The changing microbiome of poultry meat; from farm to fridge

Illumina MiSeq 16S rRNA Gene Library Preparation for Poultry Processing Microbiome Analyses

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, *a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety.This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.

Unraveling the spoilage characteristics of refrigerated pork using high-throughput sequencing coupled with UHPLC-MS/MS-based non-targeted metabolomics

The spoilage of refrigerated pork involves nutrient depletion and the production of spoilage metabolites by spoilage bacteria, yet the microbe-metabolite interactions during this process remain unclear. This study employed 16S rRNA high-throughput sequencing and non-targeted metabolomics based on ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) to reveal the core microbiota and metabolite profiles of pork during refrigeration. A total of 45 potential biomarkers were screened through random forest model analysis. Metabolic pathway analysis indicated that eleven pathways, including biogenic amine metabolism, pentose metabolism, purine metabolism, pyrimidine metabolism, phospholipid metabolism, and fatty acid degradation, were potential mechanisms of pork spoilage. Correlation analysis revealed nine metabolites-histamine, tyramine, tryptamine, D-gluconic acid, UDP-d-glucose, xanthine, glutamine, phosphatidylcholine, and hexadecanoic acid-as spoilage biomarkers, with Pseudomonas, Serratia, and Photobacterium playing significant roles. This study provides new insights into the changes in microbial and metabolic characteristics during the spoilage of refrigerated pork.

Added insult to injury? The response of meat-associated pathogens to proposed antimicrobial interventions

Modern requirements for 'green label' meat products have led to the design of novel antimicrobial innovations which prioritise quality, safety and longevity. Plasma-functionalised water (PFW), ultraviolet light and natural antimicrobial compositions have been investigated and optimised for control of foodborne pathogens like Campylobacter jejuni and Salmonella enterica serovar Typhimurium. However, given the adaptive mechanisms present in bacteria under external stresses, it is imperative to understand the effect that sublethal treatment may have on the bacterial transcriptome. In this study, Salmonella Typhimurium and C. jejuni were treated with sublethal doses of ultraviolet light, a citrus juice/essential oil marinade, and 'spark' or 'glow' cold plasma generation system-produced PFW. Immediately after treatment, cells were lysed and RNA was extracted and purified. mRNA was converted to cDNA by reverse transcription-PCR and sequenced by an Illumina MiSeq® system. Sequences were filtered and analysed using the Tuxedo workflow. Sublethal treatment of Campylobacter jejuni and Salmonella Typhimurium led to increased immediate cellular and metabolic activity, as well as diversification in protein and metabolic functioning. There was further expression of pathogenesis and virulence-associated traits associated with spark PFW and marinade treatment of Salmonella Typhimurium. However, similar concerns were not raised with glow PFW or UV-treated samples. This study provides science-based evidence of the efficacy of multi-hurdle antimicrobial system using green-label marinades and PFW or UV to inactivate pathogens without upregulating virulence traits in surviving cells. This study will inform policymakers and food industry stakeholders and reinforces the need to incorporate in-line novel technologies to ensure consumer safety. KEY POINTS: • Salmonella and C. jejuni showed increased cell activity in immediate response to stress. • Virulence genes showed increased expression when treated with natural antimicrobials and sPFW. • Reduced immediate transcriptomic response to gPFW and UV treatment indicates lower risk.

Dynamics of microbiome and resistome in a poultry burger processing line

Traditionally, surveillance programs for food products and food processing environments have focused on targeted pathogens and resistance genes. Recent advances in high throughput sequencing allow for more comprehensive and untargeted monitoring. This study assessed the microbiome and resistome in a poultry burger processing line using culturing techniques and whole metagenomic sequencing (WMS). Samples included meat, burgers, and expired burgers, and different work surfaces. Microbiome analysis revealed spoilage microorganisms as the main microbiota, with substantial shifts observed during the shelf-life period. Core microbiota of meat and burgers included Pseudomonas spp., Psychrobacter spp., Shewanella spp. and Brochothrix spp., while expired burgers were dominated by Latilactobacillus spp. and Leuconostoc spp. Cleaning and disinfection (C&D) procedures altered the microbial composition of work surfaces, which still harbored Hafnia spp. and Acinetobacter spp. after C&D. Resistome analysis showed a low overall abundance of resistance genes, suggesting that effective interventions during processing may mitigate their transmission. However, biocide resistance genes were frequently found, indicating potential biofilm formation or inefficient C&D protocols. This study demonstrates the utility of combining culturing techniques and WMS for comprehensive of the microbiome and resistome characterization in food processing lines.

Microbiological and physicochemical evaluation of chicken cuts submitted to peracetic acid application during the slaughter

Large-scale poultry slaughter is a highly automated process, which makes cross-contamination possible during the process due to failures in the cleaning and maintenance of automatic equipment, line speed, among other control parameters. To this end, using organic acids to decontaminate poultry meat is a unique strategy for reducing foodborne illnesses. Given the above, this work investigated the application of peracetic acid (PAA) in chicken breast and thigh cuts, to (a) evaluate the effectiveness of PAA as an antimicrobial against Enterobacteriaceae and aerobic mesophilic count (b) evaluate the impact of PAA on the color, texture and cooking loss of skinless chicken breast and chicken thighs with skin. Through the Central Composite Rotational Design (CCRD) with 11 trials and 3 replicates of the central point, the best conditions variable's concentration and time of application of PAA in the cuts were determined. In cuts treated with 1500 PAA solution, a reduction of 2.90 for Enterobacteriaceae in chicken breast was possible with conditions in the central point region and a reduction of 3.65 for Enterobacteriaceae in chicken thigh, when concentrations above 1800 ppm were applied. Peracetic acid (PAA) did not influence the physicochemical characteristics of chicken meat, since it did not change the appearance of fresh meat evaluated by objective analyses (color, texture, and cooking loss), which could impact consumer preference and acceptability.

