• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

• Journal of Veterinary Science
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• v.24 no.6
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• pp.82.1-82.12
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• 2023

Background: The current conventional serotyping based on antigen-antisera agglutination could not provide a better understanding of the potential pathogenicity of Salmonella enterica subsp. enterica serovar Brancaster. Surveillance data from Malaysian poultry farms indicated an increase in its presence over the years. Objective: This study aims to investigate the virulence determinants and antimicrobial resistance in S. Brancaster isolated from chickens in Malaysia. Methods: One hundred strains of archived S. Brancaster isolated from chicken cloacal swabs and raw chicken meat from 2017 to 2022 were studied. Two sets of multiplex polymerase chain reaction (PCR) were conducted to identify eight virulence genes associated with pathogenicity in Salmonella (invasion protein gene [invA], Salmonella invasion protein gene [sipB], Salmonella-induced filament gene [sifA], cytolethal-distending toxin B gene [cdtB], Salmonella iron transporter gene [sitC], Salmonella pathogenicity islands gene [spiA], Salmonella plasmid virulence gene [spvB], and inositol phosphate phosphatase gene [sopB]). Antimicrobial susceptibility assessment was conducted by disc diffusion method on nine selected antibiotics for the S. Brancaster isolates. S. Brancaster, with the phenotypic ACSSuT-resistance pattern (ampicillin, chloramphenicol, streptomycin, sulphonamides, and tetracycline), was subjected to PCR to detect the corresponding resistance gene(s). Results: Virulence genes detected in S. Brancaster in this study were invA, sitC, spiA, sipB, sopB, sifA, cdtB, and spvB. A total of 36 antibiogram patterns of S. Brancaster with a high level of multidrug resistance were observed, with ampicillin exhibiting the highest resistance. Over a third of the isolates displayed ACSSuT-resistance, and seven resistance genes (β-lactamase temoneira [bla_TEM], florfenicol/chloramphenicol resistance gene [floR], streptomycin resistance gene [strA], aminoglycoside nucleotidyltransferase gene [ant(3")-Ia], sulfonamides resistance gene [sul-1, sul-2], and tetracycline resistance gene [tetA]) were detected. Conclusion: Multidrug-resistant S. Brancaster from chickens harbored an array of virulence-associated genes similar to other clinically significant and invasive non-typhoidal Salmonella serovars, placing it as another significant foodborne zoonosis.

• Genomics & Informatics
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• v.21 no.3
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• pp.35.1-35.12
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• 2023

The Bacillus cereus group, also known as B. cereus sensu lato (B. cereus s.l.), is composed of various Bacillus species, some of which can cause diarrheal or emetic food poisoning. Several emerging highly heat-resistant Bacillus species have been identified, these include B. thermoamylovorans, B. sporothermodurans, and B. cytotoxicus NVH 391-98. Herein, we performed whole genome analysis of two thermotolerant Bacillus sp. isolates, Bacillus sp. B48 and Bacillus sp. B140, from an omelet with acacia leaves and fried rice, respectively. Phylogenomic analysis suggested that Bacillus sp. B48 and Bacillus sp. B140 are closely related to B. cereus and B. thuringiensis, respectively. Whole genome alignment of Bacillus sp. B48, Bacillus sp. B140, mesophilic strain B. cereus ATCC14579, and thermophilic strain B. cytotoxicus NVH 391-98 using the Mauve program revealed the presence of numerous homologous regions including genes responsible for heat shock in the dnaK gene cluster. However, the presence of a DUF4253 domain-containing protein was observed only in the genome of B. cereus ATCC14579 while the intracellular protease PfpI family was present only in the chromosome of B. cytotoxicus NVH 391-98. In addition, prophage Clp protease-like proteins were found in the genomes of both Bacillus sp. B48 and Bacillus sp. B140 but not in the genome of B. cereus ATCC14579. The genomic profiles of Bacillus sp. isolates were identified by using whole genome analysis especially those relating to heat-responsive gene clusters. The findings presented in this study lay the foundations for subsequent studies to reveal further insights into the molecular mechanisms of Bacillus species in terms of heat resistance mechanisms.

• Journal of Food Hygiene and Safety
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• v.38 no.5
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• pp.279-286
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• 2023

Rapid and accurate detection of pathogenic bacteria is crucial for various applications, including public health and food safety. However, existing bacteria detection techniques have several drawbacks as they are inconvenient and require time-consuming procedures and complex machinery. Recently, the precision and versatility of CRISPR/Cas system has been leveraged to design biosensors that offer a more efficient and accurate approach to bacterial detection compared to the existing techniques. Significant research has been focused on developing biosensors based on the CRISPR/Cas system which has shown promise in efficiently detecting pathogenic bacteria or virus. In this review, we present a biosensor based on the CRISPR/Cas system that has been specifically developed to overcome these limitations and detect different pathogenic bacteria effectively including Vibrio parahaemolyticus, Salmonella, E. coli O157:H7, and Listeria monocytogenes. This biosensor takes advantage of the CRISPR/Cas system's precision and versatility for more efficiently accurately detecting bacteria compared to the previous techniques. The biosensor has potential to enhance public health and ensure food safety as the biosensor's design can revolutionize method of detecting pathogenic bacteria. It provides a rapid and reliable method for identifying harmful bacteria and it can aid in early intervention and preventive measures, mitigating the risk of bacterial outbreaks and their associated consequences. Further research and development in this area will lead to development of even more advanced biosensors capable of detecting an even broader range of bacterial pathogens, thereby significantly benefiting various industries and helping in safeguard human health

