Development of a novel crAss-like phage detection method with a broad spectrum for microbial source tracking.

CrAssphage has been recognized as the most abundant and human-specific bacteriophage in the human gut. Consequently, crAssphage has been used as a microbial source tracking (MST) marker to monitor human fecal contamination. Many crAss-like phages (CLPs) have been recently discovered, expanding the classification into the new order Crassvirales. This study aims to assess CLP prevalence in South Korea and develop a detection system for MST applications. Thirteen CLPs were identified in six human fecal samples and categorized into seven genera via metagenomic analysis. The major head protein (MHP) displayed increased sequence similarity within each genus. Eight PCR primer candidates, designed from MHP sequences, were evaluated in animal and human feces. CLPs were absent in animal feces except for those from raccoons, which hosted genera VI, VIIa, and VIIb. CLPs were detected in 91.52% (54/59) of humans, with genus VI (38 out of 59) showing the highest prevalence, nearly double that of p-crAssphage in genus I (22 out of 59). This study highlights genus VI as a potent MST marker, broadening the detection range for CLPs. Human-specific and selectively targeted MST markers can significantly impact hygiene regulations, lowering public health costs through their application in screening liver, sewage, wastewater, and various environmental samples.

A Comprehensive Review Exploring the Protective Role of Specific Commensal Gut Bacteria against Salmonella.

Gut microbiota is a diverse community of microorganisms that constantly work to protect the gut against pathogens. Salmonella stands out as a notorious foodborne pathogen that interacts with gut microbes, causing an imbalance in the overall composition of microbiota and leading to dysbiosis. This review focuses on the interactions between Salmonella and the key commensal bacteria such as E. coli, Lactobacillus, Clostridium, Akkermansia, and Bacteroides. The review highlights the role of these gut bacteria and their synergy in combating Salmonella through several mechanistic interactions. These include the production of siderophores, which compete with Salmonella for essential iron; the synthesis of short-chain fatty acids (SCFAs), which exert antimicrobial effects and modulate the gut environment; the secretion of bacteriocins, which directly inhibit Salmonella growth; and the modulation of cytokine responses, which influences the host's immune reaction to infection. While much research has explored Salmonella, this review aims to better understand how specific gut bacteria engage with the pathogen, revealing distinct defense mechanisms tailored to each species and how their synergy may lead to enhanced protection against Salmonella. Furthermore, the combination of these commensal bacteria could offer promising avenues for bacteria-mediated therapy during Salmonella-induced gut infections in the future.

A comprehensive systematic review and meta-analysis of Listeria monocytogenes prevalence in food products in South Korea.

Listeria monocytogenes is a foodborne pathogen that can cause deadly severe listeriosis. While systematic review and meta-analysis are powerful tools for comprehensive analysis by pooling every related study, these approaches to L.monocytogenes contamination food have yet to be studied in South Korea. We aimed to identify high-risk L.monocytogenes foods in South Korea through a prevalence survey of retail food products for the first time. A total of 13,684 samples of 59 articles were used for meta-analysis through the systematic review, and the results were synthesized using a random-effects model considering the heterogeneity. The overall pooled prevalence was 2.26 % (95 % CI: 1.44-3.52 %). Among nine food categories, meat exhibited the highest prevalence at 8.32 % (95 % CI: 4.42-12.14 %) after sample size restriction. Specifically, a post-hoc sensitivity analysis was conducted to identify the prevalence difference among subgroups and the source of heterogeneity. Intriguingly, the analysis revealed chicken as the primary contributor to the elevated prevalence of L.monocytogenes, a key factor deriving the observed heterogeneity. This study carries significant implications for public health and food safety in Korea. Furthermore, knowledge of differences in prevalence levels in various foods will be able to be used as a predictive guideline for foodborne outbreaks.

Systematic Review and Meta-Analysis of Campylobacter Species Contamination in Poultry, Meat, and Processing Environments in South Korea.

Campylobacter spp. constitute a significant global threat as a leading cause of foodborne illnesses, with poultry meat as a prominent reservoir for these pathogens. South Korea is known for its diverse poultry consumption habits, and continuous outbreaks make it a matter of concern to perform a meta-analysis to identify the primary source of contamination. This systematic review and meta-analysis aimed to assess and compare the prevalence of Campylobacter in various poultry and meat types while also considering the importance of environmental factors in South Korea. The meta-analysis revealed that duck meat exhibited the highest prevalence of Campylobacter, with a pooled estimate of 70.46% (95% CI: 42.80% to 88.38%), followed by chicken meat at a pooled prevalence of 36.17% (95% CI: 26.44% to 47.91%). Additionally, our analysis highlighted the predominance of C. jejuni and C. coli in South Korea. These findings underscore the importance of implementing rigorous food safety measures and establishing robust surveillance programs in the poultry industry to mitigate the risk of Campylobacter-related foodborne illnesses associated with meat consumption in South Korea.