Characterization of the prevalence of Salmonella in different retail chicken supply modes using genome-wide and machine-learning analyses

Salmonella is a foodborne pathogen that causes salmonellosis, of which retail chicken meat is a major source. However, the prevalence of Salmonella in different retail chicken supply modes and the threat posed to consumers remains unclear. The prevalence, serotype distribution, antibiotic resistance, and genomic characteristics of Salmonella in three supply modes of retail chicken (live poultry, frozen, and chilled) were investigated using whole-genome sequencing (WGS) and machine learning (ML). In this study, 480 retail chicken samples from live poultry, frozen, and chilled supply modes in Guangzhou from 2020 to 2021, as well as 253 Salmonella isolates (total isolation rate = 53.1 %), were collected. The prevalence of isolates in the live poultry mode (67.5 %, 81/120) was statistically higher than in the frozen (50.0 %, 120/240) and chilled (43.3 %, 52/120) (P < 0.05) modes. Serotype identification showed significant differences in the serotype distribution of Salmonella in different supply modes. S. Enteritis (46.7 %) and S. Indiana (14.2 %) were predominant in the frozen mode. S. Agona (23.5 %) and S. Saintpaul (13.6 %) were predominant in live poultry, while S. Enteritis (40.4 %) and S. Kentucky (17.3 %) were predominant in chilled mode. Antibiotic testing showed that frozen mode isolates were more resistant; the multidrug-resistant (MDR) rate of isolates in the frozen mode reached 91.8 %, significantly higher than in the chilled (86.5 %) and live (74.1 %) (P < 0.05) modes. WGS was performed on 155 top serotypes (S. Enteritidis, S. Kentucky, S. Indiana, and S. Agona). The antibiotic resistance gene analysis showed that the abundance and carrying rate of antibiotic resistance genes of Salmonella in the frozen mode (54 types, 16.1 %) were significantly higher than in other modes (live poultry: 36 types, 9.4 %, P < 0.05; chilled: 31 types, 11.6 %). The blaNDM-1 and blaNDM-9 genes encoding carbapenem resistance were found in frozen mode isolates on a complex transposon consisting of TnAS3-IS26. Virulence factors and plasmid replicons were abundant in the studied frozen mode isolates. In addition, single nucleotide polymorphism (SNP) phylogenetic tree results showed that in the frozen supply mode, the S. Enteritidis clonal clade continued to contaminate retail chicken meat and was homologous to S. Enteritidis strains found in farm chicken embryos, slaughterhouse chicken carcasses, and patients from hospitals in China (SNP 0 = 10). Notably, the pan-genome-based ML model showed that characteristic genes in frozen and live poultry isolates differed. The narZ gene was a key characteristic gene in frozen isolates, encoding nitrate reductase, relating to anaerobic bacterial growth. The ydgJ gene is a key characteristic gene in the live mode and encodes an oxidoreductase related to oxidative function in bacteria. The high prevalence of live poultry mode Salmonella and the transmission of frozen mode MDR Salmonella in this study pose serious risks to food safety and public health, emphasizing the importance of improving disinfection and cold storage measures to reduce Salmonella contamination and transmission. In conclusion, the continued surveillance of Salmonella across different supply models and the development of an epidemiological surveillance system based on WGS is necessary.

A Microbiological and Sensory Evaluation of Modified Atmosphere-Packed (MAP) Chicken at Use-By Date and Beyond

Consumers are responsible for a large proportion of food waste, and food that has reached its use-by or best-before date is often discarded, even if edible. In this study on fresh chicken, the suitability of use-by dates currently used in the EU was evaluated by using microbial and sensory analyses. This was carried out by analyzing bacterial populations of chicken breast fillets (M. pectoralis major) at three different time points (use-by date, 2 days past use-by date, 4 days past use-by date) and two different storage temperatures (4 °C, 8 °C). A discrimination triangle test was performed to check for sensory differences between chicken breast fillets cooked at the three selected time points for both storage temperatures. A consumer preference test was also performed for chicken breast fillets that had been stored at the highest recommended temperature (4 °C) and after being cooked at the three time points. Changes in populations of total aerobic count (TAC), Enterobacteriaceae (EB), and lactic acid bacteria (LAB) were recorded over time. Despite large differences in bacterial counts at the selected time points, with TAC populations of approximately 6.5 and 8.0 log CFU/g at use-by date and four days after use-by date, respectively, storage for two or four extra days had no significant effect on the sensory parameters of cooked chicken compared with chicken consumed at its use-by date. Since the TAC populations were close to or above levels that are associated with spoilage, more work is needed to explore if shelf life can be extended.

Binding activity and specificity of tail fiber protein 35Q for Salmonella pullorum

Salmonella, a prevalent pathogen with significant implications for the poultry industry and food safety, presents a global public health concern. The rise in antibiotic resistance has exacerbated the challenge of prevention. Accurate and sensitive detection methods are essential in combating Salmonella infections. Bacteriophages, viruses capable of targeting and destroying bacteria, leverage their host specificity for accurate microbial detection. Notably, the tail fiber protein of bacteriophages plays a crucial role in recognizing specific hosts, making it a valuable tool for targeted microbial detection. This study focused on the tail fiber protein 35Q of Salmonella pullorum (SP) bacteriophage YSP2, identified through protein sequencing and genome analysis. Bioinformatics analysis revealed similarities between 35Q and other Salmonella bacteriophage tail fiber proteins. The protein was successfully expressed and purified using an Escherichia coli expression system, and its binding activity and specificity were confirmed. ELISA assays and adsorption experiments demonstrated that 35Q interacts with the outer membrane protein (OMP) receptor on bacterial surfaces. This investigation provides valuable insights for targeted Salmonella detection, informs the development of specific therapeutics, and enhances our understanding of the interaction between Salmonella bacteriophages and their hosts.

Microbial contamination pathways in a poultry abattoir provided clues on the distribution and persistence of Arcobacter spp

The consumption of contaminated poultry meat is a significant threat for public health, as it implicates in foodborne pathogen infections, such as those caused by Arcobacter. The mitigation of clinical cases requires the understanding of contamination pathways in each food process and the characterization of resident microbiota in the productive environments, so that targeted sanitizing procedures can be effectively implemented. Nowadays these investigations can benefit from the complementary and thoughtful use of culture- and omics-based analyses, although their application in situ is still limited. Therefore, the 16S-rRNA gene-based sequencing of total DNA and the targeted isolation of Arcobacter spp. through enrichment were performed to reconstruct the environmental contamination pathways within a poultry abattoir, as well as the dynamics and distribution of this emerging pathogen. To that scope, broiler's neck skin and caeca have been sampled during processing, while environmental swabs were collected from surfaces after cleaning and sanitizing. Metataxonomic survey highlighted a negligible impact of fecal contamination and a major role of broiler's skin in determining the composition of the resident abattoir microbiota. The introduction of Arcobacter spp. in the environment was mainly conveyed by this source rather than the intestinal content. Arcobacter butzleri represented one of the most abundant species and was extensively detected in the abattoir by both metataxonomic and enrichment methods, showing higher prevalence than other more thermophilic Campylobacterota. In particular, Arcobacter spp. was recovered viable in the plucking sector with high frequency, despite the adequacy of the sanitizing procedure.IMPORTANCEOur findings have emphasized the persistence of Arcobacter spp. in a modern poultry abattoir and its establishment as part of the resident microbiota in specific environmental niches. Although the responses provided here are not conclusive for the identification of the primary source of contamination, this biogeographic assessment underscores the importance of monitoring Arcobacter spp. from the early stages of the production chain with the integrative support of metataxonomic analysis. Through such combined detection approaches, the presence of this pathogen could be soon regarded as hallmark indicator of food safety and quality in poultry slaughtering.

