Resistomes of probiotic and starter cultures as potential risk factors for the spread of antibiotic resistance
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB49530 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Shotgun metagenomics reveals differences in resistomes among probiotics, starter cultures, and cheeses
| PRJEB75030 | ENA
Project description:The purpose of this study was to establish the probiotic potential of lactic acid bacteria (LAB) starter cultures, Lb. plantarum MNC 21, L. lactis MNC 24, and W. confusa MNC 20, isolated from a traditionally fermented sorghum-millet beverage from Uganda. The cultures were examined for tolerance to acid and bile salts, bile salt hydrolase (BSH) activity, antibiotic susceptibility, biogenic amine production, mucin degradation, hydrophobicity, auto-aggregation, adherence to the ileum, coaggregation, and antimicrobial properties against selected pathogenic species. Lb. rhamnosus yoba 2012, a known probiotic, was the reference. The isolates were tolerant to acid (pH?=?3) and bile (1%). W. confusa MNC 20 and Lb. plantarum MNC 21 exhibited medium BSH activity (11-15?mm diameter of hydrolysis zone) while L. lactis and Lb. rhamnosus yoba 2012 exhibited low BSH activity (<10?mm diameter of hydrolysis zone). All isolates lacked mucolytic activity. Lb. plantarum MNC 21 and W. confusa MNC 20 produced agmatine. The candidate and reference microorganisms were resistant to 10 of 21 and 5 of 21 antibiotics, respectively. The isolates exhibited hydrophobic, auto-aggregation and coaggregation properties. These three properties were exhibited more (p < 0.05) by the reference than the potential probiotics. The ability of the potential probiotics to attach onto the goat ileum (7.3-8.0 log cfu/cm2) was comparable to that of Lb. rhamnosus yoba 2012 (7.6 log cfu/cm2). The four LAB inhibited E. coli, S. aureus, and S. enterica to the same extent (p < 0.05). The findings indicated potential probiotic activity of the starter cultures. However, further in vivo examination of these isolates is required to confirm their probiotic capabilities.
| S-EPMC7424372 | biostudies-literature
Project description:The antibiotic resistances of 45 lactic acid bacteria strains belonging to the genera Lactobacillus, Streptococcus, Lactococcus, Pediococcus, and Leuconostoc were investigated. The objective was to determine antibiotic resistances and to verify these at the genetic level, as is currently suggested by the European "qualified presumption of safety" safety evaluation system for industrial starter strains. In addition, we sought to pinpoint possible problems in resistance determinations. Primers were used to PCR amplify genes involved in beta-lactam antibiotic, chloramphenicol, tetracycline, and erythromycin resistance. The presence of ribosomal protection protein genes and the ermB gene was also determined by using a gene probe. Generally, the incidences of erythromycin, chloramphenicol, tetracycline, or beta-lactam resistances in this study were low (<7%). In contrast, aminoglycoside (gentamicin and streptomycin) and ciprofloxacin resistances were higher than 70%, indicating that these may constitute intrinsic resistances. The genetic basis for ciprofloxacin resistance could not be verified, since no mutations typical of quinolone resistances were detected in the quinolone determining regions of the parC and gyrA genes. Some starter strains showed low-level ampicillin, penicillin, chloramphenicol, and tetracycline resistances, but no known resistance genes could be detected. Although some strains possessed the cat gene, none of these were phenotypically resistant to chloramphenicol. Using reverse transcription-PCR, these cat genes were shown to be silent under both inducing and noninducing conditions. Only Lactobacillus salivarius BFE 7441 possessed an ermB gene, which was encoded on the chromosome and which could not be transferred in filter-mating experiments. This study clearly demonstrates problems encountered with resistance testing, in that the breakpoint values are often inadequately identified, resistance genes may be present but silent, and the genetic basis and associated resistance mechanisms toward some antibiotics are still unknown.
