Guidance on the assessment of bacterial susceptibility to antimicrobials of human and veterinary importance

Characterisation of Lactic Acid Bacteria Isolated from the Gut of Cyprinus carpio That May Be Effective Against Lead Toxicity

The present study was conducted to isolate and characterise Pb-resistant lactic acid bacteria (LAB), and thus determine their potential for use as probiotics against Pb toxicity. A total of 107 Pb-resistant LAB strains were isolated from the gut content of Cyprinus carpio, of which 41 were established to be gram-positive and catalase-negative. Investigation of the Pb-binding ability of these isolated LAB identified seven strains (P2, P6, P7, P9, P16, P19 and P22) with comparatively high Pb-binding activities. These were selected for further screening to establish their Pb tolerance, anti-oxidative capacity and in vitro probiotic characteristics. Strain P16 exhibited both the highest Pb-binding and a relatively good antioxidant capacity. Furthermore, P16 displayed a high survival rate during 4 h of exposure to both low-pH (2.5-3.5) conditions and 10.0% fish bile, and a strong capacity to adhere to fish intestinal mucus (62.4%). Furthermore, P16 showed strong antibacterial activities against all tested fish pathogens. Strains P6, P9, P16, P19 and P22 were susceptible to a range of tested antibiotics, but not to vancomycin. Thus, of the isolated lactobacilli, strain P16 exhibited the best Pb-binding ability, a high level of antioxidant activity and satisfactory in vitro probiotic properties. Biochemical and 16S-rRNA gene analyses identified P16 as Lactobacillus reuteri. Thus, the results of the conducted in vitro tests suggest that the fish-associated P16 Lact. reuteri strain is a promising candidate probiotic, which should undergo further investigation to assess its suitability for use in protecting against lead-exposure-induced toxicities in aquaculture.

Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential

Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-β-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches.

Laboratory Evolution Assays and Whole-Genome Sequencing for the Development and Safety Evaluation of Lactobacillus plantarum With Stable Resistance to Gentamicin

The goal of this work was to use laboratory evolution assays and whole-genome sequencing to develop and test the safety of a probiotic, Lactobacillus plantarum, with high-level of resistance to gentamicin. The evolution of L. plantarum was evaluated under the selective pressure from gentamicin and subsequently when the selective pressure was removed. After 30 days of selective pressure from gentamicin, the minimum inhibitory concentration (MIC) of L. plantarum to gentamicin increased from 4 to 512 μg/mL and remained stable at this level. After removing the selective pressure, the resistance of L. plantarum to gentamicin decreased to 64 μg/mL after 20 days, and remained stable thereafter. Although the MIC declined it was still higher than the cut-off value recommended by EFSA, indicating that the acquisition of gentamicin-resistance was an irreversible process. Using whole-genome sequencing, gene mutations were identified in the strains that had undergone selection pressure from gentamicin as well as in the strains where the selection pressure was subsequently removed. Specifically, four non-synonymous mutations were detected including one single nucleotide polymorphism (SNP), one insertion, and two structural variants (SVs), of which the mutations in genes encoding the drug resistance MFS transporter and transcriptional regulator of AraC family were only detected in the strains under selective pressure from gentamicin. The results indicate that these mutations play an important role in increasing the resistant levels of L. plantarum to gentamicin. The mobility analysis of mutant genes confirmed that they were not located on mobile elements of the genome of highly resistant L. plantarum, indicating that horizontal gene transfer was not possible.

Are Probiotic Really Safe for Humans?

Probiotic bacteria have been used as a health-promoting factor for a very long time. Nowadays, products containing probiotic bacteria are becoming more and more popular on the market. The term probiotics refers to the products belonging to the following groups: probiotic drugs (medicinal products – live biotherapeutic products for human use), medical devices, probiotic foods (e.g. foods, food ingredients, dietary supplements or food for special medical purposes), directly fed microorganisms (for animal use) and designer probiotics (genetically modified probiotics). Safety assessment of bacterial strains used as probiotics should be carefully studied. Even though probiotic bacteria have the generally recognized as safe (GRAS status), there are several reports about side effects triggered by the presence of these organisms. Microorganisms used as probiotics may cause systemic infections, stimulate the immune system, disturb metabolism and participate in horizontal gene transfer.

Safety Evaluation of Oral Care Probiotics Weissella cibaria CMU and CMS1 by Phenotypic |and Genotypic Analysis

Weissella cibaria CMU and CMS1 are known to exert beneficial effects on the oral cavity but have not yet been determined to be generally recognized as safe (GRAS), although they are used as commercial strains in Korea. We aimed to verify the safety of W. cibaria CMU and CMS1 strains through phenotypic and genotypic analyses. Their safety was evaluated by a minimum inhibitory concentration assay for 14 antibiotics, DNA analysis for 28 antibiotic resistance genes (ARGs) and one conjugative element, antibiotic resistance gene transferability, virulence gene analysis, hemolysis, mucin degradation, toxic metabolite production, and platelet aggregation reaction. W. cibaria CMU showed higher kanamycin resistance than the European Food Safety Authority (EFSA) cut-off, but this resistance was not transferred to the recipient strain. W. cibaria CMU and CMS1 lacked ARGs in chromosomes and plasmids, and genetic analysis confirmed that antibiotic resistance of kanamycin was an intrinsic characteristic of W. cibaria. Additionally, these strains did not harbor virulence genes associated with pathogenic bacteria and lacked toxic metabolite production, β-hemolysis, mucin degradation, bile salt deconjugation, β-glucuronidase, nitroreductase activity, gelatin liquefaction, phenylalanine degradation, and platelet aggregation. Our findings demonstrate that W. cibaria CMU and CMS1 can achieve the GRAS status in future.

Safety and efficacy of l-tryptophan produced by fermentation with Escherichia coli KCCM 80135 for all animal species

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on l‐tryptophan produced by fermentation using Escherichia coli KCCM 80135 when used as a nutritional additive in feed and water for drinking for all animal species. The production strain and its recombinant DNA were not detected in the additive. l‐Tryptophan produced by fermentation with E. coli KCCM 80135 does not raise any safety concern with regard to the genetic modification of the production strain. The use of l‐tryptophan produced using E. coli KCCM 80135 in supplementing feed to compensate for tryptophan deficiency in feedingstuffs is safe for non‐ruminant target species. Using unprotected forms of tryptophan in ruminants can be a risk. The use of l‐tryptophan produced by fermentation using E. coli KCCM 80135 in animal nutrition presents no safety concerns to consumers of animal products. l‐Tryptophan produced by E. coli KCCM 80135 is not toxic by inhalation. The additive is not an irritant to skin and eyes, and it is not a skin sensitiser. The additive under assessment is considered safe for the environment. It is regarded as an effective source of the amino acid l‐tryptophan for all non‐ruminant species. If the additive l‐tryptophan is intended for use in ruminants, it should be protected from ruminal degradation.

Predominance of Lactobacillus plantarum Strains in Peruvian Amazonian Fruits

The objective of this research was the identification and characterization of lactic acid bacteria (LAB) isolated from Peruvian Amazonian fruits. Thirty-seven isolates were obtained from diverse Amazonian fruits. Molecular characterization of the isolates was performed by ARDRA, 16S-23S ITS RFLP and rep-PCR using GTG₅ primers. Identification was carried out by sequencing the 16S rDNA gene. Phenotypic characterization included nutritional, physiological and antimicrobial resistance tests. Molecular characterization by Amplified Ribosomal DNA Restriction Analysis (ARDRA) and 16S-23S ITS RFLP resulted in four restriction profiles while GTG₅ analysis showed 14 banding patterns. Based on the 16S rDNA gene sequence, the isolates were identified as Lactobacillus plantarum (75.7%), Weissella cibaria (13.5%), Lactobacillus brevis (8.1%), and Weissella confusa (2.7%). Phenotypic characterization showed that most of the isolates were homofermentative bacilli, able to ferment glucose, maltose, cellobiose, and fructose and grow in a broad range of temperatures and pH. The isolates were highly susceptible to ampicillin, amoxicillin, clindamycin, chloramphenicol, erythromicyn, penicillin, and tetracycline and showed great resistance to kanamycin, gentamycin, streptomycin, sulfamethoxazole/trimethoprim, and vancomycin. No proteolytic or amylolytic activity was detected. L. plantarum strains produce lactic acid in higher concentrations and Weissella strains produce exopolymers only from sucrose. Molecular methods allowed to accurately identify the LAB isolates from the Peruvian Amazonian fruits, while phenotypic methods provided information about their metabolism, physiology and other characteristics that may be useful in future biotechnological processes. Further research will focus especially on the study of L. plantarum strains.

