Effect of hot water spray on broiler carcasses for reduction of loosely attached, intermediately attached, and tightly attached pathogenic (Salmonella and Campylobacter) and mesophilic aerobic bacteria

Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics

Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.

Spoilage Bacteria Counts on Broiler Meat at Different Stages of Commercial Poultry Processing Plants That Use Peracetic Acid

In poultry processing, spoilage microbes are persistent microorganisms, which affect the quality of broiler meat. Peracetic acid (PAA) is the most common antimicrobial used by commercial processing plants, which can reduce the prevalence of these microbes. The goal of this study was to determine the concentrations of aerobic bacteria, coliforms, lactic acid bacteria, and Pseudomonas on broiler meat in processing plants that use peracetic acid in various concentrations as the primary antimicrobial. Samples were collected from three processing plants at five processing steps: post-pick (defeathering), pre-chill, post-chill, mechanically deboned meat (MDM), and drumsticks. Samples were rinsed in buffered peptone water for bacteria isolation. Over six log CFU/sample of aerobic plate counts (APC), lactic acid bacteria, and coliforms were detected on post-pick samples. All spoilage bacteria were reduced to nondetectable levels on post-chill samples (p < 0.001). However, the presence of all bacteria on mechanically deboned meat (MDM) samples indicated varying degrees of cross contamination from post-chill and MDM samples. These results suggest PAA effectively reduces spoilage microbes in chilling applications irrespective of differences in PAA concentrations. However, due to the levels of spoilage microbes detected in MDM, it may be worth investigating the potential interventions for this stage of processing.

Inhibitory Activity of Natural Synergetic Antimicrobial Consortia Against Salmonella enterica on Broiler Chicken Carcasses

The currently most utilized antimicrobial agent in poultry processing facilities is peracetic acid, a chemical increasingly recognized as hazardous to human health. We evaluated the efficacy of mixtures of natural antimicrobial compounds, namely reuterin, microcin J25, and lactic acid, for reducing the viability of Salmonella enterica and total aerobes on broiler chicken carcasses. The compounds were compared singly and in combination with water and 0.1% peracetic acid. The minimum inhibitory concentrations of reuterin, lactic acid, and microcin J25 against S. enterica serovar Enteritidis were respectively 2 mM, 0.31%, and 0.03 μM. In vitro, the combinations of reuterin + lactic acid and reuterin + microcin J25 were synergic, making these compounds effective at four times lower concentrations than those used alone. Salmonella viable counts fell to zero within 10 min of contact with reuterin + lactic acid at 10 times the concentrations used in combination, compared to 18 h in the case of reuterin + microcin J25. Sprayed onto chilled chicken carcasses, this reuterin + lactic acid mixture reduced Salmonella spp. counts by 2.02 Log CFU/g, whereas reuterin + microcin J25 and peracetic acid reduced them by respectively 0.83 and 1.13 Log CFU/g. The synergy of reuterin with lactic acid or microcin J25 as inhibitors of bacterial growth was significant. Applied as post-chill spray, these mixtures could contribute to food safety by decreasing Salmonella counts on chicken carcasses.

Inhibitory effect of ethanol and thiamine dilaurylsulfate against loosely, intermediately, and tightly attached mesophilic aerobic bacteria, coliforms, and Salmonella Typhimurium in chicken skin

