Rapid detection of Salmonella by polymerase chain reaction

Magnetic Nanoparticles Enhanced Surface Plasmon Resonance Biosensor for Rapid Detection of Salmonella Typhimurium in Romaine Lettuce

Salmonella is one of the major foodborne pathogens responsible for many cases of illnesses, hospitalizations and deaths worldwide. Although different methods are available to timely detect Salmonella in foods, surface plasmon resonance (SPR) has the benefit of real-time detection with a high sensitivity and specificity. The purpose of this study was to develop an SPR method in conjunction with magnetic nanoparticles (MNPs) for the rapid detection of Salmonella Typhimurium. The assay utilizes a pair of well-characterized, flagellin-specific monoclonal antibodies; one is immobilized on the sensor surface and the other is coupled to the MNPs. Samples of romaine lettuce contaminated with Salmonella Typhimurium were washed with deionized water, and bacterial cells were captured on a filter membrane by vacuum filtration. SPR assays were compared in three different formats-direct assay, sequential two-step sandwich assay, and preincubation one-step sandwich assay. The interaction of flagellin and MNPs with the antibody-immobilized sensor surface were analyzed. SPR signals from a sequential two-step sandwich assay and preincubation one-step sandwich assay were 7.5 times and 14.0 times higher than the direct assay. The detection limits of the assay were 4.7 log cfu/mL in the buffer and 5.2 log cfu/g in romaine lettuce samples.

Sequencing and phylogenetic analysis of the stn gene of Salmonella species isolated from different environmental sources at Lake Qarun protectorate: The role of migratory birds and public health importance

BACKGROUND AND AIM

Salmonella causes most foodborne bacterial illnesses worldwide. It is found in various hosts, including pets, farm animals, and wild animals, as well as the environment. This study aimed to examine the epidemiological relationship between Salmonella isolates from aquatic environments and those from other avian hosts.

MATERIALS AND METHODS

The study examined 12 water samples, 210 aquatic animals, and 45 migratory aquatic bird samples collected from the protected area of Lake Qarun in El-Fayoum Governorate, Egypt, during migration seasons from different waterfowl migration areas (from October 2018 to January 2019). In addition, 45 fecal samples from domestic chickens were collected from the same geographic location from poultry farms. Bacteriological examination and polymerase chain reaction assay of two virulence genes (i.e., invA and stn) were performed to isolate and identify Salmonella.

RESULTS

Salmonella was isolated from 58.3% (7/12) of Lake Qarun water samples, 13.3% (6/45) of migratory waterfowl, 6.6% of (3/45) of chickens (Gallus gallus domesticus), and 4.3% (3/70) of fish and pooled brine shrimp. In migratory aquatic bird species that were sampled, Salmonella were isolated from 23.1% (3/13) of Eurasian coot (Fulica atra), 12.5%, (1/8) of green-winged teal (Anas cardolinesis), 10% (2/20) of northern shoveler (Spatula clypeata), and 0% (0/4) of mallard duck (Anas platyrhynchos). In 35 Tilapia, Salmonella was isolated by (8.6%) 5.7% of external surfaces, 2.85% from the intestine, and 0% from the muscle. No Salmonella was isolated from the 175 brine shrimp samples. Phylogenetic analysis using the stn genes of Salmonella isolated from the aquatic environment, migratory aquatic birds, and chicken showed a strong association between these isolates. In addition, a higher nucleotide identity percentage was observed between the sequences recovered from migratory aquatic birds and Lake Qarun water samples.

CONCLUSION

Salmonella distribution was confirmed through migratory aquatic birds, based on our phylogeny tree analysis, Salmonella considered a likely carrier of zoonotic bacterial pathogens. Furthermore, the close relationship between chicken and fish sequences highlights the scenarios of using chicken manure in fish farms and its public health implications. The presence of Salmonella in different environmental sources spotlights the urgent need to control and break down its epidemiological cycle.

One-step differential detection of Salmonella enterica serovar Typhi, serovar Paratyphi A and other Salmonella spp. by using a quadruplex real-time PCR assay

