Assessment of food microbiological indicators applied on poultry carcasses by culture combined MALDI-TOF MS identification and 16S rRNA amplicon sequencing

Dual-Modal Biosensor for Staphylococcus aureus Detection Based on a Porphyrin-Based Porous Organic Polymer FePor-TPA with Excellent Peroxidase-like, Catalase-like, and Photoelectrochemical Properties

Bacterial infections seriously harm human health and cause many severe diseases, which triggered urgent demands to exploit specific and sensitive biosensor strategies for Staphylococcus aureus detection. Here, a colorimetric and photoelectrochemical dual-mode biosensor for S. aureus assay based on FePor-TPA was constructed. 2D FePor-TPA thin film and its bulk powder (FePor-TPA) were synthesized by in situ growth on ITO and a solvothermal condition, respectively, both of which exhibited excellent peroxidase-like and catalase-like activity, originating from their metalloporphyrin linkers. Benefiting from the in situ growth on ITO electrodes, the 2D FePor-TPA thin film also possessed a more ordered stacking mode and in turn exhibited good electrical conductivity, stable initial photocurrent, and high sensitivity to O2. As for bulk FePor-TPA, its porous structure and high specific surface area make it a possible scaffold to load an amount of AuNPs, the rabbit anti-Staphylococcus aureus Rosenbach tropina antibody (Ab2), and GOx for constructing the signal probe (GOx/Ab2@Au@FePor-TPA) and realizing catalytic amplification. With these satisfactory features in mind, the 2D FePor-TPA thin film and its bulk powder (FePor-TPA) were utilized to construct a dual and signal-on bioplatform for sensitively and selectively detecting S. aureus, which, as far as we know, has not been reported.

Preparation of polyclonal antibody against a universal bacterial antigen OmpA deduced by bioinformatic analysis and preliminary evaluation of concentration effects on foodborne pathogens

Rapid and ultrasensitive microbial detection in actual samples have challenges because of target pathogen diversity and low abundance. In this study, we attempted to capture and concentrate multiple pathogens by combining magnetic beads with polyclonal antibodies against a universal antigen of ompA, LAMOA-1, before further detection. A protein sequence consisting of 241 amino acids with spatial conformation similar to E. coli ompA was identified and expressed as a recombinant protein in prokaryotes according to the results of sequence alignment among 432 sequences of ompA belonging to intestinal bacteria from gram-negative bacteria. Purified from immunized rabbits, the anti-LAMOA-1 antibody was shown to effectively recognize 12 foodborne bacterial species. Antibody-conjugated beads were used to concentrate the bacteria when the bacterial concentration in artificially contaminated samples is between 10 and 100 CFU/mL, which shortens detection duration by 8-24 h. The enrichment strategy is potentially beneficial for detection of foodborne pathogens.

[Impact of preservatives in topicals on the cutaneous microbiota]

Preservatives are used to stabilize topical preparations and protect the user from the influence of pathogenic microbes. After the application of a topical preparation, the matrix undergoes a metamorphosis, and by proportional evaporation of the hydrophilic phase the preservative may accumulate on the skin surface. This is believed to lead to antiseptic effects and may influence the diversity of the cutaneous microbiota. The regulation of the cutaneous microbiome and the associated influencing factors is a complex system that results in highly individualized conditions. Therefore, investigations on the influence of defined interventions are methodologically difficult. In the present proof-of-concept study, potential antiseptic effects of preservatives were investigated in a combination of in vitro and in vivo methods using microbiological culture tests. In addition, the investigations served to develop a clinical study design to answer further questions and use of an extended range of methods. The results support the hypothesis of an antiseptic effect of the tested preservatives (methyl-4-hydroxybenzoate and propyl-4-hydroxybenzoate, potassium sorbate and propylene glycol) on prominent reference bacteria, which could also be observed in clinical settings.

