Direct triplex loop-mediated isothermal amplification assay for the point-of-care molecular detection of Salmonella genus, subspecies I, and serovar Typhimurium

An enzyme-activated loop primer probe LAMP method based on a new SNP site in the group_17537 gene for rapid on-site detection of Salmonella Pullorum

Pullorum disease (PD) is a widespread disease that causes significant economic losses within the poultry industry of developing countries. An effective strategy for its prevention and control involves the implementation of decontamination procedures utilizing highly specific on-site detection techniques. In this study, a single-nucleotide polymorphism (SNP) site within the group_17537 gene of Salmonella enterica serovar Gallinarum biovars Pullorum (S. Pullorum) was found by using bioinformatics tools. The prevalence of this SNP among 165 strains of S. Pullorum was determined to exceed 96.3 %. The SNP exhibited a specificity rate greater than 99.9 %, with only 0.08 % detected among 2490 non-target Salmonella strains. It can be concluded that this SNP can be employed to distinguish S. Pullorum from other serotypes of Salmonella, specifically Salmonella enterica serovar Enteritidis (S. Enteritidis) and Salmonella enterica serovar Gallinarum biovars Gallinarum (S. Gallinarum). Additionally, an enzyme-activated loop primer probe LAMP (EALP-LAMP) was developed based on this SNP site for the detection of S. Pullorum. This method exhibited excellent specificity and reproducibility, achieving limit of detection of 53.5 copies/µL with plasmid DNA and 0.2 pg/µL with genomic DNA. Moreover, in clinical applications involving 190 chick embryo samples from poultry farms, 24 samples identified as S. Pullorum positive, aligning with results obtained through traditional isolation and quantitative real-time PCR (qPCR) methods. These fingdings highlight the significant potential of this method, which offers accurate, rapid, on-site and visual detection of S. Pullorum.

Research progress of loop-mediated isothermal amplification in the detection of Salmonella for food safety applications

Salmonella, the prevailing zoonotic pathogen within the Enterobacteriaceae family, holds the foremost position in global bacterial poisoning incidents, thereby signifying its paramount importance in public health. Consequently, the imperative for expeditious and uncomplicated detection techniques for Salmonella in food is underscored. After more than two decades of development, loop-mediated isothermal amplification (LAMP) has emerged as a potent adjunct to the polymerase chain reaction, demonstrating significant advantages in the realm of isothermal amplification. Its growing prominence is evident in the increasing number of reports on its application in the rapid detection of Salmonella. This paper provides a systematic exposition of the technical principles and characteristics of LAMP, along with an overview of the research progress made in the rapid detection of Salmonella using LAMP and its derivatives. Additionally, the target genes reported in various levels, including Salmonella genus, species, serogroup, and serotype, are summarized, aiming to offer a valuable reference for the advancement of LAMP application in Salmonella detection. Finally, we look forward to the development direction of LAMP and expect more competitive methods to provide strong support for food safety applications.

Characterization and resistance mechanism of phage-resistant strains of Salmonella enteritidis

In the face of the increasingly severe problem of antibiotic resistance, phage therapy is regarded as a highly potential alternative. Compared with traditional antimicrobial agents, a key research area of phage therapy is the study of phage-resistant mutant bacteria. To effectively monitor and prevent this resistance, it is crucial to conduct in-depth exploration of the mechanism behind phage resistance. In this study, a strain of Salmonella enteritidis (sm140) and the corresponding phage (Psm140) were isolated from chicken liver and sewage, respectively. Using the double-layer plate method, successfully screened out phage-resistant mutant strains. Whole-genome resequencing of 3 resistant strains found that the wbaP gene of all 3 strains had mutations at a specific position (1,118), with the base changing from G to A. This mutation causes the gene-encoded glycine to be replaced by aspartic acid. Subsequent studies found that the frequency of this gene mutation is extremely high, reaching 84%, and all mutations occur at the same position. To further explore the relationship between the wbaP gene and phage resistance, knockout strains and complement strains of the wbaP gene were constructed. The experimental results confirmed the association between the wbaP gene and phage resistance. At the same time, biological characteristics and virulence were evaluated for wild strains, resistant strains, knockout strains, and complement strains. It was found that mutations or deletions of the wbaP gene lead to a decrease in bacterial environmental adaptability and virulence. Through systematic research on the mechanism and biological characteristics of phage resistance, this study provides important references and guidance for the development of new phage therapies, promoting progress in the field of antimicrobial treatment. At the same time, the emergence of phage resistance due to wbaP gene mutations is reported for the first time in salmonella, providing a new perspective and ideas for further studying phage resistance mechanisms.

