Evaluation of (GTG)5-PCR for identification of Enterococcus spp

Virulence profile of Candida spp. isolated from an anaerobic biodigester supplied with dairy cattle waste

Anaerobic biodigesters play a crucial role in enhancing animal waste management. However, the presence of pathogens in the biodigestion process poses a significant concern. Candida spp., a widespread fungus known for its opportunistic nature and adaptability to diverse environmental conditions, including reciprocal transmission between humans and animals, is one such pathogen of concern. Therefore, it is imperative to assess the virulence profile of Candida spp. originating from anaerobic biodigestion processes. Here we demonstrate that strains isolated from the biodigestion process of dairy cattle waste exhibit noteworthy virulence mechanisms, surpassing the virulence of clinical control strains. After we identified strains from affluent, effluent, and biofertilizer, we observed that all analyzed isolates produced biofilm. Additionally, a substantial proportion of these isolates demonstrated phospholipase production, while only a few strains exhibited protease production. Furthermore, all strains exhibited resistance or dose-dependent responses to amphotericin B and itraconazole, with the majority displaying resistance to fluconazole. In the in vivo test, we observed a significant correlation (p < 0.05) between the LT50 and biofilm formation as well as hyphae/pseudohyphae production. Additionally, some isolates demonstrated a quicker nematode-killing capacity compared to clinical controls. Our findings underscore the considerable pathogenic potential of certain Candida species present in the dynamics of anaerobic biodigestion. Importantly, the anaerobic biodigester system did not eliminate Candida strains from dairy cattle waste, highlighting the need for caution in utilizing biodigester products. We advocate for further studies to explore the virulence of other microorganisms in various animal production contexts. Furthermore, our results emphasize the urgency of enhancing waste treatment methods to effectively eliminate pathogens and curb their potential dissemination.

Development and validation of cost-effective SYBR Green-based RT-qPCR and its evaluation in a sample pooling strategy for detecting SARS-CoV-2 infection in the Indonesian setting

A low-cost SYBR Green-based RT-qPCR method to detect SARS-CoV-2 were developed and validated. Primers targeting a conserved and vital region of the N genes of SARS-CoV-2 were designed. In-silico study was performed to analyse the compatibility of the selected primer pair with Indonesian SARS-CoV-2 genome sequences available from the GISAID database. We determined the linearity of our new assay using serial dilution of SARS-CoV-2 RNA from clinical samples with known virus concentration. The assay was then evaluated using clinically relevant samples in comparison to a commercial TaqMan-based test kit. Finally, we applied the assay in sample pooling strategies for SARS-CoV-2 detection. The SYBR Green-based RT-qPCR method was successfully developed with sufficient sensitivity. There is a very low prevalence of genome variation in the selected N primer binding regions, indicating their high conservation. The validation of the assay using clinical samples demonstrated similar performance to the TaqMan method suggesting the SYBR methods is reliable. The pooling strategy by combining 5 RNA samples for SARS-CoV-2 detection using the SYBR RT-qPCR methods is feasible and provides a high diagnostic yield. However, when dealing with samples having a very low viral load, it may increase the risk of missing positive cases.

Resistance and virulence distribution in enterococci isolated from broilers reared in two farming systems

Background

The impact of enterococci in human health has been growing for the last decades, mainly due to their resistance to several antimicrobial agents. Human consumption of contaminated meat, especially poultry, has been identified as a possible route of transmission. The aim of the present study was to evaluate and compare the antimicrobial resistance profiles and virulence genes of enterococci isolated from Portuguese conventional and free-range broiler farms.

Results

Antibiotic susceptibility testing showed high frequencies of resistance to tetracycline in both farming systems. Resistance to erythromycin and gentamicin were detected in about half of the isolates. Resistance to penicillin was the less frequently observed and no vancomycin resistant isolates were identified. The majority of the enterococcal isolates, from either farming systems, were resistant to more than one antibiotic, and no statistical associations were found, except for penicillin resistance which associated with the genetic clusters. No differences were found between farming systems regarding the prevalence of tet(M), erm(B), aac (6′)-Ie-aph (2″)-Ia and pbp5 genes, nevertheless pbp5 prevalence was associated with the different genetic clusters. Hemolytic activity was identified in 26.47% of all isolates and gelatinase activity in 50%. The gelE gene was identified in the majority of the isolates, whereas esp and agg genes were rarely detected. The cylA determinant was not detected in any of the isolates.

Conclusions

Overall, results suggest that similar resistance patterns and virulence genes can be found in both farming systems, though enterococci in free-range conditions should be less prone to acquire further resistance genes.