Systematic review and critical reflection on the isolation and identification methods for spoilage associated bacteria in fresh marine fish

Consumers demand more fresh, safe, and high-quality food. As this is partiallycorrelated to the microbial profile, several microbiological examination tools are available. Incontrast to meat, no microbiological normalized methods to assess the microbiological quality of fresh marine fish have been agreed on. As a result, studies on the detection and diversity of spoilage associated organisms (SAOs) in fish often apply various detection, isolation, and identification techniques. This complicates the comparison and interpretation of data reported, and often results in different or inconclusive results. Therefore, the present review aimed to present a critical overview of the isolation/cultivation and detection techniques currently applied in fish microbiology. After a comprehensive search in the PubMed, Web of Science and Scopus databases, a total of 111 studies fulfilled the review selection criteria. Results revealed that when relying on culture media for the isolation of SAOs in fish, it is essential to include a salt-containing medium next to plate count agar that is currently used as the reference medium for the enumeration of bacteria on fish. In terms of identification, MALDI-TOF MS and 16S rRNA gene sequencing are currently the most promising tools, though other housekeeping genes should be targeted as well, and, the biggest challenge at this point is still the lack of comprehensive proteomic and sequence databases for SAOs. A full replacement of cultivation by next generation sequencing is difficult to recommend due to the absence of a standardized experimental methodology, especially for fish, and the relatively high sequencing costs. Additionally, a discrepancy between culture-dependent and independent methods in revealing the bacterial diversity, and abundancy, from marine fish was demonstrated by several authors. It is therefore recommended to consider both approaches as complements of one another, rather than substitutes, and to include them simultaneously to yield more complete results regarding the SAOs in fresh marine fish. As such, a thorough understanding of the biology of spoilage organisms and process will be obtained to prolong the shelf-life and deliver a high-quality product.

Consequences of Implementing Neutralizing Buffered Peptone Water in Commercial Poultry Processing on the Microbiota of Whole Bird Carcass Rinses and the Subsequent Microbiological Analyses

In 2016, the United States Department of Agriculture (USDA) Food Safety and Inspection Service (FSIS) established guidelines which modified the Buffered Peptone Water (BPW) rinsate material to include additional compounds that would better neutralize residual processing aids and allow for better recovery of sublethal injured Salmonella spp. cells. While the added compounds improved the recovery of Salmonella spp., specific data to understand how the new rinse agent, neutralizing Buffered Peptone Water (nBPW), impacts the recovery of other microorganisms such as Campylobacter spp. and indicator microorganisms are lacking. Therefore, this study evaluated the impact of rinse solutions (BPW or nBPW) used in Whole Bird Carcass rinsate (WBCR) collections on the subsequent microbiome and downstream culturing methodologies. Carcasses exiting a finishing chiller were rinsed in 400 ml of BPW or nBPW. Resulting rinsates were analyzed for Enterobacteriaceae (EB), Salmonella, and Campylobacter spp. prevalence and total aerobic bacteria (APC) and EB load. The 16S rDNA of the rinsates and the matrices collected from applied microbiological analyses were sequenced on an Illumina MiSeq^®. Log₁₀-transformed counts were analyzed in JMP 15 using ANOVA with means separated using Tukey’s HSD, and prevalence data were analyzed using Pearson’s χ² (P ≤ 0.05). Diversity and microbiota compositions (ANCOM) were analyzed in QIIME 2.2019.7 (P ≤ 0.05; Q ≤ 0.05). There was an effect of rinsate type on the APC load and Campylobacter spp. prevalence (P < 0.05), but not the quantity or prevalence of EB or Salmonella spp. prevalence. There were differences between the microbial diversity of the two rinsate types and downstream analyses (P < 0.05). Additionally, several taxa, including Streptococcus, Lactobacillus, Aeromonas, Acinetobacter, Clostridium, Enterococcaceae, Burkholderiaceae, and Staphylococcaceae, were differentially abundant in paired populations. Therefore, the rinse buffer used in a WBCR collection causes proportional shifts in the microbiota, which can lead to differences in results obtained from cultured microbial populations.