Whole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea.

Listeria monocytogenes is a foodborne pathogen that causes listeriosis in humans with severe symptoms. In South Korea, listeriosis had only been reported sporadically among hospitalized patients until the first foodborne outbreak occurred in 2018. In this study, a L. monocytogenes strain responsible for this outbreak (FSCNU0110) was characterized via whole genome sequencing and compared with publicly available L. monocytogenes genomes of the same clonal complex (CC). Strain FSCNU0110 belonged to multilocus sequence typing (MLST)-based sequence type 224 and CC224, and core genome MLST-based sublineage 6,178. The strain harbored tetracycline resistance gene tetM, four other antibiotic resistance genes, and 64 virulence genes, including Listeria pathogenicity island 1 (LIPI-1) and LIPI-3. Interestingly, llsX in LIPI-3 exhibited a characteristic SNP (deletion of A in position 4, resulting in a premature stop codon) that was missing among all CC224 strains isolated overseas but was conserved among those from South Korea. In addition, the tetM gene was also detected only in a subset of CC224 strains from South Korea. These findings will provide an essential basis for assessing the characteristics of CC224 strains in South Korea that have shown a potential to cause listeriosis outbreaks.

Assessment of Microbial Source Tracking Marker and Fecal Indicator Bacteria on Food-Contact Surfaces in School Cafeterias.

Food poisoning outbreaks in schools can affect many students, causing physical and psychological damage and time and economic loss. Fecal indicator bacteria (FIB) have been used to monitor the contamination; however, the detection is time-consuming and confirms the contamination from all warm-blooded animals. Microbial source tracking (MST) is a molecular-based detection method that is host specific. This study aimed to evaluate MSTs and FIBs for tracing contamination in the school cafeteria. The average total aerobic count was 0.89 to 3.63 log CFU/100 cm2, and the faucets in the cooking area showed a significantly high aerobic count. The stove valve, faucet, and hand-washer were the most contaminated area, with a concentration of 1.90 to 6.80 log CFU/100 cm2 from the frequent hand contact. Escherichia coli was not detected on any surfaces, and coliform was detected on five surfaces: the sink and faucet in the food preparation area, the faucet in the cooking area, the hand-washer, and the toilet seat in the restroom with 0.33 to 3.64 log CFU/100 cm2. Human-specific crAssphage appeared on a faucet in the food preparation area, while HF183 was not detected. The result indicates that the continuous monitoring of frequent hand-contact areas is recommended to maintain the hygiene condition in the school cafeteria.

Protective role of Acinetobacter and Bacillus for Escherichia coli O157:H7 in biofilms against sodium hypochlorite and extracellular matrix-degrading enzymes.

Foodborne pathogenic bacteria in multi-species biofilms in food manufacturing facilities have been suspected to be the cause of cross-contamination leading to foodborne illness. We studied if cafeteria kitchen-associated bacterial isolates can have any protective effect on E. coli O157:H7 in biofilm against extracellular polymeric substances (EPS)-degrading enzymes and sodium hypochlorite. We investigated multi-species biofilm-forming ability and the efficacy of EPS-degrading enzymes using crystal violet assay. The susceptibility of E. coli O157:H7 to sodium hypochlorite (NaClO) was evaluated using propidium monoazide combined with quantitative PCR (PMA-qPCR). Then, a combined treatment with enzymes followed by NaClO was also tested. Most cafeteria kitchen isolates of Acinetobacter and Bacillus were able to form biofilms. Several of them showed a protective effect on E. coli O157:H7 against NaClO after forming multi-species biofilms, particularly in Acinetobacter. This protective effect on E. coli O157:H7 was also noticed after the enzyme or the combined treatment with NaClO. Our results give us an insight into the protective role of food-associated environmental bacteria for E. coli O157:H7 in biofilms against common sanitizers and warrant further study to develop effective control methods. Our study also highlights the importance of preventing contamination or biofilm formation by environmental microorganisms, eventually reducing foodborne illness.

Evaluation of crAssphage as a human-specific microbial source-tracking marker in the Republic of Korea.