Status quo: Levels of Campylobacter spp. and hygiene indicators in German slaughterhouses for broiler and turkey

Poultry is a common reservoir for Campylobacter and a main source for human campylobacteriosis. With broiler being the predominant poultry for food production, most food safety related research is conducted for this species, for turkey, few studies are available. Although animals are typically colonized at the farm level, the slaughtering process is considered an important factor in re- and cross-contamination. We examined the development of Campylobacter, E. coli and total colony counts (TCC) after several processing steps in three broiler and one turkey slaughterhouses. Whole carcass rinsing and neck skin sampling was applied for broilers resulting in 486 samples in total, while 126 neck skin samples were collected for turkeys. A decrease in the loads of the different bacterial groups along the broiler slaughtering process was observed. Campylobacter mean counts dropped from 4.5 ± 1.7 log10 CFU/ml after killing to 1.6 ± 0.4 log10 CFU/ml after chilling. However, an increase in Campylobacter counts was evident after evisceration before the values again decreased by the final processing step. Although the Campylobacter prevalence in the turkey samples showed a similar development, the bacterial loads were much lower with 1.7 ± 0.3 log10 CFU/g after killing and 1.7 ± 0.4 log10 CFU/g after chilling compared to those of broilers. The loads of E. coli and total colony count of turkey were higher after killing, were reduced by scalding and remained stable until after chilling. This study highlights trends during the slaughtering process in reducing the levels of Campylobacter, E. coli, and total colony counts for broiler and turkey carcasses, from the initial step to after chilling. These results contribute to our understanding of microbial dynamics during meat processing.

Prokaryotic and eukaryotic dual-expression plasmid-mediated delivery of Campylobacter jejuni antigens by live-attenuated Salmonella: A strategy for concurrent Th1 and Th2 immune activation and protection in chickens

Salmonella and Campylobacter are food-borne pathogens that significantly affect poultry production and are transmitted to humans. Long-term protection against these pathogens in chicken relies on a balanced Th1 and Th2 response. C. jejuni antigens were screened and a fusion antigen, including CadF + FlaA adhesin and flagellin antigenic fragments was developed and safely delivered by low-endotoxicity S. Typhimurium through pJHL270, a dual-expression plasmid featuring prokaryotic (Ptrc) and eukaryotic (CMV) promoters. Antigen expression in Salmonella and host cells was confirmed by western blotting and IFA. The vaccine construct JOL2999, triggered significant increases in IgY, IgA antibodies, CD4+ and CD8+ T cells, indicating humoral, mucosal, and cell-mediated responses against both pathogens. Elevations in pro-inflammatory cytokines TNFα, INF-γ, IL-2, and IL-4 and MHC I and II cell populations further suggest simultaneous Th1 and Th2 immune activation. Reduced pathogen load and histopathological inflammatory signs in vital organs upon challenge confirmed the protective efficacy in chickens.

Low temperatures do not impair the bacterial plasmid conjugation on poultry meat

Conjugation plays an important role in the dissemination of antimicrobial resistance genes. Besides, this process is influenced by many biotic and abiotic factors, especially temperature. This study aimed to investigate the effect of different conditions of temperature and storage (time and recipient) of poultry meat, intended for the final consumer, affect the plasmid transfer between pathogenic (harboring the IncB/O-plasmid) and non-pathogenic Escherichia coli organisms. The determination of minimal inhibitory concentrations (MIC) of ampicillin, cephalexin, cefotaxime, and ceftazidime was performed before and after the conjugation assay. It was possible to recover transconjugants in the poultry meat at all the treatments, also these bacteria showed a significant increase of the MIC for all antimicrobials tested. Our results show that a non-pathogenic E. coli can acquire an IncB/O-plasmid through a conjugation process in poultry meat, even stored at low temperatures. Once acquired, the resistance genes endanger public health especially when it is about critically and highly important antimicrobials to human medicine.

Addressing Current Challenges in Poultry Meat Safety: Development of a Cultivation and Colony Hybridization Approach to Recover Enterotoxigenic Clostridium perfringens from Broiler Chicken Carcasses

Enterotoxigenic Clostridium perfringens is one of the main causes of foodborne illness in Canada. The use of a conventional bacterial culture approach to isolate enterotoxigenic C. perfringens from poultry meat is common. This approach is based on the phenotype attributable to a double hemolysis phenomenon, whereas few enterotoxigenic strains of C. perfringens produce it, which further complicates the study of the reservoirs of this important pathogen. The objectives of the current study were to validate the ability of a digoxigenin-labeled probe to detect the C. perfringens cpe gene and to validate the use of either a filtration or a direct plating approach, combined with colony hybridization to detect enterotoxigenic C. perfringens. Pure DNA and pure colonies of enterotoxigenic C. perfringens and broiler chicken carcass rinsate samples were subjected to colony hybridization. The results showed that the synthesized DNA probe can detect the cpe gene from both DNA and pure colonies of enterotoxigenic C. perfringens, and from colonies grown from carcass rinsates artificially contaminated with enterotoxigenic C. perfringens. Our study suggests that this isolation method is a promising tool for a better understanding of the epidemiology of this zoonotic pathogen.

