Abstract

Traditional fermented food products are often connected to various indigenous tribes and thus vary due to ethnicity, geography, and natural resource availability. The indigenous tribes from India greatly rely on fermentation processes for food preservation, flavor, and nutrition. Fermented foods can provide health benefits but also pose risks from harmful microbes and contaminants that grow in the food due to poor hygiene. In this study, we identified lactic acid bacteria (LAB) in fermented food collected from Northeast India, assessed their beneficial properties, and highlighted the risk from food pathogens that have antimicrobial resistance traits. A total of 113 different samples of fermented food products were collected from the local markets of five Northeastern Indian states (Nagaland, Manipur, Meghalaya, Arunachal Pradesh, and Sikkim). Standard laboratory methods were used to isolate LAB and determine their probiotic properties, conduct coliform counts, and isolate presumptive staphylococci from the fermented food samples. Antimicrobial susceptibility was determined by using the BD-Phoenix 100 automated system. We isolated 30 LAB with probiotic potential. The average aerobic colony count in different fermented food was 4.4–7.7 log·cfu/g, while coliforms were present in 43% (49/113, 95% (CI 34–53)) of the food samples, indicating low-hygiene levels. Additionally, some food samples contained staphylococci with phenotypic antibiotic-resistance markers (MRS, HLMUP, BLACT, and STAMLS). This study indicates that probiotic bacteria could be present in traditional fermented food products of Northeast India, but contamination with staphylococci and other bacterial pathogens with antibiotic resistance traits could put the health of consumers at risk.

1. Introduction

Historically, people have used various methods to preserve and enhance the shelf life of food; one extensively used practice is fermentation [1]. Fermentation involves the activity of microorganisms which play a vital role in the elimination of many pathogens and help preserve food products [2]. Some lactic acid bacteria (LAB) involved in fermentation are probiotic in nature and beneficial for human health when consumed in adequate quantities via food products [3]. LAB enhances the nutritional and therapeutic properties of the food products to provide beneficial health effects and play a vital role as gut microbiota [4, 5]. Fermentation helps improve food digestion by breaking down complex sugars into simpler forms, as well as providing essential amino acids, vitamins, and minerals, and can improve the flavor and taste [1, 2]. Protein and vitamin deficiencies are major problems in low- and middle-income countries [6, 7], and these populations could potentially be helped by increased consumption of fermented products that can help meet the requirement for healthy gut microbiota and mitigate nutrition deficiencies [812]. Traditional fermented food products are often connected to various indigenous tribes [13]. Countries like India have many tribal populations, and these tribes represent varieties of traditional fermented food due to varied ethnicity, geography, and natural resource availability [14]. Fermented foods have played a vital role in contributing to Indian diets over many centuries, partly because fermentation is a cheap and cost-effective food preservation technique [15]. The tribal people of Indian states use ethnic traditional knowledge inherited from their ancestors to prepare fermented food [16]. Although fermented foods can provide health benefits [1, 17], there is also a risk of harmful microorganisms that may grow in the food products [18] due to poor hygiene during food preparation or storage and cause adverse effects to human health [19]. Fermentation should be studied and developed further so that fermented products can be of standardized quality and safer for consumers [2023]. Reconsidering the food safety aspects of fermented food preparation would be beneficial to producers and consumers, and this could generate a more sustainable source of income for communities. However, there is a paucity of data on the food safety aspects of the fermented foods that are prepared and consumed by various tribes of Northeast India. Therefore, the present study was undertaken to assess various food safety parameters in fermented food products and the beneficial effects of the isolated LAB and identify associated pathogens, specifically, staphylococci, while also investigating their antimicrobial resistance traits.

2. Materials and Methods

The samples of fermented food products were collected and processed for isolation of indigenous LAB and associated food pathogens, followed by their identification. LAB was studied for their functional and probiotic properties by phenotypic and genotyping methods as described in the flowchart (Figure 1).