The effects of 3 ethanol levels (30, 50, and 70%) with and without thiamine dilaurylsulfate (TDS; 1,000 ppm) were evaluated for the reduction of natural mesophilic aerobic bacteria (MAB), coliforms, and inoculated Salmonella Typhimurium (S. Typhimurium) in chicken skin. The chicken skin was inoculated with a 7 log cfu/mL suspension of S. Typhimurium. Loosely, intermediately, and tightly attached cells were recovered from chicken skin through shaking at 200 rpm for 5 min, stomaching for 1 min, and blending for 1 min, respectively. Increasing the ethanol concentration reduced the number of MAB, coliforms, and S. Typhimurium on the chicken skin, whereas TDS treatment without ethanol was not effective. Intermediately and tightly attached microorganisms (total MAB, coliforms, and S. Typhimurium) were more resistant to chemical disinfectants than loosely attached microorganisms. The combination of 70% ethanol with TDS was most effective than the combination of TDS with lower concentrations of ethanol in reducing populations of loosely, intermediately, and tightly attached MAB (by 1.88 log cfu/g, 1.21 log cfu/g, and 0.84 log cfu/g, respectively), coliforms (by 1.14 log cfu/g, 1.04 log cfu/g, and 0.67 log cfu/g, respectively), and S. Typhimurium (by 1.62 log cfu/g, 1.72 log cfu/g, and 1.27 log cfu/g, respectively). However, the chicken skin treated with higher concentrations of ethanol was tougher (P < 0.05) and more yellow and less red (P < 0.05) than that treated with lower concentrations of ethanol or with water (control). On the other hand, a combination of 30% ethanol and TDS yielded the best results, showing the reduction greater than 0.5 log cfu/g in S. Typhimurium, with no negative effect on chicken skin color or texture. Thus, a combination of 30% ethanol and TDS appears to be the optimal treatment for reducing microbial contamination of skin-on chicken products to enhance poultry safety without decreasing food quality, and this treatment could be applied in the poultry industry.

Impact of ethanol and ultrasound treatment on mesophilic aerobic bacteria, coliforms, and Salmonella Typhimurium on chicken skin

The present study evaluated the efficacy of ethanol treatment (0, 30, 50, or 70%) alone or in combination with ultrasound (37 kHz, 380 W) for the reduction of natural indigenous mesophilic aerobic bacteria (MAB), coliforms, and inoculated Salmonella Typhimurium on chicken skin. Bacterial cells with loose, intermediate, or tight attachment to chicken skin were recovered by shaking in an incubator (200 rpm) for 5 min, stomaching for 1 min, or blending for 1 min, respectively. Chicken skins were inoculated with a suspension (7 log CFU/mL) of S. Typhimurium. Ethanol reduced the number of MAB, coliforms, and S. Typhimurium on the chicken skin in a concentration-dependent manner, whereas ultrasound treatment without ethanol was ineffective. A combination of 70% ethanol with ultrasound treatment was the most effective in reducing S. Typhimurium populations with loose, intermediate, and tight attachment (reduction by 2.86 log CFU/g, 2.49 log CFU/g, and 1.63 log CFU/g, respectively). However, chicken skin treated with 50% ethanol alone or with a combination of >50% ethanol and ultrasound showed significant changes in Hunter color values (a* and b*) and texture (shear force) (P > 0.05). On the other hand, a combination of 30% ethanol and ultrasound yielded the best results, leading to a reduction of S. Typhimurium by a >1.0 log CFU/g, but did not alter the color or texture of chicken skin. Thus, a combination of 30% ethanol and ultrasound appears to be the optimum treatment for reduction of microbial contamination in production and distribution of skin-on chicken products, and enhance poultry safety without decreasing food quality.

A ParDE-family toxin antitoxin system in major resistance plasmids of Enterobacteriaceae confers antibiotic and heat tolerance

Toxin-antitoxin (TA) systems were initially discovered as plasmid addiction systems on low-copy-number plasmids. Thousands of TA loci have since been identified on chromosomes, plasmids and mobile elements in bacteria and archaea with diverse roles in bacterial physiology and in maintenance of genetic elements. Here, we identified and characterised a plasmid mediated type II TA system in Enterobacteriaceae as a member of the ParDE super family. This system (hereafter, ParDE^I) is distributed among IncI and IncF-type antibiotic resistance and virulence plasmids found in avian and human-source Escherichia coli and Salmonella. It is found that ParDE^I is a plasmid stability and stress response module that increases tolerance of aminoglycoside, quinolone and β-lactam antibiotics in E. coli by ~100–1,000-fold, and thus to levels beyond those achievable in the course of antibiotic therapy for human infections. ParDE^I also confers a clear survival advantage at 42 °C and expression of the ParE^I toxin in trans induces the SOS response, inhibits cell division and promotes biofilm formation. This transmissible high-level antibiotic tolerance is likely to be an important factor in the success of the IncI and IncF plasmids which carry it and the important pathogens in which these are resident.