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China

Salmonella, especially antimicrobial resistant strains, remains one of the leading causes of foodborne bacterial disease. Retail chicken is a major source of human salmonellosis. Here, we investigated the prevalence, antimicrobial resistance (AMR), and genomic characteristics of Salmonella in 88 out of 360 (24.4%) chilled chicken carcasses, together with 86 Salmonella from humans with diarrhea in Qingdao, China in 2020. The most common serotypes were Enteritidis and Typhimurium (including the serotype I 4,[5],12:i:-) among Salmonella from both chicken and humans. The sequence types were consistent with serotypes, with ST11, ST34 and ST19 the most dominantly identified. Resistance to nalidixic acid, ampicillin, tetracycline and chloramphenicol were the top four detected in Salmonella from both chicken and human sources. High multi-drug resistance (MDR) and resistance to third-generation cephalosporins resistance were found in Salmonella from chicken (53.4%) and humans (75.6%). In total, 149 of 174 (85.6%) Salmonella isolates could be categorized into 60 known SNP clusters, with 8 SNP clusters detected in both sources. Furthermore, high prevalence of plasmid replicons and prophages were observed among the studied isolates. A total of 79 antimicrobial resistant genes (ARGs) were found, with aac(6')-Iaa, blaTEM-1B, tet(A), aph(6)-Id, aph(3″)-Ib, sul2, floR and qnrS1 being the dominant ARGs. Moreover, nine CTX-M-type ESBL genes and the genes blaNMD-1, mcr-1.1, and mcr-9.1 were detected. The high incidence of MDR Salmonella, especially possessing lots of mobile genetic elements (MGEs) in this study posed a severe risk to food safety and public health, highlighting the importance of improving food hygiene measures to reduce the contamination and transmission of this bacterium. Overall, it is essential to continue monitoring the Salmonella serotypes, implement the necessary prevention and strategic control plans, and conduct an epidemiological surveillance system based on whole-genome sequencing.

The Effect of Temperature and Storage Duration on the Quality and Attributes of the Breast Meat of Hens after Their Laying Periods

The purpose of this study was to evaluate the effect of temperature (2 °C and 6 °C) and storage duration on the quality and attributes of hens' breast meat after their laying periods. The study included physicochemical characteristics (pH, drip loss, colour, shear force), microbiological quality (total Enterobacteriaceae family and Pseudomonas count), and sensory quality. Bacterial identification was performed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. The increased meat pH and drip loss was greater at 6 than 2 °C (p < 0.05). An increase in the tenderness of the meat stored at 6 °C was found as early as day 4, as well as at 2 °C on day 8 of storage (p < 0.05). On day 4 of storage, the meat was characterised by a darker colour than on the first day, but the darkening was greater at 6 °C than at 2 °C (p < 0.05). At 6 °C, on day 4 of storage, there was an increase in yellow saturation (b*) of the meat, which was higher at 6 °C than at 2 °C (p < 0.05). At 2 °C, the total bacterial count and number of Pseudomonas spp. in the meat gradually increased along with increasing storage duration, reaching 4.64 log cfu/g and 4.48 log cfu/g, respectively, on the 8th day of storage. At 6 °C, on the sixth day of storage, the total bacterial count in the meat exceeded 7 log cfu/g, considered the limit of microbiological safety. The meat stored at 2 °C had an acceptable sensory quality until the 8th day of storage. The study shows that storage at 2 °C preserves the sensory characteristics and microbiological safety of the hen meat longer at an acceptable level after the laying period. Extended storage life may be of importance to consumers and the meat industry.

The efficiency of UV light-emitting diodes (UV-LED) in decontaminating Campylobacter and Salmonella and natural microbiota in chicken breast, compared to a UV pilot-plant scale device

This study investigated the combined effect of Ultraviolet (UV) light-emitting diode (LED) technology treatment with refrigerated storage of chicken breast meat over 7 days on Campylobacter jejuni, Salmonella enterica serovar Typhimurium, total viable counts (TVC) and total Enterobacteriaceae counts (TEC). An optimised UV-LED treatment at 280 nm for 6 min decreased inoculated S. Typhimurium and C. jejuni populations by 0.6-0.64 log CFU/g, and TVC and TEC population by 1-1.2 log CFU/g in chicken samples. During a 7-day storage at 4 °C, a 0.73 log reduction in C. jejuni was achieved compared with non-treated samples. Moreover, the UV-LED effectiveness to reduce TVC and TEC during refrigerated storage was compared with a conventional UV lamp and a similar efficiency was observed. The impact of UV-LED and UV lamp devices on the microbial community composition of chicken meat during storage was further examined using 16 S rRNA gene amplicon sequencing. Although similar bacterial reductions were observed for both technologies, the microbial communities were impacted differently. Treatment with the UV conventional lamp increased the proportion of Brochothrix spp. In meat samples, whilst Photobacterium spp. Levels were reduced.

Deciphering the growth responses and genotypic diversity of bioluminescent Photobacterium phosphoreum on chicken meat during aerobic refrigerated storage

The advent of high-throughput sequencing technologies in recent years has revealed the unexpected presence of genus Photobacterium within the chicken meat spoilage ecosystem. This study was undertaken to decipher the occurrence, the growth patterns and the genotypic biodiversity of Photobacterium phosphoreum on chicken breast fillets stored aerobically at 4 °C through conventional microbiological methods and molecular techniques. Samples were periodically cultured on marine broth agar (MA; supplemented with meat extract and vancomycin) for the enumeration of presumptive bioluminescent Photobacterium spp. In total, 90 bioluminescent bacteria were recovered from the initial (time of first appearance), middle and end stages of storage. Concomitantly, 95 total psychrotrophic/psychrophilic bacteria were isolated from the same medium to assess the presence and diversity of non-luminous photobacteria. Genetic diversity between bioluminescent isolates was assessed with two PCR-based DNA fingerprinting methods, i.e. RAPD and rep-PCR. Moreover, the characterization of selected bacterial isolates at the genus and/or species level was performed by sequencing of the 16S rRNA and/or gyrB gene. Bioluminescent bacteria were scarcely encountered in fresh samples at population levels of ca. 2.0 log CFU/g, whilst total psychrotrophic/psychrophilic bacteria were found at levels of ca. 4.4 log CFU/g. As time proceeded and close to shelf-life end, bioluminescent bacteria were encountered at higher populations, and were found at levels of 5.3 and 7.0 log CFU/g in samples from the second and third batch, respectively. In the first batch their presence was occasional and at levels up to 3.9 log CFU/g. Accordingly, total psychrotrophic/psychrophilic bacteria exceeded 8.4 log CFU/g at the end of storage, suggesting the possible underestimation of bioluminescent populations following the specific cultivation conditions. Sequence analysis assigned bioluminescent isolates to Photobacterium phosphoreum, while genetic fingerprinting revealed high intra-species variability. Respectively, total psychrotrophs/psychrophiles were assigned to genera Pseudomonas, Shewanella, Psychrobacter, Acinetobacter, Vibrio and Photobacterium. Non-luminous photobacteria were not identified within the psychrotrophs/psychrophiles. Results of the present study reveal the intra- and inter-batch variability on the occurrence and growth responses of P. phosphoreum and highlight its potential role in the chicken meat spoilage consortium.