2.1. Sampling

One hundred and thirteen samples of fermented food products were collected from five Northeastern Indian states (Nagaland, Manipur, Meghalaya, Arunachal Pradesh, and Sikkim) (Table 1). The samples were collected from traditional markets using a nonprobabilistic sampling method (convenience sampling) over a two-year period (2013 to 2015). The most prominent traditional food markets in each of the five states were identified through interactions with local residents. The fermented food samples were chosen by the vendor from a basket made of bamboo, and the samples were sometimes found wrapped in a leaf. The collected samples were placed in sterile 250 ml zip lock pouches, which were transported to the laboratory under refrigeration temperature (4°C). On arrival at the laboratory, the samples were immediately processed for further microbiological analyses. The interval between the collection of samples and the onset of analysis did not exceed 48 hours. Each sample was aseptically divided into two parts. One part was processed for isolation of LAB, and the other was analyzed for aerobic plate counts and coliform counts to assess the hygienic status.

2.2. Microbiological Analyses
2.2.1. Isolation of LAB

For isolation of LAB, the procedures reported by Tamang et al. [24] were followed with minor adaptations. Following aseptic procedures, 25 g of each sample was weighed and homogenized in 225 ml of sterile normal saline solution (0.85% NaCl) in a conical flask. The flask was left undisturbed for 10 minutes at room temperature for settling of coarse particles. From the homogenate, 10 ml was inoculated in 90 ml of sterile De Man, Rogosa, and Sharpe (MRS) broth (Hi-media, Maharashtra, India) and incubated at 37°C for 18–24 hours. Following incubation, 1 ml of enriched broth was inoculated in duplicate on MRS agar plates supplemented with 1% CaCO3. Of the duplicate MRS agar plates for each sample, one set was incubated under anaerobic conditions (Gas Pack-LE002A, Hi-media, Maharashtra, India) in an anaerobic jar at 30°C for up to 3 days. The other set of agar plates was incubated aerobically at 37°C for 24–48 hours. Presumptive colonies of LAB were identified by colony morphology (white colony with a clearing zone of CaCO3 deposition in MRS agar) and further tests including Gram staining, catalase, and oxidase production as per standard protocols [25]. A purity check of the isolates was performed by subculturing the presumptive isolates on fresh MRS agar plates, followed by microscopic examinations (Leica, Wetzlar, Germany). Presumptive isolates were then identified using the Phoenix 100 automated microbiological identification system (Becton and Dickinson, Tuas, Singapore).

2.2.2. Assessment of Hygienic Quality by the Aerobic Plate Count (APC) and Most Probable Number (MPN) of Coliforms

To assess the hygienic status of the fermented food samples, APC was determined following the procedure described in the Bacteriological Analysis Manual of Food and Drug Administration [26]. Each sample was tested on duplicate plates of plate count agar (Hi-media, Maharashtra, India), and the average count was recorded for interpretation. In addition to the aerobic plate count (APC), coliform counts were determined by the most probable number (MPN) as described previously for food samples [27]. Each sample was processed using three tube tests (1, 0.1 and 0.01 ml), and the MPN indices were recorded. The samples which were negative for all the three tubes had a MPN value < 0.3 and were assigned 0.15 in the quantitative calculation.

2.2.3. Isolation and Identification of Pathogens

Isolation of pathogens from fermented foods was undertaken by the procedures described previously with suitable modifications [28]. The isolates that grew along with LAB and were identified as staphylococci were further reconfirmed by inoculating in Brain Heart Infusion (BHI) agar (Hi-media, Maharashtra, India), followed by overnight incubation at 37°C. The bacterial colonies from BHI agar were streaked on Baird Parker Agar plates (Hi-media, Maharashtra, India) and reincubated at 37°C for 18 hours. Presumptive colonies of staphylococci (grey-black to black, with or without shine and halo) were picked (one random colony for each sample). Other suspected colonies from BHI agar were also randomly picked and characterized by using Phoenix 100 automated ID/AST system (Becton and Dickinson, Tuas, Singapore) for confirmatory identification.