• Journal of Veterinary Science
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• v.25 no.3
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• pp.39.1-39.11
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• 2024

Importance: Salmonella outbreaks linked to poultry meat have been reported continuously worldwide. Therefore, Salmonella contamination of poultry meats in slaughterhouses is one of the critical control points for reducing disease outbreaks in humans. Objective: This study examined the carry-over contamination of Salmonella species through the entire slaughtering process in South Korea. Methods: From 2018 to 2019, 1,097 samples were collected from the nine slaughterhouses distributed nationwide. One hundred and seventeen isolates of Salmonella species were identified using the invA gene-specific polymerase chain reaction, as described previously. The serotype, phylogeny, and antimicrobial resistance of isolates were examined. Results: Among the 117 isolates, 93 were serotyped into Salmonella Mbandaka (n = 36 isolates, 30.8%), Salmonella Thompson (n = 33, 28.2%), and Salmonella Infantis (n = 24, 20.5%). Interestingly, allelic profiling showed that all S. Mbandaka isolates belonged to the lineage of the sequence type (ST) 413, whereas all S. Thompson isolates were ST292. Moreover, almost all S. Thompson isolates (97.0%, 32/33 isolates) belonging to ST292 were multidrug-resistant and possessed the major virulence genes whose products are required for full virulence. Both serotypes were distributed widely throughout the slaughtering process. Pulsed-field gel electrophoretic analysis demonstrated that seven S. Infantis showed 100% identities in their phylogenetic relatedness, indicating that they were sequentially transmitted along the slaughtering processes. Conclusions and Relevance: This study provides more evidence of the carry-over transmission of Salmonella species during the slaughtering processes. ST292 S. Thompson is a potential pathogenic clone of Salmonella species possibly associated with foodborne outbreaks in South Korea.

• The Korean Journal of Applied Statistics
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• v.37 no.4
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• pp.499 -508
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• 2024

In this paper, we investigate hierarchical time series forecasting that adhere to a hierarchical structure when deriving predicted values by analyzing segmented data as well as aggregated datasets. The occurrences of food poisoning by a specific pathogen are analyzed using zero-inflated Poisson regression models and negative binomial regression models. The occurrences of major, miscellaneous, and overall food poisoning are analyzed using Poisson regression models and negative binomial regression models. For hierarchical time series forecasting, the MinT estimation proposed by Wickramasuriya et al. (2019) is employed. Negative predicted values resulting from hierarchical adjustments are adjusted to zero, and weights are multiplied to the remaining lowest-level variables to satisfy the hierarchical structure. Empirical analysis revealed that there is little difference between hierarchical and non-hierarchical adjustments in predictions based on pathogens. However, hierarchical adjustments generally yield superior results for predictions concerning major, miscellaneous, and overall occurrences. Without hierarchical adjustment, instances may occur where the predicted frequencies of the lowest-level variables exceed that of major or miscellaneous occurrences. However, the proposed method enables the acquisition of predictions that adhere to the hierarchical structure.

• Food Science of Animal Resources
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• v.33 no.3
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• pp.403-410
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• 2013

This study was performed to evaluate the microbiological contamination level of raw beef from retail markets in Seoul, Korea. The sampling and laboratory test were performed according to the procedure of "Standard for processing and ingredients specification of livestock product" and "Korean food code". Enterotoxin of Staphylococcus aureus isolates were detected using VIDAS$^{(R)}$ and PCR-based methods. Listeria monocytogenes serotyping and genotyping were carried out using Listeria antisera and L. monocytogenes Fingerprinting kit, respectively. A total of 48 samples were collected from 16 retail markets (butcher's shop: 5, department store: 6, supermarket: 5) in 2011. The level of total bacteria counts in the butcher's shop, department store and supermarket were $4.4{\times}10^3$ CFU/g, $3.9{\times}10^5$ CFU/g and $1.0{\times}10^4$ CFU/g, respectively. The concentrations of Escherichia coli of these three retail markets were $6.4{\times}10$ CFU/g, 7.6 CFU/g and $2.0{\times}10$ CFU/g, respectively. Salmonella species was not detected on all samples. However, S. aureus was isolated in the 3 samples (6.25%) from each type of three retail markets. L. monocytogenes was isolated in the 4 samples (8.3%) from department stores. The level of contamination of these foodborne bacteria was less than 100 CFU/g. The enterotoxin-encoding genes of S. aureus isolates were sea, seh, sei and sep gene. The gene similarity of L. monocytogenes isolated from two retail markets by Rep-PCR showed 57.8-98.1% and 68.1-98.1%, respectively. These results suggest that the HACCP guideline for environmental control in slaughterhouse and retail markets should be provided to prevent cross contamination and manage foodborne pathogens such as L. monocytogenes and S. aureus.