Characterization of Microbiological Quality of Whole and Gutted Baltic Herring

There is growing interest in Baltic herring (Clupea harengus membras) and other undervalued, small-sized fish species for human consumption. Gutting or filleting of small-sized fish is impractical; hence, the aim of this study was to explore the suitability of the whole (ungutted) herring for food use. The microbiological quality of commercially fished whole and gutted herring was analysed with culture-dependent methods combined with identification of bacterial isolates with MALDI-TOF Mass Spectrometry and culture-independent 16S rRNA gene amplicon sequencing. Whole and gutted herring had between 2.8 and 5.3 log₁₀ CFU g⁻¹ aerobic mesophilic and psychrotrophic bacteria and between 2.2 and 5.6 log₁₀ CFU g⁻¹ H₂S-producing bacteria. Enterobacteria counts remained low in all the analysed herring batches. The herring microbiota largely comprised the phyla Proteobacteria, Firmicutes, and Actinobacteria (71.7% to 95.0%). Shewanella, Pseudomonas, and Aeromonas were the most frequently isolated genera among the viable population; however, with the culture-independent approach, Shewanella followed by Psychrobacter were the most abundant genera. In some samples, a high relative abundance of the phylum Epsilonbacteraeota, represented by the genus Arcobacter, was detected. This study reports the bacterial diversity present in Baltic herring and shows that the microbiological quality was acceptable in all the analysed fish batches.

Perturbation on gut microbiota impedes the onset of obesity in high fat diet-induced mice

High-calorie intake has become one of the most common causes of dietary obesity, which eventually develops into type 2 diabetes mellitus (T2DM). Microbiota, along with the length of the gastrointestinal tract, is related to metabolic disorders, but its shifts and following impact on metabolic disorders due to external perturbation are still unclear. To evaluate shifts of microbiota from the proximal to the distal intestine and their impact on metabolic disorders, we profiled jejunal and colonic microbiota with the perturbation using high salt (HS) and antibiotic-induced microbiota depletion (AIMD) in diet-induced obesity (DIO) mice and analyzed the association with parameters of both obesity and blood glucose. After ten weeks of feeding DIO mice with HS intake and AIMD, they failed to develop obesity. The DIO mice with HS intake had T2DM symptoms, whereas the AIMD DIO mice showed no significant difference in blood glucose parameters. We observed that the jejunal and colonic microbiota had shifted due to settled perturbation, and jejunal microbiota within a group were more dispersed than colonic microbiota. After further analyzing jejunal microbiota using quantified amplicon sequencing, we found that the absolute abundance of Colidextribacter (R = 0.695, p = 0.001) and Faecalibaculum (R = 0.631, p = 0.005) in the jejunum was positively correlated with the changes in BW and FBG levels. The predicted pathway of glucose and metabolism of other substances significantly changed between groups (p <0.05). We demonstrated that the onset of obesity and T2DM in DIO mice is impeded when the gut microbiota is perturbed; thus, this pathogenesis depends on the gut microbiota.

Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database

According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.

SERS Sensors Based on Aptamer-Gated Mesoporous Silica Nanoparticles for Quantitative Detection of Staphylococcus aureus with Signal Molecular Release

This work describes a simple and novel biosensor for the quantitative determination of Staphylococcus aureus (S. aureus) based on target-induced release of signal molecules from aptamer-gated aminated mesoporous silica nanoparticles (MSNs) coupled with surface-enhanced Raman scattering (SERS) technology. MSNs were synthesized and then modified with amino groups by (3-aminopropyl) triethoxysilane to make them positively charged. Next, signal molecules (4-aminothiophenol, 4-ATP) were loaded into the pores of MSNs. Then, negatively charged aptamers of S. aureus were assembled on the surface of MSNs through electrostatic interactions. Upon the addition of S. aureus, the assembled aptamers were specifically bound to the bacteria. Consequently, the "gates" were opened, resulting in the release of 4-ATP from the pores of MSNs. The released molecules were measured by a Raman spectrometer, and the intensity of 4-ATP at 1071 cm^-1 was linearly related to the S. aureus concentration. A silver nanoflower silica core-shell structure (Ag NFs@SiO₂) was prepared and it served as a SERS substrate. Under optimized experimental conditions, a good linear relationship (y = 2107.93 + 1536.30x, R² = 0.9956) in the range from 4.7 × 10 to 4.7 × 10⁸ cfu/mL was observed with a limit of detection of 17 cfu/mL. The method was successfully applied for the analysis of S. aureus in fish samples and the recovery rate was 91.3-109%.

