The sources and transmission routes of microbial populations throughout a meat processing facility

Fresh pork microbiota is temporally dynamic and compositionally diverse across meat, contact surfaces, and processing lines in a pork processing facility

The goal of this study was to analyze the microbial profiles of meat and contact surfaces from two different processing lines in a pork processing plant, using a 16S rRNA gene amplicon sequencing workflow specifically designed to investigate fresh meat and environmental samples throughout a commercial production schedule. Results indicated that the microbiota differed between the meat and contact surface, both across the two processing lines and within each individual processing line. Differences in the microbiota composition were also strongly associated with both the specific processing dates and the time of day during processing. Much of this variation was associated with distinct amplicon sequence variants unique to each processing date and each processing line throughout the day. The abundance of key taxa associated with food safety and spoilage was also temporally dynamic across a production shift and was different between the meat and contact surface. Overall, the results of this study indicate significant differences in the microbial profiles of the meat and contact surfaces between two processing lines within the same plant. These differences are likely influenced by daily variation in processing and sanitation procedures, as well as differences in the design of the processing lines, which appear to affect the microbiotas of both the meat and contact surfaces.IMPORTANCEThis study provides critical knowledge that can be used as a foundation for tailored processes to improve fresh pork safety and quality, potentially customized to individual processing lines, time points within a shift, and/or production days. Additionally, this study provides a list of potential biological markers associated with food safety and quality that could be used by processors to develop and validate intervention strategies specific to different processing lines.

Microbiome characterization of two fresh pork cuts during production in a pork fabrication facility

The goal of this study was to characterize the microbial profile of two different fresh pork cuts, bootjack (BJ) trim and tenderloin (TL), through a 16S rRNA sequencing workflow developed specifically for investigating low-biomass fresh meat within a commercial production schedule. Additionally, this study aimed to determine a baseline Salmonella prevalence and enumeration profile across these two fresh pork cuts. Results showed that microbiome diversity was different between the BJ and TL, and also differed significantly by processing date. The relative abundance of key bacterial genera associated with food safety and spoilage was also different between the two meat types. However, over the course of the production shift, changes in the meat microbiome were limited in both the BJ and TL. The crude prevalence and enumerated burden of Salmonella were lower than what has been previously reported in similar fresh pork cuts, and all of the Salmonella-positive samples occurred on just two processing windows of 1-2 days each. Taken together, the results of this study suggest that the microbial profile of two fresh pork cuts is significantly different even within the same plant at the same time points, and that day-to-day variability within the production process likely influences both the fresh pork microbiome and Salmonella profile of these two meat types.IMPORTANCEModern pork processing involves a series of processes that begin with the handling and transport of the live animals, proceed through harvest and fabrication, and end with the packaging and distribution of fresh pork to the consumer. Each step in this process can alter the microbial community of fresh pork and influence the meat's safety and shelf life. However, little is known about the microbial ecology of individual, unprocessed pork cuts and if the diversity of the meat microbiome remains consistent throughout a production schedule. Additionally, the crude prevalence and enumeration of Salmonella have not been well established for individual fresh pork cuts throughout a production schedule. A more thorough understanding of the microbial profile at different stages of pork production will help processors determine processing steps that impact the microbial characteristics of fresh pork. This insight will help processors implement targeted intervention strategies to enhance food safety and quality.

Microbial Level and Microbiota Change of Laver in Dried Laver Processing Line During Production Seasons

To understand better the high microbial load in dried laver (Porphyra yezoensis or nori), this study analyzed the aerobic plate count (APC), coliform count, temperature change, and microbiota of processing water, laver materials, and food contact surface (FCS) samples from three processing plants during the dried laver processing season from December 2023 to April 2024. The seawater used for the first washing had a low microbial load (APCs < 1-2.85 log CFU/g; coliform < 1 log CFU/g) and was dominated by Proteobacteria, Firmicutes, and Bacteroidota. The microbial load of fresh laver (4.21-4.76 log CFU/g) remained unchanged after seawater washing, but significantly increased after continuous shredding, sponge dehydration, first drying, and with the seasonal temperature rise. The microbiota of laver before drying was vulnerable between processing steps and seasons, but consistently shifted back to fresh laver microflora and was dominated by Flavobacteriaceae after drying. The FCSs (except for the curtain), which had a high microbial load (APCs 5.25-8.26 log CFU/g; coliform 1.52-4.84 log CFU/g) with similar microbiota to seawater, caused the secondary contamination of laver during processing. This study revealed the microbial proliferation of laver and seawater microflora in the continuous processing line with high nutrients and with the seasonal processing water temperature rise caused by the local weather, highlighting the need for routine cleaning and sanitizing, better washing of fresh laver, and low temperature control for future dried laver production.

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonization of Listeria monocytogenes

Listeria monocytogenes is a foodborne pathogen of significant concern for the food industry due to its remarkable ability to persist through safety control efforts, posing a subsequent health threat to consumers. Understanding the microbial communities coexisting with L. monocytogenes in food processing environments provides insights into its persistence mechanisms. We investigated the microbial communities on non-food contact surfaces in a facility producing ready-to-eat foods, known to harbour a ST121 L. monocytogenes strain over multiple years. A 10-week sampling period was coordinated with the company and public health authorities. Metagenomic analysis revealed a stable microbial composition dominated by Pseudomonas fluorescens. While highly related populations were present in high-care production zones, distinctive taxa characteristic of specific areas were observed (e.g., Sphingomonas aerolata). Although Listeria spp. were not detected in metagenomes, they were detected in cultured samples, suggesting low relative abundance in factory settings. The findings suggest that a stable resident microbiota, with distinct adaptations to different areas within the factory, was selected for by their collective ability to survive control efforts in this environment. Listeria spp. was a member of this microbial community, albeit at low abundance, and may likewise benefit from the mutualism of the overall microbial community.

Polylactic Acid/Bamboo Leaf Extract Electrospun Mats with Antioxidant Activity for Food Packaging Applications

This study focuses on developing an active and biodegradable packaging using electrospinning, with polylactic acid (PLA) as the matrix and bamboo leaf extract (BLE) as the antioxidant compound. The research systematically evaluates the relationship among process parameters, material properties, and structure. The electrospun membranes were produced using different BLE contents (10 wt%, 20 wt%, 30 wt%, and 40 wt%) and characterized by their morphology, mechanical properties, wettability, and antioxidant activity. Scanning electron microscopy (SEM) revealed BLE's influence on fiber morphology, with a slight increase in diameter in PLA/BLE at 10% and 20%, attributed to higher viscosity. Conversely, PLA/BLE 30% and 40% showed a mild reduction in fiber diameter likely due to polyphenols' capacity to enhance PLA chain mobility. Mechanical tests indicated proportional reductions in modulus, maximum stress, and strain at break, upon increasing the BLE concentration, although these parameters are still suitable for packaging applications. The decrease in modulus is attributed to polyphenol capacity to increase PLA chain mobility, while increased fragility results from embedded particles acting as local defects. Wettability tests demonstrated increased hydrophilicity with higher BLE content. Total polyphenol content, estimated through FOLIN assay, increased proportionally with incorporated BLE, impacting antioxidant properties assessed via FRAP assay.