• Journal of Food Hygiene and Safety
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• v.30 no.2
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• pp.178-188
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• 2015

Microbial quality of baked egg products was evaluated by counting the levels of sanitary indicative bacteria (aerobic plate counts, coliforms, and E. coli), L. monocytogenes and Salmonella spp. at the critical control points (CCPs) of manufacturing process. In addition, the survival and growth of foodborne pathogens in various egg products (cheese, tuna, tteokgalbi, pizza omelets, baked egg, and steamed egg) were investigated at 4, 10, and $15^{\circ}C$. The contamination level of aerobic plate counts decreased from 4.67 log CFU/g at CCP 1 to 0.56 log CFU/g at CCP 3 in baked egg products. No coliforms and E. coli were detected at all CCPs. Although L. innocua and Salmonella spp. were identified at CCP 1, no L. monocytogenes and Salmonella spp. were detected in the final products. The contamination levels of aerobic plate counts and coliforms in egg strips and number of aerobic plate counts in Tteokgalbi omelet are higher than the microbiological standard of processed egg products. At $10^{\circ}C$, the growth of all pathogens was not prevented in omelet and baked egg, but the populations of S. Typhimurium and E. coli were reduced in steamed egg at $10^{\circ}C$, regardless of the presence of other pathogens. The growth of L. monocytogenes was faster than that of S. Typhimurium and E. coli in omelet. More rapid growth of S. Enteritidis than S. Typhimurium was observed in egg products, indicating the greater risk of S. Enteritidis than S. Typhimurium in egg products.

• Journal of Food Hygiene and Safety
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• v.35 no.5
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• pp.468-476
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• 2020

We aimed to analyze the microbiological quality of the ready-to-eat (RTE) side dishes collected from traditional markets, supermarkets, and cafeterias in Gyeonggi-do in 2019. A total of 108 samples were analyzed for total aerobic bacterial counts, coliforms and foodborne pathogens depending on place of purchase and cooking methods. Results show that Bacillus cereus was detected in 14 (12.9%) out of 108 samples of side dishes, while no other foodborne pathogens were detected. The mean detected level (range) of total aerobic bacteria depending on place of purchase was 5.8 log CFU/g (3.0 to 8.2 log CFU/g) for traditional markets, 4.3 log CFU/g (2.4 to 7.8 log CFU/g) for supermarkets, and 3.80 log CFU/g (0.0 to 6.8 log CFU/g) for cafeterias, indicating that there was a significant (P<0.05) difference in total aerobic bacterial counts among places of purchase. Among the samples, the highest counts of total aerobic bacteria and coliforms were detected in saengchae (raw vegetables), followed by namul (seasoned herbs, vegetables), bokkeum (stir-fried foods), and jorim (foods cooked in soy sauce). The growth of total aerobic bacteria in seasoned soybean sprouts was inhibited when the sprouts were stored at 4℃ up to 24 h, whereas bacteria rapidly grew at 20 and 35℃ after 3 and 6 h, respectively. These results reveal that storage temperature might play a significant role for the microbiological quality of seasoned soybean sprouts when they are sold in markets. Thus, this study suggests that RTE side dishes should be stored at refrigerated temperature when being sold at markets as well as after purchasing to improve their microbiological quality.

• Horticultural Science & Technology
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• v.32 no.3
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• pp.400-407
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• 2014

Urban farming supplies emotional stability and fresh vegetables to participating persons, however, no information regarding the biosafety of agricultural products from urban farming is available. Here, we collected 260 samples of Chinese cabbages and lettuce from 4 urban community gardens and 6 roof gardens in Seoul from September through October 2012, and monitored the microbiological and parasitological contamination quantitatively and/or qualitatively. The mean counts of total aerobic bacteria and coliforms were $6.1{\pm}0.8\;log\;CFU{\cdot}g^{-1}$ ( range, $5.4{\pm}0.6{\sim}7.1{\pm}0.8\;log\;CFU{\cdot}g^{-1}$) and $4.0{\pm}0.7\;log\;CFU{\cdot}g^{-1}$ (range, $2.3{\pm}0.6{\sim}6.1{\pm}0.9\;log\;CFU{\cdot}g^{-1}$), respectively. Coliforms were detected on 59.6% among 260 vegetable samples. There were no significant differences in the contamination levels of total aerobic bacteria and coliforms between the Chinese cabbages and lettuce, whereas both levels of vegetables from urban community gardens were higher than those of roof gardens (p > 0.05). Escherichia coli was isolated at 3.1% among whole vegetables, and contamination level was $1.5{\pm}0.2\;log\;CFU{\cdot}g^{-1}$. Among foodborne pathogens, Staphylococcus aureus was detected in 1.5%, however, Salmonella spp., Listeria monocytogenes and E. coli O157:H7 were not detected on any of the vegetable samples. We also found undefined parasite eggs from two samples of Chinese cabbages (0.8% of total vegetables we tested). From these study, we found the presence of microbial contamination of agricultural products from urban farming, thus we need further concern to improve the biosafety during production of agricultural products.