CrAssphage is a novel and by far the most abundant bacteriophage in the human gut and has been proposed as a human-specific microbial source tracking (MST) marker. However, its global use as a human-specific MST marker requires validation in more extensive regions. The purpose of this study was to evaluate the specificity and abundance of the human-specific MST marker crAssphage with PCR and RT-PCR assays in human and animal feces in Korea. The prevalence of crAssphage was confirmed in 94 human feces samples (subjects: 19 to 45 years old) and 56 animal feces samples (from birds, raccoons, squirrels, weasels, deer, wild boars, hares, cats, and dogs). CrAssphage showed sensitivity of 0.39 and specificity of 1.00 in Korea, with a sequencing analysis showing that genotype II was dominant at 71.9%. The quantitative analysis showed that crAssphage is sufficiently abundant in human feces given the high concentration range of 4.26 to 8.25 log gene copies (GC)/ng in human feces. In conclusion, this study confirmed the crAssphage as a specific and abundant MST marker with which to identify human fecal contamination in Korea.

Metagenomic Analysis of Microbial Composition Revealed Cross-Contamination Pathway of Bacteria at a Foodservice Facility.

Bacterial contamination of food-contact surfaces can be a potential risk factor for food quality and safety. To evaluate the spatial and temporal variations of the potential cross-contamination routes, we conducted a biogeographical assessment of bacteria in a foodservice facility based on the diversity of microflora on each surface. To this end, we performed high-throughput amplicon sequencing of 13 food-contact and non-food contact surfaces in a foodservice facility throughout a year. The results showed that Bacillus, Acinetobacter, Streptophyta, Enterobacter, Pseudomonas, Serratia, Enhydrobacter, Staphylococcus, Paracoccus, and Lysinibacillus were the dominant genera found on the kitchen surfaces of the foodservice facility. Depending on the season, changes in Firmicute/Proteobacteria ratios were observed, and the fan becomes the main source of outdoor air contamination. The microbial flow associated with spoilage was also observed throughout food preparation. Taken together, our results would be a powerful reference to hygiene managers for improvement of food processes.

Biofilm and Spore Formation of Clostridium perfringens and Its Resistance to Disinfectant and Oxidative Stress.

Clostridium perfringens is a major human pathogen that causes gastroenteritis via enterotoxin production and has the ability to form spores and biofilms for environmental persistence and disease transmission. This study aimed to compare the disinfectant and environmental resistance properties of C. perfringens vegetative cells and spores in planktonic and sessile conditions, and to examine the nucleotide polymorphisms and transcription under sessile conditions in C. perfringens strains isolated from meat. The sporulation rate of sessile C. perfringens TYJAM-D-66 (cpe+) was approximately 19% at day 5, while those of CMM-C-80 (cpe-) and SDE-B-202 (cpe+) were only 0.26% and 0.67%, respectively, at day 7. When exposed to aerobic conditions for 36 h, TYJAM-D-66, CMM-C-80, and SDE-B-202 vegetative cells showed 1.70 log, 5.36 log, and 5.67 log reductions, respectively. After treatment with sodium hypochlorite, the survival rates of TYJAM-D-66 vegetative cells (53.6%) and spores (82.3%) in biofilms were higher than those of planktonic cells (9.23%). Biofilm- and spore-related genes showed different expression within TYJAM-D-66 (-4.66~113.5), CMM-C-80 (-3.02~2.49), and SDE-B-202 (-5.07~2.73). Our results indicate the resistance of sessile cells and spores of C. perfringens upon exposure to stress conditions after biofilm formation.

Biofilm-isolated Listeria monocytogenes exhibits reduced systemic dissemination at the early (12-24 h) stage of infection in a mouse model.

Environmental cues promote microbial biofilm formation and physiological and genetic heterogeneity. In food production facilities, biofilms produced by pathogens are a major source for food contamination; however, the pathogenesis of biofilm-isolated sessile cells is not well understood. We investigated the pathogenesis of sessile Listeria monocytogenes (Lm) using cell culture and mouse models. Lm sessile cells express reduced levels of the lap, inlA, hly, prfA, and sigB and show reduced adhesion, invasion, translocation, and cytotoxicity in the cell culture model than the planktonic cells. Oral challenge of C57BL/6 mice with food, clinical, or murinized-InlA (InlAm) strains reveals that at 12 and 24 h post-infection (hpi), Lm burdens are lower in tissues of mice infected with sessile cells than those infected with planktonic cells. However, these differences are negligible at 48 hpi. Besides, the expressions of inlA and lap mRNA in sessile Lm from intestinal content are about 6.0- and 280-fold higher than the sessle inoculum, respectively, suggesting sessile Lm can still upregulate virulence genes shortly after ingestion (12 h). Similarly, exposure to simulated gastric fluid (SGF, pH 3) and intestinal fluid (SIF, pH 7) for 13 h shows equal reduction in sessile and planktonic cell counts, but induces LAP and InlA expression and pathogenic phenotypes. Our data show that the virulence of biofilm-isolated Lm is temporarily attenuated and can be upregulated in mice during the early stage (12-24 hpi) but fully restored at a later stage (48 hpi) of infection. Our study further demonstrates that in vitro cell culture assay is unreliable; therefore, an animal model is essential for studying the pathogenesis of biofilm-isolated bacteria.