Challenges, Health Risks and Recommendations on Meat Handling Practices in Africa: A Comprehensive Review

Meat handling is a crucial aspect of public health as it forms complex interactions among humans, animals, and the environment. African meat handlers continue to face various challenges in slaughterhouses that significantly impact their lives and the general public during meat processing. This paper reviews the challenges meat handlers encounter and the associated risks of improper meat handling in various African slaughterhouses. A comprehensive literature search was performed on Science Direct, Web of Science, PubMed, Scopus and Google Scholar. Articles published to investigate the challenges and health risks of meat handling practices in Africa from 1961 to 2022 were included in this review. African meat handlers face socio-economic difficulties, including inadequate returns, unpredictable working environment, market, security, and limited healthcare access. Many meat handlers work informally in unregistered facilities and are not trained by experts on proper meat handling. This results in improper meat handling, raising the possibility of meat contamination by foodborne pathogens like Salmonella sp. and E. coli on slaughter and contact surfaces, hence posing a threat to meat safety and public health. We recommended that governmental, institutional and community-level actions should be used to address the health challenges associated with improper meat handling in Africa. Government and institutional bodies play an important role in supporting and upholding the laws that guide proper meat handling and processing. Meat handlers must be educated on meat safety, handling and storage to ensure meat is safe for consumption.

The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments

Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm2) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.

In-depth characterization of food and environmental microbiomes across different meat processing plants

BACKGROUND

Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.

RESULTS

The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.

CONCLUSIONS

Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.

Slaughtering processes impact microbial communities and antimicrobial resistance genes of pig carcasses

Several steps in the abattoir can influence the presence of microbes and associated resistance genes (ARGs) on the animal carcasses used for further meat processing. We investigated how these processes influence the resistome-microbiome of groups of pigs with different on-farm antimicrobial exposure status, from the moment they entered the abattoir until the end of carcass processing. Using a targeted enrichment metagenomic approach, we identified 672 unique ARGs conferring resistance to 43 distinct AMR classes from pooled skin (N = 42) and carcass swabs (N = 63) collected sequentially before, during, and after the slaughter process and food safety interventions. We observed significant variations in the resistome and microbial profiles of pigs before and after slaughter, as well as a significant decline in ARG counts, diversity, and microbial DNA load during slaughter and carcass processing, irrespective of prior antimicrobial treatments on the farm. These results suggest that existing interventions in the abattoir are effective in reducing not only the pathogen load but also the overall bacterial burden, including ARGs on pork carcasses. Concomitant with reductions in microbial and ARG counts, we observed an increase in the relative abundance of non-drug-specific ARGs, such as those conferring resistance to metals and biocides, and in particular mercury. Using a strict colocalization procedure, we found that most mercury ARGs were associated with genomes from the Pseudomonadaceae and Enterobacteriaceae families. Collectively, these findings demonstrate that slaughter and processing practices within the abattoir can shape the microbial and ARG profiles of pork carcasses during the transition from living muscle to meat.

Transfer of beef bacterial communities onto food-contact surfaces

Introduction

Food spoilage and pathogenic bacteria on food-contact surfaces, especially biofilm-forming strains, can transfer to meats during processing. The objectives of this study were to survey the bacterial communities of beef cuts that transfer onto two commonly used food-contact surfaces, stainless steel (SS) and high-density polyethylene (HDPE) and identify potentially biofilm-forming strains.

Methods

Top round, flank, chuck, and ground beef were purchased from 3 retail stores. SS and HDPE coupons (approximately 2cm × 5cm) were placed on beef portions (3h, 10°C), after which, the coupons were submerged halfway in PBS (24h, 10°C). Bacteria from the beef cuts and coupon surfaces (n = 3) were collected, plated on tryptic soy agar plates and incubated (5 days, 25°C). Bacterial isolates were identified by 16S rRNA gene amplicon sequencing and assayed for biofilm formation using a crystal violet binding (CV) assay (72h, 10°C). Additionally, beef and coupon samples were collected for bacterial community analysis by 16S rRNA gene amplicon sequencing.

Results and discussion

Sixty-one of 972 beef isolates, 29 of 204 HDPE isolates, and 30 of 211 SS isolates were strong biofilm-formers (Absorbance>1.000 at 590 nm in the CV assay). Strong-binding isolates identified were of the genera Pseudomonas, Acinetobacter, Psychrobacter, Carnobacterium, and Brochothrix. Coupon bacterial communities among stores and cuts were distinct (p < 0.001, PERMANOVA), but there was no distinction between the communities found on HDPE or SS coupons (p > 0.050, PERMANOVA). The bacterial communities identified on the coupons may help determine the communities capable of transferring and colonizing onto surfaces, which can subsequently cross-contaminate foods.

Escherichia coli and Enterobacteriaceae Counts, Virulence Gene Profile, Antimicrobial Resistance, and Biofilm Formation Capacity during Pig Slaughter Stages

This study aimed to count Enterobacteriaceae and Escherichia coli in different locations on pig carcasses (shank, loin, abdomen, shoulder, and jowl) from two slaughterhouses (A and B) between September 2019 and July 2021 during different slaughter stages (after bleeding, after passing through the epilator machine, after manual toileting in the dirty area, before and after evisceration, and after the final washing), as well as verify antimicrobial resistance and biofilm formation capacity. The main points of Enterobacteriaceae and E. coli contamination were identified in the two slaughterhouses through three collections. The stages with the highest counts were post-bleeding and evisceration in both slaughterhouses and after manual toileting in slaughterhouse B in the first collection. Most E. coli isolates were resistant to multiple antimicrobials, with higher resistance frequencies to amoxicillin, ampicillin, chloramphenicol, sulfonamides, and streptomycin. The virulence genes eae, stx1, and stx2 were also detected. Three isolates had all three genes and exhibited resistance to at least six antimicrobial classes (β-lactams, macrolides, aminoglycosides, sulfonamides, amphenicols, and quinolones). E. coli isolates also showed a high frequency of strains with moderate and strong in vitro biofilm-forming capacity. This is the first study to characterize microbial contamination by pig slaughter stage in the Federal District region, demonstrating the critical points for hygienic production. E. coli was isolated from the surface of pig carcasses, as well as the virulence genes stx1, stx2, and eae were detected. The multi-antimicrobial resistant isolates also had a moderate-to-strong biofilm formation capacity, thus demonstrating risks to public health.

Monitoring of meat quality and change-point detection by a sensor array and profiling of bacterial communities

BACKGROUND

Real-time monitoring of food consumer quality remains challenging due to diverse bio-chemical processes taking place in the food matrices, and hence it requires accurate analytical methods. Thresholds to determine spoiled food are often difficult to set. The existing analytical methods are too complicated for rapid in situ screening of foodstuff.

