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Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture.

Noor Uddin GM, Larsen MH, Christensen H, Aarestrup FM, Phu TM, Dalsgaard A - PLoS ONE (2015)

Bottom Line: MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer.Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer.Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments.

View Article: PubMed Central - PubMed

Affiliation: Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT
Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality; however, little is known about the antimicrobial resistance properties of such probiotic bacteria and to what extent they may contribute to the development of bacterial resistance in aquaculture ponds. Concerns have been raised that the declared information on probiotic product labels are incorrect and information on bacterial composition are often missing. We therefore evaluated seven probiotics commonly used in Vietnamese shrimp culture for their bacterial species content, phenotypic antimicrobial resistance and associated transferable resistance genes. The bacterial species was established by 16S rRNA sequence analysis of 125 representative bacterial isolates. MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer. Thirteen bacterial species declared on the probiotic products could not be identified and 11 non-declared Bacillus spp. were identified. Although our culture-based isolation and identification may have missed a few bacterial species present in the tested products this would represent minor bias, but future studies may apply culture independent identification methods like pyro sequencing. Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer. Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments. Approval procedures of probiotic products must be strengthened through scientific-based efficacy trials and product labels should allow identification of individual bacterial strains and inform the farmer on specific purpose, dosage and correct application measures.

No MeSH data available.


Related in: MedlinePlus

Neighbour joining phylogenetic tree of the 16S rRNA gene sequences representing Bacillus spp. isolated from probiotic products.Type strains of Bacillus species are labeled with accession number and strain number. Strains with identical sequences are included in parenthesis after the strain selected as reference. Strains with sequences shorter than 1 kb were excluded from phylogenetic analysis and their identity only determined by similarity comparison to type strain. The scale bar represents sequence variation considering the model for nucleotide substitution (Jukes & Cantor) and tree-shape used in the neighbour joining analysis. * Strains are with too short sequences to compare.
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pone.0132338.g001: Neighbour joining phylogenetic tree of the 16S rRNA gene sequences representing Bacillus spp. isolated from probiotic products.Type strains of Bacillus species are labeled with accession number and strain number. Strains with identical sequences are included in parenthesis after the strain selected as reference. Strains with sequences shorter than 1 kb were excluded from phylogenetic analysis and their identity only determined by similarity comparison to type strain. The scale bar represents sequence variation considering the model for nucleotide substitution (Jukes & Cantor) and tree-shape used in the neighbour joining analysis. * Strains are with too short sequences to compare.

Mentions: Fig 1 shows a phylogenetic analysis based on 16S rRNA gene sequences comparing Bacillus spp. isolated from the probiotic products to type strains of the most related Bacillus species. Seven groups were observed and five included more than one species of Bacillus reflecting their close relationship based on the 16S rRNA gene sequence comparison. The analysis was also used to evaluate the degree of deviation between the declared bacterial species on the product and the species identified in the product.


Identification and Antimicrobial Resistance of Bacteria Isolated from Probiotic Products Used in Shrimp Culture.

Noor Uddin GM, Larsen MH, Christensen H, Aarestrup FM, Phu TM, Dalsgaard A - PLoS ONE (2015)

Neighbour joining phylogenetic tree of the 16S rRNA gene sequences representing Bacillus spp. isolated from probiotic products.Type strains of Bacillus species are labeled with accession number and strain number. Strains with identical sequences are included in parenthesis after the strain selected as reference. Strains with sequences shorter than 1 kb were excluded from phylogenetic analysis and their identity only determined by similarity comparison to type strain. The scale bar represents sequence variation considering the model for nucleotide substitution (Jukes & Cantor) and tree-shape used in the neighbour joining analysis. * Strains are with too short sequences to compare.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492959&req=5

pone.0132338.g001: Neighbour joining phylogenetic tree of the 16S rRNA gene sequences representing Bacillus spp. isolated from probiotic products.Type strains of Bacillus species are labeled with accession number and strain number. Strains with identical sequences are included in parenthesis after the strain selected as reference. Strains with sequences shorter than 1 kb were excluded from phylogenetic analysis and their identity only determined by similarity comparison to type strain. The scale bar represents sequence variation considering the model for nucleotide substitution (Jukes & Cantor) and tree-shape used in the neighbour joining analysis. * Strains are with too short sequences to compare.
Mentions: Fig 1 shows a phylogenetic analysis based on 16S rRNA gene sequences comparing Bacillus spp. isolated from the probiotic products to type strains of the most related Bacillus species. Seven groups were observed and five included more than one species of Bacillus reflecting their close relationship based on the 16S rRNA gene sequence comparison. The analysis was also used to evaluate the degree of deviation between the declared bacterial species on the product and the species identified in the product.

Bottom Line: MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer.Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer.Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments.

View Article: PubMed Central - PubMed

Affiliation: Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

ABSTRACT
Probiotics are increasingly used in aquaculture to control diseases and improve feed digestion and pond water quality; however, little is known about the antimicrobial resistance properties of such probiotic bacteria and to what extent they may contribute to the development of bacterial resistance in aquaculture ponds. Concerns have been raised that the declared information on probiotic product labels are incorrect and information on bacterial composition are often missing. We therefore evaluated seven probiotics commonly used in Vietnamese shrimp culture for their bacterial species content, phenotypic antimicrobial resistance and associated transferable resistance genes. The bacterial species was established by 16S rRNA sequence analysis of 125 representative bacterial isolates. MIC testing was done for a range of antimicrobials and whole genome sequencing of six multiple antimicrobial resistant Bacillus spp. used to identify resistance genes and genetic elements associated with horizontal gene transfer. Thirteen bacterial species declared on the probiotic products could not be identified and 11 non-declared Bacillus spp. were identified. Although our culture-based isolation and identification may have missed a few bacterial species present in the tested products this would represent minor bias, but future studies may apply culture independent identification methods like pyro sequencing. Only 6/60 isolates were resistant to more than four antimicrobials and whole genome sequencing showed that they contained macrolide (ermD), tetracycline (tetL), phenicol (fexA) and trimethoprim (dfrD, dfrG and dfrK) resistance genes, but not known structures associated with horizontal gene transfer. Probiotic bacterial strains used in Vietnamese shrimp culture seem to contribute with very limited types and numbers of resistance genes compared to the naturally occurring bacterial species in aquaculture environments. Approval procedures of probiotic products must be strengthened through scientific-based efficacy trials and product labels should allow identification of individual bacterial strains and inform the farmer on specific purpose, dosage and correct application measures.

No MeSH data available.


Related in: MedlinePlus