2.3. Functional Characterization of LAB by Phenotypic Tests
2.3.1. Test for Proteolysis

Isolates of LAB were inoculated in MRS broth and incubated for 24 hours at 30°C. Following incubation, bacteria were harvested by centrifugation (). Resulting pellets were washed three times in sterile phosphate buffered saline (1X PBS) (pH 7.2) and resuspended in 1 ml of PBS. The optical density of the suspension was adjusted to 0.5 MacFarland using a nephelometer (BD PhoenixSpec). Ten microliters of bacterial suspension were inoculated into each well (6 mm diameter) made in the skim milk agar (Hi-media, Maharashtra, India) plates. The plates were incubated at 37°C for 4 h and analyzed for the presence or absence of a clear zone of proteolysis around the inoculated wells. For each plate, a positive control (Pseudomonas aeruginosa ATCC 27853) and a negative control (Escherichia coli ATCC 25922) were included [29].

2.3.2. Test for Amylolysis

The amylolytic activity of the LAB isolates was estimated with bacterial suspension prepared as described in Section 2.3.1. Surface-dried plates of starch agar (Hi-media, Maharashtra, India) were inoculated with 10 µl of bacterial suspension and incubated at 37°C for 48 h. After incubation, a few drops of Gram’s iodine solution (Hi-media, Maharashtra, India) were added onto the agar surface, and the plate was allowed to stand for 10 minutes. Positive results were noted as clear zones of starch hydrolysis around the inoculation sites. In each experiment, suspensions of Aeromonas hydrophila ATCC 7966 and E. coli ATCC 25922 were included as positive and negative controls, respectively.

2.4. Antimicrobial Susceptibility Test

Susceptibility of LAB and identified pathogenic bacteria to antibiotics was tested as described elsewhere [3032]. Following presumptive identification, isolates were characterized by using the BD Phoenix-TM 100 automated ID/AST system (Becton and Dickinson, Tuas Avenue, Singapore) for minimum inhibitory concentrations of various antimicrobials employing Gram-positive combo panels (PMIC/ID-55) following the Clinical and Laboratory Standards Institute (CLSI) guidelines [33]. Manual antibiotic susceptibility testing (AST) was performed as per the Bauer–Kirby disc-diffusion test for the bacterial isolates that were not included in BD Phoenix AST taxonomy. This was performed by inoculating the overnight grown cultures on Muller–Hinton agar (MHA) (Hi-media, Maharashtra, India) plates. The bacterial suspension was set to 0.5 McFarland prior to inoculation on MHA agar. A sterile swab was used to uniformly spread the culture on the agar plate. Post inoculation, the antibiotic discs (Hi-media, Maharashtra, India) with specific antibiotic concentrations were placed on the surface of the agar plates with sterile forceps and incubated at 37°C for 18–24 hours. Isolates were considered as multidrug resistant if they show resistance to more than three classes of antibiotics or if resistance markers such as BLACT (beta-lactamase), MRS (methicillin-resistant staphylococci), HLGR (high-level gentamicin resistance), HLMUP (high-level mupirocin), mecA-RS (mecA-mediated resistant Staphylococcus), STAMLS (Staphylococcus MLSb: macrolides, lincosamides, and streptogramin B) and VRE (vancomycin resistant enterococci) carbapenems and nitrofurantoin resistance were indicated in AST results by using the automated BD Phoenix system.

2.5. Molecular Characterization
2.5.1. Isolation of Genomic DNA

Bacterial genomic DNA was extracted using a column-based bacterial genomic DNA extraction kit (Hi-media, Maharashtra, India) according to the manufacturer’s instructions.

2.5.2. Polymerase Chain Reaction

A ThermoFisher Scientific (Waltham, Massachusetts, USA) thermal cycler was used for all polymerase chain reaction (PCR) analyses. PCR was carried out to detect the presence of the following genes, for riboflavin production (ribH, ribB, and ribA genes), for tolerance to bile salt (bsh gene), for starch metabolism (amy gene), for synthesis of B vitamins, including folate synthesis (folP and folk genes), and for riboflavin synthesis (rib, ribH, and ribA genes) [34] by specific primers (Table 2). The AMR genes (tetA, tetB, tetC, TEM, CTX-M, vanA, and vanB genes) were screened by using the primers listed in Table 2.