Isolation and characterization of multidrug-resistant Salmonella-specific bacteriophages and their antibacterial efficiency in chicken breast

The use of phages as biocontrol agents against antibiotic-resistant strains of Salmonella spp. is gaining attention. This study aimed to isolate lytic bacteriophages specific for multidrug-resistant Salmonella enterica serovars Typhimurium; it also evaluated the bactericidal effect of isolated phages (STP-1, STP-2, STP-3, and STP-4) from sewage sample against S. Typhimurium as host strains. Moreover, a current study evaluated the efficacy of a bacteriophage cocktail against S. Typhimurium cocktail in chicken breast meat. The 4 phages were classified under the Caudoviricetes class by morphology characterization. On host range testing, they exhibited lytic activities against S. Typhimurium, S. Enteritidis, and S. Thompson. In the stability test, the phages exhibited resistance to heat (above 70°C for 1 h) and pH (strongly alkaline for 24 h). Additionally, the phages had comparable adsorption rates (approximately 80% adsorption in under 5 min). Additionally, the latent periods ranged from 30 to 50 min, with respective burst sizes of 31, 218, 197, and 218 PFU/CFU. In vitro, bacterial challenge demonstrated that at a multiplicity of infection (MOI) of 10, each phage consistently inhibited S. Typhimurium growth at 37°C for 24 h. In the food test, the phage cocktail (MOI = 1,000) reduced S. Typhimurium in artificially contaminated chicken breast meat stored at 4°C by 0.9 and 1.2 log CFU/g after 1 and 7 d, respectively. The results point toward a promising avenue for addressing the challenge of multidrug-resistant S. Typhimurium in the food industry through the use of recently discovered phages. Notably, the exploration of phage cocktails holds significant potential for combating S. Typhimurium in chicken breast products in the times ahead.

Peracetic acid application as an antimicrobial and its residual (HEDP): a holistic approach on the technological characteristics of chicken meat

The most significant occurrence of food-borne diseases is due to Campylobacter and Salmonella contamination from chicken meat, and for this reason, strict regulations about strategies to improve the control of food pathogens are imposed by food safety authorities. Despite the efforts of poultry industry since the beginning of risk analysis and critical control point to reduce the burden of food-borne illness, technological barriers along the way are increasingly necessary to ensure safe food. The aim of this review was to carry out a scientific approach to the influence of peracetic acid (PAA) as an antimicrobial and its toxicological safety, in particular the stabilizer used in the formulation of PAA, 1-hydroxyethylidene 1,1-diphosphonic acid (HEDP), suggesting the possibility of researching the residual HEDP in meat, which would allow the approval of the PAA by the health authorities of several countries that still restrict it. This review also aims to ascertain the effectiveness of PAA, in different cuts and carcasses, by different application methods, comparing the effectiveness of this antimicrobial with other antimicrobials, and its exclusive or combined use, for the decontamination of poultry carcasses and raw parts. The literature results support the popularity of PAA as an effective intervention against pathogenic bacteria during poultry processing.

From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production

Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.

Microbial trace investigation throughout the entire chicken supply chain based on metagenomic high-throughput sequencing

As poultry possesses a high risk of contamination by various pathogens and has repeatedly been linked to foodborne outbreaks, ensuring microbiological safety throughout the chicken production chain is essential. In this study, bacterial communities in chickens and associated environments (n = 72), including feces, floors, gloves, and worktables, were trace investigated from the broiler farm, slaughterhouse, meat processing plant, and the market by amplicon sequencing of the V4 region of the 16S rRNA. The bacterial composition in live chickens along the production chain significantly changed across the stages, with distinct microbiota noted at each step. Pseudomonas, Shewanella, Acinetobacter, and Psychrobacter were dominant in the final products. Staphylococcus was abundant in live birds originally (36.83 %) but dramatically decreased after slaughter (3.07 %, 0.06 %, and 0.42 % in slaughtered, processed, and market carcasses, respectively), which may be attributed to defeathering. The proportion of Enterobacteriaceae, Acinetobacter, and Pseudomonas increased from 0.95 %, 0.03 %, and 0.04 % before slaughter to 13.57 %, 34.19 %, and 21.90 %, respectively, after slaughter, highlighting the importance of hygiene management in the succeeding steps. Diversity analysis revealed the possibility of bacterial transmission between samples from the processing plant and the market. Source tracking was performed to identify microbial contamination routes in the chicken microbiome; the major bacterial sources in the final products were the samples from the processing plant (such as processed carcasses, gloves, and worktables), accounting for 93.53 % of the total microbial sources. These results suggest that in-depth knowledge of microbial transmission between chickens and their surroundings can facilitate a precise understanding of microbiological concerns across the poultry production system and help establish safety management measures for the poultry industry.

Green label marinades: A solution to salmonella and campylobacter in chicken products?

Introduction

The presence of meat-borne pathogens entering the home remains a concern for consumers, despite advances made in improving antimicrobial interventions and systems within the processing line. Naturally antibacterial food ingredients including citrus juice and essential oils have been proven to inhibit the proliferation of microbial growth with varying success.

Aims

This study aims to investigate the antimicrobial and sensory effects of mixtures of essential oils, fruit juices and herbs at established Minimum Inhibitory Concentrations (MICs) for their biopreservative effect on general microbiota of chicken and against chicken challenged with selected pathogenic/surrogate microorganisms.

Materials and methods

Three marinade compositions were designed for use on chicken meat; lemon juice, thyme oil and black pepper (M1), lime juice, lemongrass oil and chilli paste (M2), and olive oil, oregano oil, basil oil and garlic paste (M3). These marinades were assessed for antibacterial effects against Salmonella enterica, Campylobacter jejuni and Listeria innocua on marinaded chicken drumsticks stored in aerobic conditions at 4 °C. Consumer tasting sessions were also conducted with a small focus group using selected final marinades.

Results

M1 and M2 were effective at significantly reducing initial pathogen carriage from 6 Log CFU/g to 2 Log CFU/g on refrigerated chicken meat as well as increasing the shelf-life of the product during cold-storage from 2 days to 7 days. However, consumer studies indicate that the flavours these marinades impart to treated products can be strong.

Conclusion

These findings indicate that these designed marinades have shown excellent potential to improve food safety as well as shelf-life for the consumer, particularly in settings where food safety is often compromised such as barbecuing or in care settings. However, further recipe optimisation is required to make these marinades acceptable to consumers.