Gold nanoparticle-decorated covalent organic frameworks as amplified light-scattering probes for highly sensitive immunodetection of Salmonella in milk

Traditional immunoassays exhibit insufficient screening sensitivity for foodborne pathogens due to their low colorimetric signal intensities. Herein, we propose an ultrasensitive dynamic light scattering (DLS) immunosensor for Salmonella based on a "cargo release-seed growth" strategy enabled by a probe, namely gold nanoparticle-decorated covalent organic frameworks (COF@AuNP). Large amounts of AuNPs in COF@AuNP can be released by acid treatment-induced decomposition of the imine-linked COF, and then they are enlarged via gold growth to generate a dramatically enhanced light-scattering signal, leading to a vast improvement in detection sensitivity. Based on an immunomagnetic microbead carrier, the proposed DLS immunosensor is capable of detecting trace Salmonella in milk in the range of 2.0 × 102-2.0 × 105 CFU mL-1, with a limit of detection of 60 CFU mL-1. The immunosensor also demonstrated excellent selectivity, good accuracy and precision, and high reliability for detecting Salmonella in milk.

Label-Free Sequence-Specific Visualization of LAMP Amplified Salmonella via DNA Machine Produces G-Quadruplex DNAzyme

Salmonella is one of four key global causes of diarrhea, and in humans, it is generally contracted through the consumption of contaminated food. It is necessary to develop an accurate, simple, and rapid method to monitor Salmonella in the early phase. Herein, we developed a sequence-specific visualization method based on loop-mediated isothermal amplification (LAMP) for the detection of Salmonella in milk. With restriction endonuclease and nicking endonuclease, amplicons were produced into single-stranded triggers, which further promoted the generation of a G-quadruplex by a DNA machine. The G-quadruplex DNAzyme possesses peroxidase-like activity and catalyzes the color development of 2,2'-azino-di-(3-ethylbenzthiazoline sulfonic acid) (ABTS) as the readouts. The feasibility for real samples analysis was also confirmed with Salmonella spiked milk, and the sensitivity was 800 CFU/mL when observed with the naked eye. Using this method, the detection of Salmonella in milk can be completed within 1.5 h. Without the involvement of any sophisticated instrument, this specific colorimetric method can be a useful tool in resource-limited areas.

Adsorption-Free Self-Priming Direct Digital Dual-crRNA CRISPR/Cas12a-Assisted Chip for Ultrasensitive Detection of Pathogens

Rapid and sensitive pathogen detection methods are critical for disease diagnosis and treatment. RPA-CRISPR/Cas12 systems have displayed remarkable potential in pathogen detection. A self-priming digital PCR chip is a powerful and attractive tool for nucleic detection. However, the application of the RPA-CRISPR/Cas12 system to the self-priming chip still has great challenges due to the problems of protein adsorption and two-step detection mode of RPA-CRISPR/Cas12. In this study, an adsorption-free self-priming digital chip was developed and a direct digital dual-crRNAs (3D) assay was established based on the chip for ultrasensitive detection of pathogens. This 3D assay combined the advantages of rapid amplification of RPA, specific cleavage of Cas12a, accurate quantification of digital PCR, and point-of-care testing (POCT) of microfluidics, enabling accurate and reliable digital absolute quantification of Salmonella in POCT. Our method can provide a good linear relationship of Salmonella detection in the range from 2.58 × 10¹ to 2.58 × 10⁴ cells/mL with a limit of detection ∼0.2 cells/mL within 30 min in a digital chip by targeting the invA gene of Salmonella. Moreover, the assay could directly detect Salmonella in milk without nucleic acid extraction. Therefore, the 3D assay has the significant potential to provide accurate and rapid pathogen detection in POCT. This study provides a powerful nucleic detection platform and facilitates the application of CRISPR/Cas-assisted detection and microfluidic chips.

