Recent investigations and updated criteria for the assessment of antibiotic resistance in food lactic acid bacteria

Search for carbapenem-resistant bacteria and carbapenem resistance genes along swine food chains in Central Italy

The presence of carbapenem-resistant bacteria and carbapenem resistance genes (CRGs) in livestock is increasing. To evaluate the presence of carbapenemase-producing Enterobacteriaceae (CPE) and the main CRGs along swine food chains of the Marche Region (Central Italy), samples of faeces, feed, and animal-food derived products were collected from seven small/medium, medium, and large-scale pig farms. A total of 191 samples were analysed using a culture-dependent method, with the aim of isolating CPE. Isolates were analysed for their resistance to carbapenems using a modified Hodge test and the microdilution method for the minimum inhibitory concentration (MIC) determination. Moreover, the extraction of microbial DNA from each sample was performed to directly detect selected CRGs via qPCR. Among the 164 presumptive resistant isolates, only one strain from a liver sample, identified as Aeromonas veronii, had an ertapenem MIC of 256 μg/mL and carried a carbapenemase- (cphA) and a β-lactamase- (blaOXA-12) encoding genes. A low incidence of CRGs was found; only nine and four faecal samples tested positive for blaNDM-1 and blaOXA-48, respectively. Overall, the importance of monitoring CPE and CRGs in livestock and their food chains should be stressed to control all potential non-human CPE and CRGs reservoirs and to determine safety levels for human health.

Dry Fermented Sausages with Total Replacement of Fat by Extra Virgin Olive Oil Emulsion and Indigenous Lactic Acid Bacteria

Research background

Formulations based on vegetable or fish oil and modifications in the production technology of dry fermented sausages have emerged in recent years aiming to achieve the desirable target of reducing the fat content of these meat products. However, previous efforts have confronted many difficulties, such as high mass loss and unacceptable appearance due to intensely wrinkled surfaces and case hardening. The objective of this study is to produce and evaluate dry fermented sausages by utilising a meat protein-olive oil emulsion as fat substitute and indigenous lactic acid bacteria (LAB) with probiotic properties isolated from traditional Greek meat products.

Experimental approach

A novel formulation with extra virgin olive oil and turkey protein was developed to totally replace the conventionally added pork fat. Probiotic and safety characteristics of autochthonous LAB isolates from spontaneously fermented sausages were evaluated and three LAB isolates were finally selected as starter cultures. Physicochemical, microbiological and sensory analyses were carried out in all treatments (control, Lactobacillus acidophilus, L. casei, L. sakei and Pediococcus pentosaceus) during fermentation.

Results and conclusions

Ready-to-eat sausages were found to be microbiologically stable. The olive oil-based formulation produced in this study generated a mosaic pattern visible in the sliced product simulating the fat in conventional fermented sausages and was regarded as an ideal fat substitute for the production of fermented sausages. An autochthonous isolate of Lactobacillus casei adapted the best to the final products as it was molecularly identified to be present in the highest counts among the LAB isolates used as starter cultures.

Novelty and scientific contribution

Α novel and high-quality dry fermented meat product was produced by replacing the added pork fat with a fat substitute based on a meat protein-olive oil emulsion. Autochthonous LAB with in vitro probiotic properties could have a potential use in large-scale novel dry fermented sausage production. Such isolates could be used as starters in an effort to standardise the production process and retain the typical organoleptic and sensory characteristics. Moreover, isolates like L. casei 62 that survived in high counts in the final products can increase the safety of fermented sausages by competing not only with pathogens but also with the indigenous microbiota and could have a potential functional value for the consumer.

Distribution of Antibiotic Resistance Genes in the Saliva of Healthy Omnivores, Ovo-Lacto-Vegetarians, and Vegans

Food consumption allows the entrance of bacteria and their antibiotic resistance (AR) genes into the human oral cavity. To date, very few studies have examined the influence of diet on the composition of the salivary microbiota, and even fewer investigations have specifically aimed to assess the impact of different long-term diets on the salivary resistome. In this study, the saliva of 144 healthy omnivores, ovo-lacto-vegetarians, and vegans were screened by nested PCR for the occurrence of 12 genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and β-lactams. The tet(W), tet(M), and erm(B) genes occurred with the highest frequencies. Overall, no effect of diet on AR gene distribution was seen. Some differences emerged at the recruiting site level, such as the higher frequency of erm(C) in the saliva of the ovo-lacto-vegetarians and omnivores from Bologna and Turin, respectively, and the higher occurrence of tet(K) in the saliva of the omnivores from Bologna. A correlation of the intake of milk and cheese with the abundance of tet(K) and erm(C) genes was seen. Finally, when the occurrence of the 12 AR genes was evaluated along with geographical location, age, and sex as sources of variability, high similarity among the 144 volunteers was seen.