Lactic Acid Bacteria Diversity and Characterization of Probiotic Candidates in Fermented Meats

Probiotics are defined as live microorganisms which confer health benefits to the host when administered in adequate amounts. Many lactic acid bacteria (LAB) strains have been classified as probiotics and fermented foods are an excellent source of such LAB. In this study, novel probiotic candidates from two fermented meats (pancetta and prosciutto) were isolated and characterized. LAB populations present in pancetta and prosciutto were evaluated and Lactiplantibacillus plantarum was found to be the dominant species. The antagonistic ability of selected isolates against LAB and non-LAB strains was investigated, in particular, the ability to produce anti-microbial compounds including organic acids and bacteriocins. Probiotic characteristics including antibiotic susceptibility, hydrophobicity and autoaggregation capacity; and ability to withstand simulated gastric juice, bile salt, phenol and NaCl were assessed. Among the characterized strains, L. plantarum 41G isolated from prosciutto was identified as the most robust probiotic candidate compared. Results from this study demonstrate that artisanal fermented meat is a rich source of novel strains with probiotic potential.

Vigna spp. Root-Nodules Harbor Potentially Pathogenic Fungi Controlled By Co-habiting Bacteria

This study aimed to isolate, identify, and evaluate the pathogenicity of nodule-borne fungi of asymptomatic Vigna spp. plants, grown in soils from preserved tropical dry forests (Caatinga) areas and identify the occurrence of co-habiting bacteria from these plants, and which have potential to control the co-occurring pathogenic fungi. Fungi and bacteria were isolated from three Vigna species (V. unguiculata, V. radiata, and V. mungo), grown in soil samples collected in five preserved Caatinga areas (Northeastern, Brazil). All fungi and selected bacteria were phylogenetically characterized by the sequencing of ITS1-5.8S-ITS2, and the 16S rRNA gene, respectively. The pathogenicity of fungi in cowpea seeds germination was evaluated throughout the inoculation experiment in Petri dishes and pots containing sterile substrate. The potential of nodule-borne bacteria to control pathogenic fungi in cowpea was assessed in a pot experiment with a sterilized substrate by the co-inoculation of fungi and bacteria isolated from the respective individual plants and soils. The 23 fungal isolates recovered were classified within the genera Fusarium, Macrophomina, Aspergillus, Cladosporium, and Nigrospora. The inoculation of fungi in cowpea seeds reduced the emergence of seeds in Petri dishes and pots. Twenty-four bacteria (Agrobacterium sp., Bradyrhizobium sp., Bacillus sp., Enterobacter sp., Pseudomonas sp., Paraburkholderia sp., and Rhizobium sp.) inhibited the harmful effects of Macrophomina sp. and Fusarium sp., increasing the germination and emergency of potted cowpea plants, highlighting the strains Agrobacterium sp. ESA 686 and Pseudomonas sp. ESA 732 that controlled, respectively, the Fusarium sp. ESA 771 and Macrophomina sp. ESA 786 by 100 and 84.6% of efficiency.

Kombucha Tea as a Reservoir of Cellulose Producing Bacteria: Assessing Diversity among Komagataeibacter Isolates

Bacterial cellulose (BC) is receiving a great deal of attention due to its unique properties such as high purity, water retention capacity, high mechanical strength, and biocompatibility. However, the production of BC has been limited because of the associated high costs and low productivity. In light of this, the isolation of new BC producing bacteria and the selection of highly productive strains has become a prominent issue. Kombucha tea is a fermented beverage in which the bacteria fraction of the microbial community is composed mostly of strains belonging to the genus Komagataeibacter. In this study, Kombucha tea production trials were performed starting from a previous batch, and bacterial isolation was conducted along cultivation time. From the whole microbial pool, 46 isolates were tested for their ability to produce BC. The obtained BC yield ranged from 0.59 g/L, for the isolate K2G36, to 23 g/L for K2G30—which used as the reference strain. The genetic intraspecific diversity of the 46 isolates was investigated using two repetitive-sequence-based PCR typing methods: the enterobacterial repetitive intergenic consensus (ERIC) elements and the (GTG)5 sequences, respectively. The results obtained using the two different approaches revealed the suitability of the fingerprint techniques, showing a discrimination power, calculated as the D index, of 0.94 for (GTG)5 rep-PCR and 0.95 for ERIC rep-PCR. In order to improve the sensitivity of the applied method, a combined model for the two genotyping experiments was performed, allowing for the ability to discriminate among strains.