RESULTS

We have studied the dynamics of meat spoilage by electronic nose (e-nose) for digitizing the smell associated with volatile spoilage markers of meat, comparing the results with changes in the microbiome composition of the spoiling meat samples. We apply the time series analysis to follow dynamic changes in the gas profile extracted from the e-nose responses and to identify the change-point window of the meat state. The obtained e-nose features correlate with changes in the microbiome composition such as increase in the proportion of Brochothrix and Pseudomonas spp. and disappearance of Mycoplasma spp., and with representative gas sensors towards hydrogen, ammonia, and alcohol vapors with R2 values of 0.98, 0.93, and 0.91, respectively. Integration of e-nose and computer vision into a single analytical panel improved the meat state identification accuracy up to 0.85, allowing for more reliable meat state assessment.

SIGNIFICANCE

Accurate identification of the change-point in the meat state achieved by digitalizing volatile spoilage markers from the e-nose unit holds promises for application of smart miniaturized devices in food industry.

Early Detection of Food Safety and Spoilage Incidents Based on Live Microbiome Profiling and PMA-qPCR Monitoring of Indicators

The early detection of spoilage microorganisms and food pathogens is of paramount importance in food production systems. We propose a novel strategy for the early detection of food production defects, harnessing the product microbiome. We hypothesize that by establishing microbiome datasets of proper and defective batches, indicator bacteria signaling production errors can be identified and targeted for rapid quantification as part of routine practice. Using the production process of pastrami as a model, we characterized its live microbiome profiles throughout the production stages and in the final product, using propidium monoazide treatment followed by 16S rDNA sequencing. Pastrami demonstrated product-specific and consistent microbiome profiles predominated by Serratia and Vibrionimonas, with distinct microbial signatures across the production stages. Based on the established microbiome dataset, we were able to detect shifts in the microbiome profile of a defective batch produced under lactate deficiency. The most substantial changes were observed as increased relative abundances of Vibrio and Lactobacillus, which were subsequently defined as potential lactate-deficiency indicators. PMA-qPCR efficiently detected increased levels of these species, thus proving useful in rapidly pinpointing the production defect. This approach offers the possibility of the in-house detection of defective production events with same-day results, promoting safer food production systems.

Microbial dynamics of South Korean beef and surroundings along the supply chain based on high-throughput sequencing

Microbiological safety and quality of beef is crucial as beef can serve as a reservoir for a variety of bacteria, including spoilage-related and foodborne pathogens. Controlling microbial contamination is a critical aspect of food quality and safety, but it is difficult to prevent as there are several potential sources of contamination from production to distribution. In this study, the microbiological ecology of cattle/beef and associated environmental samples (n = 69) were trace-investigated to reveal microbiome shifts in cattle/beef and possible cross-contaminants throughout the entire supply chain using 16S rRNA gene sequencing. Pseudomonas, Psychrobacter, and Acinetobacter, known as spoilage bacteria, opportunistic pathogens, or antibiotic-resistant bacteria, were the main microorganisms present in cattle/beef, and Staphylococcus became abundant in the final products. The dominance of Acinetobacter and Pseudomonas was noticeable in the slaughtered carcasses and slaughterhouse environment, indicating that the slaughterhouse is a critical site where hygienic practices are required to prevent further contamination. Taxonomic similarities between cattle/beef and several environmental samples, as well as diversity analysis, presented a high potential for microbial transmission. Source tracking identified environmental samples that primarily contributed to the microbiota of cattle/beef. Farm floor (48%), workers' gloves (73%), and carcass splitters (20%) in the slaughterhouse were found to be major sources influencing the microbiome of cattle/beef at the farm, slaughterhouse, and processing plant, respectively. These findings demonstrated the dynamics of bacterial communities in cattle/beef according to stage and detected potential contamination sources, which may aid in a better understanding and control of microbial transmission in beef production.

Apt-Conjugated PDMS-ZnO/Ag-Based Multifunctional Integrated Superhydrophobic Biosensor with High SERS Activity and Photocatalytic Sterilization Performance

Sensitive detection and efficient inactivation of pathogenic bacteria are crucial for halting the spread and reproduction of foodborne pathogenic bacteria. Herein, a novel Apt-modified PDMS-ZnO/Ag multifunctional biosensor has been developed for high-sensitivity surface-enhanced Raman scattering (SERS) detection along with photocatalytic sterilization towards Salmonella typhimurium (S. typhimurium). The distribution of the electric field in PDMS-ZnO/Ag with different Ag sputtering times was analyzed using a finite-difference time-domain (FDTD) algorithm. Due to the combined effect of electromagnetic enhancement and chemical enhancement, PDMS-ZnO/Ag exhibited outstanding SERS sensitivity. The limit of detection (LOD) for 4-MBA on the optimal SERS substrate (PZA-40) could be as little as 10-9 M. After PZA-40 was modified with the aptamer, the LOD of the PZA-40-Apt biosensor for detecting S. typhimurium was only 10 cfu/mL. Additionally, the PZA-40-Apt biosensor could effectively inactivate S. typhimurium under visible light irradiation within 10 min, with a bacterial lethality rate (Lb) of up to 97%. In particular, the PZA-40-Apt biosensor could identify S. typhimurium in food samples in addition to having minimal cytotoxicity and powerful biocompatibility. This work provides a multifunctional nanoplatform with broad prospects for selective SERS detection and photocatalytic sterilization of pathogenic bacteria.

Emergence of potentially disinfection-resistant, naturalized Escherichia coli populations across food- and water-associated engineered environments

The Escherichia coli species is comprised of several 'ecotypes' inhabiting a wide range of host and natural environmental niches. Recent studies have suggested that novel naturalized ecotypes have emerged across wastewater treatment plants and meat processing facilities. Phylogenetic and multilocus sequence typing analyses clustered naturalized wastewater and meat plant E. coli strains into two main monophyletic clusters corresponding to the ST635 and ST399 sequence types, with several serotypes identified by serotyping, potentially representing distinct lineages that have naturalized across wastewater treatment plants and meat processing facilities. This evidence, taken alongside ecotype prediction analyses that distinguished the naturalized strains from their host-associated counterparts, suggests these strains may collectively represent a novel ecotype that has recently emerged across food- and water-associated engineered environments. Interestingly, pan-genomic analyses revealed that the naturalized strains exhibited an abundance of biofilm formation, defense, and disinfection-related stress resistance genes, but lacked various virulence and colonization genes, indicating that their naturalization has come at the cost of fitness in the original host environment.

Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features

The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.

Impact of intense sanitization procedures on bacterial communities recovered from floor drains in pork processing plants

Background

Pork processing plants in the United States (US) cease operations for 24-48 h every six or twelve months to perform intense sanitization (IS) using fogging, foaming, and further antimicrobial treatments to disrupt natural biofilms that may harbor pathogens and spoilage organisms. The impact such treatments have on short-term changes in environmental microorganisms is not well understood, nor is the rate at which bacterial communities return.

