Multiplex PCR for the Identification of Pathogenic Listeria in Flammulina velutipes Plant Based on Novel Specific Targets Revealed by Pan-Genome Analysis

Exploration of the biodiversity and mining novel target genes of Listeria monocytogenes strains isolated from beef through comparative genomics analysis

L. monocytogenes is a significant foodborne pathogen. This study aims to explore the biodiversity and evolutionary characteristics of L. monocytogenes isolated from beef through pan-genome analysis, and to provide important reference value for its specific molecular detection. This study conducted an in-depth analysis of the virulence genes, antimicrobial resistance genes, and environmental resistance genes of 344 L. monocytogenes strains isolated from beef. Pan-genomic analysis revealed that L. monocytogenes from beef have open genomes, providing a solid genetic basis for adaptation to different environments. MLST analysis revealed that the most prevalent types of L. monocytogenes isolated from beef were ST9 and CC9. A total of 50 virulence genes were detected in these strains, with 26 virulence genes such as inlA, inlB, plcA, plcB, and prfA, present in all L. monocytogenes strains. The four most prevalent antibiotic resistance genes in L. monocytogenes were norB, lin, mprF, and FosX, indicating high resistance to fluoroquinolones, lincosamides, peptides, and phosphonic acid antibiotics. A total of 416 potential target genes were identified through pan-genomic screening, which were then further filtered using a hub gene selection method to mining novel target genes. Ultimately, 10 highly connected hub genes were selected: bglF_2, tilS, group_2105, group_2431, oleD, ndk, flgG, purB, pbpB, and fni. These genes play a crucial role in the pathogenesis of L. monocytogenes. The PCR results demonstrated the excellent specificity of the bglF_2 gene for L. monocytogenes. Moreover, in the artificial contamination experiment, the bglF_2 gene was able to effectively detect L. monocytogenes in beef samples. Therefore, the bglF_2 gene holds potential as a specific molecular target for the detection of L. monocytogenes strains in beef samples.

Application of Comparative Genomics for the Development of PCR Primers for the Detection of Harmful or Beneficial Microorganisms in Food: Mini-Review

Gene markers are widely utilized for detecting harmful and beneficial microorganisms in food products. Primer sequences targeting the 16S rRNA region, recognized as a conserved region, have been conventionally employed in PCR analyses. However, several studies have highlighted limitations and false-positive results associated with the use of these primer sequences. Consequently, pan-genome analysis, a comparative genomic approach, has been increasingly applied to design more selective gene markers. This mini-review explores the application of pan-genome analysis in developing PCR primers for the detection of harmful microorganisms, such as Salmonella, Cronobacter, Staphylococcus, and Listeria, as well as beneficial microorganisms like Lactobacillus. Additionally, the review discusses the applicability, advantages, limitations, and future directions of pan-genome analysis for primer design. A comparative overview of bioinformatics tools, recent trends, and verification methods is also provided, offering valuable insights for researchers interested in leveraging pan-genome analysis for advanced primer design.

Identification of bacterial communities associated with needle mushroom (Flammulina filiformis) and its production environment

Flammulina filiformis is an important edible and medicinal mushroom widely cultivated in East Asia, with its quality and health strongly influenced by associated microbial communities. However, limited data exist on the bacterial communities associated with F. filiformis cultivation in Chinese farms. This study investigated bacterial communities associated with F. filiformis and its production environment using high-throughput 16S rRNA gene amplicon sequencing and culture-dependent methods. A total of 42 samples were collected from farms in Jilin and Guizhou provinces, China, for microbial community profiling. The analysis revealed diverse bacterial phyla, including Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Cyanobacteria. Genera such as Pseudomonas, Lactobacillus, Acinetobacter, Flavobacterium, and Phyllobacterium were identified, with notable regional variations in the relative abundance of Pseudomonas and Lactobacillus. Pathogenic species, including Pseudomonas tolaasii, Ewingella americana, Stenotrophomonas maltophilia, Pseudomonas sp., Lelliottia amnigena, and Janthinobacterium lividum, were identified through phenotypic, biochemical, and molecular analyses. Pathogenicity tests confirmed the disease-causing potential of P. tolaasii, E. americana, and J. lividum in F. filiformis. These findings highlight regional differences in bacterial community composition and emphasize the need for tailored management practices. This study contributes to safe, high-quality mushroom cultivation and provides insights into improved cultivation practices, including Mushroom Good Agricultural Practices (MGAP).