Diseases caused by typhoidal and non-typhoidal Salmonella remain a considerable threat to both developed and developing countries. Based on the clinical symptoms and serological tests, it is sometimes difficult to differentiate the Salmonella enterica serovar Paratyphi A (S. enterica serovar Paratyphi A) from serovar Typhi (S. enterica serovar Typhi). In this study, we developed a quadruplex real-time polymerase chain reaction (PCR) assay with an internal amplification control (IAC), to simultaneously differentiate S. enterica serovar Paratyphi A from serovar Typhi and to detect other Salmonella serovars which cause salmonellosis in humans. This assay was evaluated on 155 salmonellae and non-salmonellae strains and demonstrated 100% specificity in species differentiation. Inclusion of an IAC did not affect the efficiency of the assay. Further evaluation using a blind test on spiked stool, blood and food specimens showed that the detection limit was at 10³ -10⁴ CFU/mL (or g) and a high PCR efficiency with different targets (R² > 0.99), except for S. enterica serovar Paratyphi A in blood. This assay has been applied to clinical specimens to detect the causative agents of gastrointestinal infections and has successfully identified 6 salmonellosis patients from the 50 diarrhoea patients. The quadruplex real-time PCR developed in this study could enhance the detection and differentiation of salmonellae. This assay could be applied to stools, blood and food based on the notable performance in the simulation tests and field evaluation.

Multidrug resistance and prevalence of quinolone resistance genes of Salmonella enterica serotypes 4,[5],12:i:- in China

Salmonella 4,[5],12:i:- is a monophasic variant of Salmonella Typhimurium, which is responsible for global foodborne disease outbreaks. Here, 255 S. 4,[5],12:i:- strains isolated from humans (11.0%) or food-borne animals (89.0%) between 2010 and 2018 were examined. Tests of susceptibility to 19 antimicrobial agents using the broth micro dilution method showed that 99.2% (n = 253) of the isolates were resistant to at least one compound. Antibiotic susceptibility analysis demonstrated that 91.8% of the isolates were multidrug-resistant (MDR) strains with predominant resistance to tetracycline (90.6%), followed by resistance to ampicillin (86.3%), streptomycin (63.5%), chloramphenicol (62.7%), and trimethoprim-sulfamethoxazole (55.3%). The 5 major distinct patterns of multi-resistance were identified as R-type AST, R-type ACTSxt, R-type ACSTSxt, R-type ACGSTSxt and R-type ASTSxt. Among the PMQR genes examined in this study, oqxAB and aac (6')-Ib-cr were the most prevalent resistance genes in the multi-resistant isolates. Our findings highlight the prevalence of the resistance of S. 4,[5],12:i:- in some regions of China, and several common types of multidrug resistance phenotypes, to provide valuable information for epidemiological studies, risk management, and public health strategies.

Detection of Salmonella Typhimurium in Romaine Lettuce Using a Surface Plasmon Resonance Biosensor

Leafy vegetables have been associated with high-profile outbreaks causing severe illnesses. Timely and accurate identification of potential contamination is essential to ensure food safety. A surface plasmon resonance (SPR) assay has been developed for the detection of Salmonella Typhimurium in leafy vegetables. The assay utilizes a pair of well characterized monoclonal antibodies specific to the flagellin of S. Typhimurium. Samples of romaine lettuce contaminated with S. Typhimurium at different levels (between 0.9 and 5.9 log cfu/g) were pre-enriched in buffered peptone water. Three SPR assay formats, direct assay, sequential two-step sandwich assay, and pre-incubation one-step sandwich assay were evaluated. All three assay formats detect well even at a low level of contamination (0.9 log cfu/g). The SPR assay showed a high specificity for the detection of S. Typhimurium in the presence of other commensal bacteria in the romaine lettuce samples. The results also suggested that further purification of flagellin from the sample preparation using immunomagnetic separation did not improve the detection sensitivity of the SPR assay. The functional protocol developed in this study can be readily used for the detection of S. Typhimurium in leafy vegetables with high sensitivity and specificity.

Padronização de uma PCR para a autenticação do Salmo salar em pratos da culinária japonesa

RESUMO O objetivo deste trabalho foi padronizar uma PCR para a detecção do Salmo salar, a qual possa ser usada na autenticação do salmão utilizado em pratos da culinária japonesa e do pescado comercializado in natura. Para isso, dois lotes de sushi foram produzidos experimentalmente. Além disso, foram visitados 38 estabelecimentos que comercializam comida japonesa e 10 peixarias na região metropolitana de Belém, visando à coleta do sushi, do temaki e do pescado pertencente à espécie Salmo salar. Os dados demonstraram que a técnica foi eficiente para a autenticação de Salmo salar, visto que a espécie foi detectada tanto nas amostras de sushis preparados experimentalmente quanto nas alíquotas de pescados isolados, utilizados para a preparação do sushi. Em contrapartida, a espécie Salmo trutta não foi detectada nas amostras de sushis preparados com esta espécie nem nas alíquotas de pescado isolado. Além disso, foi possível a confirmação da utilização da espécie Salmo salar no preparo das amostras de sushi, temaki e de pescado. Portanto, concluiu-se que a técnica foi capaz de amplificar o DNA da referida espécie e não gerou identificação inespecífica quando a espécie Salmo trutta foi analisada, podendo ser uma ferramenta adequada para a autenticação do Salmo salar.

