506

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Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles

Journal article

Open access

Peer reviewed

Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles

Yuda Disastra, Thidathip Wongsurawat, Piroon Jenjaroenpun, David Hampson, Ratchnida Kamwa and Nuvee Prapasarakul

PloS one, Vol.20(9), e0332506

2025

DOI: https://doi.org/10.1371/journal.pone.0332506

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Abstract

Agricultural research

Antibiotics

Antimicrobial agents

Antimicrobial resistance

Bacteria

Best practice

Clindamycin

Drug resistance

E coli

Farms

Food

Gene sequencing

Gene transfer

Genes

Genomes

Genomics

Horizontal transfer

Identification

Livestock

Metabolism

Metabolites

Pediococcus acidilactici

Phylogenetics

Plasmids

Probiotics

Risk reduction

Safety

Safety analysis

Virulence

Virulence factors

Whole genome sequencing

The increasing use of probiotics in livestock necessitates rigorous safety assessments to mitigate risks such as their inadvertent contribution to antimicrobial resistance (AMR) and horizontal gene transfer (HGT). This study employs whole-genome sequencing using both long-read (GridION, Oxford Nanopore Technologies) and short-read (Illumina, San Diego, CA, USA) platforms to assess the genomic and plasmidome profiles of five Thai strains of Pediococcus acidilactici, that previously have been evaluated for probiotic potential in livestock. Our comprehensive analysis identified genes encoding AMR, virulence factors, and probiotic-related genes. Notably, strains AF2519 and AF2019 harbored plasmid-borne tet(M) and erm(B) genes, with tet(M) embedded in a novel composite genetic arrangement flanked by mobile elements, suggesting historical recombination and altered mobility potential. Strains IAF6519, IAF5919, and P72N, free from plasmid-borne AMR genes, emerged as safer candidates, lacking virulence genes. Phenotypic tests revealed discrepancies with genomic data; for instance, AF2019 was resistant to clindamycin without detectable genes, and showed susceptibility to tetracycline despite the presence of tet(M). The absence of complete transfer machinery in AF2519 and AF2019 suggests a reduced HGT risk. These findings underscore the importance of integrating genomic and phenotypic approaches in probiotic safety evaluations. The presence of plasmid-borne AMR genes in certain strains advises caution in their use, impacting probiotic selection and regulatory compliance in agriculture. This research informs policies and best practices for safe probiotic deployment, ensuring both efficacy and safety.

Details

Title: Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles
Authors/Creators: Yuda Disastra - Chulalongkorn University
Thidathip Wongsurawat - Siriraj Hospital
Piroon Jenjaroenpun - Siriraj Hospital
David Hampson
Ratchnida Kamwa - Chulalongkorn University
Nuvee Prapasarakul - Chulalongkorn University
Publication Details: PloS one, Vol.20(9), e0332506
Publisher: Public Library of Science
Identifiers: 991005816849707891
Murdoch Affiliation: School of Veterinary Medicine
Language: English
Resource Type: Journal article

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