Assessment of the application for renewal of authorisation of Bactocell® (Pediococcus acidilactici CNCM I-4622) as a feed additive for weaned piglets, pigs for fattening, minor porcine species (weaned and for fattening), chickens for fattening, laying hens and minor avian species for fattening and for laying and its extension of use to all growing pigs and all avian species

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on Bactocell® (Pediococcus acidilactici CNCM I-4622) in the context of the renewal of the authorisation for weaned piglets, pigs for fattening, minor porcine species (weaned and for fattening), chickens for fattening, laying hens and minor avian species for fattening and for laying when used as a zootechnical feed additive (gut flora stabiliser) in feed or in water for drinking. In addition, the applicant requested the extension of use for suckling piglets, minor pig species (growing/for fattening), chickens reared for laying, chickens reared for breeding purposes, chickens for breeding purposes, turkeys and minor avian species (including non-food producing/ornamental birds) reared for laying/breeding purposes and for breeding purposes when used as in feed or in water for drinking. The applicant has provided evidence that the additive currently on the market complies with the conditions of authorisation. The additive is safe for the target species, consumers and the environment as well. The additive is non-irritant to skin and eyes and is not a dermal sensitiser but should be considered a respiratory sensitiser. Considering the high dusting potential of the formulations, exposure of users by inhalation is very likely. The additive, at the level of 1 × 109 CFU/kg feed (5 × 108 when delivered in water), has the potential to be efficacious in the new species proposed: chickens reared for laying, chickens reared for breeding purposes, chickens for breeding purposes, turkeys and minor avian species reared for laying/breeding purposes and for breeding purposes (including non-food producing/ornamental birds) and in suckling piglets and minor porcine species (growing/for fattening).

Safety evaluation of the food enzyme alpha-amylase from a genetically modified Bacillus subtilis (strain NBA)

The food enzyme alpha-amylase (4-α-d-glucan glucanohydrolase; EC 3.2.1.1) is produced with a genetically modified strain of Bacillus subtilis strain NBA by DSM Food Specialities B.V. This α-amylase is intended to be used in baking processes. The genetic modifications do not give rise to safety concerns and the food enzyme is free from viable cells of the production organism and recombinant DNA. The parental strain meets the required qualifications to be considered as a Qualified Presumption of Safety (QPS) organism and is therefore presumed to be safe. Since the production strain is not cytotoxic and since the introduced genetic modifications do not raise safety concerns, the presumption of safety made for the parental strain is extended to the production strain. The conclusions on safety of the food enzyme are made following the QPS approach in relation to the production strain, with additional consideration of the conditions of manufacture. However, the Panel considers no toxicological studies other than assessment of allergenicity necessary. This is based on the QPS status of the production strain and the absence of any hazards from the product and downstream processing. Based on the maximum use level recommended for the baking processes and individual data from the European Food Safety Authority (EFSA) Comprehensive European Food Consumption Database, dietary exposure was estimated to be up to 0.093 mg TOS/kg body weight per day in European populations. The Panel considered that, under the intended conditions of use, the risk of allergic sensitisation and elicitation reactions upon dietary exposure to this food enzyme cannot be excluded, but the likelihood is considered low. Based on the data provided, the Panel concluded that this food enzyme does not raise safety concerns under the intended conditions of use.

Safety and efficacy of l-tryptophan produced by fermentation with Escherichia coli KCCM 80152 for all animal species

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on l-tryptophan produced by fermentation using Escherichia coli KCCM 80152 when used as nutritional additive in feed and water for drinking for all animal species. The production strain and its recombinant DNA were not detected in the additive. l-Tryptophan, manufactured by fermentation with E. coli KCCM 80152, does not give rise to any safety concern with regard to the genetic modification of the production strain. The use of l-tryptophan produced using E. coli KCCM 80152 in supplementing feed to compensate for tryptophan deficiency in feedingstuffs is safe for non-ruminant target species. Using unprotected forms of tryptophan in ruminants can be a risk. The use of l-tryptophan produced by fermentation using E. coli KCCM 80152 in animal feed presents no concerns to consumers of animal products. Due to the content of endotoxins, the additive poses a risk for persons handling the additive when exposed by inhalation. The additive is not considered irritant for skin or eyes and is not considered a skin sensitiser. The additive under assessment is safe for the environment. The additive under assessment is regarded as an effective source of the amino acid l-tryptophan for all non-ruminant species. If l-tryptophan is intended for use in ruminants, it should be protected from ruminal degradation.

Oral administration of bacteriocin-producing and non-producing strains of Enterococcus faecium in dogs

The current effort to incorporate microbial cultures in canine nutrition and thus intake of them on daily base increases our interest in careful and more complex study of their effects in dogs. Many of the commercially used strains have not been tested in dogs and are incorporated only on the base of beneficial effects observed in humans with specific disorders. Moreover, no information on the effects of bacteriocin-producing strains in dogs is available. Therefore, we decided to test and to compare overall effect of bacteriocin non-producing Enterococcus faecium DSM 32820 and enterocin B-producing E. faecium LMG 30881 strain (both of canine origin). Dogs were divided into three treatment groups of ten dogs each: control; DSM 32820 group; and LMG 30881 group, dosing 10⁹ CFU/day/dog. The experiment lasted 35 days with a 14-day treatment period (sample collection at days 0, 7, 14, 35). Despite bacteriocin production is believed that may provide a competitive advantage over neighbouring sensitive strains within shared environment, results indicated somewhat better survival for the DSM 32820 compared to the LMG 30881 group. Furthermore, dogs of DSM 32820 group had optimal faecal consistency throughout the experiment, significantly stimulated phagocytic activity (days 7 and 14) and metabolic burst activity of leukocytes (days 14 and 35) and lower serum glucose concentration (day 35). In contrast, dogs of LMG 30881 group showed higher faecal count of Gram-negative bacteria (day 35), lower haemoglobin and glucose concentration (day 35), and higher metabolic burst activity (days 14 and 35). These results are further evidence of the existence of inter-strain differences in efficacy despite the same origin.

Selection of carbohydrate-active probiotics from the gut of carnivorous fish fed plant-based diets

The gastrointestinal microbiota plays a critical role on host health and metabolism. This is particularly important in teleost nutrition, because fish do not possess some of the necessary enzymes to cope with the dietary challenges of aquaculture production. A main difficulty within fish nutrition is its dependence on fish meal, an unsustainable commodity and a source of organic pollutants. The most obvious sustainable alternatives to fish meal are plant feedstuffs, but their nutritive value is limited by the presence of high levels of non-starch polysaccharides (NSP), which are not metabolized by fish. The composition of fish-gut microbial communities have been demonstrated to adapt when the host is fed different ingredients. Thus, we hypothesized that a selective pressure of plant-based diets on fish gut microbiota, could be a beneficial strategy for an enrichment of bacteria with a secretome able to mobilize dietary NSP. By targeting bacterial sporulating isolates with diverse carbohydrase activities from the gut of European sea bass, we have obtained isolates with high probiotic potential. By inferring the adaptive fitness to the fish gut and the amenability to industrial processing, we identified the best two candidates to become industrially valuable probiotics. This potential was confirmed in vivo, since one of the select isolates lead to a better growth and feed utilization efficiency in fish fed probiotic-supplemented plant-based diets, thus contributing for sustainable and more cost-effective aquaculture practices.

Selection of New Probiotics for Endometrial Health

Microbiota is a crucial player in gynecologic health, in which bacteria can shift to a dysbiotic state triggering a pathogenic process. Based on an ecological understanding of the problem, the aim of this study is to select a potential probiotic strain to improve female reproductive tract based on its capacity to initially lower pH and to promote the reduction of pathogenic bacteria. Based on this rationale, strain Lactobacillus rhamnosus BPL005 was initially selected for its capacity to reduce in vitro pH levels and produce organic acids. Subsequently, strain L. rhamnosus BPL005 (CECT 8800) was demonstrated to have a protective role on endometrial infections in an in vitro model of bacterial colonization of primary endometrial epithelial cells with Atopobium vaginae, Gardnerella vaginalis, Propionibacterium acnes, and Streptococcus agalactiae. In this model, BPL005 when co-cultured with those pathogens was shown to lower pH and to produce organic acids, being lactic acid the most relevant. The co-cultivation of strain L. rhamnosus BPL005 with tested reference pathogens produced a significant reduction in P. acnes and St. agalactiae levels and a non-significant reduction in A. vaginae and G. vaginalis. The colonization of L. rhamnosus BPL005 in the culture decreased IL-6, IL-8, and MCP-1, heightened in the presence of pathogens, and increased IL-1RA and IL-1 beta. Finally, safety was evaluated showing no signs of cytotoxicity, irritation in vaginal tests, or allergic contact dermatitis potential through the Local Lymph Node Assay. Overall, these results show the potential of L. rhamnosus BPL005 strain as a probiotic in gynecological health.