Functional Properties and Sustainability Improvement of Sourdough Bread by Lactic Acid Bacteria

Preventing food spoilage without the addition of chemical food additives, while increasing functional properties of wheat-based bakery products, is an increasing demand by the consumers and a challenge for the food industry. Within this study, lactic acid bacteria (LAB) isolated from sourdough were screened in vitro for the ability to utilize the typical wheat carbohydrates, for their antimicrobial and functional properties. The dual culture overlay assay revealed varying levels of inhibition against the examined fungi, with Lactiplantibacillus plantarum S4.2 and Lentilactobacillusparabuchneri S2.9 exhibiting the highest suppression against the indicator strains Fusarium graminearum MUCL43764, Aspergillus fumigatus, A. flavus MUCL11945, A. brasiliensis DSM1988, and Penicillium roqueforti DSM1079. Furthermore, the antifungal activity was shown to be attributed mainly to the activity of acids produced by LAB. The antibacillus activity was evaluated by the spot-on-the-lawn method revealing a high inhibition potential of the majority of LAB isolated from sourdough against Bacillus cereus DSM31, B. licheniformis DSM13, B. subtilis LMG7135, and B. subtilis S15.20. Furthermore, evaluating the presence of the glutamate decarboxylase gen in LAB isolates by means of PCR showed a strain dependency of a potential GABA production. Finally, due to improved functional activities, LAB isolated from sourdoughs exhibit promising characteristics for the application as natural preservatives in wheat-based bakery products.

Genotypic diversity in multi-drug-resistant E. coli isolated from animal feces and Yamuna River water, India, using rep-PCR fingerprinting

Genotypic diversity among multi-drug-resistant (MDR) aquatic E. coli isolated from different sites of Yamuna River was analyzed using repetitive element PCR (rep-PCR) methods viz. ERIC-PCR and (GTG)₅-PCR and compared with the MDR animal fecal isolates. The 97 E. coli isolates belonging to different serotypes, phylogroups, and multi-drug resistance patterns were analyzed. High genetic diversity was observed by both the methods; however, (GTG)₅ typing showed higher discriminating potential. Combination of ERIC types (E1-E32) and (GTG)₅ types (G1-G46) generated 77 genotypes. The frequency of genotypes ranged from 0.013 to 0.065. The genotype composition of E. coli isolates was highly diverse at all the sampling sites across Yamuna River except at its entry site in Delhi. The sampling sites under the influence of high anthropogenic activities showed an increase in number of unique genotype isolates. These sites also exhibited high multiple antibiotic resistance (MAR) indexes (above 0.25) suggesting high risk of contamination. Principal coordinate analysis (PCoA) showed limited clustering of genotypes based on the sampling sites. The most frequent genotypes were grouped in the positive zone of both the principal coordinates (PC1 and PC2). The genotypes of most of the animal fecal isolates were unique and occupied a common space in the negative PC1 area forming a separate cluster. High genotypic diversity among the aquatic E. coli and the drain isolates, discharging the untreated municipal waste in the river, was observed, suggesting that the sewage effluents contribute substantially to contamination of this river system than animal feces. The presence of such a high diversity among the MDR E. coli isolates in the natural river systems is of great public health significance and highlights the need of an efficient surveillance system for better management of Indian natural water bodies.

Identification of the predominant microbiota during production of lait caillé, a spontaneously fermented milk product made in Burkina Faso

The spontaneously fermented curdled milk product from Burkina Faso, lait caillé is prepared by traditional processing from raw unpasteurised milk. The fermentation lasts 1-3 days. This study aims to identify the predominant microbiota involved in lait caillé fermentation from cow milk. A survey on lait caillé end-products from local markets showed pH ranges of 3.5 to 4.2. Counts of total lactic acid bacteria (LAB) were 7.8 ± 0.06 to 10.0 ± 0.03 log CFU/g and yeast counts were 5.3 ± 0.06 to 8.7 ± 0.01 log CFU/g, together with considerate amounts of Enterobacteriaceae < 3.00 to 8.4 ± 0.14 log CFU/g. Sampling throughout the entire fermentation of lait caillé was performed at a traditional house-hold production site. A drop in pH from 6.7 ± 0.01 at 0 h to 4.3 ± 0.08 in the end-product (59 h) was found. Total LAB counts increased to 8.6 ± 0.02 log CFU/g in the end-product, while yeast and Enterobacteriaceae counts reached 6.4 ± 0.11 and 6.7 ± 0.00 log CFU/g, respectively. LAB and yeasts isolated during the fermentation were clustered by (GTG)₅ repetitive-PCR fingerprinting followed by 16S and 26S rRNA gene sequencing, respectively. Microbial successions were observed with Leuconostoc mesenteroides being the predominant LAB followed by Pediococcus pentosaceus and Weissella paramesenteroides at the onset, while Lactococcus lactis and Enterococcus spp. where the predominant LAB after 7 h of fermentation. During the first 18 h Candida parapsilosis was the dominant yeast species, while from 35 h to the end-product, Saccharomyces cerevisiae predominated. The microbial safety risk pointed out in this study, showed the need for implementation of good manufacturing practices including pasteurisation and use of well-defined starter cultures.