Two-stage nicking enzyme signal amplification (NESA)-based biosensing platform for the ultrasensitive electrochemical detection of pathogenic bacteria

The sensitive and selective detection of pathogenic bacteria represents an essential approach in food safety analysis and clinical diagnostics. We report the development of a simple, rapid, and low-cost electrochemical biosensing strategy for the detection of pathogenic bacteria with ultrasensitivity and high specificity. The biosensor relies on the target and aptamer binding-triggered two-stage nicking enzyme signal amplification (NESA) and three-way junction probe-mediated electrochemical signal transduction. In the presence of the target S. typhimurium, the specific binding of S. typhimurium and aptamer results in the release of a primer, which hybridizes with HAP1 and initiates an extension reaction with the aid of polymerase and dNTPs. A specific recognition site for Nt.BsmaI is generated in the DNA duplex; thus, the produced DNA is nicked and the secondary primer is released (named recycle I). Subsequently, the reaction solution supplemented with a helper DNA is dropped on the electrode surface, and a three-way junction probe containing a specific recognition site for Nt.BsmaI is thus formed. The MB-labeled probe is nicked with the help of Nt.BsmaI and the dissociated primer-helper DNA duplex combines with another HAP2 (named recycle II). Thus, a remarkably decreased electrochemical signal is generated because the electroactive MB is far away from the electrode surface. As far as we know, this work is the first time that NESA and three-way junction probe-mediated electrochemical signal transduction has been used for pathogenic bacteria detection. Under optimal conditions, the results reveal that the calibration plot obtained for S. typhimurium is approximately linear from 9.6 to 9.6 × 10⁵ cfu mL^-1 with the limit of detection of 8 cfu mL^-1. Additionally, the proposed strategy has been successfully applied to the quantitative assay of S. typhimurium in the real samples. Therefore, the NESA-based biosensing strategy might create a useful and practical platform for pathogenic bacteria identification, and the related food safety analysis and clinical diagnosis.

Overview of Rapid Detection Methods for Salmonella in Foods: Progress and Challenges

Salmonella contamination in food production and processing is a serious threat to consumer health. More and more rapid detection methods have been proposed to compensate for the inefficiency of traditional bacterial cultures to suppress the high prevalence of Salmonella more efficiently. The contamination of Salmonella in foods can be identified by recognition elements and screened using rapid detection methods with different measurable signals (optical, electrical, etc.). Therefore, the different signal transduction mechanisms and Salmonella recognition elements are the key of the sensitivity, accuracy and specificity for the rapid detection methods. In this review, the bioreceptors for Salmonella were firstly summarized and described, then the current promising Salmonella rapid detection methods in foodstuffs with different signal transduction were objectively summarized and evaluated. Moreover, the challenges faced by these methods in practical monitoring and the development prospect were also emphasized to shed light on a new perspective for the Salmonella rapid detection methods applications.

Fungal Genomics in Respiratory Medicine: What, How and When?

Respiratory infections caused by fungal pathogens present a growing global health concern and are a major cause of death in immunocompromised patients. Worryingly, coronavirus disease-19 (COVID-19) resulting in acute respiratory distress syndrome has been shown to predispose some patients to airborne fungal co-infections. These include secondary pulmonary aspergillosis and mucormycosis. Aspergillosis is most commonly caused by the fungal pathogen Aspergillus fumigatus and primarily treated using the triazole drug group, however in recent years, this fungus has been rapidly gaining resistance against these antifungals. This is of serious clinical concern as multi-azole resistant forms of aspergillosis have a higher risk of mortality when compared against azole-susceptible infections. With the increasing numbers of COVID-19 and other classes of immunocompromised patients, early diagnosis of fungal infections is critical to ensuring patient survival. However, time-limited diagnosis is difficult to achieve with current culture-based methods. Advances within fungal genomics have enabled molecular diagnostic methods to become a fast, reproducible, and cost-effective alternative for diagnosis of respiratory fungal pathogens and detection of antifungal resistance. Here, we describe what techniques are currently available within molecular diagnostics, how they work and when they have been used.