Rapid detection of Salmonella in poultry environmental samples using real-time PCR coupled with immunomagnetic separation and whole genome amplification

Sampling method influences Salmonella detection and quantification in pre-harvest commercial broiler production

Effective pre-harvest Salmonella monitoring in broilers relies on accurate, reliable, and reproducible evaluation of pre-harvest Salmonella. In this study, six sampling methods were evaluated and compared to assess Salmonella prevalence and quantification during broiler production across three iterative experiments. In experiment one, bootsocks, electrostatic pad-rollers, feather swabs, cloacal swabs, fecal grabs, and litter grabs were collected from 24 houses across 10 farms (n = 288 samples). In the second experiment, bootsocks, bootsock-rollers, and feather swabs were collected in 16 houses on seven farms (n = 128). Bootsocks and bootsock-rollers were selected as the most reproducible sampling method. In experiment three both methods were performed in triplicate in 20 houses on 10 farms (n = 240). In all experiments, prevalence was determined by qPCR and by culture, then compared by Fisher's Exact test between and McNemar's test within methods. Salmonella was quantified by qPCR and Ct-values were compared using one-sided F-test. In experiment one, prevalence differed between methods by qPCR (p = 0.0150) only and the best performing sampling methods were bootsocks (42/48 culture and 41/48 qPCR positive), feather swabs (42/48 and 36/48), and electrostatic pad-rollers (35/48 and 34/48). In experiment 2, feather swabs differed by qPCR prevalence (p = 0.0004). Bootsocks (30/32 culture and 28/32 qPCR positive) and bootsock-rollers (31/32 and 32/32) performed best. In experiment 3, qPCR prevalence (210/240) was greater than culture (167/240) (p = 0.0021), but no differences were observed between methods or replicates. The average Ct-value for bootsocks and bootsock-rollers were 37.8 and 38.9, respectively and there was no difference in their variance (p = 0.8061). A linear mixed-effect model found that farm contributed 36.34 % of the variance observed while house, house-side, and replicate accounted for 24.69 %, 4.68 % and 3.85 %, respectively. This study shows that sampling methods directly influence both Salmonella detection and load recovery. For surveillance sampling, bootsocks and bootsock-rollers were found to best indicate pre-harvest Salmonella. These two methods were highly reproducible, user friendly, and provide the most reliable Salmonella results indicating the Salmonella prevalence in broiler flocks during production.

Growth assessment of Salmonella enterica multi-serovar populations in poultry rinsates with commonly used enrichment and plating media

Isolation of Salmonella from enrichment cultures of food or environmental samples is a complicated process. Numerous factors including fitness in various selective enrichment media, relative starting concentrations in pre-enrichment, and competition among multi-serovar populations and associated natural microflora, come together to determine which serovars are identified from a given sample. A recently developed approach for assessing the relative abundance (RA) of multi-serovar Salmonella populations (CRISPR-SeroSeq or Deep Serotyping, DST) is providing new insight into how these factors impact the serovars observed, especially when different selective enrichment methods are used to identify Salmonella from a primary enrichment sample. To illustrate this, we examined Salmonella-positive poultry pre-enrichment samples through the selective enrichment process in Tetrathionate (TT) and Rappaport Vassiliadis (RVS) broths and assessed recovery of serovars with each medium. We observed the RA of serovars detected post selective enrichment varied depending on the medium used, initial concentration, and competitive fitness factors, all which could result in minority serovars in pre-enrichment becoming dominant serovars post selective enrichment. The data presented provide a greater understanding of culture biases and lays the groundwork for investigations into robust enrichment and plating media combinations for detecting Salmonella serovars of greater concern for human health.