Comparative genomics analysis to explore the biodiversity and mining novel target genes of Listeria monocytogenes strains from different regions

As a common foodborne pathogen, infection with L. monocytogenes poses a significant threat to human life and health. The objective of this study was to employ comparative genomics to unveil the biodiversity and evolutionary characteristics of L. monocytogenes strains from different regions, screening for potential target genes and mining novel target genes, thus providing significant reference value for the specific molecular detection and therapeutic targets of L. monocytogenes strains. Pan-genomic analysis revealed that L. monocytogenes from different regions have open genomes, providing a solid genetic basis for adaptation to different environments. These strains contain numerous virulence genes that contribute to their high pathogenicity. They also exhibit relatively high resistance to phosphonic acid, glycopeptide, lincosamide, and peptide antibiotics. The results of mobile genetic elements indicate that, despite being located in different geographical locations, there is a certain degree of similarity in bacterial genome evolution and adaptation to specific environmental pressures. The potential target genes identified through pan-genomics are primarily associated with the fundamental life activities and infection invasion of L. monocytogenes, including known targets such as inlB, which can be utilized for molecular detection and therapeutic purposes. After screening a large number of potential target genes, we further screened them using hub gene selection methods to mining novel target genes. The present study employed eight different hub gene screening methods, ultimately identifying ten highly connected hub genes (bglF_1, davD, menE_1, tilS, dapX, iolC, gshAB, cysG, trpA, and hisC), which play crucial roles in the pathogenesis of L. monocytogenes. The results of pan-genomic analysis showed that L. monocytogenes from different regions exhibit high similarity in bacterial genome evolution. The PCR results demonstrated the excellent specificity of the bglF_1 and davD genes for L. monocytogenes. Therefore, the bglF_1 and davD genes hold promise as specific molecular detection and therapeutic targets for L. monocytogenes strains from different regions.

Listeria monocytogenes an Emerging Pathogen: a Comprehensive Overview on Listeriosis, Virulence Determinants, Detection, and Anti-Listerial Interventions

Listeria monocytogenes, the third most deleterious zoonotic pathogen, is a major causative agent of animal and human listeriosis, an infection related to the consumption of contaminated food products. Even though, this pathogen has been responsible for the outbreaks of foodborne infections in the early 1980s, the major outbreaks have been reported during the past two decades. Listeriosis infection in the host is a rare but life-threatening disease with major public health and economic implications. Extensive reports on listeriosis outbreaks are associated with milk and milk products, meat and meat products, and fresh produce. This bacterium can adapt to any environmental and stress conditions, making it a prime causative agent for major foodborne diseases. The pathogen could survive an antibiotic treatment and persist in the host cell, thereby escaping the standard diagnostic practices. The current review strives to provide concise information on the epidemiology, serotypes, and pathogenesis of the L. monocytogenes to decipher the knowledge on the endurance of the pathogen inside the host and food products as a vehicle for Listeria contaminations. In addition, various detection methods for Listeria species from food samples and frontline regimens of L. monocytogenes treatment have also been discussed.

Placental Listeriosis: Case Report and Literature Review

Listeria monocytogenes, a foodborne, facultative, intracellular gram-positive bacillus, is one of 17 species of the Listeria genus and was responsible for the world's largest outbreak of listeriosis in 2017-2018 in South Africa. Listeria monocytogenes tends to cause mild gastrointestinal symptoms in healthy individuals. However, pregnancy-associated listeriosis can be fatal to the fetus and can lead to serious adverse effects in the neonate. Listeria monocytogenes has an affinity for the placenta, as opposed to other nonreproductive organs. Herein, we present a case of placental listeriosis diagnosed in a 33-year-old female, parity 4, with unknown gestational age during the listeriosis outbreak in South Africa in 2017-2018. The patient presented with pregnancy-related complications and underwent a caesarean section. Morphological features demonstrated acute suppurative villitis and intervillositis with a heavy load of gram-positive bacilli, which is highly suggestive of placental listeriosis. Multiplex polymerase chain reaction confirmed the presence of L. monocytogenes.