Whole Genome Analysis of Lactobacillus plantarum Strains Isolated From Kimchi and Determination of Probiotic Properties to Treat Mucosal Infections by Candida albicans and Gardnerella vaginalis

Three Lactobacillus plantarum strains ATG-K2, ATG-K6, and ATG-K8 were isolated from Kimchi, a Korean traditional fermented food, and their probiotic potentials were examined. All three strains were free of antibiotic resistance, hemolysis, and biogenic amine production and therefore assumed to be safe, as supported by whole genome analyses. These strains demonstrated several basic probiotic functions including a wide range of antibacterial activity, bile salt hydrolase activity, hydrogen peroxide production, and heat resistance at 70°C for 60 s. Further studies of antimicrobial activities against Candida albicans and Gardnerella vaginalis revealed growth inhibitory effects from culture supernatants, coaggregation effects, and killing effects of the three probiotic strains, with better efficacy toward C. albicans. In vitro treatment of bacterial lysates of the probiotic strains to the RAW264.7 murine macrophage cell line resulted in innate immunity enhancement via IL-6 and TNF-α production without lipopolysaccharide (LPS) treatment and anti-inflammatory effects via significantly increased production of IL-10 when co-treated with LPS. However, the degree of probiotic effect was different for each strain as the highest TNF-α and the lowest IL-10 production by the RAW264.7 cell were observed in the K8 lysate treated group compared to the K2 and K6 lysate treated groups, which may be related to genomic differences such as chromosome size (K2: 3,034,884 bp, K6: 3,205,672 bp, K8: 3,221,272 bp), plasmid numbers (K2: 3, K6 and K8: 1), or total gene numbers (K2: 3,114, K6: 3,178, K8: 3,186). Although more correlative inspections to connect genomic information and biological functions are needed, genomic analyses of the three strains revealed distinct genomic compositions of each strain. Also, this finding suggests genome level analysis may be required to accurately identify microorganisms. Nevertheless, L. plantarum ATG-K2, ATG-K6, and ATG-K8 demonstrated their potential as probiotics for mucosal health improvement in both microbial and immunological contexts.

Detection of vaginal lactobacilli as probiotic candidates

The vaginal microbiota of healthy women is dominated by lactobacilli, which exerts important health-promoting effects to the host. In the present study, 261 lactobacilli isolated from vagina of healthy women were screened for their potential probiotic characteristics. Safety features (haemolytic activity, antibiotic susceptibility, bile salt hydrolase activity) and functional properties (resistance to low pH and bile salts, lysozyme tolerance, gastrointestinal survival, antagonistic activity against pathogens, hydrophobicity, auto-aggregation, and co-aggregation abilities, hydrogen peroxide production, biofilm formation, exopolysaccharide production, adhesion capacity to both normal human vagina epithelial cells and Caco-2 epithelial cells, and lactic acid production) were in depth evaluated. Seven strains, identified as Lactobacillus rhamnosus, Lactobacillus helveticus and Lactobacillus salivarius fulfilled the criteria described above. Therefore, the vaginal ecosystem represents a suitable source of probiotic candidates that could be used in new functional formulates for both gastrointestinal and vaginal eubiosis.

Safety and efficacy of Beltherm MP/ML (endo-1,4-beta-xylanase) as a feed additive for chickens for fattening, chickens reared for laying, turkeys for fattening, turkeys reared for breeding, turkeys for breeding purposes and minor poultry species

Beltherm MP/ML contains endo-1,4-beta-xylanase and is intended to be used as a zootechnical additive for poultry species. The safety and efficacy of the additive have been evaluated by the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP Panel) in 2017. In that assessment, the additive and the production strain, a genetically modified strain of Bacillus subtilis, were characterised in full. No viable cells of the production strain were detected in the final additive, but recombinant DNA from the production strain was detected. Considering that the production strain does not carry genetic sequences of concern, the presence of DNA was considered per se of no safety concern by the Panel. The safety of the additive for the target species, consumers and environment was established, but the Panel concluded that the additive should be considered as a respiratory sensitiser. Regarding the efficacy, it was concluded that the additive has a potential to be efficacious in chickens for fattening and extended/extrapolated the conclusion to chickens reared for laying and minor poultry species for fattening. However, the Panel could not conclude on the efficacy of the additive in turkeys for fattening, reared for breeding or for breeding purposes. The Panel concluded, based on the new guidance on the efficacy for feed additives, that the conclusion on the efficacy in chickens for fattening can be extrapolated to turkeys for fattening/reared for breeding purposes. New data in turkeys for fattening would support the extrapolation. No data has been provided to support the efficacy in turkeys for breeding purposes and therefore no conclusion could be drawn. Finally, the applicant has proposed, in the current submission, a modification of the manufacturing process to remove the presence of DNA from the production strain in the final product, the removal was confirmed by analyses.

Safety and efficacy of l-valine produced using Corynebacterium glutamicum CGMCC 11675 for all animal species

The product subject of this assessment is l-valine produced by fermentation with a strain of Corynebacterium glutamicum (CGMCC 11675). It is intended to be used in feed and water for drinking for all animal species and categories. Owing to the uncertainties regarding the possible genetic modification of the original production strain, the FEEDAP Panel cannot conclude on the safety of the additive l-valine produced with C. glutamicum CGMCC 11675 for the target species, the consumers, the users and the environment. The FEEDAP Panel has concerns on the safety for the target animals of the simultaneous oral administration of valine-containing additives via feed and water for drinking. In the absence of data, the FEEDAP Panel cannot conclude on the potential of l-valine produced with C. glutamicum CGMCC 11675 to be toxic by inhalation, irritant to skin or eyes, or on its potential to be a dermal sensitiser. The product is considered an efficacious source of the amino acid l-valine for all animal species. The supplemental l-valine requires protection against rumen degradations in order to be as efficacious in ruminant as in non-ruminant species.

Safety and efficacy of Cinergy® Life B3 HiCon (Bacillus amyloliquefaciens NRRL B-50508, B. amyloliquefaciens NRRL B-50509 and Bacillus subtilis NRRL B-50510) as a feed additive for pigs for fattening and minor porcine species

The additive contains viable spores of two strains of Bacillus amyloliquefaciens and a single strain of Bacillus subtilis and is intended to be used with pigs for fattening and minor porcine species at a minimum inclusion level of 1.5 × 108 colony forming units (CFU)/kg complete feedingstuffs. The two bacterial species are considered suitable for the qualified presumption of safety (QPS) approach to safety assessment, which requires the identity of the strains to be established and evidence that they lack toxigenic potential and acquired antimicrobial resistance determinants for antibiotics of human and veterinary importance. The identity of the three active agents is established and the lack of toxigenic potential confirmed. The two B. amyloliquefaciens strains do not show resistance to relevant antibiotics, and are presumed safe for the target species, consumers and the environment. The B. subtilis strain showed a low level of resistance to streptomycin, for which acquired resistance genes were not identified. Therefore, it also complies with the QPS qualifications and is presumed safe for the target species, consumer and the environment. Since no other component give rise to concerns, Cinergy® Life B3 HiCon is also considered safe for the target species, consumers and the environment. In the absence of data, no conclusions can be made on the skin or eye irritancy or the potential for dermal sensitisation of the additive. Owing to the proteinaceous nature of the active agents, the additive is considered a potential respiratory sensitiser. However, the low dusting potential makes it unlikely that additive poses a risk for the respiratory system. Cinergy® Life B3 HiCon showed a potential to improve the feed to gain ratio in pigs for fattening given the additive at a minimum inclusion level of 1.5 × 108 CFU/kg complete feed. This conclusion is extrapolated to minor porcine species at the same application rate and for an equivalent growth phase.