Preparation of polyclonal antibody against a universal bacterial antigen OmpA deduced by bioinformatic analysis and preliminary evaluation of concentration effects on foodborne pathogens

Rapid and ultrasensitive microbial detection in actual samples have challenges because of target pathogen diversity and low abundance. In this study, we attempted to capture and concentrate multiple pathogens by combining magnetic beads with polyclonal antibodies against a universal antigen of ompA, LAMOA-1, before further detection. A protein sequence consisting of 241 amino acids with spatial conformation similar to E. coli ompA was identified and expressed as a recombinant protein in prokaryotes according to the results of sequence alignment among 432 sequences of ompA belonging to intestinal bacteria from gram-negative bacteria. Purified from immunized rabbits, the anti-LAMOA-1 antibody was shown to effectively recognize 12 foodborne bacterial species. Antibody-conjugated beads were used to concentrate the bacteria when the bacterial concentration in artificially contaminated samples is between 10 and 100 CFU/mL, which shortens detection duration by 8-24 h. The enrichment strategy is potentially beneficial for detection of foodborne pathogens.

Development of a lateral flow dipstick test for the detection of 4 strains of Salmonella spp. in animal products and animal production environmental samples based on loop-mediated isothermal amplification

OBJECTIVE

This study aimed to develop loop-mediated isothermal amplification (LAMP) combined with lateral flow dipstick (LFD) and compare it with LAMP-AGE, polymerase chain reaction (PCR), and standard Salmonella culture as reference methods for detecting Salmonella contamination in animal products and animal production environmental samples.

METHODS

The SalInvA01 primer, derived from the InvA gene and designed as a new probe for LFD detection, was used in developing this study. Adjusting for optimal conditions by temperature, time, and reagent concentration includes evaluating the specificity and limit of detection. The sampling of 120 animal product samples and 350 animal production environmental samples was determined by LAMP-LFD, comparing LAMP-AGE, PCR, and the culture method.

RESULTS

Salmonella was amplified using optimal conditions for the LAMP reaction and a DNA probe for LFD at 63°C for 60 minutes. The specificity test revealed no cross-reactivity with other microorganisms. The limit of detection of LAMP-LFD in pure culture was 3×102 CFU/mL (6 CFU/reaction) and 9.01 pg/μL in genomic DNA. The limit of detection of the LAMP-LFD using artificially inoculated in minced chicken samples with 5 hours of pre-enrichment was 3.4×104 CFU/mL (680 CFU/reaction). For 120 animal product samples, Salmonella was detected by the culture method, LAMP-LFD, LAMP-AGE, and PCR in 10/120 (8.3%). In three hundred fifty animal production environmental samples, Salmonella was detected in 91/350 (26%) by the culture method, equivalent to the detection rates of LAMP-LFD and LAMP-AGE, while PCR achieved 86/350 (24.6%). When comparing sensitivity, specificity, positive predictive value, and accuracy, LAMP-LFD showed the best results at 100%, 95.7%, 86.3%, and 96.6%, respectively. For Kappa index of LAMP-LFD, indicated nearly perfect agreement with culture method.

CONCLUSION

The LAMP-LFD Salmonella detection, which used InvA gene, was highly specific, sensitive, and convenient for identifying Salmonella. Furthermore, this method could be used for Salmonella monitoring and primary screening in animal products and animal production environmental samples.

Effects of Cinnamon Essential Oil on Oxidative Damage and Outer Membrane Protein Genes of Salmonella enteritidis Cells