3. Results

3.1. Identification of LAB

LAB were isolated from 20 of the 113 (17.7%; 95% confidence interval (CI) (11–26%)) samples. In total, 30 LAB (including duplicates) were identified by using the BD PhoenixTM100 automated ID/AST system as Pediococcus parvulus (10), Pediococcus pentosaceus (9), Pediococcus acidilactici (5), Leuconostoc mesenteroides (3), Pediococcus damnosus (1), Aerococcus viridans (1), and Lactococcus plantarum (1). The dominant genus in the fermented products was Pediococcus (isolated from 9 samples of fermented dry fish and 8 samples of fermented bamboo shoots). No LAB were isolated from yak cheese, milk products, and fish and meat pickles.

3.2. APC and MPN of Coliforms

The fermented food samples showed varied aerobic colony counts. The average APC was found to be highest in fermented soyabean (average 7.7 log cfu/g), followed by fermented milk (average 6.4 log cfu/g), meat pickles (average 6.1 log cfu/g), yak cheese (average 5.9 log cfu/g), fish pickles (average 5.1 log cfu/g), and dry fish (average log 5.1 cfu/g). The lowest colony count was observed in fermented bamboo shoots (average 4.4 log cfu/g) (Table 3), (Supplementary Materials, Table S1). According to the compendium of microbiological criteria for food 2018 [39], fermented food falls under category 5, and there are no interpretation criteria available to interpret the result as satisfactory, marginal, or unsatisfactory.

The overall coliform prevalence in the fermented food samples was 43% (49/113; 95% CI (34–53)). Coliforms were detected in all tested samples of fermented milk, fish pickle, and meat pickle, while the prevalence levels of coliforms were higher in soyabeans (67%), followed by dry fish (39%) and bamboo shoots (22%). The average concentration of coliforms in the fermented food samples was 0.50 log MPN/ml (g), and the range was from −0.82 to 0.04 log MPN/ml (g) (Table 4) (Supplementary Materials, Table S1).

3.3. Identification of Pathogens

Fifty-three percent (60/113; 95% CI (42–63)) of the fermented food samples were found to contain different pathogens (Table 5). A total of 145 presumptive pathogens (including duplicates) were found in the samples identified by using the BD Phoenix ID/AST system. Among the isolated presumptive pathogens, only staphylococci were reconfirmed by growing them in a selective medium followed by microscopic examination and reidentified using the BD phoenix system. The rest of the isolates were not reconfirmed and hence cannot be concluded to be pathogens (Table 5), (Supplementary Materials, Table S1).

3.4. Proteolytic and Amylolytic Activity by the Phenotypic Method

Amylolytic activity was observed in 33% (10/30; 95% (CI 17–53)) of LAB, and none of the LAB isolates exhibited proteolytic activity. Amylolytic activity was observed in the following LAB: Pediococcus pentosaceus (5), Pediococcus acidilactici (1), Leuconostoc mesenteroides (2), Lactococcus plantarum (1), and Pediococcus parvulus (1) (Supplementary Materials, Table S2).

3.5. Molecular Detection of Functional and Antibiotic Resistance Genes by PCR

By screening the LAB (30) for the functional genes, 80% (24/30; 95% CI (50–85)) possessed riboflavin synthesis capacity (ribA gene), 20% (6/30; 95% CI (7–38)) had the combination (ribA + ribB genes), 70% (21/30; 95% CI (50–85)) were starch metabolizers (possessing amy gene), and 60% (18/30; 95% CI (40–77)) were bile salt metabolizers (bsh gene). While screening the LAB for AMR genes such as vanA, vanB, blaTEM, blaCTX-M, qnrA, qnrB, tetA, and tetB, none of the LAB were found to carry these antibiotic resistance genes (Supplementary Materials, Table S2).

3.6. Antibiotic Susceptibility Testing

The antibiotic susceptibility testing by using the BD Phoenix-TM 100 automated ID/AST system indicated that all the LAB were resistant to teicoplanin and vancomycin.