Synergistic anti-biofilm effects of Brassicaceae plant extracts in combination with proteinase K against Escherichia coli O157:H7.

Bacteria can form biofilms, complex microbial communities protected from environmental stress, on food contact surfaces. Brassicaceae plant has been shown to contain bioactive compounds with antimicrobial activities. The objective of this study was to evaluate the synergistic effects of Brassicaceae species and proteinase K against E. coli O157:H7 biofilm. We determined the minimum biofilm inhibitory concentration, the fractional inhibitory concentration indexes, and the synergistic inhibitory effect of Raphanus sativus var. longipinnatus, R. sativus, and Brassica oleracea var. acephala extracts with proteinase K on E. coli O157:H7. The biofilm showed a 49% reduction with 2 mg/mL R. sativus. The combination of proteinase K 25 µg/mL significantly increased the effect of 2 mg/mL R. sativus var. longipinnatus and the combined treatment yielded up to 2.68 log reduction on stainless steel coupons. The results showed that the combination of R. sativus var. longipinnatus extract and proteinase K could serve as an anti-biofilm agent with synergistic effects for inhibiting E. coli O157:H7 biofilm on stainless steel surfaces.

Survival of foodborne pathogens on stainless steel soiled with different food residues.

Insufficient and ineffective cleaning practices can cause food residues to remain in kitchen and can facilitate bacterial attachment and persistence by protective films. The present study investigated the survival of five major foodborne pathogens on stainless steel coupons, in the presence of cooked rice, whole eggs, and soymilk. Foodborne pathogens showed different survival rates by desiccation and disinfection depending on food residues. Overall, the pathogens showed stronger survival than the control at 0.13-3.97 log CFU/coupon with 5% residues, and at 0.75-5.29 log CFU/coupon with 50% residues. Staphylococcus aureus was not affected by the food residue with showing the least difference in concentration, while Escherichia coli O157:H7 showed the most significant increase by food residue. The cells with cooked rice were observed using FE-SEM, and demonstrated bacterial binding or embedment. All results suggest that food safety can be practically ensured by food residue types and appropriate cleaning and disinfectants.

Anti-attachment, anti-biofilm, and antioxidant properties of Brassicaceae extracts on Escherichia coli O157:H7.

Bacteria can survive and persist in food processing environments by attachment and biofilm formation and transfer to food products, causing serious foodborne illness. In this study, we investigated natural substances that belong to the family Brassicaceae to determine whether they have potential anti-attachment activities against Escherichia coli O157:H7. The inhibition of biofilm formation was evaluated by crystal violet and resazurin assays at different stages of biofilm formation (initial attachment, biofilm formation, and after biofilm development) of E. coli O157:H7. The sessile cells were reduced to a range of 13.8-31.3% by young radish, radish, radish sprout, red cabbage, and kale extracts, and the viability was reduced to between 5.83 and 51.5%. The radical scavenging activities and the presence of polyphenolic compounds were compared. The presence of phenolic compounds such as gallic acid, caffeic acid, and phenylethyl ITC in the Brassicaceae family verified the potential use as a natural anti-biofilm substituent against E. coli O157:H7.

Bio-enzymes for inhibition and elimination of Escherichia coli O157:H7 biofilm and their synergistic effect with sodium hypochlorite.

Escherichia coli O157:H7 is one of the most important pathogens worldwide. In this study, three different kinds of enzymes, DNase I, proteinase K and cellulase were evaluated for inhibitory or degrading activity against E. coli O157:H7 biofilm by targeting extracellular DNA, proteins, and cellulose, respectively. The cell number of biofilms formed under proteinase K resulted in a 2.43 log CFU/cm2 reduction with an additional synergistic 3.72 log CFU/cm2 reduction after NaClO post-treatment, while no significant reduction occurred with NaClO treatment alone. It suggests that protein degradation could be a good way to control the biofilm effectively. In preformed biofilms, all enzymes showed a significant reduction of 16.4-36.7% in biofilm matrix in 10-fold diluted media (p < 0.05). The sequential treatment with proteinase K, cellulase, and NaClO showed a significantly higher synergistic inactivation of 2.83 log CFU/cm2 compared to 1.58 log CFU/cm2 in the sequence of cellulase, proteinase K, and NaClO (p < 0.05). It suggests that the sequence of multiple enzymes can make a significant difference in the susceptibility of biofilms to NaClO. This study indicates that the combination of extracellular polymeric substance-degrading enzymes with NaClO could be useful for the efficient control of E. coli O157:H7 biofilms.