Methods

Swab samples were collected from floor drains to provide representative environmental microorganisms at two US pork processing plants before, during, and after an IS procedure. Samples were collected from four coolers where finished carcasses were chilled and from four locations near cutting tables. Each sample was characterized by total mesophile count (TMC), total psychrophile count (TPC), and other indicator bacteria; their biofilm-forming ability, tolerance of the formed biofilm to a quaternary ammonium compound (300 ppm, QAC), and ability to protect co-inoculated Salmonella enterica. In addition, bacterial community composition was determined using shotgun metagenomic sequencing.

Results

IS procedures disrupted bacteria present but to different extents depending on the plant and the area of the plant. IS reduced TPC and TMC, by up to 1.5 Log10 CFU only to return to pre-IS levels within 2-3 days. The impact of IS on microorganisms in coolers was varied, with reductions of 2-4 Log10, and required 2 to 4 weeks to return to pre-IS levels. The results near fabrication lines were mixed, with little to no significant changes at one plant, while at the other, two processing lines showed 4 to 6 Log10 reductions. Resistance to QAC and the protection of Salmonella by the biofilms varied between plants and between areas of the plants as well. Community profiling of bacteria at the genus level showed that IS reduced species diversity and the disruption led to new community compositions that in some cases did not return to the pre-IS state even after 15 to 16 weeks.

Discussion

The results found here reveal the impact of using IS to disrupt the presence of pathogen or spoilage microorganisms in US pork processing facilities may not have the intended effect.

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.

Understanding the quality and safety of food production through the lens of The Microbiome of The Built Environment

The Microbiome of the Built Environment (MoBE) is profoundly implicated in various sectors, including food science. The balance between beneficial and pathogenic microbes in these facilities directly influences product quality and public health. Maintaining a careful check on MoBE and external microbes is vital to the food industry to ensure quality control. There is also a risk of contamination in the meat processing facility as well. However, over-sanitization can increase drug-resistant microbes, highlighting the importance of balanced microbial management. Additionally, facility design, influenced by understanding MoBE, can optimize the growth of beneficial microbes and inhibit pathogenic microbes. Microbial mapping, an emerging practice, offers insights into microbial hotspots within facilities, resulting in targeted interventions. As the food industry evolves, the intricate understanding and management of MoBE will be pivotal to ensuring optimal food quality, safety, and innovation.

Salmonella-induced microbiome profile in response to sanitation by quaternary ammonium chloride

Salmonella enterica is a prominent cause of foodborne disease in the United States. However, the mechanism and route of pathogen transmission that leads to Salmonella infection in commercial processing plants are poorly understood. This study aimed to investigate the effect of mixed-species biofilms on S. enterica survival and persistence under sanitizer stress [Quaternary ammonium compounds (QACs)] by analyzing 78 floor drain samples from a meat processing facility and three S. enterica strains (serovars Cerro, Montevideo, and Typhimurium) isolated from that facility and an unrelated source. The four test groups were as follows: control, QAC treatment, Salmonella addition, and QAC treatment with Salmonella addition. DNAs were extracted, and 16S rRNA gene based on the variable region V4 amplicon sequencing was performed to analyze the relative abundance, core microbiome, and Alpha and Beta diversity using the qiime2 pipeline. At the genus level, the Brochothrix (45.56%), Pseudomonas (38.94%), Carnobacterium (6.18%), Lactococcus (4.68%), Serratia (3.14%), and Staphylococcus (0.82%) were shown to be the most prevalent in all drain samples. The results demonstrate that the relative abundance of different bacterial genera was affected by both QAC treatment and Salmonella addition, with some genera showing increases or decreases in abundance. Notably, the correlation network was constructed to understand the relationships between the different bacteria. Nitrospira had the greatest number of connections in the floor drain environment network, with two negative and eight positive correlations. The results suggest that Nitrospira in the mixed-species biofilm community may play a role in converting ammonium in the QAC sanitizer into nitrites. Thus, Nitrospira could be a potentially important genus in providing sanitizer resistance to pathogen-encompassed mixed-species biofilms.IMPORTANCESalmonella contamination in meat processing facilities can lead to foodborne illness outbreaks. Our study characterized the microbiome dynamics in beef facility drains and their response to Salmonella addition and common sanitizer (QAC). Nitrospira could be an important genus in providing sanitizer resistance to pathogen-encompassed mixed-species biofilms. The results provide insight into the impact of mixed-species biofilms on Salmonella survival and persistence under sanitizer stress in meat processing facilities. The results highlight the need to consider mixed-species biofilm effects when developing targeted interventions to enhance food safety.

Driving forces shaping the microbial ecology in meat packing plants

Meat production is a complex system, continually receiving animals, water, air, and workers, all of which serve as carriers of bacteria. Selective pressures involved in different meat processing stages such as antimicrobial interventions and low temperatures, may promote the accumulation of certain residential microbiota in meat cutting facilities. Bacteria including human pathogens from all these sources can contaminate meat surfaces. While significant advancements have been made in enhancing hygienic standards and pathogen control measures in meat plants, resulting in a notable reduction in STEC recalls and clinical cases, STEC still stands as a predominant contributor to foodborne illnesses associated with beef and occasionally with pork. The second-and third-generation sequencing technology has become popular in microbiota related studies and provided a better image of the microbial community in the meat processing environments. In this article, we reviewed the potential factors influencing the microbial ecology in commercial meat processing facilities and conducted a meta-analysis on the microbiota data published in the last 10 years. In addition, the mechanisms by which bacteria persist in meat production environments have been discussed with a focus on the significant human pathogen E. coli O157:H7 and generic E. coli, an indicator often used for the hygienic condition in food production.

Bacterial profile of pork from production to retail based on high-throughput sequencing

Pork is a common vehicle for foodborne pathogens, including Salmonella spp. and Yersinia enterocolitica. Cross-contamination can occur at any stage of the pork production chain, from farm to market. In the present study, high-throughput sequencing was used to characterize bacterial profiles and track their changes along the whole supply chain. Tracked meat samples (pig on the farm, carcass in the slaughterhouse, unprocessed carcass and processed meat in the processing plant, and fresh pork at the local retail stores) and their associated environmental samples (e.g., water, floor, feed, feces, and workers' gloves) were collected from sequential stages (n = 96) and subjected to 16S rRNA metataxonomic analyses. At the farm, a total of 652 genera and 146 exclusive genera were identified in animal and environmental samples (pig, drain, floor, fan, and feces). Based on beta diversity analysis, it was demonstrated that the microbial composition of animal samples collected at the same processing step is similar to that of environmental samples (e.g., drain, fan, feces, feed, floor, gloves, knives, tables, and water). All animal and environmental samples from the slaughterhouse were dominated by Acinetobacter (55.37 %). At the processing plant, belly meat and neck meat samples were dominated by Psychrobacter (55.49 %). At the retail level, key bacterial players, which are potential problematic bacteria and important members with a high relative abundance in the samples, included Acinetobacter (8.13 %), Pseudomonas (6.27 %), and Staphylococcus (2.13 %). In addition, the number of confirmed genera varied by more than twice that identified in the processing plant. Source tracking was performed to identify bacterial contamination routes in pork processing. Animal samples, including the processing plant's carcass, the pig from the farm, and the unwashed carcass from the slaughterhouse (77.45 %), along with the processing plant's gloves (5.71 %), were the primary bacterial sources in the final product. The present study provides in-depth knowledge about the bacterial players and contamination points within the pork production chain. Effective control measures are needed to control pathogens and major pollutants at each stage of pork production to improve food safety.