Heightened variability observed in resistance and virulence genes across salmonella Kentucky isolates from poultry environments in British Columbia, Canada

Many niche-dependent barriers along the poultry production continuum favour the survival of certain Salmonella serovars over others. Historically, the presence of particular serovars has been determined by niche-specific genes which encode resistance to selective pressures such as host defenses and industrial antimicrobial practices. Over the past decade, Canada has witnessed unexplained shifts in the Salmonella landscape in the poultry sector. Several formerly minor Salmonella serovars, including S. Kentucky and S. Reading, have recently increased in prevalence in live chickens and turkeys, respectively, in British Columbia (BC). The purpose of this research was to investigate the genomic features of the top poultry-associated Salmonella spp. in BC, to probe for serovar-specific characteristics that could address the recently shifting balance of serovars along the poultry continuum. By examining the quantity and diversity of antimicrobial resistance (AMR) genes, virulence factors (VFs), Salmonella Pathogenicity Islands (SPIs), and plasmids across 50 poultry-associated S. enterica isolates using whole genome sequencing and antimicrobial resistance profiling, we have identified serovar-specific differences that likely influence niche survival. Specifically, isolates in our collection from predominantly human pathogenic serovars (S. I 4, [5], 12:i: , S. Typhimurium, and S. Enteritidis) were found to share the IncFIB(S) and IncFII(S) plasmids which carry important VFs known to aid in human host infection. Additionally, these strains held the lowest number of AMR genes, and the highest number of unique SPIs which also facilitate virulence. However, other serovars containing a greater diversity and abundance of resistance genes have been increasing across the poultry sector. S. Kentucky was found to carry unique AMR genes, VFs, SPIs, and plasmids that could bolster persistence in farm and processing environments. Overall, S. Kentucky also had comparatively high levels of intra-serovar genetic variability when compared to other prominent serovars from our collection. In addition, one of our two S. Reading isolates had high carriage of both AMR genes and VFs relative to other isolates in our collection. As the poultry-associated Salmonella landscape continues to evolve in Canada, future studies should monitor the genetic composition of prominent serovars across poultry production to maintain up-to-date risk assessments of these foodborne pathogens to consumers.

The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia

The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, and post-chill carcass rinsate were collected from a large-scale abattoir in Australia. DNA was extracted using the Wizard^® Genomic DNA Purification Kit, and the 16S rRNA v3-v4 gene region was sequenced using Illumina MiSeq. The results revealed that the Firmicutes decreased from scalding to evisceration (72.55%) and increased with chilling (23.47%), with the Proteobacteria and Bacteroidota changing inversely. A diverse bacterial community with 24 phyla and 392 genera was recovered from the post-chill chicken, with Anoxybacillus (71.84%), Megamonas (4.18%), Gallibacterium (2.14%), Unclassified Lachnospiraceae (1.87%), and Lactobacillus (1.80%) being the abundant genera. The alpha diversity increased from scalding to chilling, while the beta diversity revealed a significant separation of clusters at different processing points (p = 0.01). The alpha- and beta-diversity revealed significant contamination during the defeathering, with a redistribution of the bacteria during the chilling. This study concluded that the genetic diversity during the defeathering is strongly associated with the extent of the post-chill contamination, and may be used to indicate the microbial quality of the chicken meat.

Current and future interventions for improving poultry health and poultry food safety and security: A comprehensive review

Poultry is thriving across the globe. Chicken meat is the most preferred poultry worldwide, and its popularity is increasing. However, poultry also threatens human hygiene, especially as a fomite of infectious diseases caused by the major foodborne pathogens (Campylobacter, Salmonella, and Listeria). Preventing pathogenic bacterial biofilm is crucial in the chicken industry due to increasing food safety hazards caused by recurring contamination and the rapid degradation of meat, as well as the increased resistance of bacteria to cleaning and disinfection procedures commonly used in chicken processing plants. To address this, various innovative and promising strategies to combat bacterial resistance and biofilm are emerging to improve food safety and quality and extend shelf-life. In particular, natural compounds are attractive because of their potential antimicrobial activities. Natural compounds can also boost the immune system and improve poultry health and performance. In addition to phytochemicals, bacteriophages, nanoparticles, coatings, enzymes, and probiotics represent unique and environmentally friendly strategies in the poultry processing industry to prevent foodborne pathogens from reaching the consumer. Lactoferrin, bacteriocin, antimicrobial peptides, cell-free supernatants, and biosurfactants are also of considerable interest for their prospective application as natural antimicrobials for improving the safety of raw poultry meat. This review aims to describe the feasibility of these proposed strategies and provide an overview of recent published evidences to control microorganisms in the poultry industry, considering the human health, food safety, and economic aspects of poultry production.

Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal

The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.

16S rRNA gene-based assessment of common broiler chicken sampling methods: Evaluating intra-flock sample size, cecal pair similarity, and cloacal swab similarity to other alimentary tract locations

16S rRNA gene sequencing for characterization of microbiomes has become more common in poultry research and can be used to both answer specific research questions and help inform experimental design choices. The objective of this study was to use 16S rRNA gene sequencing to examine common sampling practices in broiler chicken studies such as: the required number of birds selected from a flock to adequately capture microbiome diversity, the differences between cecal pairs within the same bird, and whether cloacal swabs are representative of other alimentary tract (AT) locations. To do this, nine market age broilers were euthanized and immediately sampled in ten AT locations: crop, gizzard, proventriculus, duodenum, jejunum, ileum, cecal samples from each pouch, colon, and cloacal swab. DNA was extracted and subjected to 16S rRNA gene amplification and sequencing. Each location within the broiler AT hosts distinct microbial communities. When each sampling location was considered, it was found that sampling after 2.8 birds (range 2-4) resulted in less than 10% new amplicon sequencing variants (ASV) being added while sampling after 7.6 birds (range 6-10) increases new observed ASVs by less than 1%. Additionally, when cecal pairs from the same bird were evaluated, it was found that cecal pair mates are an adequate replication if interested in the total cecal microbiome but may be less useful if a rare lineage is of interest. Furthermore, when compared to other AT locations, the cecal microbiome was enriched in Firmicutes and Bacteroides while several lineages, most notably Lactobacillus, were under-represented. Finally, when cloacal swabs were compared to other AT locations, community similarity exhibited a direct distance relationship, i.e., the more aborad samples were the more similar they were to the swab. These findings indicate that while cloacal swabs can approximate overall changes in microbiome composition, they are not adequate for inferring changes to specific taxa in other parts of the AT tract-even those that are highly abundant within the microbial community. These data provide new insights guiding appropriate sample size selection within flocks and add to the consensus data regarding cecal pair similarity and destructive versus non-destructive sampling methods.