Safety and efficacy of l-tryptophan produced by fermentation with Escherichia coli CGMCC 7.248 for all animal species

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on l-tryptophan produced by fermentation with a genetically modified strain of Escherichia coli CGMCC 7.248 when used as a nutritional additive in feed and water for drinking for all animal species and categories. The production strain E. coli CGMCC 7.248 and its recombinant DNA were not detected in the final product. The product l-tryptophan, manufactured by fermentation with E. coli CGMCC 7.248, does not give rise to any safety concern with regard to the genetic modification of the production strain. l-Tryptophan produced by E. coli CGMCC 7.248 is safe for non-ruminant target species. The use of unprotected l-tryptophan in ruminant feed should be avoided. l-Tryptophan produced by fermentation by E. coli CGMCC 7.248 is safe for the consumer. The level of endotoxins present in the product and its dusting potential indicate an inhalation risk for the user. l-Tryptophan produced by E. coli CGMCC 7.248 is not a skin or eye irritant but it is a dermal sensitiser. The use of l-tryptophan produced by E. coli CGMCC 7.248 in animal nutrition does not pose a risk to the environment. The product under assessment is regarded as an effective source of the amino acid l-tryptophan for all non-ruminant species. For the supplemental l-tryptophan to be as efficacious in ruminants as in non-ruminant species, it requires protection against degradation in the rumen.

Safety and efficacy of l-valine produced by fermentation using Corynebacterium glutamicum KCCM 11201P for all animal species

The product subject of this assessment is l‐valine produced by fermentation using a non‐genetically modified strain of Corynebacterium glutamicum (KCCM 11201P). It is intended to be used in feed and water for drinking for all animal species and categories. Species identity of the production organism was confirmed and the strain was sensitive to antibiotics at concentrations below thresholds specified by EFSA, thus C. glutamicum KCCM 11201P may be considered safe by the qualified presumption of safety (QPS) approach. No viable cells of C. glutamicum were detected in the final product. The amount of identified material exceeded ■■■■■% on ‘as is’ basis, and no impurities of concern were detected. The use of l‐valine produced by C. glutamicum KCCM 11201P is safe for target species when supplemented to diets in appropriate amounts, for the consumer and the environment. The product l‐valine produced by C. glutamicum (KCCM 11201P) is considered not to be an irritant or a dermal sensitiser, and does not cause acute inhalation toxicity. The additive is an effective source of valine for all species. For the supplemental l‐valine to be as efficacious in ruminants as in non‐ruminant species, it requires protection against microbial degradation in the rumen.

Peer review of the pesticide risk assessment of the active substance Verticillium albo-atrum strain WCS850

The conclusions of EFSA following the peer review of the initial risk assessments carried out by the competent authorities of the rapporteur Member State Sweden and co-rapporteur Member State the Netherlands for the pesticide active substance Verticillium albo-atrum strain WCS850 are reported. The context of the peer review was that required by Commission Implementing Regulation (EU) No 844/2012. The conclusions were reached on the basis of the evaluation of the representative use of Verticillium albo-atrum strain WCS850 as a fungicide on elm trees. The reliable end points, appropriate for use in regulatory risk assessment, are presented. Missing information identified as being required by the regulatory framework is listed.

Safety and efficacy of Lactobacillus reuteri NBF-1 (DSM 32203) as a feed additive for dogs

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of Lactobacillus reuteri NBF-1 when used in feed for dogs at a minimum dose of 6 × 109 colony forming units (CFU) per animal and day. The additive is a preparation of viable cells of L. reuteri DSM 32203. This species is considered by the European Food Safety Authority to be suitable for the qualified presumption of safety (QPS) approach establishing safety for the target species and the environment. The active agent fulfils the requirements of the QPS approach to the assessment of safety. Consequently, in the absence of concerns from other components of the additive, Lactobacillus reuteri NBF-1 is presumed safe for the target animals and the environment. Lactobacillus reuteri NBF-1 should be considered a potential respiratory sensitiser. In the absence of data, the FEEDAP Panel cannot conclude on the irritancy of the additive to skin and eyes or on its dermal sensitisation. The FEEDAP Panel is not in the position to conclude on the efficacy of Lactobacillus reuteri NBF-1 for dogs.

Safety and efficacy of l-lysine monohydrochloride and concentrated liquid l-lysine (base) produced by fermentation using Corynebacterium glutamicum strain NRRL B-50775 for all animal species based on a dossier submitted by ADM

The European Commission asked EFSA for an opinion on the safety for the target animals, consumer, user and the environment and on the efficacy of a l-lysine monohydrochloride (HCl, minimum 98.5%) and of a concentrated liquid l-lysine (base, minimum 50%) produced by a genetically modified strain of Corynebacterium glutamicum (NRRL B-50775). They are intended to be used in feed or water for drinking for all animal species and categories. Neither the production strain C. glutamicum NRRL B-50775 nor its recombinant DNA was detected in the final product. Therefore, the product does not pose any safety concern associated with the genetic modification of the production strain. l-Lysine HCl and concentrated liquid l-lysine (base) produced by C. glutamicum NRRL B-50775 are considered safe for the target species, for the consumer and for the environment. l-Lysine HCl produced by C. glutamicum NRRL B-50775 is considered not irritant to skin or eyes and not a skin sensitiser. In the absence of data, the FEEDAP Panel cannot conclude on the potential toxicity by inhalation of l-lysine HCl produced by C. glutamicum NRRL B-50775. Concentrated liquid l-lysine (base) produced by C. glutamicum NRRL B-50775, due to its high pH (11) it is anticipated to be corrosive to skin and eyes and poses a risk by inhalation. l-Lysine HCl and concentrated liquid l-lysine (base) produced by C. glutamicum NRRL B-50775 are considered as efficacious sources of the essential amino acid l-lysine for non-ruminant animal species. For the supplemental l-lysine to be as efficacious in ruminants as in non-ruminant species, it would require protection against degradation in the rumen.

Safety and efficacy of Lactobacillus reuteri NBF-2 (DSM 32264) as a feed additive for cats

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of Lactobacillus reuteri NBF-2 when used in feed for cats at a minimum dose of 6 × 109 colony forming units (CFU) per animal and day. The additive is a preparation of viable cells of L. reuteri DSM 32264. This species is considered by EFSA to be suitable for the qualified presumption of safety (QPS) approach establishing safety for the target species and the environment. The active agent fulfils the requirements of the QPS approach to the assessment of safety. Consequently, in the absence of concerns form other components of the additives, Lactobacillus reuteri NBF-2 is presumed safe for the target animals and the environment. Lactobacillus reuteri NBF-2 should be considered a potential respiratory sensitiser. In the absence of data, the FEEDAP Panel cannot conclude on the irritancy of the additive to skin and eyes or on its dermal sensitisation. The FEEDAP the Panel is not in the position to conclude on the efficacy of Lactobacillus reuteri NBF-2 for cats.

In vitro Assessment of the Probiotic Properties and Bacteriocinogenic Potential of Pediococcus pentosaceus MZF16 Isolated From Artisanal Tunisian Meat "Dried Ossban"

Pediococcus pentosaceus MZF16 has been isolated from artisanal Tunisian meat so called "Dried Ossban," an original ecological niche, and identified by MALDI-TOF mass spectrometry and 16S rDNA sequencing. This bacterium showed a high tolerance to gastric stress conditions, and toward bile salts. P. pentosaceus MZF16 also demonstrated a hydrophobic surface profile (high adhesion to xylene), autoaggregation, and adhesive abilities to the human intestinal Caco-2/TC7 cell line. These properties may help the bacterium colonizing the gut. Furthermore, MZF16 was found to be resistant to gentamycin and chloramphenicol but did not harbor any transferable resistance determinants and/or virulence genes. The data also demonstrated absence of cytotoxicity of this strain. Conversely, P. pentosaceus MZF16 can slightly stimulate the immune system and enhance the intestinal epithelial barrier function. Moreover, this bacterium has been shown to be highly active against Listeria spp. due to bacteriocin production. Characterization of the bacteriocin by PCR amplification, sequencing and bioinformatic analyses revealed that MZF16 produces a bacteriocin 100% identical to coagulin, a pediocin-like inhibitory substance produced by Bacillus coagulans. To our knowledge, this is the first report that highlights the production of a pediocin 100% identical to coagulin in a Pediococcus strain. As coagulin, pediocin MZF16 has the consensus sequence YYGNGVXCXXXXCXVXXXXA (X denotes any amino acid), which confirms its belonging to class IIa bacteriocins, and its suitability to preserve foods from Listeria monocytogenes development. According to these results, P. pentosaceus MZF16 can be proposed as a probiotic and bioprotective agent for fermented foods, including Tunisian dry meat and sausages. Further investigations will aim to study the behavior of this strain in meat products as a component of functional food.