Effect of some chemical decontaminants on the survival of Listeria monocytogenes and Salmonella Typhimurium with different attachment times on chicken drumstick and breast meat

The aim of this study was to investigate the efficacy of some decontaminant agents on the survival of Salmonella Typhimurium and Listeria monocytogenes with different attachment periods to chicken drumstick with skin and skinless breast meat. For this purpose, S. Typhimurium and L. monocytogenes were given periods of 0.5 (30 s), 20 and 210 min to attach to the chicken drumstick and breast meat. At the end of the each attachment period, the meat samples were treated with lactic acid, (2 and 4%), cetylpyridinium chloride (0.5%) and acidified sodium chlorite (1200 ppm). In the drumstick sample treated with cetylpyridinium chloride, the reduction level of L. monocytogenes with 30 s attachment period was 3.2 log10 CFU/ml while the reduction level was found to be 2.2 log10 CFU/ml with 20 min attachment period. Decontamination with acidified sodium chlorite resulted in reduction of 1.8 log10 CFU/ml in S. Typhimurium attached to the chicken drumstick for 30 s while the reduction levels of S. Typhimurium with 20 and 210 min attachment periods were 1.2 and 1.3 log10 CFU/ml, respectively. The results indicated that some antimicrobial agents have more strong effect on L. monocytogenes and S. Typhimurium on the chicken meat parts in the first 30 s of attachment. However, there were no changes in the efficacy of the decontaminants on the survival of L. monocytogenes and S. Typhimurium on chicken meat when the attachment time of these bacteria were extended from 20 min to 210 min.

Antimicrobial Activities of Phenolic Extracts Derived from Seed Coats of Selected Soybean Varieties

Soybean hulls or seed coats consist of complex carbohydrates, proteins, lipids, and polyphenols such as anthocyanidins, proanthocyanidins, and isoflavones. The polyphenolics in the seed coats give them various colors such as black, brown, green, yellow, or even a mottled appearance. In this study, the antimicrobial effects of phenolic extracts from the seed coats of different colored soybeans (yellow, dark brown, brown, and black) were evaluated against foodborne pathogens such as Salmonella Typhimurium, Escherichia coli O157:H7, and Campylobacter jejuni in broth-cultures as well as on chicken skin. The highest total phenolic content was observed for the phenolic extract from soybean variety (R07-1927) with black colored seed coat (74.1 ± 2.1 mg chlorogenic acid equivalent [CAE]/g extract) and was significantly different (P <0.0001) from the extract of the conventional soybean variety (R08-4004) with yellow colored seed coat (7.4 ± 1.2 mg CAE/g extract). The extract from black colored soybean produced reductions of 2.10 ± 0.08 to 2.20 ± 0.08-log CFU/mL for both E. coli O157:H7 and C. jejuni after 3 d when incubated in broth-culture having 4-log CFU/mL of bacteria, whereas a 6 d incubation was found to reduce S. Typhimurium and E. coli O157:H7 at 2.03 ± 0.05 and 3.3 ± 0.08-log CFU/mL, respectively. The extract also reduced S. Typhimurium and E. coli O157:H7 attached to chicken skin by 1.39 ± 0.03 and 1.24 ± 0.06-log CFU/g, respectively, upon incubation for 6 d. Soybean seed coat extracts may have a potency as antimicrobial agents to reduce foodborne bacteria contaminating poultry products.

Heat Survival and Phenotype Microarray Profiling of Salmonella Typhimurium Mutants

Contamination of food products by pathogenic microorganisms continues to be a major public health and food industry concern. Non-typhoidal Salmonella species have led to numerous outbreaks associated with various foods. A wide variety of methods have been applied and introduced for treatment of fresh foods to eliminate pathogenic as well as spoilage microorganisms. Salmonella can become exposed to elevated temperatures while associated with hosts such as poultry. In addition, heat treatment is also applied at various stages of processing to retain the shelf life of food products. Despite this, these microorganisms may overcome exposure to such treatments through the efficient expression of stress response mechanisms and result in illness following consumption. Thermal stress induces a range of destructive exposures to bacterial cells such as protein damage and DNA damage caused by reactive oxygen species. In this study, we chose three genes (∆recD, ∆STM14_5307, and ∆aroD) associated with conditionally essential genes required for different aspects of optimal growth at 42 °C and evaluated the responses of wild type and mutant Salmonella Typhimurium strains to uncover potential mechanisms that may enable survival and resistance under thermal stress. The RecBCD complex that initiates repair of double-stranded DNA breaks through homologous recombination. STM14_5307 is a transcriptional regulator involved in stationary phase growth and inositol metabolism. The gene aroD is involved in metabolism and stationary phase growth. These strains were characterized via high throughput phenotypic profiling in response to two different growth temperatures (37 °C (human host temperature) and 42 °C (poultry host temperature)). The ∆aroD strain exhibited the highest sensitivity to the various temperatures followed by the ∆recD and ∆STM14_5307 strains, respectively. Achieving more understanding of the molecular mechanisms of heat survival may lead to the development of more effective strategies to limit Salmonella in food products through thermal treatment by developing interventions that specifically target the pathways these genes are involved in.