Beef carcass microbiota after slaughtering and primary cooling: A metataxonomic assessment to infer contamination drivers

The impact of primary cooling on beef microbiota was investigated on six beef carcasses consecutively processed with the parallel use of metataxonomic and culture-dependent analysis. Samples were collected immediately after slaughtering (AS) and after the 24th-hour post-cooling (PC) from three different surfaces, namely neck, flank and thigh. The main objective was to examine whether the microbiota composition of beef carcasses changes as function of the surface sampled, primary cooling (from AS to PC) and animal's origin (breeder). The outcomes underline that primary cooling did not affect qualitatively the composition of the potentially active microbiota or the carcass superficial counts. Although slight changes in chemical-physical parameters like volatile organic compounds (VOCs) were observed after cooling, the carcasses microbiota and its inferred metabolic pathways varied among animals as a function of their origin. Co-occurrence and co-exclusion analyses underlined competition for the colonisation of the carcass surface between Brochothrix-Psychrobacter and Carnobacterium-Serratia-Pseudomonas. Once integrated in a comprehensive monitoring of the supply chain, the metataxonomic characterisation of the beef carcasses microbiota might represent a valid integrative approach to define the cuts' perishability and their appropriateness to specific packaging and storage methods. These new bits of knowledge could be the base to define good strategies for the prevention of meat spoilage.

Tracking the contamination sources of microbial population and characterizing Listeria monocytogenes in a chicken slaughterhouse by using culture-dependent and -independent methods

Listeria monocytogenes is the etiologic agent of listeriosis, a foodborne disease that poses a threat to public health globally. Chicken meat exhibits heightened susceptibility to L. monocytogenes contamination during butchery. The persistence of this pathogen in the slaughterhouse environment enables recurring contamination of meat products. This study aimed at identifying the sources and transmission routes of L. monocytogenes contamination within an abattoir where it was consistently detected for three consecutive years (2019-2021). Furthermore, the environmental factors aiding contamination along chicken processing lines were determined by surveying the microbiome within the facility. Samples collected in 2019 to 2021 were subjected to culture-dependent analysis to assess the prevalence, serotypes, and multi-locus sequence typing (MLST) of L. monocytogenes. Additionally, the specimens collected in 2021 underwent culture-independent analysis via real-time quantitative polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing to identify the contamination sources and characterize the entire microbial community within the slaughterhouse. L. monocytogenes was isolated only from the clean zone, where the final slaughtering stage occurs. Most strains isolated from the final carcasses showed the same genetic cluster as the isolate in the chilling water and were assigned to MLST profile ST3. Culture-independent qPCR confirmed L. monocytogenes contamination in all samples, excluding post-scalding carcasses, prewashed post-evisceration carcasses, and the bleeding areas. Consequently, qPCR enabled more comprehensive identification of L. monocytogenes contamination points than culture-dependent approaches. Moreover, 16S rRNA gene amplicon sequencing demonstrated that psychro-tolerant and spoilage-related bacteria with L. monocytogenes-like attributes exhibited enhanced viability in the clean zone and immersion-chilling water. Metagenomics-based source tracking analysis further revealed that the shackles and chilling waters represent predominant sources of cross-contamination between different slaughterhouse zones, whereas the grading and packaging workstations and chilling water in the clean zone were deemed crucial sources affecting final carcass contamination. Collectively, these findings demonstrate through culture-dependent and -independent methods that L. monocytogenes spreads along the slaughter line, contaminating the slaughterhouse. Moreover, by investigating changes in microbial community and bacterial flow along the slaughter line within the facility, the sources influencing carcass contamination can be effectively traced.

ROS generating BODIPY loaded nanoparticles for photodynamic eradication of biofilms

Bacterial biofilms can pose a serious health risk to humans and are less susceptible to antibiotics and disinfection than planktonic bacteria. Here, a novel method for biofilm eradication based on antimicrobial photodynamic therapy utilizing a nanoparticle in conjunction with a BODIPY derivative as photosensitizer was developed. Reactive oxygen species are generated upon illumination with visible light and lead to a strong, controllable and persistent eradication of both planktonic bacteria and biofilms. One of the biggest challenges in biofilm eradication is the penetration of the antimicrobial agent into the biofilm and its matrix. A biocompatible hydrophilic nanoparticle was utilized as a delivery system for the hydrophobic BODIPY dye and enabled its accumulation within the biofilm. This key feature of delivering the antimicrobial agent to the site of action where it is activated resulted in effective eradication of all tested biofilms. Here, 3 bacterial species that commonly form clinically relevant pathogenic biofilms were selected: Escherichia coli, Staphylococcus aureus and Streptococcus mutans. The development of this antimicrobial photodynamic therapy tool for biofilm eradication takes a promising step towards new methods for the much needed treatment of pathogenic biofilms.

A South African Perspective on the Microbiological and Chemical Quality of Meat: Plausible Public Health Implications

Meat comprises proteins, fats, vitamins, and trace elements, essential nutrients for the growth and development of the body. The increased demand for meat necessitates the use of antibiotics in intensive farming to sustain and raise productivity. However, the high water activity, the neutral pH, and the high protein content of meat create a favourable milieu for the growth and the persistence of bacteria. Meat serves as a portal for the spread of foodborne diseases. This occurs because of contamination. This review presents information on animal farming in South Africa, the microbial and chemical contamination of meat, and the consequential effects on public health. In South Africa, the sales of meat can be operated both formally and informally. Meat becomes exposed to contamination with different categories of microbes, originating from varying sources during preparation, processing, packaging, storage, and serving to consumers. Apparently, meat harbours diverse pathogenic microorganisms and antibiotic residues alongside the occurrence of drug resistance in zoonotic pathogens, due to the improper use of antibiotics during farming. Different findings obtained across the country showed variations in prevalence of bacteria and multidrug-resistant bacteria studied, which could be explained by the differences in the manufacturer practices, handling processes from producers to consumers, and the success of the hygienic measures employed during production. Furthermore, variation in the socioeconomic and political factors and differences in bacterial strains, geographical area, time, climatic factors, etc. could be responsible for the discrepancy in the level of antibiotic resistance between the provinces. Bacteria identified in meat including Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, Campylobacter spp., Salmonella spp., etc. are incriminated as pathogenic agents causing serious infections in human and their drug-resistant counterparts can cause prolonged infection plus long hospital stays, increased mortality and morbidity as well as huge socioeconomic burden and even death. Therefore, uncooked meat or improperly cooked meat consumed by the population serves as a risk to human health.