Safety and efficacy of Monimax® (monensin sodium and nicarbazin) for chickens for fattening and chickens reared for laying

The coccidiostat Monimax® (monensin sodium and nicarbazin) is considered safe for chickens for fattening and chickens reared for laying at the highest use level of 50 mg monensin and 50 mg nicarbazin/kg complete feed. This conclusion is extended to chickens reared for laying. For both active substances, the metabolic pathways in the chicken are similar to those in the turkey and rat. Nicarbazin, when ingested, is rapidly split in its two components dinitrocarbanilide (DNC) and 2-hydroxy-4,6-dimethylpyrimidine (HDP) which behave independently. Monimax® does not represent a genotoxic risk. No safety concerns would arise from the nicarbazin impurities p-nitroaniline and methyl(4-nitrophenyl) carbamate. The lowest no observed effect level (NOEL) identified for monensin sodium in a developmental study in rabbits is 0.3 mg monensin sodium/kg body weight (bw) per day for maternal toxicity in rabbits. The lowest no observed adverse effect level (NOAEL) identified in a 52-week study in rat using DNC + HDP was 20 mg DNC + 8 mg HDP/kg bw per day based on the absence of microcrystals in urine and related microscopic renal observations. No significant interaction between monensin sodium and nicarbazin is expected from toxicological studies. The use of Monimax® at the highest proposed dose will not pose a risk to persons consuming animal products from treated chickens for fattening. This conclusion is extended to chickens reared for laying. No withdrawal time is required for Monimax® in chickens for fattening. Residue data comply with the established maximum residue limits (MRLs) for monensin and DNC. Based on the available data, the FEEDAP Panel cannot conclude on the safety of Monimax® for the environment. Monimax® has the potential to control coccidiosis in chickens for fattening at a minimum concentration of 40 mg monensin and 40 mg nicarbazin/kg complete feed.

Safety and efficacy of Monteban® G100 (narasin) for chickens for fattening

The feed additive Monteban® G100, containing the active substance narasin, an ionophore anticoccidial, is intended to control coccidiosis in chickens for fattening at a dose of 60-70 mg/kg complete feed. Narasin is produced by fermentation. Limited data on the taxonomic identification of the production strain did not allow the proper identification of strain NRRL 8092 as Streptomyces aureofaciens. The FEEDAP Panel cannot conclude on the absence of genetic determinants for antimicrobial resistance in Streptomyces spp. under assessment. Based on the available data set, the FEEDAP Panel cannot conclude on the safety of Monteban® G100 for chickens for fattening. The simultaneous use of Monteban® G100 and certain antibiotic drugs (e.g. tiamulin) is contraindicated. Narasin is not genotoxic. No indication of carcinogenicity or developmental toxicity was found at the doses tested in the mouse, rat and rabbit. The lowest no observed effect level (NOEL) identified in the oral toxicity studies was 0.5 mg/kg body weight (bw) per day for the neuropathy seen in a one-year dog study. The acceptable daily intake (ADI) derived from this NOEL is 0.005 mg narasin/kg bw applying a uncertainty factor of 100. Monteban® G100 is safe for the consumer. Maximum residue limits (MRLs) of 50 μg narasin/kg for all wet tissues ensure consumer safety. Monteban® G100 is irritatant to the eyes but not to the skin. It has the potential to induce skin sensitisation. Inhalation exposure would pose a risk to persons handling the additive. Narasin, when used as a feed additive for chickens for fattening at 70 mg/kg feed, is not expected to pose a risk to the environment. The risk for sediment compartment cannot be assessed. The FEEDAP Panel cannot conclude on the efficacy of Monteban® at the minimum applied dose of 60 mg narasin/kg complete feed for chickens for fattening.

Safety and efficacy of Lactobacillus hilgardii CNCM I-4785 and Lactobacillus buchneri CNCM I-4323/NCIMB 40788 as a silage additive for all animal species

Following a request from the European Commission, the Panel on Additives and Products or Substances used in Animal Feed was asked to deliver a scientific opinion on the safety and efficacy of a strain of Lactobacillus hilgardii and of Lactobacillus buchneri when used as a technological additive intended to improve ensiling at a proposed application rate of 3.0 x 10⁸ colony forming units (CFU)/kg fresh material. The two bacterial species are considered by EFSA to be suitable for the qualified presumption of safety approach to safety assessment. In previous opinions the identity of the strains has been clearly established and no antibiotic resistance of concern was detected. Therefore, the use of the strains as a silage additive is considered safe for livestock species, for consumers of products from animals fed the treated silage and for the environment. In the absence of data, no conclusion can be drawn on the skin and eye irritancy or skin sensitisation of the additive. The additive should be considered a potential respiratory sensitiser. In a previous application, three studies involving both strains used in combination at the same concentration were made with samples of whole crop maize with varied dry matter content. The same studies have been submitted in this application. The Panel reiterates its previous conclusions that Lactobacillus hilgardii CNCM I-4785 and Lactobacillus buchneri NCIMB 40788/CNCM I-4323 at 1.5 × 10⁸ CFU of each active agent per kg of fresh forage, equivalent to 3 x 10⁸ CFU total lactobacilli/kg of forage significantly improve the aerobic stability of the silage.

Identification and antibiotic susceptibility of lactobacilli isolated from turkeys

Background

The aim of this study was to identify Lactobacillus isolates derived from turkeys from six Polish farms and to characterize their phenotypic and genotypic antibiotic resistance profiles.

Results

Among 62 isolates identified by MALDI-TOF mass spectrometry and restriction analysis of 16S rDNA, the dominant species was L. salivarius (35%), followed by L. crispatus (21%), L. ingluviei (14.5%) and L. johnsonii (10%). A high prevalence of resistance to tetracycline (68% resistant isolates), lincomycin (64.5%) and enrofloxacin (60%) among the lactobacilli tested was observed. Fewer than 50% isolates were resistant to ampicillin (47%), erythromycin (45%), streptomycin (31%), chloramphenicol (29%) and gentamicin (10%). As many as 64,5% of the isolates showed multidrug resistance. High MIC values for ampicillin (≥64 μg/ml) were usually accompanied by elevated MICs for cephalosporins (≥16 μg/ml) and high MICs for tiamulin, i.e. ≥32 μg/ml, were noted in most of the turkey lactobacilli (61%). The occurrence of resistance genes was associated with phenotypic resistance, with the exception of five phenotypically susceptible isolates that contained the tetM, tetL, ermC, ermB or cat genes. The most frequently identified were ermB (45% isolates), tetL (40%), tetW (37%) and tetM (29%), and the occurrence of lnuA (18%), cat (10%), ermC (6%), ant(6)-Ia (5%) and aadE (5%) was less frequent. The mechanism of ampicillin resistance has not been elucidated, but the results of nitrocefin test confirmed that it is not involved in the production of beta-lactamases.

Conclusions

The high rate of antibiotic resistance observed in this study indicates the need to implement the principles of rational use of antibiotics in poultry. The presence of transmissible resistant genes in lactobacilli may contribute to the development of antibiotic resistant pathogenic strains that pose a threat to both poultry and consumers. The results of these studies may be useful for committees providing guidance on antibiotic susceptibility of microorganisms in order to revise and supplement current microbiological cut-offs values within the genus Lactobacillus.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1269-6) contains supplementary material, which is available to authorized users.

Safety evaluation of the food enzyme endo‐1,4‐β‐xylanase from a genetically modified Bacillus subtilis (strain LMG S‐24584)

The food enzyme endo‐1,4‐β‐xylanase (EC 3.2.1.8) is produced with the genetically modified Bacillus subtilis strain LMG S‐24584 by Puratos N. V. The genetic modifications do not give rise to safety concerns. The Panel noted that, although the production strain was not detected in the food enzyme, recombinant DNA was present in all batches of the food enzyme tested. The food enzyme is intended to be used in baking processes. Based on the maximum use levels recommended for the baking processes and individual consumption data from the EFSA Comprehensive European Food Consumption Database, dietary exposure to the food enzyme–Total Organic Solids (TOS) was estimated to be up to 0.017 mg TOS/kg body weight (bw) per day in European populations. Genotoxicity tests did not raise a safety concern. The systemic toxicity was assessed by means of a repeated dose 90‐day oral toxicity study in rodents. A comparison of the no observed adverse effect level of 37 mg TOS/kg bw per day from this study with the dietary exposure results in a sufficiently high margin of exposure. The amino acid sequence of the food enzyme did not match those of known allergens. The Panel considered that, under the intended condition of use, the risk of allergic sensitisation and elicitation reactions upon dietary exposure to this food enzyme cannot be excluded, but the likelihood of such reactions occurring is considered to be low. Based on the data provided, the Panel concluded that this food enzyme does not give rise to safety concerns under the intended conditions of use.

