Simultaneous enumeration of Cronobacter sakazakii and Staphylococcus aureus in powdered infant foods through duplex TaqMan real-time PCR

Rapid detection methods for foodborne pathogens based on nucleic acid amplification: Recent advances, remaining challenges, and possible opportunities

This article presents a review of recent advancements in the utilization of NAA-based techniques for detecting foodborne pathogens in food products, focusing on studies conducted within the past five years. This review revealed that recent research efforts have primarily aimed at enhancing sensitivity and specificity by improving sample pre-treatment/preparation, DNA isolation, and readout methods. Isothermal-based amplification methods, such as LAMP, RPA, RAA, and RCA, have emerged as promising approaches, providing rapid results within one h and often demonstrating comparable or superior sensitivity to conventional or qPCR methods. However, the attention paid to specific pathogens varies, with Salmonella spp., Listeria spp., E. coli, and V. parahaemolyticus receiving more focus than norovirus and other similar pathogens. NAA-based methods have the potential to significantly contribute to food safety and public health protection. However, further advancements are necessary to fully realize their benefits.

Isothermal Amplification and CRISPR/Cas12a-System-Based Assay for Rapid, Sensitive and Visual Detection of Staphylococcus aureus

Staphylococcus aureus exists widely in the natural environment and is one of the main food-borne pathogenic microorganisms causing human bacteremia. For safe food management, a rapid, high-specificity, sensitive method for the detection of S. aureus should be developed. In this study, a platform for detecting S. aureus (nuc gene) based on isothermal amplification (loop-mediated isothermal amplification-LAMP, recombinase polymerase amplification-RPA) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas12a) proteins system (LAMP, RPA-CRISPR/Cas12a) was proposed. In this study, the LAMP, RPA-CRISPR/Cas12a detection platform and immunochromatographic test strip (ICS) were combined to achieve a low-cost, simple and visualized detection of S. aureus. The limit of visual detection was 57.8 fg/µL of nuc DNA and 6.7 × 102 CFU/mL of bacteria. Moreover, the platform could be combined with fluorescence detection, namely LAMP, RPA-CRISPR/Cas12a-flu, to establish a rapid and highly sensitive method for the detection of S. aureus. The limit of fluorescence detection was 5.78 fg/µL of genomic DNA and 67 CFU/mL of S. aureus. In addition, this detection platform can detect S. aureus in dairy products, and the detection time was ~40 min. Consequently, the isothermal amplification CRISPR/Cas12a platform is a useful tool for the rapid and sensitive detection of S. aureus in food.

Co-culture of Cronobacter sakazakii and Staphylococcus aureus: Explore the influence of mixed biofilm formation and regulation of Cronobacter sakazakii biofilm formation genes

Bacterial biofilm is a protective matrix composed of metabolites secreted by bacteria that envelop bacteria. By forming a biofilm, bacteria can considerably improve their environmental tolerance. In food-related processing environment, different types of microorganisms are often present in biofilms. The main contaminating strain in the powdered infant formula (PIF) processing environment, Cronobacter sakazakii and Staphylococcus aureus continues to pollute the PIF processing environment after biofilm production. This study selected Cronobacter sakazakii with a weak biofilm-forming ability as one of the test organisms. The coexistence of Cronobacter sakazakii and Staphylococcus aureus on the surface of production equipment was simulated to analyze the interaction. Biofilm formation in the co-culture group was significantly higher than the others. In-depth study of the effect of Staphylococcus aureus on the biofilm formation genes of Cronobacter sakazakii. Results show two bacteria can coexist on the surface of a metal device, forming a more compact hybrid biofilm structure. Under co-culture conditions, S. aureus increased bcsA and fliD expression in Cronobacter sakazakii, whereas decreased bcsC expression. Signaling molecules produced by Staphylococcus aureus (Autoinducer 2) significantly promoted the biofilm formation of Cronobacter sakazakii at the concentration of 0-500 ng/mL (0.099-0.177) and up-regulated the expression of bcsA, filD and flhD genes.