Molecular Identification and Probiotic Potential Characterization of Lactic Acid Bacteria Isolated from Human Vaginal Microbiota

Purpose: The increased demand for probiotics because of their health purposes provides the context for this study, which involves the molecular identification of lactic acid bacteria (LAB) obtained from the vaginal microbiota of healthy fertile women. The isolates were subjected for examination to prove their probiotic potential. In particular, the isolates were subjected to various tests, including acid/bile tolerance, antimicrobial activity, antibiotic susceptibility, Gram staining, and catalase enzyme activity assessment. Methods: Several methods were utilized for the molecular identification of the isolates, including ARDRA, (GTG)5-PCR fingerprinting, and the PCR sequencing of 16S-rDNA amplified fragments. Disc diffusion and well diffusion methods were used to assess antibiotic susceptibility and antibacterial activity of isolates. Tolerance to acid and bile was performed at pH 2.5 and 0.3% bile oxgall. Results: A total of 45 isolates of 88 separate organisms was selected. All of the isolates demonstrated an antibacterial effect on the exploited indicator microorganisms. All selected strains also maintained their viability at low-pH and high-bile salt conditions and exhibited abroad variation in their survival. Only the Enterococcus avium strain showed resistance to all 9 tested antibiotics. Based on the molecular identification and clustering, the 45 isolated bacteria were classified into three major groups of LAB: Enterococcus, Lactobacillus and Lactococcus. Conclusion: LAB are microorganisms that have a particularly important function in maintaining the health of the vaginal and gastrointestinal tract and in protecting it from infection by other pathogenic organisms. The isolates found to be a promising probiotic candidate by showed desirable characteristics. Therefore, strain DL3 can be used as natural food preservative with some more potential investigations.

Assessment of Coagulase-Negative Staphylococci and Lactic Acid Bacteria Isolated from Portuguese Dry Fermented Sausages as Potential Starters Based on Their Biogenic Amine Profile

The aim of this study was to evaluate the decarboxylase activity of coagulase-negative staphylococci (CNS) and lactic acid bacteria (LAB) involved in meat products fermentation, in order to characterize and select the strains most suitable to be used as safe starter cultures. Isolates were obtained from traditional Portuguese dry fermented meat sausages, identified by PCR and characterized according to their technological properties. Lactobacilli and enterococci were assessed for their bacteriocinogenic potential. Biogenic amines (BA) were screened by culture method and analyzed by RP-HPLC/UV. The screening method, compared with chromatographic analysis, was not reliable for CNS and LAB strains selection. Tyramine decarboxylase activity was present in CNS strains, with a slight production of amines. No other hazardous BA were produced. Among lactobacilli, moderate production of tyramine was related only to Lactobacillus curvatus, with some strains producing putrescine or 2-phenylethylamine. Enterococci were high and moderate producers of tyramine and 2-phenylethylamine, respectively. Staphylococcus xylosus, Staphylococcus equorum, and Staphylococcus carnosus, independent of their genetic and technological profiles and BA production, were adequate for use in meat products, according to the data. Lactobacillus plantarum and Lactobacillus sakei strains could also be selected for starters.

PRACTICAL APPLICATION

The selection of coagulase-negative staphylococci and lactic acid bacteria (LAB) isolates were based on their production of biogenic amines in order to avoid this potential hazard production in meat products. The most suitable isolates could be used as safe starter cultures in meat products industry. The staphylococci and LAB selected will achieve particular organoleptic characteristics in meat products and bioprotection from pathogens.

Screening, Characterization and In Vitro Evaluation of Probiotic Properties Among Lactic Acid Bacteria Through Comparative Analysis

The present work aimed to identify probiotic bacteria from healthy human infant faecal and dairy samples. Subsequently, an assay was developed to evaluate the probiotic properties using comparative genetic approach for marker genes involved in adhesion to the intestinal epithelial layer. Several in vitro properties including tolerance to biological barriers (such as acid and bile), antimicrobial spectrum, resistance to simulated digestive fluids and cellular hydrophobicity were assessed. The potential probiotic cultures were rapidly characterized by morphological, physiological and molecular-based methods [such as RFLP, ITS, RAPD and (GTG)5]. Further analysis by 16S rDNA sequencing revealed that the selected isolates belong to Lactobacillus, Pediococcus and Enterococcus species. Two cultures of non-lactic, non-pathogenic Staphylococcus spp. were also isolated. The native isolates were able to survive under acidic, bile and simulated intestinal conditions. In addition, these cultures inhibited the growth of tested bacterial pathogens. Further, no correlation was observed between hydrophobicity and adhesion ability. Sequencing of probiotic marker genes such as bile salt hydrolase (bsh), fibronectin-binding protein (fbp) and mucin-binding protein (mub) for selected isolates revealed nucleotide variation. The probiotic binding domains were detected by several bioinformatic tools. The approach used in the study enabled the identification of potential probiotic domains responsible for adhesion of bacteria to intestinal epithelial layer, which may further assist in screening of novel probiotic bacteria. The rapid detection of binding domains will help in revealing the beneficial properties of the probiotic cultures. Further, studies will be performed to develop a novel probiotic product which will contribute in food and feed industry.