Multiplex detection of bacteria on an integrated centrifugal disk using bead-beating lysis and loop-mediated amplification

Although culture-based identification of bacteria is the gold-standard for the diagnosis of infectious diseases, it is time consuming. Recent advances in molecular diagnostics and microfluidic technologies have opened up new avenues for rapid detection of bacteria. Here, we describe a centrifugal-microfluidic chip for the detection of bacteria by integrating the cell lysis, clarification, and loop-mediated amplification (LAMP). The major advantages of this chip are as follows. Firstly, bacteria lysis was innovatively achieved by rotating a pair of magnets to generate bead-beating while the chip was kept stationary during lysis, which simplified the chip design because no additional valve was needed. Secondly, the on-chip assay time was short (within 70 min), which was competitive in emergency situations. Thirdly, results of the analysis can be interpreted by using a fluorescence detector or by the naked-eye, making it versatile in many areas, especially the resource-limited areas. The on-chip limits of detection of six types of bacteria were valued by gel electrophoresis, showing the similar results compared to the bench-top LAMP protocol. This chip can be used for rapid, sensitive, accurate and automated detection of bacteria, offering a promising alternative for simplifying the molecular diagnostics of infectious diseases.

Efficient and Specific Detection of Salmonella in Food Samples Using a stn-Based Loop-Mediated Isothermal Amplification Method

The Salmonella enterotoxin (stn) gene exhibits high homology among S. enterica serovars and S. bongori. A set of 6 specific primers targeting the stn gene were designed for detection of Salmonella spp. using the loop-mediated isothermal amplification (LAMP) method. The primers amplified target sequences in all 102 strains of 87 serovars of Salmonella tested and no products were detected in 57 non-Salmonella strains. The detection limit in pure cultures was 5 fg DNA/reaction when amplified at 65°C for 25 min. The LAMP assay could detect Salmonella in artificially contaminated food samples as low as 220 cells/g of food without a preenrichment step. However, the sensitivity was increased 100-fold (~2 cells/g) following 5 hr preenrichment at 35°C. The LAMP technique, with a preenrichment step for 5 and 16 hr, was shown to give 100% specificity with food samples compared to the reference culture method in which 67 out of 90 food samples gave positive results. Different food matrixes did not interfere with LAMP detection which employed a simple boiling method for DNA template preparation. The results indicate that the LAMP method, targeting the stn gene, has great potential for detection of Salmonella in food samples with both high specificity and high sensitivity.

Paratyphoid fever: splicing the global analyses

The incidence of enteric fever caused by Salmonella enterica serovar Paratyphi A (S. Paratyphi A) is increasing in many parts of the world. Although there is no major outbreak of paratyphoid fever in recent years, S. Paratyphi A infection still remains a public health problem in many tropical countries. Therefore, surveillance studies play an important role in monitoring infections and the emergence of multidrug resistance, especially in endemic countries such as India, Nepal, Pakistan and China. In China, enteric fever was caused predominantly by S. Paratyphi A rather than by Salmonella enterica serovar Typhi (S. Typhi). Sometimes, S. Paratyphi A infection can evolve into a carrier state which increases the risk of transmission for travellers. Hence, paratyphoid fever is usually classified as a "travel-associated" disease. To date, diagnosis of paratyphoid fever based on the clinical presentation is not satisfactory as it resembles other febrile illnesses, and could not be distinguished from S. Typhi infection. With the availability of Whole Genome Sequencing technology, the genomes of S. Paratyphi A could be studied in-depth and more specific targets for detection will be revealed. Hence, detection of S. Paratyphi A with Polymerase Chain Reaction (PCR) method appears to be a more reliable approach compared to the Widal test. On the other hand, due to increasing incidence of S. Paratyphi A infections worldwide, the need to produce a paratyphoid vaccine is essential and urgent. Hence various vaccine projects that involve clinical trials have been carried out. Overall, this review provides the insights of S. Paratyphi A, including the bacteriology, epidemiology, management and antibiotic susceptibility, diagnoses and vaccine development.