A Method to Directly Identify Cronobacter sakazakii in Liquid Medium by MALDI-TOF MS

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry has been widely used as an emerging technology for the rapid identification of microorganisms. Cronobacter sakazakii (C. sakazakii) is a food-borne pathogen of particular importance to the powdered infant formula (PIF) processing environment due to its high lethality in infants. However, the traditional solid spotting detection method of pretreating samples for MALDI-TOF MS leads only to qualitative detection of C. sakazakii. We developed a new, low-cost, robust liquid spotting pretreatment method and used a response surface methodology to optimize its parameters. The applicability, accuracy, and quantitative potential were measured for different types of samples. The optimal parameters of this method were as follows: a volume of 70% formic acid of 25 μL, treatment with ultrasound at 350 W for 3 min, and a volume of acetonitrile added of 75 μL. These conditions led to the highest identification score for C. sakazakii (1926.42 ± 48.497). This method was found to detect bacteria accurately and reproducibly. When 70 strains of C. sakazakii isolates were analyzed with this method, the identification accuracy was 100%. The detection limit of C. sakazakii in environmental and PIF samples was 4.1 × 10¹ cfu/mL and 2.72 × 10³ cfu/mL, respectively.

Electrochemical Detection of ompA Gene of C. sakazakii Based on Glucose-Oxidase-Mimicking Nanotags of Gold-Nanoparticles-Doped Copper Metal-organic Frameworks

The present work developed an electrochemical genosensor for the detection of virulence outer membrane protein A (ompA, tDNA) gene of Cronobacter sakazakii (C. sakazakii) by exploiting the excellent glucose-oxidase-mimicking activity of copper Metal-organic frameworks (Cu-MOF) doped with gold nanoparticle (AuNPs). The signal nanotags of signal probes (sDNA) that biofunctionalized AuNPs@Cu-MOF (sDNA-AuNPs@Cu-MOF) were designed using an Au-S bond. The biosensor was prepared by immobilization capture probes (cDNA) onto an electrodeposited AuNPs-modified glassy carbon electrode (GCE). AuNPs@Cu-MOF was introduced onto the surface of the GCE via a hybridization reaction between cDNA and tDNA, as well as tDNA and sDNA. Due to the enhanced oxidase-mimicking activity of AuNPs@Cu-MOF to glucose, the biosensor gave a linear range of 1.0 × 10^-15 to 1.0 × 10^-9 mol L^-1 to tDNA with a detection limit (LOD) of 0.42 fmol L^-1 under optimized conditions using differential pulse voltammetry measurement (DPV). It can be applied in the direct detection of ompA gene segments in total DNA extracts from C. sakazakii with a broad linear range of 5.4-5.4 × 10⁵ CFU mL^-1 and a LOD of 0.35 CFU mL^-1. The biosensor showed good selectivity, fabricating reproducibility and storage stability, and can be used for the detection of ompA gene segments in real samples with recovery between 87.5% and 107.3%.

Visual detection of Cronobacter sakazakii on a microfluidic chip fabricated by a 3D molding method

Cronobacter sakazakii (C. sakazakii) is a pathogenic bacterium associated with life-threatening neonatal infections that have been linked to contaminated powdered infant formula (PIF). Most C. sakazakii testing is still limited in microbiology laboratories due to the need for sophisticated equipment and professional technicians. Microfluidic chips combined with isothermal amplification analysis are shown to be one of the most attractive microbiological on-site detection platforms. In this study, PDMS microfluidic chips were fabricated by a simple 3D molding method and sealed with "PDMS glue". The chip consisted of an inlet, a microchannel, six reaction wells, and six vent holes. And based on the 16S rRNA and ITS genes of C. sakazakii, we have successfully proposed a multiplex competitive annealing mediated isothermal amplification (mCAMP) assay on the microfluidic chip for the visual detection of C. sakazakii in PIF samples. The primers were fixed in the reaction wells of the chip before detection, which can be preserved for 60 days at 4 °C. The results showed that the established mCAMP assay had high specificity, and the limit of detection was 2.2 × 10³ CFU g^-1. With enrichment culture, even if the initial inoculation level is 1 CFU g^-1, the mCAMP assay can still detect the presence of C. sakazakii in spiked PIF samples. The test results are visible to the naked eye, which is suitable for rapid analysis in resource-limited settings.

