Characterization of antimicrobial resistance in lactobacilli and bifidobacteria used as probiotics or starter cultures based on integration of phenotypic and in silico data
ID Rozman, Vita (Author), ID Mohar Lorbeg, Petra (Author), ID Accetto, Tomaž (Author), ID Bogovič Matijašić, Bojana (Author)

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Lactic acid bacteria and bifidobacteria deliberately introduced into the food chain may act as a reservoir of antimicrobial resistance genes (ARGs), which is considered a safety concern. In the present study, resistance to antimicrobials of commercial probiotic strains, probiotic candidate strains, and starter cultures (n = 20) was characterised based on integration of phenotypic and in silico data. Minimum inhibitory concentrations (MICs) of 16 antimicrobials were determined for lactobacilli and bifidobacteria that were isolated from pharmaceutical products or obtained from the manufacturers or culture collections. Using different databases and bioinformatic tools, we predicted ARGs, mutations, genomic islands, and mobile genetic elements (MGEs) in their whole genome sequences. In addition, a comprehensive in silico analysis of the prevalence of the tetW gene and its genetic environment across lactobacilli and bifidobacteria (n = 1423) was conducted. Several strains exhibited phenotypic resistance to kanamycin, tetracycline, chloramphenicol, quinupristin-dalfopristin, ciprofloxacin, or neomycin. These resistances, however, did not always correspond to the presence of ARGs and vice versa. We detected an acquired tetW gene in four commercial strains of Bifidobacterium animalis subsp. lactis, whereas homologs of antimicrobial resistance (AR) proteins were predicted in all 20 proteomes. The prevalence of the tetW gene, which was often flanked by MGEs, was higher in analysed bifidobacteria (31.9%) than lactobacilli (6.3%). In addition, sequences flanking tetW were associated with putative genomic islands and were conserved in several strains, including potential pathogens. Our findings provide an insight into AR of probiotics, probiotic candidates, and starter cultures with an emphasis on tetracycline and into the safety of these strains in the context of AR.

Keywords:antimicrobial resistance, Bifidobacterium, genomic island, Lactobacillus, mobile genetic element, tetracycline
Work type:Article (dk_c)
Typology:1.01 - Original Scientific Article
Organization:BF - Biotechnical Faculty
Publication status in journal:Published
Article version:Publisher's version of article
Number of pages:11 str.
Numbering:Vol. 314, art. 108388
PID:20.500.12556/RUL-113246 This link opens in a new window
ISSN on article:1879-3460
DOI:10.1016/j.ijfoodmicro.2019.108388 This link opens in a new window
COBISS.SI-ID:4320904 This link opens in a new window
Publication date in RUL:30.01.2020
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Record is a part of a journal

Title:International journal of food microbiology
Shortened title:Int. j. food microbiol.
COBISS.SI-ID:23238661 This link opens in a new window


License:CC BY-NC-ND 4.0, Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
Description:The most restrictive Creative Commons license. This only allows people to download and share the work for no commercial gain and for no other purposes.

Secondary language

Keywords:mikrobiologija, laktobacili, bifidobakterije, probiotiki, odpornost


Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Project number:6316-1/2017-273

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Project number:603-1/2017-13

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Project number:J4-1769
Name:Rezistomi probiotičnih in starterskih kultur kot potencialni dejavnik tveganja za širjenje odpornosti proti antibiotikom

Funder:ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
Project number:P4-0097
Name:Prehrana in mikrobna ekologija prebavil

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