TRS-PCR profiling for discrimination of Escherichia coli strains isolated from children with diarrhea under 5 years of age in Lodz region, Poland

Escherichia coli is one of the most frequently isolated gram-negative pathogens in cases of foodborne diseases and hospital infections. What is more, diarrheal diseases, including these associated with pathogenic E. coli strains, are leading causes of morbidity and mortality worldwide, especially among children. Improvements of the management of diarrheal diseases caused by these bacteria are in the spotlight of the World Health Organization. Therefore, there is still a need to develop new methods or improve ones that are commonly used to characterize and distinguish E. coli strains more precisely. In this work, TRS-based PCRs were effectively used for discrimination of 123 E. coli strains isolated from children with diarrhea in the Lodz region (Poland). The composite TRS-PCR approach, based on similarity comparisons of GTG-PCR and CGG-PCR fingerprints, enabled us to distinguish strains with very good efficacy. This was confirmed by the high diversity index (0.991) and high reproducibility of the band patterns obtained (95.0 %). These results showed the great variation in strains that may cause infections in children under 38 months. However, the stains were grouped in three separate clusters, which were different in terms of their phylogenetic affiliation and virulence factor repertoire. The obtained results support and are consistent with the need of public health surveillance for searching new and fast assays as far as children’s health is concerned. TRS-PCR profiling is an effective tool for genotyping of E. coli strains isolated from children with diarrhea.

Innovative Analysis of the Sequenced Patterns of Vancomycin-Resistant Enterococci Strains to Determine Clonal Transmission in a Hospital Setting

Isolates from patients who acquired vancomycin-resistant enterococci (VRE) were examined for the frequency of genetically indistinguishable strains on leukemia and stem cell transplant units at a major cancer center for 1 year. A total of 14 strains recurred, primarily on the same floor and in the same service unit an average of 49 days apart.

Characterization of Enterococci from Food and Food-Related Settings

Enterococcus species are ubiquitous in nature, exist at high levels in food, and can cause severe diseases in humans. Thus, surveillance of enterococci harboring antibiotic resistance and virulence factors in food and food-related environments is needed. In the present study, 89 samples from food and food processing surfaces were collected in a cheese factory, a swine slaughterhouse, and a supermarket, and 132 Enterococcus isolates were recovered. Most isolates were identified as E. faecalis, which is considered the most pathogenic member of this genus. Safety analysis covering antibiotic resistance revealed that all isolates were resistant to sulfamethoxazole-trimethoprim and sensitive to amoxicillin-clavulanate, ampicillin, ciprofloxacin, gentamicin, levofloxacin, linezolid, nitrofurantoin, or teicoplanin. More than half of the isolates were resistant to quinupristin-dalfopristin, tetracycline, and bacitracin, and less than half were resistant to the other antibiotics evaluated. Regarding virulence factors, 52% the isolates were beta-hemolytic, 39% were gelatinase producers, and 45% contained the gelE gene. For the remaining genes evaluated, efaAfs was detected in more than half of the isolates, and agg, esp, and efaAfm were found in less than half of the isolates. The present investigation revealed that food-related enterococci obtained from very different settings have multidrug resistance and virulence factors, highlighting the importance of effective surveillance networks to avoid the spread of putative pathogenic enterococci.

Thermotolerant Campylobacter during Broiler Rearing: Risk Factors and Intervention

Thermotolerant Campylobacters are one of the most important bacterial causative agents of human gastrointestinal illness worldwide. In most European Union (EU) member states human campylobacteriosis is mainly caused by infection with Campylobacter jejuni or Campylobacter coli following consumption or inadequate handling of Campylobacter-contaminated poultry meat. To date, no effective strategy to control Campylobacter colonization of broilers during rearing is available. In this review, we describe the public health problem posed by Campylobacter presence in broilers and list and critically review all currently known measures that have been researched to lower the numbers of Campylobacter bacteria in broilers during rearing. We also discuss the most promising measures and which measures should be investigated further. We end this review by elaborating on readily usable measures to lower Campylobacter introduction and Campylobacter numbers in a broiler flock.

Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal

A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215(T), was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215(T) had 98.74-99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus (Lactobacillus farciminis BCRC 14043(T), Lactobacillus futsaii BCRC 80278(T) and Lactobacillus crustorum JCM 15951(T)). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215(T) was well separated from the reference strains of species of the genus Lactobacillus. DNA-DNA hybridization results indicated that strain S215(T) had DNA related to the three type strains of species of the genus Lactobacillus (33-66 % relatedness). The DNA G+C content of strain S215(T) was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus, for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215(T) ( = NBRC 109509(T) = BCRC 80582(T)).

Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms

The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.

Enterococcus saccharolyticus subsp. taiwanensis subsp. nov., isolated from broccoli

A coccal strain isolated from fresh broccoli was initially identified as Enterococcus saccharolyticus ; however, molecular identification and phenotypic traits did not support this identification. DNA–DNA hybridization with the type strain of E. saccharolyticus (76.4 % relatedness), DNA G+C content (35.7 mol%), phylogenetic analysis based on 16S rRNA, pheS and rpoA gene sequences, rep-PCR fingerprinting and profiles of cellular fatty acids, whole-cell proteins and enzyme activities, together with carbohydrate metabolism characteristics, indicated that this strain is distinct and represents a novel subspecies, for which the name Enterococcus saccharolyticus subsp. taiwanensis subsp. nov. is proposed. The type strain is 812T ( = NBRC 109476T = BCRC 80575T). Furthermore, we present an emended description of Enterococcus saccharolyticus and proposal of Enterococcus saccharolyticus subsp. saccharolyticus subsp. nov. (type strain ATCC 43076T = CCUG 27643T = CCUG 33311T = CIP 103246T = DSM 20726T = JCM 8734T = LMG 11427T = NBRC 100493T = NCIMB 702594T).

Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC)

When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group "8651 Probiotics" to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling.

Lactobacillus porcinae sp. nov., isolated from traditional Vietnamese nem chua

A species diversity study of lactic acid bacteria occurring in traditional Vietnamese nem chua yielded an isolate, LMG 26767T, that could not be assigned to a species with a validly published name. The isolate was initially investigated by 16S rRNA gene sequence analysis, which revealed that it belonged to the genus Lactobacillus , with Lactobacillus manihotivorans and Lactobacillus camelliae as the closest relatives (98.9 % and 96.9 % gene sequence similarity to the type strains, respectively). Comparative (GTG)5-PCR genomic fingerprinting confirmed the unique taxonomic status of the novel strain. DNA–DNA hybridization experiments, DNA G+C content determination, sequence analysis of the phenylalanyl-tRNA synthase (pheS) gene, and physiological and biochemical characterization demonstrated that strain LMG 26767T represents a novel species, for which the name Lactobacillus porcinae sp. nov. is proposed; the type strain is LMG 26767T ( = CCUG 62266T). Biochemically, L. porcinae can be distinguished from L. manihotivorans and L. camelliae by its carbohydrate fermentation profile, absence of growth at 45 °C, and production of d- and l-lactate as end products of glucose metabolism.

Enterococcus alcedinis sp. nov., isolated from common kingfisher (Alcedo atthis)

Two Gram-positive, catalase-negative bacterial strains were isolated from the cloaca of common kingfishers (Alcedo atthis). Repetitive sequence-based PCR fingerprinting using the (GTG)5 primer grouped these isolates into a single cluster separated from all known enterococcal species. The two strains revealed identical 16S rRNA gene sequences placing them within the genus Enterococcus with Enterococcus aquimarinus LMG 16607(T) as the closest relative (97.14 % similarity). Further taxonomic investigation using sequencing of the genes for the superoxide dismutase (sodA), phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) as well as application of whole-cell protein fingerprinting, automated ribotyping and extensive phenotyping confirmed that both strains belong to the same species. Based on data from this polyphasic study, these strains represent a novel species of the genus Enterococcus, for which the name Enterococcus alcedinis sp. nov. is proposed. The type strain is L34(T) (= CCM 8433(T) = LMG 27164(T)).

Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam

AIMS

To evaluate the potential use of MALDI-TOF MS for fast and reliable classification and identification of lactic acid bacteria (LAB) from traditional fermented foods.