Development of cobalt oxyhydroxide-aptamer-based upconversion sensing nano-system for the rapid detection of Staphylococcus aureus

Staphylococcus aureus (S. aureus) is a common pathogen that is dangerous to humans' health. Herein, a novel upconversion fluorescent biosensor based on fluorescence resonance energy transfer from aptamer-labeled upconversion nanoparticles (UCNPs-apt) as donor and cobalt oxyhydroxide (CoOOH) nanosheets as acceptor was designed to detect S. aureus in complex matrices. The principle of the work relies on fluorescence resonance energy transfer as UCNPs-apt can self-assemble on CoOOH nanosheet surfaces by van der Waals forces to effectively quench the fluorescence. When S. aureus was added, the aptamer was able to preferentially capture the target, resulting in the dissociation of donor and acceptor and the recovery of fluorescence. The structure and morphology of the nanostructures were assigned in detail by a series of characterizations, and the energy transfer mechanism was evaluated by time-resolved lifetime measurements. Under the optimal conditions, a linear calibration plot was obtained in a concentration range of 45-4.5 × 10⁶ CFU/mL with a limit of detection of 15 CFU/mL. In addition, the proposed biosensor was used for S. aureus detection in real samples (e.g., pork, beef), and the detection result showed no significant difference (p > 0.05) compared with the conventional plate count approach. Hence, the fabricated biosensor holds a potential application for S. aureus in food analysis and public health.

Research progress on detection techniques for point-of-care testing of foodborne pathogens

The global burden of foodborne disease is enormous and foodborne pathogens are the leading cause of human illnesses. The detection of foodborne pathogenic bacteria has become a research hotspot in recent years. Rapid detection methods based on immunoassay, molecular biology, microfluidic chip, metabolism, biosensor, and mass spectrometry have developed rapidly and become the main methods for the detection of foodborne pathogens. This study reviewed a variety of rapid detection methods in recent years. The research advances are introduced based on the above technical methods for the rapid detection of foodborne pathogenic bacteria. The study also discusses the limitations of existing methods and their advantages and future development direction, to form an overall understanding of the detection methods, and for point-of-care testing (POCT) applications to accurately and rapidly diagnose and control diseases.

A lab-on-a-tube biosensor for automatic detection of foodborne bacteria using rotated Halbach magnetic separation and Raspberry Pi imaging

A lab-on-a-tube biosensor was established to rapidly, sensitively and automatically detect foodborne bacteria through a rotatable Halbach magnet to form and rotate magnetic nanobead (MNB) chains for specific isolation of target bacteria, gold@platinum nanocatalysts (Au@PtNCs) to label target bacteria for efficient amplification of detection signal and Raspberry Pi App to collect and analyze the image of catalysate. First, the glass tube was successively preloaded with the mixture of MNBs, sample and Au@PtNCs, the washing buffer (skim milk) and the substrate (hydrogen peroxide-3,30,5,50-tetramethylbenzidine), and they were separated by air gaps. After the tube was placed on the biosensor, the MNB chains were stably formed and continuously rotated using the Halbach magnet and the mixture was moved back and forth using a programmable peristaltic pump, thus making the formation of MNB-bacteria-Au@PtNCs complexes. After the washing buffer was moved to wash the complexes, the substrate was then moved to resuspend the complexes, resulting in the catalytic reaction that changed the color of the substrate. Finally, the catalysate was moved to the designated area, the image of which was analyzed by the Raspberry Pi App to quantitatively determine the concentration of bacteria in the samples. This biosensor was able to detect Salmonella in spiked chicken samples in 1 h with lower detection limit of 8 CFU/50 μL and a recovery from 88.96% to 99.74%. This biosensor based on a single tube is very promising to automatically detect foodborne bacteria due to its low cost, high integration and simple operation.

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.