Out of 53% (n = 60) isolated presumptive pathogens, 42% (n = 46) of the isolates were antibiotic resistance (including duplicates). Staphylococci 39% (n = 42) made up the majority of the resistant isolates and exhibited beta-lactamase (BLACT), methicillin-resistant Staphylococcus (MRS), high-level mupirocin (HLMUP), vancomycin-resistantStaphylococcus aureus, (VRSA) or Staphylococcus MLSb: macrolides, lincosamides, and streptogramin B (STAMLS) phenotype by antibiotic susceptibility testing.

After staphylococci, the other antibiotic-resistant isolates were Enterococcus spp. (2% (n = 2)), vancomycin-resistant enterococci (VRE), and Providencia stuartii (1% (n = 1)) with potential carbapenemase producer and Micrococcus lylae (1% (n = 1)) with nitrofurantoin resistance (Table 6) (Supplementary Materials, Table S1).

4. Discussion

In this study, we analyzed 113 fermented food samples and found 30 potential LAB isolates within four different genera and seven different species, identified as Pediococcus pentosaceus, P. parvulus, P. acidilactici, P. damnosus, Leuconostoc mesenteroides, Aerococcus viridans, and Lactococcus plantarum. Functional characterization of LAB isolates revealed that 80% of the LAB isolates were producers of riboflavin synthesis, 70% showed starch metabolism, and 60% possessed bile salt indicating their beneficial role in fermented food.

Amylolytic activity was observed in 33% of LAB by the phenotypic test, whereas the presence of the amy gene was observed in 70% of LAB by the molecular method, indicating higher sensitivity of the molecular method than the phenotypic test in detecting starch metabolism. Detection of the amy gene among LAB isolates indicates that these isolates were capable of sustaining growth in starchy substrates through the production of amylase [40].

None of the LAB were found to exhibit proteolytic activity; this could be due to absence or poor synthesis of proteinase enzyme in the isolated LAB. The proteolytic activity does not operate for many LAB [41], and this could be the reason that all the LAB in our study were negative for proteolytic activity.

In addition to probiotic effects, the LAB isolates revealed the potential for nutritional enhancement of foods by the production of riboflavin. The probiotic potential of LAB was further strengthened by their tolerance to bile salt, which might ensure their survival inside the gastrointestinal tract. Our results indicated a great diversity of LAB among the traditional fermented foods of Northeastern India with probiotic potential, but interestingly, in most of the food samples, LAB were absent and in fact had potential pathogens that sometimes carried antibiotic resistance.

Although there are several earlier studies about bacterial diversity in fermented foods [42, 43], we still know very little about the antimicrobial resistance implications on the safety of these foods in India. Our study found that all the LAB were resistant to antibiotics such as teicoplanin and vancomycin. The resistance to glycopeptides such as teicoplanin and vancomycin should be a point of concern as vancomycin is a last resort antibiotic in treating infections associated with multidrug-resistant Gram-positive bacteria [44, 45]. Though LAB have been reported to be intrinsically resistant to a number of antibiotics [46, 47], however in our study, none of the LAB were positive for AMR genes (VanA, VanB, TEM, CTX, Qnr, TetA, and TetB) by the molecular method, indicating the absence of transferable antibiotic resistance genes [48, 49] and their safety with respect to AMR.

Assessment of food safety parameters revealed a wide variation in APC among the samples. This variation may be attributable to hygienic standards followed in the preparation of foods, but other factors such as the physiochemical nature of the food could also influence the likelihood of the food product to be a good medium for bacterial growth [50].

Coliforms were present in 43% of the fermented food samples, indicating poor hygienic standards. The majority (53%) of the fermented food samples were contaminated with different food pathogens, among which staphylococci were most dominant. This indicates a possible risk of foodborne disease from fermented foods. However, some foods are cooked before consumption [5153], and some studies have even suggested that fermented food be cooked prior to consumption [18, 54] to reduce the risk of foodborne outbreaks. Nonetheless, episodes of food poisoning due to the consumption of traditional fermented food in India, such as Hawaijar, are occasionally reported [55], and there have been reports of food poisoning from fermented food products in other parts of the world as well [20, 23].

