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Open Access CC BY-NC-ND V4.0
Journal article
Whole-genome sequencing reveals hidden antimicrobial resistance genes in phenotypically susceptible probiotic candidate lactic acid bacteria
Scientific reports, Vol.16, 27986
2026
PMID: 42315553
Abstract
Phenotypic assays commonly used to evaluate probiotic safety may fail to detect clinically relevant antimicrobial resistance (AMR), potentially allowing genetically concerning strains to appear acceptable based on MIC testing alone. To explore this issue, we applied whole-genome sequencing (WGS) to three lactic acid bacteria (LAB) isolates previously identified as probiotic candidates based on acid and bile tolerance, antagonism against enteric pathogens, and biofilm formation in vitro: Lactiplantibacillus plantarum L25F and L22F (from pigs) and Ligilactobacillus salivarius AF2319 (from a chicken). Genome annotation identified extensive repertoires of probiotic-associated genes (46-47 per strain) linked to stress tolerance, adhesion, immunomodulation, and quorum sensing, supporting functional potential. The two L. plantarum strains exhibited broader predicted metabolic capacities than L. salivarius AF2319. However, genomic analysis revealed acquired AMR genes with complex genotype-phenotype relationships not fully apparent from phenotypic testing. The L. plantarum strains harbored lnu(A) (99.79% identity) on extrachromosomal DNA, conferring the L-phenotype (lincomycin resistance, clindamycin susceptibility); clindamycin MICs (1 mg/L) were concordant with this genotype, though lincomycin MICs were not determined. L. salivarius AF2319 carried tet(M), tet(L), and erm(C) (99.48%, 99.49%, and 99.45% identity by ResFinder, respectively) on extrachromosomal DNA; notably, the erythromycin MIC (1 mg/L) was precisely at the EFSA breakpoint (≤ 1 mg/L), representing borderline genotype-phenotype discordance potentially due to silent gene expression. Under current EFSA QPS criteria, these acquired ARGs would preclude all three strains from approval as probiotic feed additives despite favorable functional profiles, underscoring the indispensable role of WGS-based AMR gene detection in modern probiotic safety evaluation.
Details
- Title
- Whole-genome sequencing reveals hidden antimicrobial resistance genes in phenotypically susceptible probiotic candidate lactic acid bacteria
- Authors/Creators
- Yuda Disastra - Chulalongkorn UniversityThidathip Wongsurawat - Siriraj HospitalPiroon Jenjaroenpun - Siriraj HospitalDavid John Hampson - Murdoch UniversityRatchnida Kamwa - Chulalongkorn UniversityNuvee Prapasarakul - Chulalongkorn University
- Publication Details
- Scientific reports, Vol.16, 27986
- Publisher
- Springer Nature
- Grant note
- (FOOD_FF681253100014) / the 2568-Fundamental Fund, Thailand Science Research and Innovation
- Identifiers
- 991005896087407891
- Copyright
- © The Author(s) 2026.
- Murdoch Affiliation
- School of Veterinary Medicine
- Language
- English
- Resource Type
- Journal article
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