Salmonella is an important pathogen causing food poisoning. Food safety and health are the themes of today′s society. As a class of food-borne pathogens, Salmonella enteritidis had become one of the common zoonotic pathogens. Cinnamon essential oil (CEO) had been reported as an antibacterial agent, but there are few studies on its antibacterial mechanism. This study investigated the effects of CEO on oxidative damage and outer membrane protein genes of Salmonella enteritidis cells. First, the reactive oxygen species content in bacteria treated with different concentrations of cinnamon essential oil was determined by fluorescence spectrophotometry, and the effects of superoxide dismutase (SOD), catalase (CAT) and superoxide dismutase (SOD), and catalase (CAT) and peroxidase (POD) were determined by the kit method. The activity of POD and the content of malondialdehyde (MDA) were investigated to investigate the oxidative damage of CEO to Salmonella enteritidis cells. By analyzing the effect of CEO on the Salmonella enteritidis cell membrane’s outer membrane protein gene expression, the mechanism of CEO′s action on the Salmonella enteritidis cell membrane was preliminarily discussed. The results showed that CEO treatment had an obvious oxidative damaging effect on Salmonella enteritidis. Compared with the control group, the increase in CEO concentration caused a significant increase in the bacteria ROS content. The observation technique experiment found that with the increase in CEO concentration, the number of stained cells increased, which indicated that CEO treatment would increase the ROS level in the cells, and it would also increase with the increase in CEO concentration, thus causing the oxidation of cells and damage. In addition, CEO treatment also caused the disruption of the balance of the cellular antioxidant enzymes (SOD, CAT, POD) system, resulting in an increase in the content of MDA, a membrane lipid metabolite, and increased protein carbonylation, which ultimately inhibited the growth of Salmonella enteritidis. The measurement results of cell membrane protein gene expression levels showed that the Omp genes to be detected in Salmonella enteritidis were all positive, which indicated that Salmonella enteritidis carried these four genes. Compared with the control group, the relative expressions of OmpF, OmpA and OmpX in the CEO treatment group were significantly increased (p < 0.05), which proved that the cell function was disturbed. Therefore, the toxicity of CEO to Salmonella enteritidis could be attributed to the damage of the cell membrane and the induction of oxidative stress at the same time. It was speculated that the antibacterial mechanism of CEO was the result of multiple effects. This work was expected to provide a theoretical basis for the development of new natural food preservatives and the prevention and control of Salmonella enteritidis.

Molecular-based monitoring of live vaccines in dust samples from experimental and commercial chicken flocks and its potential use as a screening test

Despite the high cost of vaccination programmes, conventional methods to evaluate vaccine uptake are often impractical and costly. More recently, molecular-based testing of poultry dust has been used to monitor the "take" of Marek's disease virus and infectious laryngotracheitis virus (ILTV) live vaccines. This study aimed to provide proof-of-concept for detecting other poultry pathogens by using molecular detection of vaccine microorganisms in poultry dust of vaccinated flocks. Dust and choanal cleft and cloacal swabs were collected from chickens vaccinated against avian encephalomyelitis virus (AEV), fowlpox virus (FPV), Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) using live vaccines in an experimental flock. Dust samples were collected weekly from 5 commercial breeder or layer flocks from day-old up to 25 weeks of age. These flocks were vaccinated against Newcastle disease virus (NDV), infectious bronchitis virus (IBV), infectious bursal disease virus (IBDV), ILTV, fowl adenovirus (FAdV), MG and MS. Samples were tested for nucleic acids of these microorganisms by PCR or reverse transcriptase PCR. Genomes of all targeted vaccines were detected in dust samples from the experimental and commercial flocks except for FPV, which was detected only in the experimental flock. FAdV was detected in unvaccinated commercial flocks. These findings suggest that PCR detection of target organisms in dust samples has potential as a relatively simple and inexpensive population-level test to monitor vaccine take and/or pathogen status in chicken flocks. Further studies comparing the detection of each of these microorganisms in poultry dust with individual birds samples are required to validate this approach.

Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment

In this study, we addressed different aspects regarding the implementation of quasimetagenomic sequencing as a hybrid surveillance method in combination with enrichment for early detection of Listeria monocytogenes in the food industry. Different experimental enrichment cultures were used, comprising seven L. monocytogenes strains of different sequence types (STs), with and without a background microbiota community. To assess whether the proportions of the different STs changed over time during enrichment, the growth and population dynamics were assessed using dapE colony sequencing and dapE and 16S rRNA amplicon sequencing. There was a tendency of some STs to have a higher relative abundance during the late stage of enrichment when L. monocytogenes was enriched without background microbiota. When coenriched with background microbiota, the population dynamics of the different STs was more consistent over time. To evaluate the earliest possible time point during enrichment that allows the detection of L. monocytogenes and at the same time the generation of genetic information that enables an estimation regarding the strain diversity in a sample, quasimetagenomic sequencing was performed early during enrichment in the presence of the background microbiota using Oxford Nanopore Technologies Flongle and Illumina MiSeq sequencing. The application of multiple displacement amplification (MDA) enabled detection of L. monocytogenes (and the background microbiota) after only 4 h of enrichment using both applied sequencing approaches. The MiSeq sequencing data additionally enabled the prediction of cooccurring L. monocytogenes strains in the samples.