Characterization of robust Lactobacillus plantarum and Lactobacillus pentosus starter cultures for environmentally friendly low-salt cucumber fermentations

Seven candidates for starter cultures for cucumber fermentations belonging to the Lactobacillus pentosus and Lactobacillus plantarum species were characterized based on physiological features desired for pickling. The isolates presented variable carbohydrate utilization profile on API^® 50CHL test strips. The L. pentosus strains were unable to utilize d-xylose in MRS broth or the M medium. The lactobacilli were unable to produce histamine, tyramine, putrescine, and cadaverine in biogenic amine broth containing the necessary precursors. Production of d-lactic acid by the lactobacilli, detected enzymatically, was stimulated by growth in MRS broth as compared to cucumber juice medium (CJM). The lactobacilli utilized malic acid in the malate decarboxylase medium. Exopolyssacharide biosynthesis related genes were amplified from the lactobacilli. A sugar type-dependent-ropy phenotype was apparent for all the cultures tested in MRS and CJM. The genes associated with bacteriocin production were detected in the lactobacilli, but not the respective phenotypes. The antibiotic susceptibility profile of the lactobacilli mimics that of other L. plantarum starter cultures. It is concluded that the lactobacilli strains studied here are suitable starter cultures for cucumber fermentation. PRACTICAL APPLICATION: The availability of such starter cultures enables the implementation of low salt cucumber fermentations that can generate products with consistent biochemistry and microbiological profile.

Safety Aspects of Genetically Modified Lactic Acid Bacteria

Lactic acid bacteria (LAB) have a long history of use in the food industry. Some species are part of the normal human microbiota and have beneficial properties for human health. Their long-standing use and considerable biotechnological potential have led to the development of various systems for their engineering. Together with novel approaches such as CRISPR-Cas, the established systems for engineering now allow significant improvements to LAB strains. Nevertheless, genetically modified LAB (GM-LAB) still encounter disapproval and are under extensive regulatory requirements. This review presents data on the prospects for LAB to obtain 'generally recognized as safe' (GRAS) status. Genetic modification of LAB is discussed, together with problems that can arise from their engineering, including their dissemination into the environment and the spread of antibiotic resistance markers. Possible solutions that would allow the use of GM-LAB are described, such as biocontainment, alternative selection markers, and use of homologous DNA. The use of GM-LAB as cell factories in closed systems that prevent their environmental release is the least problematic aspect, and this is also discussed.

Techno-functional characterization of indigenous Lactobacillus isolates from the traditional fermented foods of Meghalaya, India

The rural tribal people of Meghalaya depend mostly on their ethnic fermented foods as a part of their regular diet and these fermented foods are considered to be a hub of healthy microorganisms. However, the efficacy of probiotic microorganisms is considered to be population-specific because of gut microflora variation in food habits and specific host-microbial interactions. Hence, a strong need for exploring novel indigenous microorganisms with rich probiotic potentiality is required. A few indigenous Lactobacillus isolates (from traditional fermented foods of Meghalaya) were studied extensively for its technological and probiotic attributes. The isolates could survive at pH 2–3 (L. fermentum K16 showed high cell count: pH 2–5.12 log CFU/ml; pH 3–5.76 log CFU/ml), against bile salts (L. fermentum K7 showed high cell count-5.36 log CFU/ml), gastric juices (pepsin and trypsin), and intestinal juice (pancreatin). The isolates showed α-galactosidase activity from 0.104-0.412 μM/ml and β-glucosidase activity ranging from 0.122-0.409 μM/ml. Exopolysaccharide production was in between 410 and 950 mg/L. Cell surface hydrophobicity was 71.57% (L. rhamnosus K4E) and auto-aggregation was 83% (L. fermentum K16) during the study. Highest proteolytic activity (0.671 nm) and cholesterol assimilation (52.57%) was exhibited by L. fermentum K16. The isolates showed high free radical scavenging activity by ABTS method up to 80.78% by isolate L. fermentum K7. Antibacterial activity and co-aggregation efficacy was also tested against B. cereus, E. faecalis, S. dysenteriae, S. aureus, E. coli, L. monocytogenes, S. typhi. These indigenous Lactobacillus isolates with high probiotic potentials could be exploited in the development of the traditional fermented foods of Meghalaya.