Assessment of the potential use of MALDI-TOF MS for the identification of bacteria associated with chilled vacuum-packaged lamb meat

The focus of this study was to compare the effectiveness of MALDI-TOF MS and partial 16S rRNA gene sequencing for the identification of bacteria isolated from VP lamb meat stored chilled at 5 °C for 21 days, at the same time gaining insights into bacterial changes over time. The identity of bacterial isolates on non-selective and selective agars was determined by both methods and results compared. Results showed that total bacterial numbers increased over the 21 days (as expected) with Staphylococcus and Pseudomonas (day 0) being replaced by Carnobacterium, Brochothrix and members of the Enterobacteriaceae family by day 21. A high level of agreement (86-100%) for bacterial isolates' identity at genus level was observed between MALDI-TOF MS and partial 16S rRNA gene-based sequencing for isolates where identification was possible. With its cheaper cost and faster turnaround time, once optimized, MALDI-TOF MS could become a useful alternative to 16S rRNA gene-sequencing for the rapid identification of red meat bacterial isolates.

Bacterial shifts on broiler carcasses at retail upon frozen storage

Freezing broiler carcasses, industrially or at home, not only delays spoilage, but also is expected to increase food safety by hampering growth of food pathogens. However, detailed knowledge on microbial changes after a short or longer freezing period of fresh broiler meat in home freezing setting is lacking and no comparison between different freezing periods has been published yet. The present study combined classical isolation techniques and identification by MALDI-TOF MS with 16S rRNA amplicon sequencing to assess bacterial contamination on broiler carcasses that were either bought fresh and then frozen for short periods (total n = 20) in home freezing, or industrial frozen one (total n = 4) at retail. Changes in total aerobic bacteria (TAB) were also studied on 78 freshly bought broiler carcasses that were then stored frozen for up to 6 months in domestic freezers. Salmonella and Campylobacter were examined to assess the effect of freezing on controlling common foodborne pathogens. The contamination level of mesophilic and psychrotrophic TAB was numerically equal on carcasses at retail, either fresh or frozen at different time points. After short and long freezing period, a decrease in counts of mesophilic TAB was observed, while changes in counts of psychrotrophic TAB were rarely observed. No correlation between home freezing period and TAB load, either mesophilic (R = -0.006, p = 0.949) or psychrotrophic (R = 0.080, p = 0.389), was observed. No Salmonella and Campylobacter was detected on industrial frozen carcasses but on fresh carcasses at retail, either pre-freezing or after freezing. The bacterial communities were influenced by freezing, in which some genera showed significantly changes in relative abundance after freezing. In conclusion, from a food safety point of view, freezing of meat products does not serve as safety hurdle, and freezing should only be considered as a method for extending shelf life compared with fresh chicken meat. Applying hygienic slaughter procedures to keep the initial contamination as low as possible, and the maintenance of the cold chain during further processing are the key factors in food safety.

Evaluation of microbial contamination of different pork carcass areas through culture-dependent and independent methods in small-scale slaughterhouses

Routine evaluation of the slaughter process is performed by the enumeration of the aerobic colony count, Enterobacteriaceae and Salmonella spp. on the carcass through destructive or non-destructive methods. With non-destructive methods, bacteria are counted from a minimum area of 100 cm² in different sampling sites on the pork carcasses, and the results of these investigated areas are pooled to one value for the complete carcass evaluation (a total of 400 cm²). However, the composition of the bacterial community present on the different sampling areas remains unknown. The aim of the study was to characterize the microbial population present on four areas (ham, back, jowl and belly) of eight pork carcasses belonging to two different slaughterhouses through culture-dependent (Matrix-assisted laser desorption/ionization time-of-flight Mass Spectrometry MALDI-TOF MS, combined with 16S rRNA gene sequencing) and complementary culture-independent (16S rRNA amplicon sequencing) methods. The presence of Salmonella spp. and Y. enterocolitica was additionally assessed. Using MALDI-TOF MS, Staphylococcus, Pseudomonas, and Escherichia coli were found to dominate the bacterial cultures isolated from the 8 carcasses. Based on the 16S rRNA amplicon sequencing analyses however, no specific genus clearly dominated the bacterial community composition. By using this culture-independent method, the most abundant genera in microbial populations of the ham, back, jowl and belly were found to be similar, but important differences between the two slaughterhouses were observed. Thus, present data suggests that the indigenous bacterial population of individual animals is overruled by the microbial population of the slaughterhouse in which the carcass is handled. Also, our data suggests that sampling of only one carcass area by official authorities may be appropriate for the evaluation of the hygienic status of the carcasses and therefore of the slaughter process.