Microbial succession during button mushroom (Agaricus bisporus) production evaluated via high-throughput sequencing

Button mushrooms (Agaricus bisporus), are one of the most widely consumed mushrooms in the world. However, changes within its microbial community as it relates to the use of different raw materials and cultivation methods, as well as potential points of microbial contamination throughout the production process have not been investigated extensively. In the present study, button mushroom cultivation was investigated in each of the four stages (raw materials, composting (phase I, Ⅱ, and Ⅲ), casing, and harvesting), and samples (n = 186) from mushrooms and their related environments were collected from four distinct mushroom-growing farms (A-D) in Korea. Shifts within the bacterial consortium during mushroom production were characterized with 16 S rRNA amplicon sequencing. The succession of bacterial communities on each farm was dependent on the raw material incorporated, aeration, and the farm environment. The dominant phyla of the compost stack at the four farms were Pseudomonadota (56.7%) in farm A, Pseudomonadota (43.3%) in farm B, Bacteroidota (46.0%) in farm C, and Bacillota (62.8%) in farm D. During the Phase Ⅰ, highly heat-resistant microbes, such as those from the phylum Deinococcota (0.6-65.5%) and the families Bacillaceae (1.7-36.3%), Thermaceae (0.1-65.5%), and Limnochordaceae (0.3-30.5%) greatly proliferated. The microbial diversity within compost samples exhibited a marked decline as a result of the proliferation of thermophilic bacteria. In the spawning step, there were considerable increases in Xanthomonadaceae in the pasteurized composts of farms C and D - both of which employed an aeration system. In the harvesting phase, beta diversity correlated strongly between the casing soil layer and pre-harvest mushrooms, as well as between gloves and packaged mushrooms. The results suggest that gloves may be a major source of cross-contamination for packaged mushrooms, highlighting the need for enhanced hygienic practices during the harvesting phase to ensure product safety. These findings contribute to the current understanding of the influence of environmental and adjacent microbiomes on mushroom products to benefit the mushroom industry and relevant stakeholders by ensuring quality production.

Screening, molecular identification, population diversity, and antibiotic susceptibility pattern of Actinomycetes species isolated from meat and meat products of slaughterhouses, restaurants, and meat stores of a developing country, Iran

Introduction

Actinomycetes can colonize surfaces of tools and equipment and can be transferred to meat and meat products during manufacture, processing, handling, and storage. Moreover, washing the meat does not eliminate the microorganisms; it only spreads them. As a result, these opportunistic pathogens can enter the human body and cause various infections. Therefore, the aim of the current study was to screen, identify, and determine the antibiotic susceptibility of Actinomycetes species from meat and meat products in the Markazi province of Iran.

Methods

A total of 60 meat and meat product samples, including minced meat, mutton, beef, chicken, hamburgers, and sausages, were collected from slaughterhouses, butchers, and restaurants in the Markazi province of Iran. The samples were analyzed using standard microbiological protocols for the isolation and characterization of Actinomycetes. PCR amplification of hsp65 and 16SrRNA genes and sequence analysis of 16SrRNA were used for genus and species identification. The minimum inhibitory concentrations (MICs) of antimicrobial agents were determined by the broth microdilution method and interpreted according to the CLSI guidelines.

Results

A total of 21 (35%) Actinomycetes isolates from 5 genera and 12 species were isolated from 60 samples. The most prevalent Actinomycetes were from the genus Mycobacterium, with six (28.6%) isolates (M. avium complex, M. terrae, M. smegmatis, and M. novocastrense), followed by the genus Rhodococcus with five (23.8%) isolates (R. equi and R. erythropolis), the genus Actinomyces with four (19.1%) isolates (A. ruminicola and A. viscosus), the genus Nocardia with four (19.1%) isolates (N. asiatica, N. seriolae, and N. niigatensis), and the genus Streptomyces with two (9.5%) isolates (S. albus). Chicken and sausage samples had the highest and lowest levels of contamination, with six and one isolates. Respectively, the results of drug susceptibility testing (DST) showed that all isolates were susceptible to Ofloxacin, Amikacin, Ciprofloxacin, and Levofloxacin, whereas all of them were resistant to Doxycycline and Rifampicin.

Discussion

The findings suggest that meat and meat products play an important role as a reservoir for the transmission of Actinomycetes to humans, thus causing life-threatening foodborne diseases such as gastrointestinal and cutaneous disorders. Therefore, it is essential to incorporate basic hygiene measures into the cycle of meat production to ensure food safety.

A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities

Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.

Transition of microbial contamination on the surface of carcass during the cattle slaughter process

In this study, we aimed to investigate how microbial contamination progresses on the carcass surface during the slaughter process. Cattle carcasses were tracked during a series of slaughter processes (five steps), and carcass surfaces (four parts) and equipment (nine types) were swabbed to investigate the bacterial contamination. Results showed that the outer surface (near the rear region of the flank [Top round] and [Top sirloin butt]) had significantly higher total viable counts (TVCs) than inner surface (p < 0.01) and that TVCs gradually decreased along the process. Enterobacteriaceae (EB) counts were high on the splitting saw and in top round region, and EB was detected on the inner surface of the carcasses. Furthermore, in some carcasses, Yersinia spp., Serratia spp., and Clostridium spp. present on top round and top sirloin butt immediately after skinning and remained on the carcass surface after the final process. These bacterial groups are detrimental to beef quality as they can grow in the package during cold distribution. Our results show that the skinning process is the most prone to microbial contamination, including psychrotolerant microorganisms. Moreover, this study provides information for understanding the dynamics of microbial contamination in the cattle slaughter process.

Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9 % of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.