METHODS AND RESULTS

A total of 119 strains of LAB from fermented meat (nem chua) were analysed with both (GTG)(5)-PCR fingerprinting and MALDI-TOF MS. Cluster analysis of the profiles revealed five species represented by a single isolate both in (GTG)(5)-PCR and in MALDI-TOF MS; five species grouped alike for (GTG)(5)-PCR and for MALDI-TOF MS; however, differences in minimal similarity between the delineated (GTG)(5)-PCR and MALDI-TOF MS clusters could be observed; three species showed more heterogeneity in their MALDI-TOF MS profiles compared to their (GTG)(5)-PCR profiles; two species, each represented by a single MALDI-TOF cluster, were subdivided in the corresponding (GTG)(5)-PCR dendrogram. As proof of the identification potential of MALDI-TOF MS, LAB diversity from one fermented mustard sample was analysed using MALDI-TOF MS. PheS gene sequencing was used for validation.

CONCLUSIONS

MALDI-TOF MS is a powerful, fast, reliable and cost-effective technique for the identification of LAB associated with the production of fermented foods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Food LAB can be identified using MALDI-TOF MS, and its application could possibly be extended to other food matrices and/or other food-derived micro-organisms.

A wide variety of Clostridium perfringens type A food-borne isolates that carry a chromosomal cpe gene belong to one multilocus sequence typing cluster

Of 98 suspected food-borne Clostridium perfringens isolates obtained from a nationwide survey by the Food and Consumer Product Safety Authority in The Netherlands, 59 strains were identified as C. perfringens type A. Using PCR-based techniques, the cpe gene encoding enterotoxin was detected in eight isolates, showing a chromosomal location for seven isolates and a plasmid location for one isolate. Further characterization of these strains by using (GTG)(5) fingerprint repetitive sequence-based PCR analysis distinguished C. perfringens from other sulfite-reducing clostridia but did not allow for differentiation between various types of C. perfringens strains. To characterize the C. perfringens strains further, multilocus sequence typing (MLST) analysis was performed on eight housekeeping genes of both enterotoxic and non-cpe isolates, and the data were combined with a previous global survey covering strains associated with food poisoning, gas gangrene, and isolates from food or healthy individuals. This revealed that the chromosomal cpe strains (food strains and isolates from food poisoning cases) belong to a distinct cluster that is significantly distant from all the other cpe plasmid-carrying and cpe-negative strains. These results suggest that different groups of C. perfringens have undergone niche specialization and that a distinct group of food isolates has specific core genome sequences. Such findings have epidemiological and evolutionary significance. Better understanding of the origin and reservoir of enterotoxic C. perfringens may allow for improved control of this organism in foods.

Enterococcus plantarum sp. nov., isolated from plants

Eight Gram-positive, catalase-negative bacterial strains were isolated during screening of enterococcal populations on plants. rep-PCR fingerprinting using the (GTG)5 primer showed that the isolates constituted a single cluster that was separate from all known enterococcal species. 16S rRNA gene sequence phylogenetic analysis of three representative strains showed that the isolates belonged to the genus Enterococcus and that they clustered with the Enterococcus faecalis species group. Sequencing of the genes for the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) also revealed the isolates’ separate taxonomic position. Application of whole-cell protein fingerprinting, automated ribotyping and extensive phenotyping demonstrated the genetic and phenotypic homogeneity of the isolates and confirmed their separate position within the E. faecalis species group. The isolates represent a novel species of the genus Enterococcus , for which the name Enterococcus plantarum sp. nov. is proposed; the type strain is CCM 7889T ( = LMG 26214T = C27T).

Genotypic characterization and safety assessment of lactic acid bacteria from indigenous African fermented food products

Background

Indigenous fermented food products play an essential role in the diet of millions of Africans. Lactic acid bacteria (LAB) are among the predominant microbial species in African indigenous fermented food products and are used for different applications in the food and biotechnology industries. Numerous studies have described antimicrobial susceptibility profiles of LAB from different parts of the world. However, there is limited information on antimicrobial resistance profiles of LAB from Africa. The aim of this study was to characterize 33 LAB previously isolated from three different African indigenous fermented food products using (GTG)₅-based rep-PCR, sequencing of the 16S rRNA gene and species-specific PCR techniques for differentiation of closely related species and further evaluate their antibiotic resistance profiles by the broth microdilution method and their haemolytic activity on sheep blood agar plates as indicators of safety traits among these bacteria.