Safety and Growth Optimization of Lactic Acid Bacteria Isolated From Feedlot Cattle for Probiotic Formula Design

In order to eliminate the widespread use of antibiotics in livestock production, the research for alternatives has increased lately. This study examined the safety of 40 lactic acid bacteria (LAB) isolated from bovine feedlot environment and previously selected as potential probiotics. A high sensitivity prevalence to ampicillin (AMP, 100%), gentamicin (GEN, 96.3%), kanamycin (KAN, 96.3%), clindamycin (CLI, 85.2%), chloramphenicol (CHL, 92.6%) and streptomycin (STR, 88.9%) while moderate and high resistance against erythromycin (ERY, 48%) and tetracycline (TET, 79%) respectively, were determined. Feedlot enterococci and pediococci displayed high resistance to CLI, ERY, GEN and TET (73, 100, 54.5, and 73%, respectively). Among fifteen resistance genes investigated, seven were identified in lactobacilli; their presence not always was correlated with phenotypic resistance. STR resistance genes, aadA and ant(6) were observed in 7.4 and 3.7% of isolates, respectively; genes responsible for aminoglycosides resistance, such as bla (7.4%), and aph(3”)-III (3.7%) were also recognized. In addition, resistance cat and tetS genes (3.7 and 7.4%, respectively) were harbored by feedlot lactobacilli strains. The presence of ermB gene in 22.3% of isolates, including two of the six strains phenotypically resistant to ERY, exhibited the highest prevalence among the assessed antibiotics. None of the feedlot lactobacilli harbored virulence factors genes, while positive PCR amplification for ace, agg, fsrA, and atpA genes was found for enterococci. With the objective of producing large cell biomass for probiotic delivery, growth media without peptone but containing glucose and skim milk powder (Mgl and Mlac) were selected as optimal. Lactobacillus acidophilus CRL2074, L. amylovorus CRL2115, L. mucosae CRL2069, and L. rhamnosus CRL2084 were strains selected as free of antibiotic resistance and virulence determinants, able to reach high cell numbers in non-expensive culture media and being compatible among them.

Antimicrobial Susceptibility Testing and Tentative Epidemiological Cutoff Values for Five Bacillus Species Relevant for Use as Animal Feed Additives or for Plant Protection

Bacillus megaterium (n = 29), Bacillus velezensis (n = 26), Bacillus amyloliquefaciens (n = 6), Bacillus paralicheniformis (n = 28), and Bacillus licheniformis (n = 35) strains from different sources, origins, and time periods were tested for the MICs for nine antimicrobial agents by the CLSI-recommended method (Mueller-Hinton broth, 35°C, for 18 to 20 h), as well as with a modified CLSI method (Iso-Sensitest [IST] broth, 37°C [35°C for B. megaterium], 24 h). This allows a proposal of species-specific epidemiological cutoff values (ECOFFs) for the interpretation of antimicrobial resistance in these species. MICs determined by the modified CLSI method were 2- to 16-fold higher than with the CLSI-recommended method for several antimicrobials. The MIC distributions differed between species for five of the nine antimicrobials. Consequently, use of the modified CLSI method and interpretation of resistance by use of species-specific ECOFFs is recommended. The genome sequences of all strains were determined and used for screening for resistance genes against the ResFinder database and for multilocus sequence typing. A putative chloramphenicol acetyltransferase (cat) gene was found in one B. megaterium strain with an elevated chloramphenicol MIC compared to the other B. megaterium strains. In B. velezensis and B. amyloliquefaciens, a putative tetracycline efflux gene, tet(L), was found in all strains (n = 27) with reduced tetracycline susceptibility but was absent in susceptible strains. All B. paralicheniformis and 23% of B. licheniformis strains had elevated MICs for erythromycin and harbored ermD The presence of these resistance genes follows taxonomy suggesting they may be intrinsic rather than horizontally acquired. Reduced susceptibility to chloramphenicol, streptomycin, and clindamycin could not be explained in all species.IMPORTANCE When commercializing bacterial strains, like Bacillus spp., for feed applications or plant bioprotection, it is required that the strains are free of acquired antimicrobial resistance genes that could potentially spread to pathogenic bacteria, thereby adding to the pool of resistance genes that may cause treatment failures in humans or animals. Conversely, if antimicrobial resistance is intrinsic to a bacterial species, the risk of spreading horizontally to other bacteria is considered very low. Reliable susceptibility test methods and interpretation criteria at the species level are needed to accurately assess antimicrobial resistance levels. In the present study, tentative ECOFFs for five Bacillus species were determined, and the results showed that the variation in MICs followed the respective species. Moreover, putative resistance genes, which were detected by whole-genome sequencing and suggested to be intrinsic rather that acquired, could explain the resistance phenotypes in most cases.

Peer review of the pesticide risk assessment of the active substance ABE‐IT 56 (components of lysate of Saccharomyces cerevisiae strain DDSF623)

The conclusions of EFSA following the peer review of the initial risk assessments carried out by the competent authority of the rapporteur Member State, France, for the pesticide active substance ABE‐IT 56 (components of lysate of Saccharomyces cerevisiae strain DDSF623) are reported. The context of the peer review was that required by Regulation (EC) No 1107/2009 of the European Parliament and of the Council. The conclusions were reached on the basis of the evaluation of the representative use of ABE‐IT 56 as a fungicide on grapes. The reliable endpoints, appropriate for use in regulatory risk assessment, are presented. Missing information identified as being required by the regulatory framework is listed.

Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

Enterococcus durans KLDS6.0930 has previously been shown to have probiotic potential. However, being a potential clinical pathogen, it becomes necessary to evaluate its safety status for novel potential probiotic use. The purpose of this study is to systematically evaluate the safety of E. durans KLDS6.0930 based on its genomics, phenotypic characteristics and oral toxicity. The complete genome of E. durans KLDS6.0930 was sequenced and analyzed for safety-related genes. Antibiotic susceptibility and the production of harmful metabolites were tested. A 28-day repeated oral dose toxicity test was implemented in rats. In vitro, E. durans KLDS6.0930 was resistant to five antibiotics, with intrinsic resistances to four antibiotics and no identified genes for the last. E. durans KLDS6.0930 was not hemolytic and virulence factors were non-functional in its genome. E. durans KLDS6.0930 produced a small amount of tyramine and phenethylamine; genes encoding tyramine decarboxylase were identified. In addition, genotype and phenotype analyses showed that the strain did not have the ability to generate D-lactic acid, indole, or nitroreductase. In vivo, E. durans KLDS6.0930 did not induce adverse effects on the organs, hematological and serum biochemical parameters, or cecal bacterial populations in the oral toxicity test. These results indicate that E. durans KLDS6.0930 can be safely used as a potential probiotic for human consumption and animal feed.

Probiotic potential of Lactobacillus isolates of chicken origin with anti-Campylobacter activity

Campylobacteriosis is currently the most frequent zoonosis in humans and the main source of infection is contaminated poultry meat. As chickens are a natural host for Campylobacter species, one strategy to prevent infection in humans is to eliminate these bacteria on poultry farms. A study was conducted to evaluate the probiotic potential of 46 Lactobacillus isolates from chickens faeces or cloacae. All lactobacilli were able to produce active compounds on solid media with antagonistic properties against C. jejuni and C. coli, with L. salivarius and L. reuteri exhibiting particularly strong antagonism. The cell-free culture supernatants had a much weaker inhibitory effect on the growth of Campylobacter, and the neutralization of organic acids caused them to completely lose their inhibitory properties. The ability to produce H2O2 was exhibited by 93% of isolates; most of isolates had a hydrophobic surface, showed excellent survival at pH 2.0 or 1.5, and displayed tolerance to bile; 50% isolates displayed the ability to biofilm formation. Determination of MICs of various antibiotics showed that as much as 80.4% of Lactobacillus isolates were resistant to at least one antimicrobial agent. Seven ultimately selected isolates that met all the basic criteria for probiotics may have potential application in reducing Camylobacter spp. in chickens and thus prevent infections in both birds and humans.