Ileal and cecal microbiota response to Salmonella Typhimurium challenge in conventional and slow-growing broilers

Despite the negative impacts of Salmonella intestinal colonization on human health, Salmonella is a natural colonizer of the gastrointestinal tract and is not overtly pathogenic to the avian host. It is of interest to understand the impacts and colonization rates of Salmonella across selected genetic lines such as slow-growing (SG) and conventional (CONV) broilers. The objective of this study was to characterize the relationship between Salmonella enterica serovar Typhimurium challenge and selected broiler genetic lines on the ileal and cecal microbiome. Male chicks of two broiler breeds (n = 156/breed) were cohoused in an open floor pen until day 7. On day 13, the chicks were then separated into 12 isolators per breed (4 rooms, 6 isolators/room, 11 chicks/isolator). On day 14, chicks in the 12 treatment isolators (6 isolators/breed, 108 total) were challenged with Salmonella Typhimurium (ST) (1 × 108 CFU/ml) via oral gavage while the remaining chicks (n = 108) were given an oral gavage of sterile tryptic soy broth control (C). Ileal and cecal contents were collected on day 7 from 24 chicks of each breed, and on days 13, 17, 21, and 24 from two chicks per isolator. Samples underwent DNA extraction and PCR amplification to obtain 16S rRNA amplicons that were sequenced with Illumina MiSeq. Salmonella Typhimurium colonization in the cecum was not different in the two broiler breeds. The main effect of breed had the greatest impact on the ileum microbiota of broilers 7 days of age where SG broilers had significantly lower diversity and richness compared to CONV broilers (p < 0.05). Salmonella Typhimurium challenge consistently caused a change in beta diversity. Regardless of day or intestinal location, challenged broilers had many amplicon sequence variants (ASVs) with decreased abundance of likely beneficial bacteria such as Mollicutes RF39, Shuttleworthia, Flavonifractor, and Oscillibacter compared to broilers that were unchallenged with Salmonella Typhimurium (p < 0.05). Additionally, there was a difference in the timing of when the microbiota alpha and beta diversity of each breed responded to Salmonella Typhimurium challenge. Thus, both broiler breed and Salmonella Typhimurium can impact the intestinal microbiota.

Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast

BACKGROUND

Sequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental artefacts. Sample handling and processing are key sources of variation that require standard approaches. Extracting sufficient quantities of high quality DNA from food matrices is challenging because target bacterial species are usually minor components of the microbiota and foods contain an array of compounds that are inhibitory to downstream DNA applications. Here, three DNA extraction methods are compared for their ability to extract high quality bacterial DNA from retail chicken breast rinses, with or without enrichment. Method performance was assessed by comparing ease of use, DNA yield, DNA quality, PCR amplicon yield, and the detection of bacterial taxa by 16S rRNA amplicon sequencing.

RESULTS

All three DNA extraction methods yielded DNA of sufficient quantity and quality to perform quantitative PCR and 16S rRNA amplicon sequencing. The extraction methods differed in ease of use, with the two commercial kits (PowerFood, PowerSoil) offering considerable time and cost savings over a hybrid method that used laboratory reagents for lysis and commercial column based kits for further purification. Bacterial richness as determined by 16S rRNA amplicon sequencing was similar across the three DNA extraction methods. However, differences were noted in the relative abundance of bacterial taxa, with significantly higher abundance of Gram-positive genera detected in the DNA samples prepared using the PowerFood DNA extraction kit.

CONCLUSION

The choice of DNA extraction method can affect the detection of bacterial taxa by 16S rRNA amplicon sequencing in chicken meat rinses. Investigators should be aware of this procedural bias and select methods that are fit for the purposes of their investigation.

Gut microbiota and meat quality

Sustainable meat production is important to providing safe and quality protein sources for humans worldwide. Intensive artificial selection and high energy input into the diet of many commercial animals for the last decade has significantly increased the daily gain of body weight and shortened the raising period, but unexpectedly decreased the meat quality. The gastrointestinal tract of animals harbors a diverse and complex microbial community that plays a vital role in the digestion and absorption of nutrients, immune system development, pathogen exclusion, and meat quality. Fatty acid composition and oxidative stress in adipose and muscle tissue influences meat quality in livestock and poultry. Recent studies showed that nutraceuticals are receiving increased attention, which could alter the intestinal microbiota and regulate the fat deposition and immunity of hosts to improve their meat quality. Understanding the microbiota composition, the functions of key bacteria, and the host-microbiota interaction is crucial for the development of knowledge-based strategies to improve both animal meat quality and host health. This paper reviews the microorganisms that affect the meat quality of livestock and poultry. A greater understanding of microbial changes that accompany beneficial dietary changes will lead to novel strategies to improve livestock and poultry meat product quality.

Microbiological Safety and Shelf-Life of Low-Salt Meat Products-A Review

Salt is widely employed in different foods, especially in meat products, due to its very diverse and extended functionality. However, the high intake of sodium chloride in human diet has been under consideration for the last years, because it is related to serious health problems. The meat-processing industry and research institutions are evaluating different strategies to overcome the elevated salt concentrations in products without a quality reduction. Several properties could be directly or indirectly affected by a sodium chloride decrease. Among them, microbial stability could be shifted towards pathogen growth, posing a serious public health threat. Nonetheless, the majority of the literature available focuses attention on the sensorial and technological challenges that salt reduction implies. Thereafter, the need to discuss the consequences for shelf-life and microbial safety should be considered. Hence, this review aims to merge all the available knowledge regarding salt reduction in meat products, providing an assessment on how to obtain low salt products that are sensorily accepted by the consumer, technologically feasible from the perspective of the industry, and, in particular, safe with respect to microbial stability.