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Technological and probiotic attributes (in vitro) of eight indigenous Lactobacillus strains were studied.

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Lactobacillus strains were isolated from the traditional fermented foods of Meghalaya, India.

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L. rhamnosus K4E, L. fermentum K16, L. fermentum K7 and L. plantarum RD7 were considered predominant over the rest of the strains.

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The isolates could be employed for development of novel functional fermented foods.

Gut commensal bacteria show beneficial properties as wildlife probiotics

Probiotics are noninvasive, environmentally friendly alternatives for reducing infectious diseases in wildlife species. Our aim in the present study was to evaluate the potential of gut commensals such as lactic acid bacteria (LAB) as wildlife probiotics. The LAB selected for our analyses were isolated from European badgers (Meles meles), a wildlife reservoir of bovine tuberculosis, and comprised four different genera: Enterococcus, Weissella, Pediococcus, and Lactobacillus. The enterococci displayed a phenotype and genotype that included the production of antibacterial peptides and stimulation of antiviral responses, as well as the presence of virulence and antibiotic resistance genes; Weissella showed antimycobacterial activity owing to their ability to produce lactate and ethanol; and lactobacilli and pediococci modulated proinflammatory phagocytic responses that associate with protection against pathogens, responses that coincide with the presence of immunomodulatory markers in their genomes. Although both lactobacilli and pediococci showed resistance to antibiotics, this was naturally acquired, and almost all isolates demonstrated a phylogenetic relationship with isolates from food and healthy animals. Our results show that LAB display probiotic benefits that depend on the genus, and that lactobacilli and pediococci are probably the most obvious candidates as probiotics against infectious diseases in wildlife because of their food-grade status and ability to modulate protective innate immune responses.

Critical insights into antibiotic resistance transferability in probiotic Lactobacillus

Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host, with respect to metabolism, immune function, and nutrition. Any perturbation of these beneficial microbes leads to gut dysbiosis, which triggers the development of various disorders in the gastrointestinal system. Probiotics play a key role in resolving the dysbiosis posed by external factors such as antibiotics, other substances, or interventions. Supplementing probiotics with antibiotics is favorable in reducing the harmful effects of antibiotics on gut flora. These microbes also possess specific intrinsic drug resistance mechanisms that aid their survival in the internal environment. According to US Food and Drug Administration reports, species belonging to Lactobacillus and Bifidobacterium genera are the most common probiotics consumed by humans through commercial products. However, various studies have reported the tendency of microbes to acquire specific drug resistance, in recent years, through various mechanisms. The reports on transferable resistance among probiotics are of major concern, of which minimal information is available to date. The aim of this review was to describe the pros and cons of drug resistance among these beneficial microorganisms with emphasis on the recommended selection criteria for specific probiotics, devoid of transferable drug resistance genes, suitable for human consumption.

Current knowledge on the microbiota of edible insects intended for human consumption: A state-of-the-art review