Staphylococci were discovered to be the most prevalent pathogens, and the prevalence of antibiotic-resistant bacterial pathogens was found to be 42%. Some of the staphylococci showed resistance against many classes of antimicrobials including beta-lactam, gentamicin, macrolides, and others. The major phenotypic resistance markers observed in staphylococci were BLACT, MRS, HLGR, HLMuRS, mecA-RS, and Staph MLSb. After staphylococci, other antibiotic-resistant pathogens identified were Enterococcus spp., Providencia stuartii, and Micrococcus lylae that were vancomycin-resistant enterococci (VRE), potential carbapenemase producers, and nitrofurantoin resistant.

The presence of antimicrobial resistance traits among isolates in fermented food indicates potential risks to consumers due to the transfer of antimicrobial resistance [56] to other microorganisms [57] in the gastrointestinal tract and may lead to possible treatment failure of infections [58].

According to the World Health Organization (WHO), food-handling personnel plays an important role in ensuring food safety throughout the chain of food production, processing, storage, and preparation [59]. Mishandling and disregarding hygienic measures on the part of food vendors may enable pathogens to contaminate the food [60] and, in some cases, to survive and multiply in sufficient numbers to cause illness to consumers [61]. Traditional fermented foods occupy an important food niche in Northeast India [16]. The fermentation process is an alternative method of food preservation of raw food and thus helps in increasing the shelf life [62] of the food product. Fermented food influences the gut microbiota of consumers and could have potential health advantages [15, 63].

Our study was limited by the small number of samples, particularly from some regions, and the wide variety of products. The differences in the quantity of the collected fermented food samples were caused due to seasonal variations in the availability of raw material and reduced local production of fermented food. Given that the study is not representative, the prevalence of food pathogens in the samples was less conclusive than would have been the case with a more representative sampling frame. The virulence of the pathogenic isolates in fermented food is also unknown because a molecular approach was not used to confirm the pathogenicity of the isolates. Therefore, extensive and systemic future studies are required with larger sample frames in order to understand the actual scenario with regard to the safety of traditional fermented food products in Northeast India.

5. Conclusions

Our findings revealed a mixed picture of opportunity, with a large variety of LAB with probiotic potential on the one hand, and a significant risk, with poor hygienic quality, the presence of pathogens, and the prevalence of drug resistance traits on the other. This is the first study of LAB in conjunction with foodborne bacterial pathogens and their antibiotic resistance in traditional fermented foods found in Northeast India. This was, however, only a small study, and more extensive studies are required with larger samples in order to understand the actual scenario with regard to the safety of traditional fermented food products and the role of LAB.

Data Availability

Data are made available from the authors upon reasonable request.

Conflicts of Interest

The authors declare no conflicts of interest.

Authors’ Contributions

S.G and T.K.D were responsible for conceptualization. S.G and T.K.D were responsible for methodology. T.K.D and S.G were responsible for validation. T.K.D was responsible for formal analysis. T.K.D was responsible for investigation. S.G and T.K.D were responsible for resources. T.K.D, S.G, and J.F.L were responsible for writing the original draft. T.K.D, J.F.L, S.G, Å.L, R.S, A.A.P.M, S.D, P.K, and A.S were responsible for writing, reviewing, and editing the manuscript. J.F.L, T.K.D, S.G, and Å.L were responsible for visualization. S.G and J.F.L were responsible for supervision. S.G was responsible for project administration. T.K.D and S.G were responsible for funding acquisition. All the authors have read and agreed to the published version of the manuscript.

Acknowledgments

The authors thankfully acknowledge funding and laboratory support received from the Division of Animal and Fisheries Sciences, Indian Council for Agricultural Research, Northeastern Hill Region, Meghalaya, India. The authors also thankfully acknowledge the support received from the scientists and colleagues from the Division of Animal and Fisheries Sciences, Indian Council for Agricultural Research, Meghalaya, India, for helping in sample collection.

Supplementary Materials

The following supporting information can be downloaded at https://www.hindawi.com. Table S1: details of fermented foods, including their aerobic plate count (APC), most probable number (MPN), associated pathogens, and resistance markers for those pathogens and Table S2: details of fermented foods and lactic acid bacteria (LAB) identification with functional and antibiotic resistance genes. (Supplementary Materials)