Analyses of the Bacterial Contamination on Belgian Broiler Carcasses at Retail Level

Broilers are not equally exposed to bacterial contamination during rearing and processing, resulting in areas with different bacterial communities on carcasses at retail. The determination of these communities is also affected by the examination methods applied. The present study aimed to assess the bacterial communities on neck, breast, and back skin on broiler carcasses at retail through classical International Organization of Standardization based isolation methods combined with identification by matrix-assisted laser desorption ionization time-of-flight mass spectrum (MALDI-TOF MS) and 16S amplicon sequencing. Twelve commercially and eight organically reared broilers slaughtered in four slaughterhouses were examined. Significantly higher anaerobic bacterial counts were observed on the neck skin than on the breast and back skin. By the combination of cultivation and amplicon sequencing, remarkable shifts in bacterial communities were determined on the breast and back skin, but not on the neck skin. Although the aerobic bacteria contamination levels were not different between the areas, different bacterial communities were observed. The impact of the slaughterhouse to the overall microbial composition was rather small. Organically reared broilers had unique bacterial communities. In conclusion, compared to the breast skin, the neck, and back skin had a larger potential for bacterial spoilage, in particular when anaerobic storage conditions are applied. The distribution of bacteria on the different areas could be related to the contamination during slaughter as well as the bird-rearing methods.

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing

Complex interactions occur within microbial communities during the fermentation process of kimchi. Identification of these microorganisms provides the essential information required to improve food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community changes during the fermentation of kimchi by comparing a culture-dependent (MALDI-TOF MS analysis) and a culture-independent method (high-throughput sequencing) of 16S rRNA gene fragment). Members of the Lactobacillus-related genera, Leuconostoc, and Weissella were identified as the predominant microorganisms by both methods. The culture-independent method was able to additionally identify non-lactic acid bacteria and yeasts, such as Kazachstania in kimchi. However, high-throughput sequencing failed to accurately recognize Latilactobacillus sakei, Latilactobacillus curvatus, Lactiplantibacillus plantarum, and W. cibaria, which played an important role in kimchi fermentation, as this method only allowed for identification at the genus level. Conversely, MALDI-TOF MS analysis could identify the isolates at the species level. Also, culture-dependent method could identify predominant species in viable cell communities. The culture-dependent method and culture-independent method provided complementary information by producing a more comprehensive view of the microbial ecology in fermented kimchi.

Detection and quantification of Campylobacter in foods: New analytic approaches to detect and quantify Campylobacter spp. in food samples

The aim of the present study was to develop rapid qualitative and quantitative methods based on the use of Real-Time PCR and Droplet Digital PCR (ddPCR), in order to have reliable techniques to detect and quantify Campylobacter spp. in food samples. The gene 16S-rRNA was used as specific target for Campylobacter spp. Real- Time PCR evaluation assay and a not competitive internal control was ushered in it. To investigate the selectivity of the method, 26 Campylobacter strains and 40 non-Campylobacter strains were tested and in order to verify the application of Real- Time PCR method, 5 pork meat samples were experimentally inoculated with a Campylobacter jejuni strain. Subsequently, dilutions with a bacterial load of Campylobacter jejuni within 10-106 CFU/mL were chosen for the optimization of the ddPCR assay. Lastly, a total of 54 naturally contaminated foods samples were analyzed through molecular (Real-Time PCR and ddPCR) and traditional methods. The Real-Time PCR protocol demonstrated to amplify only the Campylobacter spp. strains and when Campylobacter jejuni was experimentally inoculated in meat samples the pathogen was always detected. The ddPCRs assay allowed to quantify a level of contamination of 10 CFU/mL, but it was unable to quantify levels of 105 - 106 CFU/mL. Lastly, Campylobacter spp. was never detected in the 54 samples tested. In conclusion, the novel analytic approach proposed, based on an initial screening of the samples with Real-Time PCR and then on quantification of Campylobacter spp. with a ddPCR on those positive, represents a quick monitoring tool and, if used correctly, it would allow the implementation of food safety.