Because of their positive nutritional characteristics and low environmental impact, edible insects might be considered a 'food of the future'. However, there are safety concerns associated with the consumption of insects, such as contaminating chemical and biological agents. The possible presence of pathogenic and toxigenic microorganisms is one of the main biological hazards associated with edible insects. This review presents an overview of the microbiota of edible insects, highlighting the potential risks for human health. Detailed information on the microbiota of edible insects from literature published in 2000-2019 is presented. These data show complex ecosystems, with marked variations in microbial load and diversity, among edible insects as well as stable and species-specific microbiota for some of the most popular edible insect species, such as mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria). Raw edible insects generally contain high numbers of mesophilic aerobes, bacterial endospores or spore-forming bacteria, Enterobacteriaceae, lactic acid bacteria, psychrotrophic aerobes, and fungi, and potentially harmful species (i.e. pathogenic, mycotoxigenic, and spoilage microbes) may be present. Several studies have focused on reducing the microbial contamination of edible insects by applying treatments such as starvation, rinsing, thermal treatments, chilling, drying, fermentation, and marination, both alone and, sometimes, in combination. Although these studies show that various heat treatments were the most efficient methods for reducing microbial numbers, they also highlight the need for species-specific mitigation strategies. The feasibility of using edible insects as ingredients in the food industry in the development of innovative insect-based products has been explored; although, in some cases, the presence of spore-forming bacteria and other food-borne pathogens is a concern. Recent studies have shown that a risk assessment of edible insects should also include an evaluation of the incidence of antibiotic-resistance (AR) genes and antibiotic-resistant microorganisms in the production chain. Finally, as proposed in the literature, microbial hazards should be limited through the implementation of good hygienic practices during rearing, handling, processing, and storage, as well as the implementation of an appropriate HACCP system for edible insect supply chains. Another issue frequently reported in the literature is the need for a legislative framework for edible insect production, commercialisation, and trading, as well as the need for microbiological criteria specifically tailored for edible insects. Microbiological criteria like those already been established for the food safety and hygiene (e.g. those in the European Union food law) of different food categories (e.g. ready-to-eat products) could be applied to edible insect-based products.

Fate of tetracycline and sulfonamide resistance genes in a grassland soil amended with different organic fertilizers

This study provided an assessment of the environmental fate of antibiotic resistance genes (ARGs) in a Scottish grassland field repeatedly treated with different organic fertilizers. The impacts of manure, biosolids and municipal food-derived compost on the relative abundances of tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), sulfonamide ARGs (sul1 and sul2) and class 1 integron-integrase gene (IntI1) in soils were investigated, with inorganic fertilizer (NPK) as a comparison. The background soil with a history of low intensity farming showed a higher total relative abundance of tet ARGs over sul ARGs, with tetracycline efflux genes occurring in a higher frequency. In all treatments, the relative abundances of most ARGs detected in soils decreased over time, especially IntI1 and tet ARGs. This general attenuation of soil ARGs is a reflection of changes in the soil microbial community, which is supported by the result that almost all the soils at the end of the experiment had different bacterial communities from the untreated soil at the beginning of the experiment. Multiple applications of organic fertilizers to some extent counteracted the decreasing trend of soil ARGs relative abundances, which resulted in higher ARGs relative abundances in comparison to NPK, either by a lesser decrease of IntI1 and tet ARGs or an increase of sul ARGs. The enhancement of existing soil ARG prevalence by organic fertilizers was strongly dependent on the organic fertilizer type and the particular ARG. Compost contained the lowest relative abundance of inherent ARGs and had the least effect on the soil ARG decrease after application. The relative increase of tet ARGs caused by biosolids was larger than that of sul ARGs, while manure caused the opposite effect. Fertilization practices did not exert effective impacts on the soil bacterial community, although it caused significant changes in the profile of the ARG pool. Organic fertilization may thus accelerate the dissemination of ARGs in soil mainly through horizontal gene transfer (HGT), consistent with the enrichment of IntI1 in organic fertilized soils.

Investigation of the Dominant Microbiota in Ready-to-Eat Grasshoppers and Mealworms and Quantification of Carbapenem Resistance Genes by qPCR