Quantification of loosely associated and tightly associated bacteria on broiler carcass skin using swabbing, stomaching, and grinding methods

This research was conducted to quantify bacterial populations after swabbing or stomaching, followed by grinding the swabbed or stomached broiler skins. For each of 3 replications, 3 eviscerated broilers were randomly taken from a processing line in a local broiler processing plant. Ten swabs and 10 stomachs per bird were conducted on the left- and the right-side skins (10×7 cm), respectively, which were then finally ground. Results indicated that mesophilic aerobic bacteria (MAB) in the first swabbed sample were significantly lower than those in the first stomached sample (P<0.05), with no difference seen for the remaining sampling times (P>0.05). During 10 swabbings followed by final grinding, 8, 9, and 83% of MAB were detected after the first swabbing, after the second through 10th swabbings, and after final grinding of the skin, respectively. During 10 stomachings followed by the final grinding, 17, 18, and 65% of MAB were detected after the first stomaching, after the second through 10th stomachings, and after final grinding of the skin, respectively. Escherichia coli (E. coli) and coliforms were significantly higher in the first stomaching than those in the first swabbing (P<0.05), with no difference seen between the 2 sampling methods for the rest sampling times (P>0.05). Populations of E. coli and coliforms decreased step-wisely from the highest after grinding to the intermediate after first and second sampling, and to the least after 10th sampling (P<0.05), regardless of swabbing or grinding. In this study, less than 35% of MAB seemed loosely associated in the skin of eviscerated broiler, whereas more than 65% of MAB looked tightly associated, which were not recovered by stomaching or swabbing even 10 times but were recovered by grinding the skin.

The evaluation of combined chemical and physical treatments on the reduction of resident microorganisms and Salmonella Typhimurium attached to chicken skin

This study was conducted to evaluate the efficacy of sodium hypochlorite (NaOCl, 0-200 mg/kg), thiamine dilauryl sulfate (TDS, 1,000 mg/kg), and ultrasound (37 kHz, 380 W) on reducing Salmonella Typhimurim, mesophilic aerobic bacteria (MAB), and coliforms on chicken skin. Chemical and physical treatments were applied for 5 min either singly or jointly, and Salmonella previously inoculated on chicken skin were quantitatively assessed using brilliant green agar, and the populations of MAB and coliforms in the native flora were enumerated using plate count agar and violet red bile agar, respectively. In the evaluation of bacterial attachment/detachment, chicken skin was quantitatively assessed for loosely, intermediately, and tightly attached bacteria. The treatment effects on bacteria detachment were also visualized using field emission scanning electron microscopy. In addition, color and textural properties of the skin after treatments were evaluated using a color difference meter and texture analyzer. Antimicrobial activity of NaOCl increased as the NaOCl concentration was increased, especially for loosely attached cells. The combination of 200 mg/kg NaOCl and ultrasound (NaOCl/ultrasound) significant reduced loosely, intermediately, and tightly attached bacteria populations by 0.75 to 0.47, 0.43 to 0.41, and 0.83 to 0.54 log cfu/g for MAB, coliforms, and Salmonella Typhimurium, respectively. However, the combination of NaOCl and TDS (NaOCl/TDS) did not sufficiently reduce those cells on chicken skins, except for loosely attached MAB and coliforms. The NaOCl/ultrasound combination produced a higher reduction in numbers of inoculated and native bacteria flora than any single application, with no negative effect on skin color or texture. Generally, the loosely attached bacteria were less resistant to the chemical and physical treatments than the intermediately and tightly attached bacteria in chicken skin, presumably due to their location in deeper skin layer and crevices. Further research is needed to investigate how the intermediately and tightly attached microorganisms can be effectively eliminated from chicken skin.