Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data

Rozman, Vita; Lorbeg, Petra Mohar; Accetto, Tomaž; Matijašić, Bojana Bogovič

doi:10.1016/j.ijfoodmicro.2019.108388

Cited by 63 publications

(38 citation statements)

References 78 publications

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“…This hypothesis is also supported by an earlier report suggesting that tetracycline resistance genes in the human intestinal bifidobacteria might have been acquired from intestinal pathogens [87]. Although it is important that LAB for the food and probiotic applications should be free of antibiotic resistance and the associated genes, some previous reports have shown the absence of a correlation between the antibiotic resistance phenotype and genotype [86, 88]. Thus, the mechanism of antibiotic resistance in the strains lacking related ARGs and that of the antibiotic susceptibility in spite of having the ARGs needs to be studied in detail in Lactobacillaceae .…”

Section: Resultsmentioning

confidence: 65%

Plasmids encode niche-specific traits in Lactobacillaceae

2021

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Species belonging to the family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbour plasmids that encode important genes. In this study, we performed comparative genomic analysis of publicly available data for 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-thirds of the species had at least one plasmid-harbouring strain. Plasmid abundance and GC content were significantly lower in vertebrate-adapted species as compared to nomadic and free-living species. Hierarchical clustering highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the vertebrate-adapted species. EggNOG-assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin–antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters and the major facilitator superfamily were overrepresented on the plasmids of the vertebrate-adapted species. These genomic signatures correlate with the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of vertebrate-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to their respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.

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Section: Resultsmentioning

confidence: 65%

Plasmids encode niche-specific traits in Lactobacillaceae

2021

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“…However, there is an increasing concern that LAB may act as reservoirs of AR determinants, from which they could ultimately be transferred to pathogens [3,20]. Indeed, the existence of lactobacilli and bifidobacteria strains resistant to several antibiotics, by either acquiring mutations or exogenous genes, has been repeatedly reported [21][22][23][24][25]. Therefore, during the selection of probiotics, the susceptibility of lactobacilli and bifidobacteria to antibiotics has to be assessed and the absence in the selected strains of transferable AR genes should be assured [26].…”

Section: Discussionmentioning

confidence: 99%

Antibiotic Susceptibility Profiles of Lactic Acid Bacteria from the Human Vagina and Genetic Basis of Acquired Resistances

Sirichoat

Flórez

Vázquez

et al. 2020

IJMS

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Lactic acid bacteria can act as reservoirs of antibiotic resistance genes that can be ultimately transferred to pathogens. The present work reports on the minimum inhibitory concentration (MIC) of 16 antibiotics to 25 LAB isolates of five Lactobacillus and one Bifidobacterium species from the human vagina. Acquired resistances were detected to kanamycin, streptomycin, chloramphenicol, gentamicin, and ampicillin. A PCR analysis of lactobacilli failed to identify genetic determinants involved in any of these resistances. Surprisingly, a tet(W) gene was detected by PCR in two Bifidobacterium bifidum strains, although they proved to be tetracycline-susceptible. In agreement with the PCR results, no acquired genes were identified in the genome of any of the Lactobacillus spp. strains sequenced. A genome analysis of B. bifidum VA07-1AN showed an insertion of two guanines in the middle of tet(W) interrupting the open reading frame. By growing the strain in the presence of tetracycline, stable tetracycline-resistant variants were obtained. An amino acid substitution in the ribosomal protein S12 (K43R) was further identified as the most likely cause of VA07-1AN being streptomycin resistance. The results of this work expand our knowledge of the resistance profiles of vaginal LAB and provide evidence for the genetic basis of some acquired resistances.

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“…This hypothesis is also supported by an earlier report suggesting that the tetracycline resistance genes in the human intestinal bifidobacteria might have been acquired from the intestinal pathogens (87). Although it is important that LAB for the food and probiotic applications should be free of antibiotic resistance and the associated genes, some of the previous reports have shown the absence of correlation between the antibiotic resistance phenotype and genotype (86), (88). Thus, the mechanism of antibiotic resistance in the strains lacking the related ARGs and that of the antibiotic susceptibility in spite of having the ARGs needs to be deeply studied in Lactobacillaceae .…”

Section: Resultsmentioning

confidence: 99%

Plasmids encode niche-specific traits in Lactobacillaceae

Davray

Deo

Kulkarni

2020

Preprint

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The species of family Lactobacillaceae are found in highly diverse environments and play an important role in fermented foods and probiotic products. Many of these species have been individually reported to harbor plasmids that encode important genes. In this study, we performed comparative genomic analysis of the publically available data of 512 plasmids from 282 strains represented by 51 species of this family and correlated the genomic features of plasmids with the ecological niches in which these species are found. Two-third of the species had at least one plasmid-harboring strain. Plasmid abundance and GC content were significantly lower in the host-adapted species as compared to the nomadic and free-living species. Hierarchical clustering (HCL) highlighted the distinct nature of plasmids from the nomadic and free-living species than those from the host-adapted species. EggNOG assisted functional annotation revealed that genes associated with transposition, conjugation, DNA repair and recombination, exopolysaccharide production, metal ion transport, toxin-antitoxin system, and stress tolerance were significantly enriched on the plasmids of the nomadic and in some cases nomadic and free-living species. On the other hand, genes related to anaerobic metabolism, ABC transporters, and major facilitator superfamily were found to be overrepresented on the plasmids of the host-adapted species. These genomic signatures are correlated to the comparatively nutrient-depleted, stressful and dynamic environments of nomadic and free-living species and nutrient-rich and anaerobic environments of the host-adapted species. Thus, these results indicate the contribution of the plasmids in the adaptation of lactobacilli to the respective habitats. This study also underlines the potential application of these plasmids in improving the technological and probiotic properties of lactic acid bacteria.

show abstract

Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data

Cited by 63 publications

References 78 publications

Plasmids encode niche-specific traits in Lactobacillaceae

Plasmids encode niche-specific traits in Lactobacillaceae

Antibiotic Susceptibility Profiles of Lactic Acid Bacteria from the Human Vagina and Genetic Basis of Acquired Resistances

Plasmids encode niche-specific traits in Lactobacillaceae

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