Results

Using molecular biology based methods and selected phenotypic tests such as catalase reaction, CO₂ production from glucose, colonies and cells morphology, the isolates were identified as Lactobacillus delbrueckii, Lactobacillus fermentum, Lactobacillus ghanensis, Lactobacillus plantarum, Lactobacillus salivarius, Leuconostoc pseudomesenteroides, Pediococcus acidilactici, Pediococcus pentosaceus and Weissella confusa. The bacteria were susceptible to ampicillin, chloramphenicol, clindamycin and erythromycin but resistant to vancomycin, kanamycin and streptomycin. Variable sensitivity profiles to tetracycline and gentamicin was observed among the isolates with Lb. plantarum, Lb. salivarius, W. confusa (except strain SK9-5) and Lb. fermentum strains being susceptible to tetracycline whereas Pediococcus strains and Lb. ghanensis strains were resistant. For gentamicin, Leuc. pseudomesenteroides, Lb. ghanensis and Ped. acidilactici strains were resistant to 64 mg/L whereas some W. confusa and Lb. plantarum strains had a MIC value of 16 mg/L and 32 mg/L respectively. No β-haemolytic activity was observed, however, α-haemolytic activity was observed in 27% (9) of the strains comprising Lb. salivarius (6), W. confusa (2) and Lb. delbrueckii (1) isolates.

Conclusions

The resistance to kanamycin and vancomycin is probably an intrinsic feature since similar observations were reported in the literature for LAB. Low prevalence of pathogenicity indicator traits were observed among the isolates especially with the presence of poor haemolytic activities and they could therefore be considered as interesting candidates for selection of starter cultures or probiotics for different applications.

Genotypic intraspecies heterogeneity of Enterococcus italicus: data from dairy environments

The diversity of a collection of 19 Enterococcus italicus strains isolated from different dairy sources was explored using a molecular polyphasic approach, comprising random amplification of polymorphic DNA (RAPD-PCR), repetitive element PCR (REP-PCR), plasmid profiling and ribotyping. The data obtained showed a high-level of biodiversity, not always correlated to the niche of isolation. Particularly, REP-PCR with primer BOXA1R and plasmid profiling allowed the best discrimination at strain level. Exploiting the genome shotgun sequence of the type strain of the species, available in public database, genes related to insertion sequences present on enterococcal Pathogenic Islands (ISEf1, IS905), determinants related to virulence factors (codifying for hemolysin and cell wall surface proteins), exogenously DNA (conjugal transfer protein, replication plasmid protein, pheromone shutdown protein, phage integrase/recombinase) and penicillin binding proteins system were detected. The presence of most of these genes seemed a common genetic trait in the Enterococcus genus, sur gene (cell wall surface protein) was only detected in strains of E. italicus. To our knowledge, this is the first time that specific primers, with the expection of the species-specific probe targeted to 16S rRNA gene, have been designed for this species.

Enterococcus ureilyticus sp. nov. and Enterococcus rotai sp. nov., two urease-producing enterococci from the environment

A set of 25 urease-producing, yellow-pigmented enterococci was isolated from environmental sources. Phenotypic classification divided the isolates into two phena. Both phena were characterized using 16S rRNA gene sequence analysis, DNA base composition, rep-PCR fingerprinting and automated ribotyping. The obtained data distinguished the isolates from all members of the genus Enterococcus with validly published names and placed them in the Enterococcus faecalis species group. DNA-DNA hybridization experiments, pheS and rpoA sequencing and whole-cell protein electrophoresis provided conclusive evidence for the classification of each phenon as a novel species of the genus Enterococcus, for which the names Enterococcus ureilyticus sp. nov. (type strain CCM 4629(T)  = LMG 26676(T)  = CCUG 48799(T)), inhabiting water and plants, and Enterococcus rotai sp. nov. (type strain CCM 4630(T)  = LMG 26678(T)  = CCUG 61593(T)), inhabiting water, insects (mosquitoes) and plants, are proposed.

Antibiotic resistance and virulence factors among Enterococci isolated from chouriço, a traditional Portuguese dry fermented sausage

Enterococci are ubiquitous microorganisms, found as part of the normal intestinal microbiota of many animals. They can be present in food products, for example, the Portuguese dry fermented sausage chouriço. Twenty enterococci were isolated from chouriço in two processing units; after identification and typification by conventional-molecular methods, the isolates were screened for virulence factors and antibiotic resistance. Identification allocated all enterococci to the species Enterococcus faecalis, and PCR fingerprinting demonstrated that each isolate was specific to the processing unit and chouriço from which it was recovered. Regarding the screening for virulence factors, 1 strain produced cytolysin and 4 were gelatinase positive, but none produced lipase. The ace gene was detected in 1 enterococci, ebpABC and efaA(fs) in 16 isolates each, esp in 3, fsrB in 5, gelE in 7, and cylA in 1. A multiresistant phenotype was observed in 8 isolates, 6 belonging to factory A. The antibiotic resistance gene ere(B) was detected in 9 enterococci, whereas the genes tet(M), aac(6')-Ie-aph(2''), and vanA were detected in 8 isolates each. As some of the E. faecalis chouriço isolates present a multiresistant profile and harbor virulence and/or resistance genes, to assess further the safety of Portuguese dry sausages, a larger number of products and processing units must by analyzed.