IMPORTANCE We showed that a combination of a short primary enrichment combined with MDA and Nanopore sequencing can accelerate the traditional process of cultivation and identification of L. monocytogenes. The use of Illumina MiSeq sequencing additionally allowed us to predict the presence of cooccurring L. monocytogenes strains. Our results suggest quasimetagenomic sequencing is a valuable and promising hybrid surveillance tool for the food industry that enables faster identification of L. monocytogenes during early enrichment. Routine application of this approach could lead to more efficient and proactive actions in the food industry that prevent contamination and subsequent product recalls and food destruction, economic and reputational losses, and human listeriosis cases.

Immunomagnetic separation: An effective pretreatment technology for isolation and enrichment in food microorganisms detection

The high efficiency and accurate detection of foodborne pathogens and spoilage microorganisms in food are a task of great social, economic, and public health importance. However, the contamination levels of target bacteria in food samples are very low. Owing to the background interference of food ingredients and negative impact of nontarget flora, the establishment of efficient pretreatment techniques is very crucial for the detection of food microorganisms. With the significant advantages of high specificity and great separation efficiency, immunomagnetic separation (IMS) assay based on immunomagnetic particles (IMPs) has been considered as a powerful system for the separation and enrichment of target bacteria. This paper mainly focuses on the development of IMS as well as their application in food microorganisms detection. First, the basic principle of IMS in the concentration of food bacteria is presented. Second, the effect of different factors, including the sizes of magnetic particles (MPs), immobilization of antibody and operation parameters (the molar ratio of antibody to MPs, the amount of IMPs, incubation time, and bacteria concentration) on the immunocapture efficiency of IMPs are discussed. The performance of IMPs in different food samples is also evaluated. Finally, the combination of IMS and various kinds of detection methods (immunology-based methods, nucleic acid-based methods, fluorescence methods, and biosensors) to detect pathogenic and spoilage organisms is summarized. The challenges and future trends of IMS are also proposed. As an effective pretreatment technique, IMS can improve the detection sensitivity and shorten their testing time, thus exhibiting broad prospect in the field of food bacteria detection.

Combining impedance biosensor with immunomagnetic separation for rapid screening of Salmonella in poultry supply chains

Salmonella screening is a key to ensure food safety in poultry supply chains. Currently available Salmonella detection methods including culture, polymerase chain reaction and enzyme-linked immuno-sorbent assay could not achieve rapid, sensitive, and in-field detection. In this study, different strategies for separation and detection of Salmonella were proposed, compared, and improved based on our previous studies on immunomagnetic separation and impedance biosensor. First, the coaxial capillary for immunomagnetic separation of target bacteria was improved with less contamination, and 3 strategies based on the improved capillary and immunomagnetic nanoparticles were compared to separate the target bacteria from sample and form the magnetic bacteria. The experimental results showed that the strategy of capture in tube and separation in capillary was the most suitable with separation efficiency of approximately 88%. Then, the immune gold nanoparticles coated with urease were used to label the magnetic bacteria, resulting in the formation of enzymatic bacteria, which were injected into the capillary. After the urea was catalyzed by the urease on the enzymatic bacteria in the capillary, different electrodes were compared to measure the impedance of the catalysate and the screen-printed electrode with higher sensitivity and better stability was the most suitable. This impedance biosensor-based bacterial detection strategy was able to detect Salmonella as low as 102 CFU/mL in 2 h without complex operations. Compared to the gold standard culture method for practical screening of Salmonella in poultry supply chains, this proposed strategy had an accuracy of approximately 90% for 75 real poultry samples.