| S-EPMC1800751 | biostudies-literature
Project description:The objective of this study was to investigate probiotic microorganisms for use as starter cultures in dry fermented sausages production. A total of eight strains were studied evaluating technological and safety characteristics including the ability to grow, lactic acid production, gas formation, catalase activity, nitrate reductase activity, proteolytic activity, lipolytic activity, hydrogen peroxide production, salt tolerance, performance at low temperatures, decarboxylation of amino acids and antimicrobial activity against pathogens associated with the product. Lactobacillus rhamnosus R0011, L. rhamnosus Lr-32, Lactobacillus paracasei Lpc-37, Lactobacillus casei Shirota and Enterococcus faecium MXVK29 were good candidates for use as fermented sausages starters cultures because they showed the best technological and safety properties since they did not demonstrate amino acid decarboxylation but showed antimicrobial activity against Listeria monocytogenes, Escherichia coli, Salmonella Dublin and Staphylococcus aureus. L. rhamnosus Lr-32 was the strain best tolerating the levels of salt, nitrate and low pH during the simulated stages of fermentation and ripening of sausage. The strain was thus the most promising of the tested probiotics as sausage starter culture. The findings warrant studies in a meat matrix, such as that of raw-cured sausage, to evaluate the effects of L. rhamnosus Lr-32 under actual conditions.
| S-EPMC7278822 | biostudies-literature
Project description:Fermented foods are thought to provide a source of probiotics that promote gut health. Consequently, isolation and characterization of fermented food strains and their applications in a controlled fermentation process or as probiotics present a new facet in this area of research. Therefore, the current study sought to identify dominant strains in sorghum-fermented foods (ting) and characterize their probiotic potential in vitro. Recovered isolates were identified as Lactobacillus helveticus, Lactobacillus amylolyticus, Lacticaseibacillus paracasei, Lacticaseibacillus paracasei subsp paracasei, Lactiplantibacillus plantarum, Levilactobacillus brevis, Loigolactobacillus coryniformis and Loigolactobacillus coryniformis subsp torquens based on the their 16S rRNA sequences. Increased biomass was noted in seven out of nine under a low pH of 3 and a high bile concentration of 2% in vitro. Bactericidal activities of isolated LABs presented varying degrees of resistance against selected pathogenic bacteria ranging between (1.57 to 41 mm), (10 to 41 mm), and (11.26 to 42 mm) for Salmonella typhimurium ATTC 14028, Staphylococcus aureus ATTC 6538 and Escherichia coli ATTC8739, respectively. Ampicillin, erythromycin, mupirocin, tetracycline and chloramphenicol were able to inhibit growth of all selected LABs. Thus, isolates recovered from ting partially satisfy the potential candidacy for probiotics by virtue of being more tolerant to acid and bile, antibacterial activity and antibiotic resistance.
| S-EPMC10054160 | biostudies-literature
Project description:Antibiotic resistance genes are ubiquitous in the environment. However, only a fraction of them are mobile and able to spread to pathogenic bacteria. Until now, studying the mobility of antibiotic resistance genes in environmental resistomes has been challenging due to inadequate sensitivity and difficulties in contig assembly of metagenome based methods. We developed a new cost and labor efficient method based on Inverse PCR and long read sequencing for studying mobility potential of environmental resistance genes. We applied Inverse PCR on sediment samples and identified 79 different MGE clusters associated with the studied resistance genes, including novel mobile genetic elements, co-selected resistance genes and a new putative antibiotic resistance gene. The results show that the method can be used in antibiotic resistance early warning systems. In comparison to metagenomics, Inverse PCR was markedly more sensitive and provided more data on resistance gene mobility and co-selected resistances.
| S-EPMC5073339 | biostudies-literature
Project description:The aim of this study is to characterise and examine the biochemical properties of 40 Lactococcus lactis strains isolated from indigenous Montenegrin dairy products in order to explore their potential to be used as starter cultures for producing typical Montenegrin cheese, such as 'bijeli sir', 'masni sir' and 'njeguški sir'. Their safety regarding the production of biogenic amines, the presence of antimicrobial resistance and the antibacterial activity against relevant pathogens and spoilage microorganisms has also been tested. Based on the characterisation, all strains belong to L. lactis ssp. lactis. Out of these 40 strains, 23 displayed rapid acidification ability and proteolysis. However, none of the strains exhibited the ability of lipid degradation. Most of the strains were not associated with any health risk investigated. Summing up, a large percentage (27.5%) of the tested strains showed good properties. These strains should be further examined for their possible application as specific starter cultures in the production of indigenous cheese in Montenegro.