Safety Evaluations of Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI

Over the past decade, a variety of lactic acid bacteria have been commercially available to and steadily used by consumers. However, recent studies have shown that some lactic acid bacteria produce toxic substances and display properties of virulence. To establish safety guidelines for lactic acid bacteria, the Food and Agriculture Organization of the United Nations (FAO)/World Health Organization (WHO) has suggested that lactic acid bacteria be characterized and proven safe for consumers’ health via multiple experiments (e.g., antibiotic resistance, metabolic activity, toxin production, hemolytic activity, infectivity in immune-compromised animal species, human side effects, and adverse-outcome analyses). Among the lactic acid bacteria, Bifidobacterium and Lactobacillus species are probiotic strains that are most commonly commercially produced and actively studied. Bifidobacterium bifidum BGN4 and Bifidobacterium longum BORI have been used in global functional food markets (e.g., China, Germany, Jordan, Korea, Lithuania, New Zealand, Poland, Singapore, Thailand, Turkey, and Vietnam) as nutraceutical ingredients for decades, without any adverse events. However, given that the safety of some newly screened probiotic species has recently been debated, it is crucial that the consumer safety of each commercially utilized strain be confirmed. Accordingly, this paper details a safety assessment of B. bifidum BGN4 and B. longum BORI via the assessment of ammonia production, hemolysis of blood cells, biogenic amine production, antimicrobial susceptibility pattern, antibiotic resistance gene transferability, PCR data on antibiotic resistance genes, mucin degradation, genome stability, and possession of virulence factors. These probiotic strains showed neither hemolytic activity nor mucin degradation activity, and they did not produce ammonia or biogenic amines (i.e., cadaverine, histamine or tyramine). B. bifidum BGN4 and B. longum BORI produced a small amount of putrescine, commonly found in living cells, at levels similar to or lower than that found in other foods (e.g., spinach, ketchup, green pea, sauerkraut, and sausage). B. bifidum BGN4 showed higher resistance to gentamicin than the European Food Safety Authority (EFSA) cut-off. However, this paper shows the gentamicin resistance of B. bifidum BGN4 was not transferred via conjugation with L. acidophilus ATCC 4356, the latter of which is highly susceptible to gentamicin. The entire genomic sequence of B. bifidum BGN4 has been published in GenBank (accession no.: CP001361.1), documenting the lack of retention of plasmids capable of transferring an antibiotic-resistant gene. Moreover, there was little genetic mutation between the first and 25th generations of B. bifidum BGN4. Tetracycline-resistant genes are prevalent among B. longum strains; B. longum BORI has a tet(W) gene on its chromosome DNA and has also shown resistance to tetracycline. However, this research shows that its tetracycline resistance was not transferred via conjugation with L. fermentum AGBG1, the latter of which is highly sensitive to tetracycline. These findings support the continuous use of B. bifidum BGN4 and B. longum BORI as probiotics, both of which have been reported as safe by several clinical studies, and have been used in food supplements for many years.

Anti-biofilm Properties of the Fecal Probiotic Lactobacilli Against Vibrio spp

Diarrheal disease caused by Vibrio cholerae is endemic in developing countries including India and is associated with high rate of mortality especially in children. V. cholerae is known to form biofilms on the gut epithelium, and the biofilms once formed are resistant to the action of antibiotics. Therefore agents that prevent the biofilm formation and disperse the preformed biofilms are associated with therapeutic benefits. The use of antibiotics for the treatment of cholera is associated with side effects such as gut dysbiosis due to depletion of gut microflora, and the increasing problem of antibiotic resistance. Thus search for safe alternative therapeutic agents is warranted. Herein, we screened the lactobacilli spp. isolated from the fecal samples of healthy children for their abilities to prevent biofilm formation and to disperse the preformed biofilms of V. cholerae and V. parahaemolyticus by using an in vitro assay. The results showed that the culture supernatant (CS) of all the seven isolates of Lactobacillus spp. used in the study inhibited the biofilm formation of V. cholerae by more than 90%. Neutralization of pH of CS completely abrogated their antimicrobial activities against V. cholera, but had negligible effects on their biofilm inhibitory potential. Further, CS of all the lactobacilli isolates caused the dispersion of preformed V. cholerae biofilms in the range 62–85%; however, pH neutralization of CS reduced the biofilm dispersal potential of the 4 out of 7 isolates by 19–57%. Furthermore, the studies showed that CS of none of the lactobacilii isolates had antimicrobial activity against V. parahaemolyticus, but 5 out of 7 isolates inhibited the formation of its biofilm in the range 62–82%. However, none of the CS dispersed the preformed biofilms of V. parahaemolyticus. The ability of CS to inhibit the adherence of Vibrio spp. to the epithelial cell line was also determined. Thus, we conclude that the biofilm dispersive action of CS of lactobacilli is strain-specific and pH-dependent. As Vibrio is known to form biofilms in the intestinal niche having physiological pH in the range 6–7, the probiotic strains that have dispersive action at high pH may have better therapeutic potential.

Use of a Potential Probiotic, Lactobacillus plantarum L7, for the Preparation of a Rice-Based Fermented Beverage

This study aimed to isolate potential probiotic lactic acid bacteria from a traditional rice-based fermented beverage "bhaati jaanr" and to evaluate their role during preparation of the beverage. Among various isolates, Lactobacillus plantarum strain L7 exhibited satisfactory in vitro probiotic characteristics such as acid resistance and bile tolerance, cell surface hydrophobicity, auto-aggregation, antibiotic susceptibility, and antimicrobial activities. Therefore, performance of L7 as a starter culture in rice fermentation was determined during a 6-day rice fermentation study. L. plantarum L7 decreased the pH, associated with an increase in total titratable acidity and organic acid production up to the 4th day of fermentation. The highest concentrations of succinic acid (0.37 mg/g), lactic acid (4.95 mg/g), and acetic acid (0.36 mg/g) were recorded on the 3rd, 4th, and 5th days of fermentation, respectively. Saccharifying (148.13 μg/min g-1) and liquefying (89.47 μg/min g-1) activities were the highest on days 3 and 2, respectively, and thereafter, they decreased. Phytase activity and the cleavage of free minerals (sodium, calcium, magnesium, manganese, and ferrous) increased up to days 3-4. The concentration of various accumulated malto-oligosaccharides (glucose, fructose, maltotriose, and maltoterose) was noted to be the maximum on days 4 and 5. Furthermore, gas chromatography-mass spectrometry analysis indicated the presence of various volatile compounds. The fermented material also exhibited 1,1-diphenyl-2-picrylhydrazyl and 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) radical scavenging activity. Therefore, the probiotic, L. plantarum L7, has a significant role in the fermentation of this beverage and enhances its functional properties.

Beneficial and Safety Properties of a Corynebacterium vitaeruminis Strain Isolated from the Cow Rumen

Corynebacterium vitaeruminis MRU4 was isolated from the cow rumen and was differentiated from other isolates by rep-PCR and RAPD and identified by 16S rRNA sequencing. This strain presented higher survival rates for low pH and bile salts treatments, and it was able to survive and multiply in simulated gastric and intestinal environments. C. vitaeruminis MRU4 had a 53.2% auto-aggregation rate, 42.4% co-aggregation rate with Listeria monocytogenes Scott A, 41.6% co-aggregation rate with Enterococcus faecalis ATCC 19443, 10.0% co-aggregation rate with Lactobacillus sakei ATCC 15521, and 98.2% cell surface hydrophobicity rate. PCR analysis showed the presence of EFTu and map genes. The strain possessed positive results for deconjugation of bile salts (taurocholic acid, taurodeoxycholic acid, glycocholic acid, and glycodeoxycholic acid) and positive results for β-galactosidase activity and lactose assimilation activity (glucose of 8.15 ± 0.01 CFU/ml and lactose of 9.24 ± 0.02 CFU/ml). No virulence was observed by phenotypical tests. C. vitaeruminis MRU4 was resistant to oxacillin, gentamicin, erythromycin, clindamycin, sulfa/trimethoprim, and rifampicin by the disc diffusion method and showed resistance just for vancomycin by the Etest® strips test. The strain was negative for 50 tested virulence and resistance genes based on performed PCR. Based on our knowledge, this is the first report regarding the beneficial potential of one C. vitaeruminis strain.