In this study, 30 samples of processed edible mealworms (Tenebrio molitor L.) and 30 samples of grasshoppers (Locusta migratoria migratorioides) were obtained from producers located in Europe (Belgium and the Netherlands) and Asia (Thailand) and subjected to PCR-DGGE analyses. The PCR-DGGE analyses showed that species in the genus Staphylococcus were predominant in the samples of mealworms from Belgium and grasshoppers from the Netherlands; species in the genus Bacillus were detected in the samples of mealworms and grasshoppers from Thailand. Moreover, Weissella cibaria/confusa/spp. was found in grasshoppers from Belgium. Since data concerning the role of novel foods such as edible insects in the dissemination of carbapenem resistance are currently lacking, the quantification of five carbapenemase encoding genes (bla NDM-1, bla VIM, bla GES, bla OXA-48, and bla KPC) by qPCR was also carried out in all the samples under study. The genes coding for GES and KPC were not detected in the analyzed samples. A very low frequency of bla OXA-48 (3%) and bla NDM-1 (10%) genes was detected among mealworms. In contrast, grasshoppers were characterized by a high incidence of the genes for OXA-48 and NDM-1, accounting for 57 and 27% of the overall grasshopper samples, respectively. The bla VIM gene was detected exclusively in two grasshopper samples from Thailand, showing only 7% positivity. The analysis of variance showed that all the effects (producers, species, and producers × species) were statistically significant for bla NDM-1, whereas for bla OXA-48 and bla VIM, no significant effects were detected for the same source of variation. Further studies are necessary to assess the possible role of edible insects as reservoirs for the resistance to carbapenems and to understand the correlation with the insect microbiota. Furthermore, an intensified surveillance plan examining the occurrence of carbapenemase encoding genes in the food chain and in environmental compartments is needed for a proper risk assessment. In such a context, the appropriate use of antimicrobials represents the main preventive action that should always be applied.

Distribution of Transferable Antibiotic Resistance Genes in Laboratory-Reared Edible Mealworms (Tenebrio molitor L.)

In the present study, the distribution of antibiotic resistance genes in laboratory-reared fresh mealworm larvae (Tenebrio molitor L.), their feeding substrates (carrots and wheatmeal), and frass was assessed. Microbial counts on selective media added with antibiotics highlighted the presence of lactic acid bacteria resistant to ampicillin and vancomycin and, more specifically, enterococci resistant to the latter antibiotic. Moreover, staphylococci resistant to gentamicin, erythromycin, tetracycline, and vancomycin were detected. Enterobacteriaceae resistant to ampicillin and gentamicin were also found, together with Pseudomonadaceae resistant to gentamicin. Some of the genes coding for resistance to macrolide-lincosamide-streptogramin B (MLSB) [erm(A), erm(C)], vancomycin [vanA, vanB], tetracycline [tet(O)], and β-lactams [mecA and blaZ] were absent in all of the samples. For the feeding substrates, organic wheatmeal was positive for tet(S) and tet(K), whereas no AR genes were detected in organic carrots. The genes tet(M), tet(K), and tet(S) were detected in both mealworms and frass, whereas gene aac-aph, coding for resistance to amynoglicosides was exclusively detected in frass. No residues for any of the 64 antibiotics belonging to 10 different drug classes were found in either the organic wheatmeal or carrots. Based on the overall results, the contribution of feed to the occurrence of antibiotic resistance (AR) genes and/or antibiotic-resistant microorganisms in mealworm larvae was hypothesized together with vertical transmission via insect egg smearing.

Prevalence and risk factors for thermotolerant species of Campylobacter in poultry meat at retail in Europe

The thermotolerant species Campylobacter jejuni, Campylobacter coli, Campylobacter lari and Campylobacter upsaliensis are the causative agents of the human illness called campylobacteriosis. This infection represents a threat for the health of consumers in Europe. It is well known that poultry meat is an important food vehicle of Campylobacter infection. As emerged from the reported scientific literature published between 2006 and 2016, poultry meat sold at retail level in Europe represents an important source of the pathogen. The contamination level of poultry meat sold at retail can vary depending on pre- and post-harvest factors. Among the pre-harvest measures, strict biosecurity practices must be guaranteed; moreover, among post-harvest control measures scalding, chilling and removal of faecal residues can reduce the contamination level of Campylobacter. An additional issue is represented by increasing proportion of Campylobacter isolates resistant to tetracyclines, ciprofloxacin, and nalidixic acid, thus feeding a serious concern on the effectiveness of antibiotic treatment for human campylobacteriosis in a near future.