Molecular genotyping, biofilm formation and antibiotic resistance of enterotoxigenic Clostridium perfringens isolated from meat supplied to school cafeterias in South Korea.

Clostridium perfringens is one of the leading causes of food poisoning worldwide. The aims of this study were to investigate the presence of C. perfringens in food supplied to school cafeterias, to assess the presence of toxin genes in the isolates, and to investigate the biofilm formation and antibiotic susceptibility of the isolates. A total of 30 C. perfringens strains (12.9%) from 232 samples of beef, pork, chicken, and duck meat were isolated. Toxin genes, including cpa, cpe, cpb2, and netB, were detected, while the cpb, etx, iap and tpeL genes were absent. Biofilm formation was analyzed, and all the isolates were able to form biofilm. Antibiotic resistance was observed against penicillin (97%), lincomycin (20%), bacitracin (97%), oxytetracycline (73%), trimethoprim (7%), gentamicin (10%), tetracycline (93%), erythromycin (83%), ampicillin (100%), amikacin (7%), and streptomycin (3%). In conclusion, the results showed that students are exposed to a potentially high risk of food poisoning by C. perfringens; therefore, precaution is required for these types of catering services.

Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea.

The purpose of this study was to characterize the microbial community in ground pork using molecular approaches. Forty six ground pork products were purchased from local stores in the north central area of South Korea. Aerobic plate counts varied 4.23 ± 5.14 × 10(5) CFU/g with the range between 5.00 × 10(3) and 1.85 × 10(6) CFU/g for ground pork samples. Four ground meat samples were further processed for metagenomic analysis. Pseudomonas species was the most relative abundant with a wide range occurring (1.72 to 77.7%) as part of the microbial genera in ground pork. Bacteria such as Carnobacterium, Yersinia, Photobacterium were also identified in ground pork. Despite the prominence of certain genera across all samples there was still extensive microbial diversity among ground pork products that originated from different slaughter houses and were processed in different markets. Such diversity indicates that designing interventions to extend shelf life may be hampered by the extensive variability in the microbial consortia associated with pork products. However, this diversity may be useful for developing microbial traceability signatures unique to a slaughter house or a particular market.

Acridine orange as an alternative to optical density to study growth kinetics of Lactobacillus bulgaricus ATCC 7517.

In this study we assessed the use of acridine orange as an alternative to optical density to quantify the growth of Lactobacillus bulgaricus ATCC 7517. The growth of bacteria in Lactobacillus de Man Rogosa Sharpe (MRS) medium was measured by both acridine orange (AO) and optical density (OD) measurements for 24 h. The relationship between both methods was compared via correlation analysis. The doubling time of bacteria based on the values of OD600 and AO obtained during 24 h growth were also calculated. The result shows strong correlation of cell growth between OD600 and AO during the first 10 hours of growth, but the correlation was less strong when analyzing the data from 0 to 24 hours. Growth rates, generation time and lag time were also similar. This study indicates that AO could be used in place of OD to prepare growth curves of Lactobacillus bulgaricus during the exponential phase of growth, and to compare growth rates, generation times or lag times.

Enhancement of chicken macrophage cytokine response to Salmonella Typhimurium when combined with bacteriophage P22.

Salmonella infections are reported as the second most common pathogen caused foodborne disease in the United States, and several Salmonella serovars can colonize in the intestinal tracts of poultry. Reducing Salmonella in poultry is crucial to decrease the incidence of salmonellosis in humans. In this study, we evaluated the immune response of chicken macrophage cells (HD-11) and effects of bacteriophage P22 against the extra- and intracellular S. Typhimurium LT2. Four treatments, (1) HD-11 cells as control, (2) HD-11 cells with LT2, (3) HD-11 cells with LT2 and P22, and (4) HD-11 cells with P22, were administered, and IL-8 responses of HD-11 cells were measured using an ELISA. Also, four cytokine (IL-4, IL-8, IL-10, and IFN-γ) gene expression levels in the presence of LT2 and/or P22 were quantified by qRT-PCR. We found that P22 lysed the extra- and intracellular LT2, which adhered and were taken up by the HD-11 cells. The ELISA indicated that HD-11 cells produced significantly higher IL-8 cytokine levels in the supernatant during the intracellular lyses of LT2 by P22 (P < 0.05). The IL-8 expression levels measured by qRT-PCR also exhibited similar results with the IL-8 production based on ELISA measurements.