Yersinia enterocolitica detection in pork products: Evaluation of isolation protocols

Conventional methods for Yersinia enterocolitica detection in food samples are generally considered inadequate. Problems arise from the presence of the so-called "background flora", coupled to the low contamination level of the pathogen. Since, data on the microbial ecology occurring in competitive microflora are still lacking, MALDI TOF MS was used for strains 'identification after enrichment in PSB or ITC broths, and after plating on selective CIN medium at different incubation times. SYBR Green Real time PCR was used for the Y. enterocolitica strains' detection (4/O:3, 1A/O:5) in experimentally contaminated foods, as well as in naturally contaminated samples. A higher number of different bacterial genera (10 on CIN and 18 on PCA) was recorded after enrichment in PSB, whilst enrichment in ITC led to recovery of 6 and 10 genera on CIN and PCA, respectively. Yersiniaceae was the dominant family on the first day of incubation, but on the second day the percentage of isolation considerably decreased. By testing experimentally contaminated samples, substantial difficulties were encountered. The biotype 1A was always detected, whereas strain 4/O:3 proved to be poorly competitive. Based on the data, the enrichment media PSB and ITC, currently proposed for Y. enterocolitica detection, need to be improved to promote a successful pathogen's recovery.

Paper-Based Diagnostic System Facilitating Escherichia coli Assessments by Duplex Coloration

Laboratory support for low-resource regions is a rising global issue. As microbiological contamination is closely associated with other issues like food safety, water supply sustainability, and public health, bacterial assessments in this setting need to be improved. Herein, we demonstrate a paper-based diagnostic device for point-of-need testing, in which fecal-indicating Escherichia coli and highly pathogenic E. coli are detected by duplex coloration. This device was functionalized by mixing different chromogenic substrates that reflect each bacterial enzymatic phenotype. In the final part of the paper, we describe this microbiological diagnostic system tested with bacteria-contaminated food samples. The device sensitivity was shown to have greatly reduced the total analysis time (below to 4 h) when combined with an enrichment amplification procedure. Notably, this paper device successfully detected 10 cfu/mL of target bacteria in a contaminated milk sample. Our diagnostic system shows acceptable accuracy, short analysis time, and a user-friendly interface, thereby eliminating demands for high-end equipment and a highly trained staff. We expect that this diagnostic system will be a sustainable solution in supporting microbiological or clinical laboratories in low-income countries.

Assessment of microbial communities on freshly killed wild boar meat by MALDI-TOF MS and 16S rRNA amplicon sequencing

Wild boars (Sus scrofa) are the most widely distributed large mammals and recent increase in consumption of wild boar meat urges the need of microbiological quality criteria. The aim of the study was to characterize the initial bacterial contamination on freshly-killed wild boar meat using a culture-dependent approach with ISO-methods combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification and 16S rRNA amplicon sequencing. Moreover, the presence of foodborne pathogens was examined using Real-Time-PCR and confirmed by classical isolation. Analysing 22 unrelated wild boar meat samples showed a higher bacterial contamination level compared to pork, with Salmonella present in almost one third of the samples. A great variability of the microbial contamination between the samples was recorded, as well as complementary results between culturing and 16S rRNA amplicon sequencing as frequently isolated genera were not always detected, and vice versa. Furthermore, the foodborne pathogen Salmonella was never detected with 16S rRNA amplicon sequencing, demonstrating the necessity for a cautious approach in the implementation of new analysis techniques in food safety. The present work determines that attention should be paid to the trade of non-inspected meat directly to retail or consumers.