Microbial Profiles of Meat at Different Stages of the Distribution Chain from the Abattoir to Retail Outlets

Meat has been found to be a prime vehicle for the dissemination of foodborne pathogens to humans worldwide. Microbial meat contaminants can cause food-borne diseases in humans. The threat to consumers by microbial meat contaminants necessitates the studying of meat microbial loads to prevent potential illnesses in consumers. Studies investigating the meat microbial loads in South Africa are limited. The objective of this study was to compare microbial contamination of different meat types from low-throughput (LTA) and high-throughput abattoirs (HTA) at three stages of the distribution chain from abattoir to retail outlets. Beef, pork, and mutton (n = 216) carcasses were sampled: during the loading process at the abattoirs, when off-loading at the supply points and during marketing. All samples were subjected to total bacterial count (TBC), coliform count (CC), presumptive Escherichia coli (E. coli) (PEC) and Staphylococcus aureus (S. aureus) detection. In mutton, TBC dominated at loading, CC was similar across distribution chain stages, PEC was the predominant microbial contaminant at the offloading stage at the HTA, but TBC was affected at loading, CC was similar across distribution chain stages, PEC was affected at loading, and S. aureus was affected at the display stage at the LTAs. In beef, TBC had similar levels at loading; CC and PEC dominated at the display stage for the HTAs. However, TBC was affected at the display stage; CC was similar across stages; PEC was affected at the offloading stage at the LTAs. In pork, higher contamination levels were discovered at the display stage, CC dominated at the loading stage, with PEC detected at offloading at the HTAs but TBC, CC, PEC and S. aureus were similar across stages at the LTAs. TBC, CC and PEC were affected by the storage period and meat supplier to meat shop distance whereas distance affected the TBC, CC and PEC. Meat supplier to meat shop distance negatively correlated with meat distribution chain stage but positively correlated with TBC, CC and PEC such as temperature. Temperature positively correlated with meat distribution chain stage and shop class. Meat distribution chain stage was negatively correlated with storage period, TBC, CC and PEC but positively correlated with shop class. Shop class negatively correlated with storage period, TBC, CC and PEC. Storage period positively correlated with TB, CC and PEC. TBC and meat type positively correlated with CC and PEC. CC positively correlated with PEC but negatively correlated with S. aureus such as PEC. In conclusion, mutton, pork and beef meat are susceptible to microbial contamination at distribution chain stages in abattoirs.

Thériault W, Longpré J, Thibodeau A, Hocine MN, Fravalo P. Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse

The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.

Pernicious Attitude of Microbial Biofilms in Agri-Farm Industries: Acquisitions and Challenges of Existing Antibiofilm Approaches

Biofilm is a complex matrix made up of extracellular polysaccharides, DNA, and proteins that protect bacteria against physical, chemical, and biological stresses and allow them to survive in harsh environments. Safe and healthy foods are mandatory for saving lives. However, foods can be contaminated by pathogenic microorganisms at any stage from farm to fork. The contaminated foods allow pathogenic microorganisms to form biofilms and convert the foods into stigmatized poison for consumers. Biofilm formation by pathogenic microorganisms in agri-farm industries is still poorly understood and intricate to control. In biofilms, pathogenic bacteria are dwelling in a complex manner and share their genetic and physicochemical properties making them resistant to common antimicrobial agents. Therefore, finding the appropriate antibiofilm approaches is necessary to inhibit and eradicate the mature biofilms from foods and food processing surfaces. Advanced studies have already established several emerging antibiofilm approaches including plant- and microbe-derived biological agents, and they proved their efficacy against a broad-spectrum of foodborne pathogens. This review investigates the pathogenic biofilm-associated problems in agri-farm industries, potential remedies, and finding the solution to overcome the current challenges of antibiofilm approaches.

Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting

Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.

Distribution and Characterization of Antimicrobial Resistant Pathogens in a Pig Farm, Slaughterhouse, Meat Processing Plant, and in Retail Stores

The emergence of antibiotic resistance in foodborne pathogens isolated from meat pro-ducts and their producing environment has been an increasing and leading threat to public health. The aim of the study was to identify pathogens and their antimicrobial resistance isolated from pig production to pork meat distribution phases. Through this study, food spoilage and foodborne or clinical pathogenic bacteria were isolated and identified from pork (belly and neck) meat product and its related environmental samples that include pig swabs, diets, feces, liquid manure, workers’ gloves, dust fan swabs, carcass swabs, floor swabs, and drain water in the affiliated farm, slaughterhouse, meat processing plant, and in retail stores. All carcasses at the slaughterhouse and meat products at the meat processing plant were tracked from pigs at a targeted farm. Nine different selective media agars were used to effectively isolate various pathogenic bacteria. A total of 283 presumptive pathogenic bacteria isolated from 126 samples were selected and identified using MALDI-ToF MS. Twenty-three important foodborne pathogens were identified, and some of them, Shiga-toxin-producing E. coli (STEC), Listeria monocytogenes, Staphylococcus aureus, and Yersinia enterocolitica, were further confirmed using PCR. The PFGE patterns of 12 STEC isolates were grouped by sample source or site. All the foodborne pathogens used in the study were not resistant to amoxicillin/clavulanate, ciprofloxacin, and gentamicin, whereas some of the STEC, L. monocytogenes, and S. aureus isolates were resistant to various antibiotics, including ampicillin, erythromycin, tetracycline, and vancomycin. The most common antimicrobial resistance pattern in the pathogenic STEC isolates was AMP-KAN-STR-SXT-TET. Consequently, this study provides valuable information for the distribution of antimicrobial-resistant pathogens along the pork meat production chain and can assist farmers and stakeholders to develop a systematic strategy for reducing the current emergence and spread of antimicrobial resistance in the different phases of pig production and distribution.

A Pilot Study: the Development of a Facility-Associated Microbiome and Its Association with the Presence of Listeria Spp. in One Small Meat Processing Facility

Microbial communities which persist in food processing facilities may have a detrimental impact on food safety and spoilage. In meat processing, Listeria monocytogenes is an organism of concern due to its ability to cause significant human illnesses and persist in refrigerated environments. The microbial ecology of Listeria spp. in small meat processing facilities has not been well characterized. Therefore, we collected samples from a newly constructed meat processing facility as an opportunity to investigate several research objectives: (i) to determine whether a stable, consistent microbiome develops in a small meat processing facility during the first 18 months of operation, (ii) to evaluate the environmental factors that drive microbial community formation, and (iii) to elucidate the relationship between microbial communities and the presence of Listeria species. We evaluated microbiomes using 16S rRNA gene sequencing and Listeria presence using quantitative PCR. We demonstrated that microbial communities differentiate by the functional room type, which is representative of several environmental differences such as temperature, sources of microbes, and activity. Temperature was an especially important factor; in rooms with low temperatures, communities were dominated by psychotrophs, especially Pseudomonas, while warmer rooms supported greater diversity. A stable core community formed in facility drains, indicating that mechanisms which cause persistence are present in the communities. The overall presence of Listeria in the facility was low but could be tied to specific organisms within a room, and the species of Listeria could be stratified by room function. IMPORTANCE This study provides critical knowledge to improve meat safety and quality from small meat processing facilities. Principally, it demonstrates the importance of facility design and room condition to the development of important microbial communities; temperature, sanitation regimen, and physical barriers all influence the ability of microorganisms to join the stable core community. It also demonstrates a relationship between the microbial community and Listeria presence in the facility, showing the importance of managing facility sanitation plans for not only pathogens, but also the general facility microbiome.