Tetracycline resistance in lactobacilli isolated from Serbian traditional raw milk cheeses

The aim of this study was to investigate the presence of tetracycline resistance in lactobacilli isolated from traditional Serbian white brined raw milk cheeses (Homolje, Sjenica, Zlatar). Isolation of presumptive lactobacilli was initially performed using MRS-S agar without tetracycline, or supplemented with 16 and 64 µg/mL of tetracycline. Rep-PCR (GTG)₅ genotyping showed a high diversity of the isolates obtained, as examination of 233 isolates resulted in 156 different Rep-PCR fingerprints. Ninety out of 156 (57.69%) of the strains, representatives with different (GTG)₅ fingerprints, were identified by MALDI-TOF MS as lactobacilli, while 66 out of 156 (42.31%) strains were identified as members of other LAB genera. All except one out of 90 Lactobacillus isolates further tested by microdilution method, demonstrated unimodal distribution of tetracycline MIC values which were equal to or lower from the breakpoint MIC values (EFSA in EFSA J 10: 1-10, 2012. 10.2903/j.efsa.2012.2740). Only one Lb. paracasei isolate showed the presence of tet(M) gene, while the other analyzed tet genes [tet(A), tet(B), tet(C) tet(K), tet(L), tet(O) and tet(W)] were not detected in any of the isolates. The results of this study indicates that lactobacilli from traditional Serbian raw milk cheeses do not present considerable tetracycline resistance reservoirs. For final conclusions about the safety of these autochthonous cheeses regarding the possible tetracycline resistance transferability, the assessment of the entire cheese microbiota is needed.

New Insight into Biofilm Formation Ability, the Presence of Virulence Genes and Probiotic Potential of Enterococcus sp. Dairy Isolates

Enterococci have controversial status due to their emerging role in nosocomial infections and transmission of antibiotic resistance genes, while some enterococci strains are used as probiotics for humans and animals and starter cultures in dairy industry. In order to improve our understanding of factors involved in the safe use of enterococci as potential probiotics, the antibiotic susceptibility, virulence and probiotic traits of 75 dairy enterococci isolates belonging to Enterococcus durans (50), En. faecium (15), En. faecalis (6), En. italicus (3), and En. hirae (1) were evaluated. The results revealed that ciprofloxacin resistance and biofilm formation are correlated with isolates originated from Golija mountain (Serbia), while gelatinase activity was more common in isolates from Prigorje region (Croatia), pointing to uncontrolled use of antibiotics and anthropogenic impact on dairy products' microbiota in these regions. The virulence genes were sporadically present in 13 selected dairy enterococci isolates. Interestingly, biofilm formation was correlated with higher ability of strains to reduce the adhesion of E. coli and Salmonella Enteritidis to HT29-MTX cells. To our knowledge this is the first study reporting the presence of the esp gene (previously correlated with pathogenesis) in dairy enterococci isolates, mostly associated with the genes involved in adhesion property. Hence, the results of this study revealed that the virulence genes are sporadically present in dairy isolates and more correlated to adhesion properties and biofilm formation, implicating their role in gut colonization rather than to the virulence traits.

In vitro and in silico characterisation of Lactobacillus paraplantarum D2-1, a starter culture for soymilk fermentation

Soymilk contains several functional nutrients and is thus a promising ingredient for production of functional foods. The present research aimed to study starter properties, functional characteristics and safety of Lactobacillus paraplantarum D2-1, a promising starter culture for soymilk fermentation. Strain D2-1 actively fermented soymilk within 24 h but had weak activity of additional acid production after 7 d. Succinate and acetoin, which could be linked to flavour and taste, were accumulated in fermented soymilk. In vitro study revealed that the organism has several beneficial properties, including high survival ability in artificial gastric juice, high abilities of mucus adhesion and biofilm formation and production of γ-aminobutyric acid and conjugated linoleic acid, without any significant risks for consumption. Genome sequencing supported the desirable metabolic properties of the strain. These results indicate that L. paraplantarum D2-1 is a suitable starter for soymilk fermentation and is a promising probiotic candidate that can be used safely.

Investigating the transmissibility of tet(W) in bifidobacteria exposed to acid and bile stress

Transfer of antibiotic resistance genes from probiotic bacteria to pathogens poses a safety concern. Orally administered probiotics are exposed to stressful conditions during gastrointestinal transit. In this study, filter mating experiments were performed to investigate the potential role of exposure of Bifidobacterium isolates to acid and bile stress on the transfer of a tetracycline resistance gene, tet(W), to Enterococcus faecalis ATCC 51299. No E. faecalis transconjugants were obtained after mating with either stressed or unstressed Bifidobacterium, thereby suggesting that tet(W) could not be transferred as a result of exposure to gastrointestinal stresses.

Antibiotic Resistance-Susceptibility Profiles of Streptococcus thermophilus Isolated from Raw Milk and Genome Analysis of the Genetic Basis of Acquired Resistances

The food chain is thought to play an important role in the transmission of antibiotic resistances from commensal and beneficial bacteria to pathogens. Streptococcus thermophilus is a lactic acid bacterium of major importance as a starter for the dairy industry. This study reports the minimum inhibitory concentration (MIC) of 16 representative antimicrobial agents to 41 isolates of S. thermophilus derived from raw milk. Strains showing resistance to tetracycline (seven), erythromycin and clindamycin (two), and streptomycin and neomycin (one) were found. PCR amplification identified tet(S) in all the tetracycline-resistant strains, and ermB in the two erythromycin/clindamycin-resistant strains. Hybridisation experiments suggested each resistance gene to be located in the chromosome with a similar genetic organization. Five antibiotic-resistant strains -two resistant to tetracycline (St-2 and St-9), two resistant to erythromycin/clindamycin (St-5 and St-6), and one resistant to streptomycin/neomycin (St-10)- were subjected to genome sequencing and analysis. The tet(S) gene was identified in small contigs of 3.2 and 3.7 kbp in St-2 and St-9, respectively, flanked by truncated copies of insertion sequence (IS) elements. Similarly, ermB in St-6 and St-5 was found in contigs of 1.6 and 28.1 kbp, respectively. Sequence analysis and comparison of the largest contig showed it to contain three segments (21.9, 3.7, and 1.4 kbp long) highly homologous to non-collinear sequences of pRE25 from Enterococcus faecalis. These segments contained the ermB gene, a transference module with an origin of transfer (oriT) plus 15 open reading frames encoding proteins involved in conjugation, and modules for plasmid replication and segregation. Homologous stretches were separated by short, IS-related sequences, resembling the genetic organization of the integrative and conjugative elements (ICEs) found in Streptococcus species. No gene known to provide aminoglycoside resistance was seen in St-10. Four strain-specific amino acid substitutions in the RsmG methyltransferase were scored in this strain; these might be associated to its streptomycin/neomycin resistance. Under yogurt manufacturing and storage conditions, no transfer of either tet(S) or ermB from S. thermophilus to L. delbrueckii was detected. The present results contribute toward characterisation of the antibiotic resistance profiles in S. thermophilus, provide evidence for the genetic basis of acquired resistances and deepen on their transference capability.

Analysis of newly detected tetracycline resistance genes and their flanking sequences in human intestinal bifidobacteria

Due to tetracycline abuse, the safe bifidobacteria in the human gastrointestinal intestinal tract (GIT) may serve as a reservoir of tetracycline resistance genes. In the present investigation of 92 bifidobacterial strains originating from the human GIT, tetracycline resistance in 29 strains was mediated by the tet(W), tet(O) or tet(S) gene, and this is the first report of tet(O)- and tet(S)-mediated tetracycline resistance in bifidobacteria. Antibiotic resistance genes harbored by bifidobacteria are transferred from other bacteria. However, the characteristics of the spread and integration of tetracycline resistance genes into the human intestinal bifidobacteria chromosome are poorly understood. Here, conserved sequences were identified in bifidobacterial strains positive for tet(W), tet(O), or tet(S), including the tet(W), tet(O), or tet(S) and their partial flanking sequences, which exhibited identity with the sequences in multiple human intestinal pathogens, and genes encoding 23 S rRNA, an ATP transporter, a Cpp protein, and a membrane-spanning protein were flanking by the 1920-bp tet(W), 1920-bp tet(O), 1800-bp tet(O) and 252-bp tet(S) in bifidobacteria, respectively. These findings suggest that tetracycline resistance genes harbored by human intestinal bifidobacteria might initially be transferred from pathogens and that each kind of tetracycline resistance gene might tend to insert in the vicinity of specific bifidobacteria genes.