Development of a Teat Bio-sealant and Evaluation of its Technological and Functional Properties

A teat bio-sealant was developed using Weissella cibaria, and the bio-sealant's technological and functional properties were assessed. The development included four experimental phases that were analyzed using independent experimental designs. Initially, sterilized or pasteurized Aloe vera gels were used, and the effect of heat treatment was investigated. In the second phase, the effects of time, storage temperature, and addition of cryopreservatives on the viability of the probiotic were observed. The third phase consisted of evaluating the synergistic effects of the cryopreservatives. The fourth phase involved selecting a material that would provide viscosity to the teat sealant. Technological and functional properties were measured in terms of viability of W. cibaria, and antimicrobial activity against Staphylococcus aureus and Streptococcus agalactiae was also analyzed. A mixture of milk powder and glycerol preserved this antimicrobial activity. Pullulan provided greater viscosity and maintained the technological and functional properties of the bio-sealant for 29 days. This teat bio-sealant can be used as an alternative for the prevention of bovine mastitis.

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.

Occurrence of antibiotic resistance genes in the fecal DNA of healthy omnivores, ovo-lacto vegetarians and vegans

SCOPE

The effects of long-term omnivore, ovo-lacto vegetarian and vegan diets on the occurrence of 12 antibiotic resistance (AR) genes in the human gut were studied.

METHODS AND RESULTS

The feces of 144 healthy volunteers recruited from Turin, Bari, Bologna, and Parma were screened for the occurrence of genes conferring resistance to tetracyclines, macrolide-lincosamide-streptogramin B, vancomycin, and β-lactams. Overall, erm(B), tet(W) and tet(M) were detected at the highest frequency. A low effect from the diet on the AR gene distribution emerged, with tet(K) and vanB occurring at a lower and higher frequency in vegans and omnivores, respectively. A correlation of the intake of eggs, milk from animal sources and cheese with an increased occurrence of tet(K) was observed, together with a higher incidence of vanB in consumers of eggs, poultry meat, fish and seafood. When the detection frequencies of AR genes in volunteers from Bari and the other sites were comparatively evaluated, a north-to-south gradient was observed, whereas no effect of sex or age was highlighted. Except for tet(K), a negligible three-factor interaction was seen.

CONCLUSION

A high impact of the geographical location on AR gene distribution was seen in the cohort of subjects analyzed, irrespective of their dietary habits.

Transferable Antibiotic Resistances in Marketed Edible Grasshoppers (Locusta migratoria migratorioides)

Grasshoppers are the most commonly eaten insects by humans worldwide, as they are rich in proteins and micronutrients. This study aimed to assess the occurrence of transferable antibiotic resistance genes in commercialized edible grasshoppers. To this end, the prevalence of 12 selected genes [aac(6')-Ie aph(2″)-Ia, blaZ, erm(A), erm(B), erm(C), mecA, tet(M), tet(O), tet(S), tet(K), vanA, vanB] coding for resistance to antibiotics conventionally used in clinical practice was determined. The majority of samples were positive for tet(M) (70.0%), tet(K) (83.3%) and blaZ (83.3%). A low percentage of samples were positive for erm(B) (16.7%), erm(C) (26.7%), and aac(6')-Ie aph(2″)-Ia (13.3%), whereas no samples were positive for erm(A), vanA, vanB, tet(O), and mecA. Cluster analysis identified 4 main clusters, allowing a separation of samples on the basis of their country of origin.

Functional screening of antibiotic resistance genes from a representative metagenomic library of food fermenting microbiota

Lactic acid bacteria (LAB) represent the predominant microbiota in fermented foods. Foodborne LAB have received increasing attention as potential reservoir of antibiotic resistance (AR) determinants, which may be horizontally transferred to opportunistic pathogens. We have previously reported isolation of AR LAB from the raw ingredients of a fermented cheese, while AR genes could be detected in the final, marketed product only by PCR amplification, thus pointing at the need for more sensitive microbial isolation techniques. We turned therefore to construction of a metagenomic library containing microbial DNA extracted directly from the food matrix. To maximize yield and purity and to ensure that genomic complexity of the library was representative of the original bacterial population, we defined a suitable protocol for total DNA extraction from cheese which can also be applied to other lipid-rich foods. Functional library screening on different antibiotics allowed recovery of ampicillin and kanamycin resistant clones originating from Streptococcus salivarius subsp. thermophilus and Lactobacillus helveticus genomes. We report molecular characterization of the cloned inserts, which were fully sequenced and shown to confer AR phenotype to recipient bacteria. We also show that metagenomics can be applied to food microbiota to identify underrepresented species carrying specific genes of interest.