A Family of 2D-MXenes: Synthesis, Properties, and Gas Sensing Applications

Gas sensors, capable of detecting and monitoring trace amounts of gas molecules or volatile organic compounds (VOCs), are in great demand for numerous applications including diagnosing diseases through breath analysis, environmental and personal safety, food and agriculture, and other fields. The continuous emergence of new materials is one of the driving forces for the development of gas sensors. Recently, 2D materials have been gaining huge attention for gas sensing applications, owing to their superior electrical, optical, and mechanical characteristics. Especially for 2D MXenes, high specific area and their rich surface functionalities with tunable electronic structure make them compelling for sensing applications. This Review discusses the latest advancements in the 2D MXenes for gas sensing applications. It starts by briefly explaining the family of MXenes, their synthesis methods, and delamination procedures. Subsequently, it outlines the properties of MXenes. Then it describes the theoretical and experimental aspects of the MXenes-based gas sensors. Discussion is also extended to the relation between sensing performance and the structure, electronic properties, and surface chemistry. Moreover, it highlights the promising potential of these materials in the current gas sensing applications and finally it concludes with the limitations, challenges, and future prospects of 2D MXenes in gas sensing applications.

Temporal variation of antibiotic resistome and pathogens in food waste during short-term storage

The massive food wastes pose a growing health concern for spreading of antibiotic resistance and pathogens due to food spoilage. However, little is known about these microbial hazards during collection, classification, and transportation before eventual treatment. Here, we profiled the temporal variations of antibiotic resistance genes (ARGs), pathogens, bacterial and fungal communities across four typical food wastes (vegetable, fish, meat, and rice) during storage at room temperature in summer (maximum 28-29 °C) of typical southeast city in China. A total of 171 ARGs and 32 mobile genetic elements were detected, and the absolute abundance of ARGs significantly increased by up to 126-fold with the storage time. Additionally, five bacterial pathogens containing virulence factor genes were detected, and Klebsiella pneumoniae was persistently detected throughout the storage time in all food types except rice. Moreover, fungal pathogens (e.g., Aspergillus, Penicillium, and Fusarium) were also frequently detected. Notably, animal food wastes were demonstrated to harbor higher abundance of ARGs and more types of pathogens, indicating a higher level of hazard. Mobile genetic elements and food types were demonstrated to mainly impact ARG profiles and pathogens, respectively. This work provides a comprehensive understanding of the microbial hazards associated with food waste recycling, and will contribute to optimize the food waste management to ensure biosecurity and benefit human health.

Microbiome Research as an Effective Driver of Success Stories in Agrifood Systems – A Selection of Case Studies

Increasing knowledge of the microbiome has led to significant advancements in the agrifood system. Case studies based on microbiome applications have been reported worldwide and, in this review, we have selected 14 success stories that showcase the importance of microbiome research in advancing the agrifood system. The selected case studies describe products, methodologies, applications, tools, and processes that created an economic and societal impact. Additionally, they cover a broad range of fields within the agrifood chain: the management of diseases and putative pathogens; the use of microorganism as soil fertilizers and plant strengtheners; the investigation of the microbial dynamics occurring during food fermentation; the presence of microorganisms and/or genes associated with hazards for animal and human health (e.g., mycotoxins, spoilage agents, or pathogens) in feeds, foods, and their processing environments; applications to improve HACCP systems; and the identification of novel probiotics and prebiotics to improve the animal gut microbiome or to prevent chronic non-communicable diseases in humans (e.g., obesity complications). The microbiomes of soil, plants, and animals are pivotal for ensuring human and environmental health and this review highlights the impact that microbiome applications have with this regard.

Comparative Study of Different Sampling Methods of Biofilm Formed on Stainless-Steel Surfaces in a CDC Biofilm Reactor

The formation of biofilms in dairy processing plants can reduce equipment efficiency, contribute to surface deterioration, and contaminate dairy products by releasing the microorganisms they contain, which may cause spoilage or disease. However, a more representative identification of microbial communities and physico-chemical characterization requires to detach and recover adequately the entire biofilm from the surface. The aim of this study is to develop an efficient technique for in-plant biofilm sampling by growing a strain of Pseudomonas azotoformans PFl1A on stainless-steel surface in a dynamic CDC biofilm reactor system using tryptic soy broth (TSB) and milk as growth media. Different techniques, namely, swabbing, scraping, sonic brushing, synthetic sponge, and sonicating synthetic sponge were used and the results were compared to a standard ASTM International method using ultrasonication. Their efficiencies were evaluated by cells enumeration and scanning electron microscopy. The maximum total viable counts of 8.65 ± 0.06, 8.75 ± 0.08, and 8.71 ± 0.09 log CFU/cm2 were obtained in TSB medium using scraping, synthetic sponge, and sonicating synthetic sponge, respectively, which showed no statistically significant differences with the standard method, ultrasonication (8.74 ± 0.02 log CFU/cm2). However, a significantly (p &lt; 0.05) lower cell recovery of 8.57 ± 0.10 and 8.60 ± 0.00 log CFU/cm2 compared to ultrasonication were achieved for swabbing and sonic brushing, respectively. Furthermore, scanning electron microscopy showed an effective removal of biofilms by sonic brushing, synthetic sponge, and sonicating synthetic sponge; However, only the latter two methods guaranteed a superior release of bacterial biofilm into suspension. Nevertheless, a combination of sonication and synthetic sponge ensured dislodging of sessile cells from surface crevices. The results suggest that a sonicating synthetic sponge could be a promising method for biofilm recovery in processing plants, which can be practically used in the dairy industries as an alternative to ultrasonication.

Similar Carcass Surface Microbiota Observed Following Primary Processing of Different Pig Batches

Bacterial contamination during meat processing is a concern for both food safety and for the shelf life of pork meat products. The gut microbiota of meat-producing animals is one of the most important sources of surface contamination of processed carcasses. This microbiota is recognized to vary between pigs from different farms and could thus be reflected on the bacterial contamination of carcasses at time of processing. In this study, the microbiota of 26 carcasses of pigs originating from different farms (i.e., batches) were compared to determine if an association could be observed between carcass surface microbiota (top and bottom) and the origin of slaughtered animals. The microbiota of the top and bottom carcass surface areas was analyzed by culturing classical indicator microorganisms (mesophilic aerobic bacteria, Enterobacteria, Escherichia coli, Pseudomonas, and lactic bacteria), by the detection of Salmonella, and by 16S rRNA gene sequencing. Culture results showed higher Enterobacteria, E. coli, and lactic bacteria counts for the bottom areas of the carcasses (neck/chest/shoulder) when compared to the top areas. Salmonella was not detected in any samples. Globally, 16S rRNA gene sequencing showed a similar composition and diversity between the top and bottom carcass areas. Despite the presence of some genera associated with fecal contamination such as Terrisporobacter, Escherichia-Shigella, Turicibacter, Clostridium sensustricto1, and Streptococcus on the carcass surface, sequencing analysis suggested that there was no difference between the different batches of samples from the top and bottom areas of the carcasses. The primary processing therefore appears to cause a uniformization of the carcass global surface microbiota, with some specific bacteria being different depending on the carcass area sampled.

Microbial Community Analysis and Food Safety Practice Survey-Based Hazard Identification and Risk Assessment for Controlled Environment Hydroponic/Aquaponic Farming Systems

Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans.