A novel multiplex PCR for the simultaneous detection of Salmonella enterica and Shigella species

Advances in aptamer-based biosensors for monitoring foodborne pathogens

Biosensors are analytical devices for detecting a wide range of targets, including cells, proteins, DNA, enzymes, and chemical and biological compounds. They mostly rely on using bioprobes with a high binding affinity to the target for specific detection. However, low specificity and effectiveness of the conventional biosensors has led to the search for novel materials, that can specifically detect biomolecules. Aptamers are a group of single-stranded DNA or RNA oligonucleotides, that can bind to their targets with high specificity and serve as effective bioprobes for developing aptamer-based biosensors. Aptamers have a shorter production time, high stability, compared to traditional bioprobes, and possess ability to develop them for specific target molecules for tailored applications. Thus, various aptasensing approaches, including electrochemical, optical, surface plasmon resonance and chip-dependent approaches, have been investigated in recent times for various biological targets, including foodborne pathogens. Hence, this article is an overview of various conventional foodborne pathogen detection methods, their limitations and the ability of aptamer-based biosensors to overcome those limitations and replace them. In addition, the current status and advances in aptamer-based biosensors for the detection of foodborne pathogens to ensure food safety were also discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-023-05889-8.

PathoSense: a rapid electroanalytical device platform for screening Salmonella in water samples

Salmonella contamination is a major global health challenge, causing significant foodborne illness. However, current detection methods face limitations in sensitivity and time, which mostly rely on the culture-based detection techniques. Hence, there is an immediate and critical need to enhance early detection, reduce the incidence and impact of Salmonella contamination resulting in outbreaks. In this work, we demonstrate a portable non-faradaic, electrochemical sensing platform capable of detecting Salmonella in potable water with an assay turnaround time of ~ 9 min. We evaluated the effectiveness of this sensing platform by studying two sensor configurations: one utilizing pure gold (Au) and the other incorporating a semiconductor namely a zinc oxide thin film coated on the surface of the gold (Au/ZnO). The inclusion of zinc oxide was intended to enhance the sensing capabilities of the system. Through comprehensive experimentation and analysis, the LoD (limit of detection) values for the Au sensor and Au/ZnO sensor were 0.9 and 0.6 CFU/mL, respectively. In addition to sensitivity, we examined the sensing platform's precision and reproducibility. Both the Au sensor and Au/ZnO sensor exhibited remarkable consistency, with inter-study percentage coefficient of variation (%CV) and intra-study %CV consistently below 10%. The proposed sensing platform exhibits high sensitivity in detecting low concentrations of Salmonella in potable water. Its successful development demonstrates its potential as a rapid and on-site detection tool, offering portability and ease of use. This research opens new avenues for electrochemical-based sensors in food safety and public health, mitigating Salmonella outbreaks and improving water quality monitoring.

Beneficial effects of coconut oil (Cocos nucifera) on hematobiochemicl and histopathological markers in CCL4-intoxicated rabbits

The study was designed to investigate the effect of Coconut Oil on the levels of some liver and hematological parameters in carbon tetrachloride intoxicated rabbits. Also the antioxidant capacity of Coconut Oil for various concentrations was assessed on the basis of percent scavenging of (DPPH) free radical. Experimental animals were divided into five groups, eight rabbits in each group. These were: group A (Normal control), group B (Toxic control), group C (Standard control), group D (Treated with Coconut Oil 50 mL/kg body weight after CCl4 intoxication), group E (Treated with Coconut Oil 200 mL/kg body weight after CCl4 intoxication). The effects observed were compared with a standard hepatoprotective drug silymarine (50 mL/kg body weight). The Coconut Oil (200 mL/kg body weight) significantly (P<0.05) reduced the elevated serum levels of alanine transaminase (ALT), aspartate transaminase (AST) and alkaline phosphatase (ALP) when compared to a toxic control rabbits. The results of extract treated rabbits were similar to silymarine administered rabbits group. Treatment with Coconut Oil root and silymarine caused no significant changes in RBC, Platelets, (Hb), (MCH) concentration and (HCT) values. However, significant (P<0.05) increase was observed in the total WBC count. The present study suggested that Coconut Oil can be used as an herbal alternative (need further exploration i.e to detect its bioactive compound and its efficacy) for hepatoprotective activity.

Development of high-resolution melting (HRM) assay to differentiate the species of Shigella isolates from stool and food samples

Shigella species, a group of intracellular foodborne pathogens, are the main causes of bacillary dysentery and shigellosis in humans worldwide. It is essential to determine the species of Shigella in outbreaks and food safety surveillance systems. The available immunological and molecular methods for identifying Shigella species are relatively complicated, expensive and time-consuming. High resolution melting (HRM) assay is a rapid, cost-effective, and easy to perform PCR-based method that has recently been used for the differentiation of bacterial species. In this study, we designed and developed a PCR-HRM assay targeting rrsA gene to distinguish four species of 49 Shigella isolates from clinical and food samples and evaluated the sensitivity and specificity of the assay. The assay demonstrated a good analytical sensitivity with 0.01–0.1 ng of input DNA template and an analytical specificity of 100% to differentiate the Shigella species. The PCR-HRM assay also was able to identify the species of all 49 Shigella isolates from clinical and food samples correctly. Consequently, this rapid and user-friendly method demonstrated good sensitivity and specificity to differentiate species of the Shigella isolates from naturally contaminated samples and has the potential to be implemented in public health and food safety surveillance systems.

Fluoroquinolone resistance in non-typhoidal Salmonella enterica isolated from slaughtered pigs in Thailand

Introduction. The emergence and spread of non-typhoidal Salmonella enterica (NTS) serovars resistant to fluoroquinolones and third- and higher-generation cephalosporins is a matter of great concern. Antimicrobial-resistant NTS is increasingly being discovered in humans, animals, food animals, food products, and agricultural environments. Pigs are considered a major reservoir of antimicrobial-resistant Salmonella spp.Hypothesis/Gap Statement. Fluoroquinolone-resistant Salmonella spp. warrant further surveillance and characterization for a better understanding of the bacteria isolated from animals.Aim. NTS isolated from pork from slaughterhouses across Thailand were characterized in terms of their serovars; resistance to fluoroquinolones, third-generation cephalosporins, and carbapenems; and antimicrobial resistance genes.Methodology. A total of 387 NTS isolates, collected from slaughtered pigs in ten provinces across Thailand between 2014 and 2015, were characterized based on their serovars, antimicrobial resistance genes, and susceptibility to fluoroquinolones, third-generation cephalosporins, and carbapenems.Results. Among all NTS isolates, S. enterica serovar Rissen was predominant. Antimicrobial resistance was exhibited in 93/387 isolates (24 %). Although 24 (6.2 %) isolates were susceptible to all the tested antimicrobials, they were found to possess β-lactamase genes, such as bla _TEM, bla _SHV, or bla _CTX-M. Mobilized colistin-resistant genes (mcr) and resistance to colistin were not observed in any tested isolate. Carbapenem resistance was detected in ten isolates (10.7 %); however, bla _KPC, bla _NDM, bla _OXA-48-like, and bla _IMP were not present. Among the 93 antimicrobial-resistant isolates, 87.1 % showed fluoroquinolone resistance with the quinolone resistance gene (qnrS) combined with topoisomerase genes parC (T57S) or gyrA (S83E/Y and D124E/G) substitutions, or topoisomerase gene substitutions alone.Conclusion. We found high fluoroquinolone resistance rates among the NTS isolates from pigs from slaughterhouses. The fluoroquinolone resistance mechanism in NTS was associated with the combination of qnrS and substitutions in gyrA, parC, or both. To prevent the transmission of antimicrobial-resistant NTS between animals and humans, continuous monitoring, surveillance, and regulation of Salmonella in the pork supply chain are pivotal.

Rapid Detection of Salmonella typhimurium in Drinking Water by a White Light Reflectance Spectroscopy Immunosensor

Biosensors represent an attractive approach for fast bacteria detection. Here, we present an optical biosensor for the detection of Salmonella typhimurium lipopolysaccharide (LPS) and Salmonella bacteria in drinking water, based on white light reflectance spectroscopy. The sensor chip consisted of a Si die with a thin SiO₂ layer on top that was transformed into a biosensor through the immobilization of Salmonella LPS. The optical setup included a reflection probe with seven 200 μm fibers, a visible and near-infrared light source, and a spectrometer. The six fibers at the reflection probe circumference were coupled with the light source and illuminated the biosensor chip vertically, whereas the central fiber collected the reflected light and guided it to the spectrometer. A competitive immunoassay configuration was adopted for the analysis. Accordingly, a mixture of LPS or bacteria solution, pre-incubated for 15 min, with an anti-Salmonella LPS antibody was pumped over the chip followed by biotinylated secondary antibody and streptavidin for signal enhancement. The binding of the free anti-Salmonella antibody to chip-immobilized LPS led to a shift of the reflectance spectrum that was inversely related to the analyte concentration (LPS or bacteria) in the calibrators or samples. The total assay duration was 15 min, and the detection limits achieved were 4 ng/mL for LPS and 320 CFU/mL for bacteria. Taking into account the low detection limits, the short analysis time, and the small size of the chip and instrumentation employed, the proposed immunosensor could find wide application for bacteria detection in drinking water.

DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables

The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.

Prevalence and antimicrobial profile of Shigella isolates in a tertiary care hospital of North Karnataka: A 12-year study

Context

Shigella is a common cause of bacillary dysentery. Although it is reported worldwide, the majority of the infections are seen in developing countries with Shigella flexneri being the most common isolate. Prevalence of Shigella species and their antibiotic susceptibility profiles vary according to geographic area and season.

Aims

In the present study, the epidemiology and antimicrobial profile of Shigella from stool samples received at our hospital for a period of 12 years (January 2006 to December 2017) was evaluated.

Subjects and Methods

A total of 4578 stool samples were collected from the cases of acute gastroenteritis and diarrhoea. Samples were processed for culture and sensitivity according to standard microbiological techniques. The presumptive identification of Shigella species was done using standard conventional biochemical tests and confirmed using antisera.

Results

A total of 189 (4.2%) samples yielded Shigella spp. Isolation of Shigella spp. were more frequent from males (58.2%). S. flexneri was the commonest species isolated (47.6%) followed by Shigella sonnei(11.6%), Shigella dysenteriae (4.2%) and Shigella boydii (2.1%). Non-typeable Shigella was commonly recovered. The isolates showed high resistance to ampicillin (76.7%) and co-trimoxazole (75%) while highest susceptibility was observed to ceftriaxone (79.2%).

Conclusions

S. flexneri was the most prevalent species isolated at this centre. Shigella isolates from the study showed alarming resistance to recommended antibiotics. Non-typeable Shigella accounted for 34.4% isolates. Molecular discrimination between Shigella and Escherichia coli is essential.

Precise, direct, and rapid detection of Shigella Spa gene by a novel unmodified AuNPs-based optical genosensing system

Early detection of infectious bacteria is a necessity for combating infectious diseases. Due to low infectious dose of Shigella, rapid and sensitive detection is needed. Compared to the presented genes, Spa gene can be introduced as a novel sequence for all species of Shigella detection. Herein, the possibility of Spa genes for detection of four species of Shigella was investigated for the first time by AuNPs-based optical genosensing system. In this method, AuNP-DNA probes were hybridized with Spa gene sequence. When the complementary target is present, it prevents the aggregation of the complex under acid environment and the solution remains red whereas in the absence of the specific sequence, it turns to purple. Therefore, visual detection is possible with bare eye. The comparison of this Optical DNA biosensor and PCR-based method showed that the proposed method is simple, cost-effective, rapid operation, with high or comparable detection limit of (LOD and LOQ: 8.14 and 26.6 ng mLl^-1, respectively), without need of any expensive techniques, and equipments compared to the conventional methods. In conclusion, the described method may develop into a platform that could be utilized for detection of various bacterial species with high accuracy and prompt screening of samples.

A review of methods for the detection of pathogenic microorganisms

The testing and rapid detection of pathogenic organisms is a crucial protocol in the prevention and identification of crises related to health, safety and wellbeing. Pathogen detection has become one of the most challenging aspects in the food and water industries, because of the rapid spread of waterborne and foodborne diseases in the community and at significant costs. With the prospect of inevitable population growth, and an influx of tourism to certain water bodies testing will become a requirement to control and prevent possible outbreaks of potentially fatal illnesses. The legislation is already particularly rigorous in the food industry, where failure to detect pathogenic materials represents a catastrophic event, particularly for the elderly, very young or immune-compromised population types. In spite of the need and requirement for rapid analytical testing, conventional and standard bacterial detection assays may take up to seven days to yield a result. Given the advent of new technologies, biosensors, chemical knowledge and miniaturisation of instrumentation this timescale is not acceptable. This review presents an opportunity to fill a knowledge gap for an extremely important research area; discussing the main techniques, biology, chemistry, miniaturisation, sensing and the emerging state-of-the-art research and developments for detection of pathogens in food, water, blood and faecal samples.

Rapid and specific detection of Salmonella infections using chemically modified nucleic acid probes

Salmonella is a leading source of bacterial foodborne illness in humans, causing gastroenteritis outbreaks with bacteraemia occurrences that can lead to clinical complications and death. Eggs, poultry and pig products are considered as the main carriers of the pathogenic Salmonella for humans. To prevent this relevant zoonosis, key changes in food safety regulations were undertaken to improve controls in the food production chain. Despite these measures, large outbreaks of salmonellosis were reported worldwide in the last decade. Thus, new strategies for Salmonella detection are a priority for both, food safety and public health authorities. Such detection systems should provide significant reduction in diagnostic time (hours) compared to the currently available methods (days). Herein, we report on the discovery and characterization of nucleic acid probes for the sensitive and specific detection of live Salmonella within less than 8 h of incubation. We are the first to postulate the nuclease activity derived from Salmonella as biomarker of infection and its utility to develop innovative detection strategies. Our results have shown the screening and identification of two oligonucleotide sequences (substrates) as the most promising probes for detecting Salmonella - Sal-3 and Sal-5. The detection limits for both probes were determined with the reference Salmonella Typhimurium (STM 1) and Salmonella Enteritidis (SE 1) cultures. Sal-3 has reported LOD values around 10⁵ CFU mL^-1 for STM 1 and 10⁴ CFU mL^-1 for SE 1, while Sal-5 proves to be a slightly better probe, with LODs of 10⁴ CFU mL^-1 for STM 1 and 10⁴ CFU mL^-1 for SE 1. Both selected probes have shown the capability to recognize 49 out of 51 different Salmonella serotypes tested in vitro and the most frequent serotypes in porcine mesenteric lymph nodes as a standard sample used in fattening-pig salmonellosis baseline studies. Notably, our results showed 100% correlation between nuclease detection and the PCR-InvA or ISO-6579 standard method, underlining the great potential of this innovative nucleic acids technology to be implemented as a rapid method for food safety testing.

Inhibition of biofilm formation on the surface of water storage containers using biosand zeolite silver-impregnated clay granular and silver impregnated porous pot filtration systems

Development of biofilms occurring on the inner surface of storage vessels offers a suitable medium for the growth of microorganisms and consequently contributes to the deterioration of treated drinking water quality in homes. The aim of this study was to determine whether the two point-of-use technologies (biosand zeolite silver-impregnated clay granular (BSZ-SICG) filter and silver-impregnated porous pot (SIPP) filter) deployed in a rural community of South Africa could inhibit the formation of biofilm on the surface of plastic-based containers generally used by rural households for the storage of their drinking water. Culture-based methods and molecular techniques were used to detect the indicator bacteria (Total coliforms, faecal coliform, E. coli) and pathogenic bacteria (Salmonella spp., Shigella spp. and Vibrio cholerae) in intake water and on the surface of storage vessels containing treated water. Scanning electron microscopy was also used to visualize the development of biofilm. Results revealed that the surface water source used by the Makwane community was heavily contaminated and harboured unacceptably high counts of bacteria (heterotrophic plate count: 4.4–4.3 Log₁₀ CFU/100mL, total coliforms: 2.2 Log₁₀ CFU/100 mL—2.1 Log₁₀ CFU/100 mL, faecal coliforms: 1.9 Log₁₀ CFU/100 mL—1.8 Log₁₀ CFU/100 mL, E. coli: 1.7 Log₁₀ CFU/100 mL—1.6 Log₁₀ CFU/100 mL, Salmonella spp.: 3 Log₁₀ CFU/100 mL -8 CFU/100 mL; Shigella spp. and Vibrio cholerae had 1.0 Log₁₀ CFU/100 mL and 0.8 Log₁₀ CFU/100 mL respectively). Biofilm formation was apparent on the surface of the storage containers with untreated water within 24 h. The silver nanoparticles embedded in the clay of the filtration systems provided an effective barrier for the inhibition of biofilm formation on the surface of household water storage containers. Biofilm formation occurred on the surface of storage plastic vessels containing drinking water treated with the SIPP filter between 14 and 21 days, and on those containing drinking water treated with the BSZ-SICG filter between 3 and 14 days. The attachment of target bacteria on the surface of the coupons inoculated in storage containers ranged from (0.07 CFU/cm2–227.8 CFU/cm²). To effectively prevent the development of biofilms on the surface of container-stored water, which can lead to the recontamination of treated water, plastic storage containers should be washed within 14 days for water treated with the SIPP filter and within 3 days for water treated with the BSZ-SICG filter.

Molecular Tools To Study Preharvest Food Safety Challenges

Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.

Serotype determination of Salmonella by xTAG assay

Currently, no protocols or commercial kits are available to determine the serotypes of Salmonella by using Luminex MAGPIX®. In this study, an xTAG assay for serotype determination of Salmonella suitable for Luminex MAGPIX® is described and 228 Salmonella isolates were serotype determined by this xTAG assay. The xTAG assay consists of two steps: 1) Multiplex PCR to amplify simultaneously O, H and Vi antigen genes of Salmonella, and 2) Magplex-TAG™ microsphere hybridization to identify accurately the specific PCR products of different antigens. Compared with the serotyping results of traditional serum agglutination test, the sensitivity and specificity of the xTAG assay were 95.1% and 100%, respectively. The agreement rate of these two assays was 95.2%. Compared with Luminex xMAP® Salmonella Serotyping Assay (SSA) kit, the advantages of this xTAG assay are: First, the magnetic beads make it applicable to both the Luminex®100/200™ and MAGPIX® systems. Second, only primers rather than both primers and probes are needed in the xTAG assay, and the process of coupling antigen-specific oligonucleotide probes to beads is circumvented, which make the xTAG assay convenient to be utilized by other laboratories. The xTAG assay may serve as a rapid alternative or complementary method for traditional Salmonella serotyping tests, especially for laboratories that utilize the MAGPIX® systems.

A review on detection methods used for foodborne pathogens

Foodborne pathogens have been a cause of a large number of diseases worldwide and more so in developing countries. This has a major economic impact. It is important to contain them, and to do so, early detection is very crucial. Detection and diagnostics relied on culture-based methods to begin with and have developed in the recent past parallel to the developments towards immunological methods such as enzyme-linked immunosorbent assays (ELISA) and molecular biology-based methods such as polymerase chain reaction (PCR). The aim has always been to find a rapid, sensitive, specific and cost-effective method. Ranging from culturing of microbes to the futuristic biosensor technology, the methods have had this common goal. This review summarizes the recent trends and brings together methods that have been developed over the years.

Multiple- locus variable-number tandem-repeat analysis (MLVA) of Shigella sonnei isolates of 2012 outbreak I. R. Iran

Shigella sonnei is a major cause of diarrhea especially in children. Molecular study can help to determine the outbreak of this bacterium. Multiple-Locus Variable number tandem repeat Analysis (MLVA) will largely influence the public health field by introducing newer, faster, safer, and effective procedure for typing of microorganisms. A total of fifty shigella isolates were collected between November 2012 to October 2013 in Tehran, Iran. The strains were identified base on biochemical and molecular tests. Subsequently, all shigella species were confirmed by species-specific polymerase chain reaction (PCR). Virulence factors were detected using PCR for ial, set1A, and set1B genes. The strains were genotyped by MLVA typing method. All of the isolates were identified as S. sonnei by biochemical and molecular (PCR) methods. Virulence genes identified among all isolates included ial, and set1A genes in 20% and 5% of all isolates, respectively. On the other hand, none of isolates were positive for set1B gene. Using MLVA method 22 MLVA types were identified. MLVA type 11 accounted for 32% of isolates. Moreover, all virulence factors were only detected in MLVA type 11, 9, 5, 4. The results of this study indicate that the Iranian 2012-2013 S. sonnei outbreak isolates were virulent and clonaly related. Furthermore, this study showed that MLVA can be used as useful method for S. sonnei genotyping in epidemiological investigations.

Nano-materials for use in sensing of salmonella infections: Recent advances

Salmonella infectious diseases spreading every day through food have become a life-threatening problem for millions of people and growing menace to society. Health expert's estimate that the yearly cost of all the food borne diseases is approximately $5-6 billion. Traditional methodologies for salmonella analysis provide high reliability and very low limits of detection. Among them immunoassays and Nucleic acid-based assays provide results within 24h, but they are expensive, tedious and time consuming. So, there is an urgent need for development of rapid, robust and cost-effective alternative technologies for real-time monitoring of salmonella. Several biosensors have been designed and commercialized for detection of this pathogen in food and water. In this overview, we have updated the literature concerning novel biosensing methods such as various optical and electrochemical biosensors and newly developed nano- and micro-scaled and aptamers based biosensors for detection of salmonella pathogen. Furthermore, attention has been focused on the principal concepts, applications, and examples that have been achieved up to diagnose salmonella. In addition, commercial biosensors and foreseeable future trends for onsite detecting salmonella have been summarized.