An Outdoor Access Period Improves Chicken Cecal Microbiota and Potentially Increases Micronutrient Biosynthesis

Characterizing the gut microbiota of free-range and alternative poultry production systems provides information, which can be used to improve poultry welfare, performance, and environmental sustainability. Gut microbiota influence not only the health and metabolism of the host but also the presence of zoonotic agents contaminating food of animal origin. In this study, the composition and diversity of the cecal microbiota community of free-range grown chickens were characterized by 16S rDNA high-throughput Illumina sequencing. Significant differences were observed in the composition of chicken cecal microbiota at the time points of 28 days of age (Indoor group) and 56 days of age (Outdoor group), i.e., before and after the outdoor access period of chicken groups. The Outdoor group showed a richer and more complex microbial community, characterized by the onset of new phyla such as Deferribacterota and Synergistota, while the Indoor group showed an increase in Campylobacterota. At the species level, it is noteworthy that the occurrence of Mucispirillum schaedleri in Outdoor group is known to potentially stimulate mucus layer formation in the distal intestinal tract, thus being associated with a healthy gut. We also report a significant decrease in the Outdoor group of Helicobacter pullorum, highlighting that the lower abundance at the age of slaughter reduced the possibility to contaminate chickens' carcasses and, consequently, its zoonotic potential. As revealed by a mutual exclusion study in network analysis, H. pullorum was present only if Bacteroides barnesiae, an uncultured organism of the genus Synergistes, and Bacteroides gallinaceum were absent. Finally, microbiome predictive analysis revealed an increase of vitamins and micronutrient biosyntheses such as queuosine (Q) and its precursor pre Q0, in the Outdoor group, suggesting that the outdoor evolved microbiota of chickens do contribute to the vitamin pool of the gut and the biosynthesis of micronutrients involved in vital cell processes.

NRJ Media as the Gold-Standard Arcobacter-Specific Detection System: Applications in Poultry Testing

Arcobacter species are ubiquitous emerging pathogens with an impact that has been underestimated due to limitations in isolation and detection methods. Our group recently developed the novel NRJ Arcobacter-detection system, with major improvements in specificity and selectivity compared to other culture-based methods. In this work, the NRJ detection system was evaluated using retail whole broiler chicken carcass. Nanopore 16S rRNA gene amplicon sequencing demonstrated that Arcobacter species are found in very low abundance in retail chicken and that indigenous microbiota could be a major factor interfering with detection. Comparison of the microbiome obtained from modified Houf broth (HB) method, as the standard detection system, and the novel NRJ method, showed Arcobacter abundances of <15% and >97%, respectively. The NRJ system significantly inhibits the growth of non-target microbiota, and specifically allows the multiplication of Arcobacter species. In this report, we describe the gold-standard of Arcobacter-specific culture-based method to test food matrices, which can be used for other applications, such as clinical and environmental sampling.

Critical review and recent advances of 2D materials-Based gas sensors for food spoilage detection

Many people around the world are concerned about meat safety and quality, which has resulted in the ongoing advancement of packaged food technology. Since the emergence of graphene in 2004, the number of studies on layered two-dimensional materials (2DMs) for applications ranging from food packaging to meat quality monitoring has been expanding quickly. Recently, scientists have been working hard to develop a novel class of 2DMs that keep the good things about graphene but don't have zero bandgaps at room temperature. Much work has been done on layered transition metal dichalcogenides (TMDCs) like different metal sulfides and selenides for meat spoilage gas sensors. This review looks at (i) the main indicators of meat spoilage and (ii) the detection methods that can be used to find out if meat has been spoiled, such as chemiresistive, electrochemical, and optical methods. (iii) the role of 2DMs in meat spoilage detection and (iv) the emergence of advanced methods for selective classification of target analytes in meat/food spoilage detection in recent years. Thus, this review demonstrates the potential scope of 2DMs for developing intelligent sensor systems for food and meat spoilage detection with high viability, simplicity, cost-effectiveness, and other multipurpose tools.

A Probabilistic Structural Equation Model to Evaluate Links between Gut Microbiota and Body Weights of Chicken Fed or Not Fed Insect Larvae

Simple Summary

Feeding poultry with insects could reduce production costs, but the impact of this diet on their gut microbiota and growth is little known because the network of relationships between their weights, the composition of their microbiota and their diet is complex and potentially biased by confounding factors (such as the gut compartment, age and sex of the birds). In this study, we were able to unravel these relationships in local breed chickens fed or not fed with black soldier fly larvae thanks to a technique of artificial intelligence (the probabilistic structural equation model). Bacteria were grouped into few entities with distinctive metabolic attributes and were probably linked nutritionally. Birds’ age influenced body weights and bacterial composition. The proposed methodology was thus able to simplify the complex dependencies among bacteria present in the gut and to highlight links potentially important in the response of chicken to insect feed.

Abstract

Feeding chicken with black soldier fly larvae (BSF) may influence their rates of growth via effects on the composition of their gut microbiota. To verify this hypothesis, we aim to evaluate a probabilistic structural equation model because it can unravel the complex web of relationships that exist between the bacteria involved in digestion and evaluate whether these influence bird growth. We followed 90 chickens fed diets supplemented with 0%, 5% or 10% BSF and measured the strength of the relationship between their weight and the relative abundance of bacteria (OTU) present in their cecum or cloaca at 16, 28, 39, 67 or 73 days of age, while adjusting for potential confounding effects of their age and sex. Results showed that OTUs (62 genera) could be combined into ten latent constructs with distinctive metabolic attributes. Links were discovered between these constructs that suggest nutritional relationships. Age directly influenced weights and microbiotal composition, and three constructs indirectly influenced weights via their dependencies on age. The proposed methodology was able to simplify dependencies among OTUs into knowledgeable constructs and to highlight links potentially important to understand the role of insect feed and of microbiota in chicken growth.

The Prevalence and Epidemiology of Salmonella in Retail Raw Poultry Meat in China: A Systematic Review and Meta-Analysis

Foodborne disease caused by Salmonella is an important public health concern worldwide. Animal-based food, especially poultry meat, is the main source of human salmonellosis. The objective of this study was to evaluate the prevalence and epidemiology of Salmonella contamination in raw poultry meat commercialized in China. Following the principle of systematic review, 98 sets of prevalence data were extracted from 74 publications conducted in 21 Chinese provincial regions. The random-effect model was constructed for subgrouping analysis by meat category, preservation type, and geographical location. The prevalence levels differed from high to low among raw poultry meat, including chicken, 26.4% (95% CI: 22.4-30.8%); pigeon, 22.6% (95% CI: 18.2-27.8%); duck, 10.1% (95% CI: 5.3-18.2%); and other poultry meat, 15.4% (95% CI: 12.0-19.5%). Prevalence data on the preservation type revealed that chilled poultry meat might be more likely to experience cross-contamination than non-chilled poultry meat in China. The distribution map of Salmonella for raw poultry meat showed that a higher prevalence level was found in the Shaanxi, Henan, Sichuan, and Beijing regions. All subgroups possessed high amounts of heterogeneity (I² > 75%). The scientific data regarding the differences in prevalence levels between meat category, preservation method, and geographical region sources might be useful to improve specific interventions to effectively control the incidence of Salmonella in poultry meat.