Listeria monocytogenes Strains Persisting in a Meat Processing Plant in Central Italy: Use of Whole Genome Sequencing and In Vitro Adhesion and Invasion Assays to Decipher Their Virulence Potential

In this study, we used both a WGS and an in vitro approach to study the virulence potential of nine Listeria monocytogenes (Lm) strains belonging to genetic clusters persisting in a meat processing plant in Central Italy. The studied clusters belonged to CC1-ST1, CC9-ST9, and CC218-ST2801. All the CC1 and CC218 strains presented the same accessory virulence genes (LIPI-3, gltA, gltB, and aut_IVb). CC1 and CC9 strains presented a gene profile similarity of 22.6% as well as CC9 and CC218 isolates. CC1 and CC218 showed a similarity of 45.2% of the same virulence profile. The hypervirulent strains of lineage I (CC1 and CC218) presented a greater ability to adhere and invade Caco-2 cells than hypovirulent ones (CC9). CC1 strains were significantly more adhesive and invasive compared with CC9 and CC218 strains, although these last CCs presented the same accessory virulence genes. No statistically significant difference was found comparing CC218 with CC9 strains. This study provided for the first time data on the in vitro adhesiveness and invasiveness of CC218-ST2801 and added more data on the virulence characteristics of CC1 and CC9. What we observed confirmed that the ability of Lm to adhere to and invade human cells in vitro is not always decipherable from its virulence gene profile.

A review of rapid food safety testing: using lateral flow assay platform to detect foodborne pathogens

The detrimental impact of foodborne pathogens on human health makes food safety a major concern at all levels of production. Conventional methods to detect foodborne pathogens, such as live culture, high-performance liquid chromatography, and molecular techniques, are relatively tedious, time-consuming, laborious, and expensive, which hinders their use for on-site applications. Recurrent outbreaks of foodborne illness have heightened the demand for rapid and simple technologies for detection of foodborne pathogens. Recently, Lateral flow assays (LFA) have drawn attention because of their ability to detect pathogens rapidly, cheaply, and on-site. Here, we reviewed the latest developments in LFAs to detect various foodborne pathogens in food samples, giving special attention to how reporters and labels have improved LFA performance. We also discussed different approaches to improve LFA sensitivity and specificity. Most importantly, due to the lack of studies on LFAs for the detection of viral foodborne pathogens in food samples, we summarized our recent research on developing LFAs for the detection of viral foodborne pathogens. Finally, we highlighted the main challenges for further development of LFA platforms. In summary, with continuing improvements, LFAs may soon offer excellent performance at point-of-care that is competitive with laboratory techniques while retaining a rapid format.

Recent advances in quality preservation of postharvest golden needle mushroom (Flammulina velutiper)

The golden needle mushroom (Flammulina velutiper) is one of the most productive mushrooms in the world. However, F. velutiper experiences continuous quality degradation in terms of changes in color and textural characteristics, loss of moisture, nutrition and flavor, and increased microbial populations due to its high respiratory activity during the postharvest phase. Postharvest preservation techniques, including physical, chemical and biological methods, play a vital role in maintaining postharvest quality and extending the shelf life of mushrooms. Therefore, in this study, the decay process of F. velutiper and the factors affecting its quality were comprehensively reviewed. Additionally, the preservation methods (e.g., low-temperature storage, packaging, plasma treatment, antimicrobial cleaning and 1-methylcyclopropene treatment) for F. velutiper used for the last 5 years were compared to provide an outlook on future research directions. Overall, this review aims to provide a reference for developing novel, green and safe preservation techniques for F. velutiper. © 2023 Society of Chemical Industry.