| S-EPMC5434366 | biostudies-literature
Project description:Antibiotic resistance reservoirs within food-producing animals are thought to be a risk to animal and human health. This study describes the minimum natural resistome of pig faeces as the bacteria are under no direct antibiotic selective pressure. The faecal resistome of 257 different genes comprised 56 core and 201 accessory resistance genes. The genes present at the highest relative abundances across all samples were tetW, tetQ, tet44, tet37, tet40, mefA, aadE, ant(9)-1, ermB and cfxA2. This study characterized the baseline resistome, the microbiome composition and the metabolic components described by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in healthy pig faeces, without antibiotic selective pressures. The microbiome hierarchical analysis resulted in a cluster tree with a highly similar pattern to that of the accessory resistome cluster tree. Functional capacity profiling identified genes associated with horizontal gene transfer. We identified a statistically significant positive correlation between the total antibiotic resistome and suggested indicator genes, which agree with using these genes as indicators of the total resistomes. The correlation between total resistome and total microbiome in this study was positive and statistically significant. Therefore, the microbiome composition influenced the resistome composition. This study identified a core and accessory resistome present in a cohort of healthy pigs, in the same conditions without antibiotics. It highlights the presence of antibiotic resistance in the absence of antibiotic selective pressure and the variability between animals even under the same housing, food and living conditions. Antibiotic resistance will remain in the healthy pig gut even when antibiotics are not used. Therefore, the risk of antibiotic resistance transfer from animal faeces to human pathogens or the environment will remain in the absence of antibiotics.
| S-EPMC6562245 | biostudies-literature
Project description:Enterococci represent the most controversial group of dairy bacteria. They are found to be the main constituent of many traditional Mediterranean dairy products and contribute to their characteristic taste and flavor. On the other hand, during the last 50 years antibiotic-resistant enterococci have emerged as leading causes of nosocomial infections worldwide. The aim of this study was to determine the diversity, technological properties, antibiotic susceptibility and virulence traits of 636 enterococci previously isolated from 55 artisan dairy products from 12 locations in the Western Balkan countries (WBC) of Serbia, Croatia and Bosnia and Herzegovina. All strains were identified both by microbiological and molecular methods. The predominant species was Enterococcus durans, followed by Enterococcus faecalis and Enterococcus faecium. Over 44% of the isolates were resistant to ciprofloxacin and erythromycin, while 26.2% of the isolates were multi-resistant to three or more antibiotics belonging to different families. 185 isolates (29.1%) were susceptible to all 13 of the antibiotics tested. The antibiotic-susceptible isolates were further tested for possible virulence genes and the production of biogenic amines. Finally, five enterococci isolates were found to be antibiotic susceptible with good technological characteristics and without virulence traits or the ability to produce biogenic amines, making them possible candidates for biotechnological application as starter cultures in the dairy industry.
| S-EPMC4563272 | biostudies-literature
Project description:Microbial strains for starter culture-initiated sourdough productions are commonly isolated from a fermenting flour-water mixture. Yet, starter culture strains isolated from matrices other than sourdoughs could provide the dough with interesting metabolic properties and hence change the organoleptic properties of the concomitant breads. Furthermore, the selection of sourdough starter cultures does not need to be limited to lactic acid bacteria (LAB), as other food-grade microorganisms are sometimes found in sourdoughs. Therefore, different strains belonging to LAB, acetic acid bacteria (AAB), and coagulase-negative staphylococci (CNS) that originated from different fermented food matrices (fermenting cocoa pulp-bean mass, fermented sausage, and water kefir), were examined as to their prevalence in a wheat sourdough ecosystem during 72-h fermentations. Limosilactobacillus fermentum IMDO 222 (fermented cocoa pulp-bean mass isolate) and Latilactobacillus sakei CTC 494 (fermented sausage isolate) seemed to be promising candidates as sourdough starter culture strains, as were the AAB strains Acetobacter pasteurianus IMDO 386B and Gluconobacter oxydans IMDO A845 (both isolated from fermented cocoa pulp-bean mass), due to their competitiveness in the wheat flour-water mixtures. Wheat breads made with G. oxydans IMDO A845 sourdoughs were significantly darker than reference wheat breads.
| S-EPMC7599913 | biostudies-literature