Use of β-cyclodextrin and activated carbon for quantification of Salmonella enterica ser. Enteritidis from ground beef by conventional PCR without enrichment

The high level of PCR inhibitors present in ground beef is a major factor that affects molecular based techniques, such as the polymerase chain reaction (PCR), for the detection of Salmonella enterica. In this study, the use of β-cyclodextrin and milk protein coated activated carbon (MP-CAC) allowed the PCR to detect low numbers of Salmonella seeded into ground beef without enrichment of samples. invA was used as target gene in the conventional PCR protocol. With 25 g samples of ground beef containing 7.0, 15, and 27% fat, treatment of stomached samples with 5.0, 10, and 15% β-cyclodextrin respectively followed by treatment with MP-CAC, resulted in the detection of 3 CFU/g (equivalent to 75 CFU in a 25 g sample). The total assay time was 4.5 h. The methodology described in this study for the detection of S. enterica in ground beef without enrichment is rapid, sensitive, and has the potential to be applied to a number of complex food matrices to detect low numbers of food-borne bacterial pathogens.

Real-time PCR-based rapid and culture-independent detection of Salmonella in dairy milk--addressing some core issues

In this study, methodologies were developed for cost-effective, rapid and user-friendly culture-independent detection of Salmonella in milk by real-time PCR. The SYBR Green-based real-time PCR assay was standardized with primers targeting the Salmonella enterotoxin gene (stn) that have been earlier used for its detection by conventional PCR. Inclusivity tests generated the specific amplifications with a Tm corresponding to 81 ± 0·5°C. The specificity of the reaction was evaluated with a panel of 36 non-Salmonella strains. Standard curves generated, with different number of cells of this organism in milk, depicted the detection of five cells with a CT value of 37·17 (SD 0·43). To make the assays user-friendly and suitable for field applications, protocols were also established for the immobilization of the SYBR Green reaction mixes in the reaction tubes. The immobilized master mixes were stable at 25°C for 4 months and at 8°C for over 6 months. Total DNA was prepared from 150 samples of full-fat dairy milk and subjected to real-time PCR detection wherein 31 samples tested positive for Salmonella. The time of analysis was <5 h.

Rapid detection of Salmonella in foods using real-time PCR

Conventional methods for detection of Salmonella serovars in foods are generally time-consuming and labor intensive. A real-time PCR method has been developed with custom designed primers and a TaqMan probe to detect the presence of a 262-bp fragment of the Salmonella-specific invA gene. The method has been tested with a total of 384 field-isolated Salmonella serovars and non-Salmonella stock strains, as well as 420 U.S. Food and Drug Administration food samples, comprising a variety of food matrices. The method was highly specific in detecting Salmonella in spiked chili powder and shrimp samples, with a sensitivity of 0.04 CFU/g. In addition, the method is faster, more accurate, and less costly than the traditional U.S. Food and Drug Administration's Bacteriological Analytical Manual cell-culturing and the AOAC International-approved VIDAS methods to detect Salmonella in foods.

Evaluation of three different molecular markers for the detection of Staphylococcus aureus by polymerase chain reaction

The aim of this study was to target three genes of Staphylococcus aureus-fmhA (coding for a factor of unknown function), catalase and femA (coding for a factor essential for methicillin resistance) to establish and validate a PCR assay for the detection of this pathogen. Two pairs of primers were designed for fmhA and one pair each for catalase and femA genes. The PCR assays were standardized and found to give specific amplicons under similar reaction parameters. Target specificity of the primers was confirmed by DNA sequencing of the amplicons. While the initial inclusivity and exclusivity test reactions were in agreement in case of three of the primer pairs, one pair based on fmhA gene produced a non-specific product with a template DNA used in exclusivity test reactions. Forty-five strains of S. aureus were subjected to these PCR assays for their evaluation. Three among the four pairs of primers, one against each gene detected all the 45 strains precisely whereas one of the PCR assays using primers targeting the fmhA gene did not generate the specific amplicon with several of the strains. Seven unidentified strains of Gram-positive cocci subjected to these PCR assays produced negative results for each culture. Six of the strains were identified as Staphylococcus haemolyticus and one strain as Staphylococcus arlettae by 16S ribosomal gene analyses. All the three assay systems showed a detection limit of 100 cells per 20mul reaction assay. For validation of these assay systems, 80 coded samples of 11% skimmed milk spiked with different pathogens were received from NICED (National Institute of Cholera and Enteric Diseases), Kolkata and subjected to these PCR assays. All the three assays could detect S. aureus correctly in two of the samples. Amongst 150 raw milk samples, 36 (24%) were found positive for S. aureus. We conclude that fmhA, catalase and femA genes are conserved in S. aureus and, therefore, could be used as specific targets for its detection and identification by PCR. The protocols developed herein could be used for rapid and specific detection of this pathogen in food, clinical and environmental samples, especially milk.