Listeria monocytogenes Isolates from Meat Products and Processing Environment in Poland Are Sensitive to Commonly Used Antibiotics, with Rare Cases of Reduced Sensitivity to Ciprofloxacin

Antibiotic resistance is a global health problem, causing not only an increased mortality rate of bacterial infections but also economic losses due to, among other reasons, the need for longer hospital stays. Listeria monocytogenes is one of the foodborne pathogens with the ability to induce a serious illness called listeriosis, with approximately 20-30% fatal outcomes. The treatment regimen of listeriosis in humans includes the administration of antibiotics (in most cases, ampicillin or trimethoprim with sulfamethoxazole in case of allergies to β-lactams), so the resistance of this pathogen to antibiotics can potentially lead to increased mortality. The antibiotic sensitivity status of n = 153 L. monocytogenes isolates originating from meat food samples (raw and processed) and meat-processing environment (both contacting and non-contacting with food) collected between October 2020 and November 2021 in Poland was examined in this study. Susceptibility to antibiotics was determined using the disc diffusion method on Mueller-Hinton agar plates. All collected samples were susceptible to 9 antibiotics: ampicillin (10 µg), chloramphenicol (30 µg), erythromycin (15 µg), gentamicin (10 µg), penicillin (10 IU), streptomycin (10 µg), sulfamethoxazole/trimethoprim (1.25/23.75 µg), tetracycline (30 µg) and vancomycin (30 µg). Some of the isolates (n = 10; 6.5%) showed reduced susceptibility to ciprofloxacin (5 µg), which was classified as an intermediate response. All these ten isolates were collected from surfaces contacting with food in food-processing facilities.

Virulence Characteristics and Distribution of the Pathogen Listeria ivanovii in the Environment and in Food

Listeria ivanovii and L. monocytogenes, are the only pathogenic species of the genus Listeria and share many virulence factors and mechanisms of pathogenicity. L. ivanovii shows host tropism towards small ruminants and rodents and much lower virulence for humans compared to L. monocytogenes. However, severe infections caused by L. ivanovii, resulting in bacteremia, abortion and stillbirth, occasionally occurred in immunocompromised persons and in pregnant women, while in immunocompetent hosts L. ivanovii can cause gastroenteritis. In this review, the updated knowledge on virulence aspects and distribution of L. ivanovii in the environment and in food is summarized. Recent research on its virulence characters at genome level gave indications on how pathogenicity evolved in this bacterial species. As for L. monocytogenes, L. ivanovii infections occurred after the ingestion of contaminated food, so an overview of reports regarding its distribution in food products was carried out to obtain indications on the categories of foods exposed to contamination by L. ivanovii. It was found that a wide variety of food products can be a source of this microorganism and that, like L. monocytogenes, L. ivanovii is able to persist in the food production environment. Studies on its ability to grow in enrichment and isolation media suggested that its occurrence in nature might be underestimated. Moreover, virulence varies among strains for differences in virulence character regulation, presence/absence of genetic regions and the possible instability of a Listeria pathogenicity genomic island, LIPI-2, which is unique to L. ivanovii. We can conclude that L. ivanovii, as a possible pathogen for animals and humans, requires more focused investigations regarding its occurrence in the environment and in food and on intra-species variability of pathogenic potential.

Real-Time PCR Method for the Rapid Detection and Quantification of Pathogenic Staphylococcus Species Based on Novel Molecular Target Genes

Coagulase-positive Staphylococcus aureus is a foodborne pathogen considered one of the causes of food-related disease outbreaks. Like S. aureus, Staphylococcus capitis, Staphylococcus caprae, and S. epidermidis are opportunistic pathogens causing clinical infections and food contamination. The objective of our study was to develop a rapid, accurate, and monitoring technique to detect four Staphylococcus species in food. Four novel molecular targets (GntR family transcriptional regulator for S. aureus, phosphomannomutase for S. epidermidis, FAD-dependent urate hydroxylase for S. capitis, and Gram-positive signal peptide protein for S. caprae) were mined based on pan-genome analysis. Primers targeting molecular target genes showed 100% specificity for 100 non-target reference strains. The detection limit in pure cultures and artificially contaminated food samples was 10² colony-forming unit/mL for S. aureus, S. capitis, S. caprae, and S. epidermidis. Moreover, real-time polymerase chain reaction successfully detected strains isolated from various food matrices. Thus, our method allows an accurate and rapid monitoring of Staphylococcus species and may help control staphylococcal contamination of food.