PCR-ELISA detection of Escherichia coli in milk

Review of paper-based microfluidic analytical devices for in-field testing of pathogens

Pathogens cause various infectious diseases and high morbidity and mortality which is a global public health threat. The highly sensitive and specific detection is of significant importance for the effective treatment and intervention to minimise the impact. However, conventional detection methods including culture and molecular method gravely depend on expensive equipment and well-trained skilled personnel, limiting in the laboratory. It remains challenging to adapt in resource-limiting areas, e.g., low and middle-income countries (LMICs). To this end, low-cost, rapid, and sensitive detection tools with the capability of field testing e.g., a portable device for identification and quantification of pathogens, has attracted increasing attentions. Recently, paper-based microfluidic analytical devices (μPADs) have shown a promising tool for rapid and on-site diagnosis, providing a cost-effective and sensitive analytical approach for pathogens detection. The fast turn-round data collection may also contribute to better understanding of the risks and insights on mitigation method. In this paper, critical developments of μPADs for in-field detection of pathogens both for clinical diagnostics and environmental surveillance are reviewed. The future development, and challenges of μPADs for rapid and onsite detection of pathogens are discussed, including using the cross-disciplinary development with, emerging techniques such as deep learning and Internet of Things (IoT).

Bacterial drug-resistance and viability phenotyping upon disinfectant exposure revealed by single-nucleotide resolved-allele specific isothermal RNA amplification

Disinfectant abuse poses a risk of bacterial evolution against stresses, especially during the coronavirus disease 2019 (COVID-19) pandemic. However, bacterial phenotypes, such as drug resistance and viability, are hard to access quickly. Here, we reported an allele specific isothermal RNA amplification (termed AlleRNA) assay, using an isothermal RNA amplification technique, i.e., nucleic acid sequence-based amplification (NASBA), integrated the amplification refractory mutation system (ARMS), involving the use of sequence-specific primers to allow the amplification of the targets with complete complementary sequences. AlleRNA assay enables rapid and simultaneous detection of the single nucleotide polymorphism (SNP) (a detection limit, a LOD of 0.5 % SNP) and the viability (a LOD of 80 CFU) of the quinolone resistant Salmonella enterica. With the use of AlleRNA assay, we found that the quinolone resistant S. enterica exhibited higher survival ability during exposure toquaternary ammonium salt, 75 % ethanol and peracetic acid, which might be attributed to the upregulation of stress response-associated genescompared with the susceptible counterparts. Additionally, the AlleRNA assay indicated the potential risk in a high-frequency occurrence of viable but nonculturable (VBNC) quinolone resistant S. enterica induced by disinfectants due to the depression of ATP biosynthesis. The excessive usage of disinfectants during the COVID-19 pandemic should be carefully evaluated due to the latent threat to ecological and human health.

SERS-based immunosensor for E. coli contaminants detection in milk using silver-coated nanoporous silicon substrates

The dairy sector is frequently affected by contagious and environmental factors that spread between animals by numerous means and induce the inflammatory disease of bovine mastitis (BM). Herein, silver decorated porous silicon (Ag-pSi) SERS platform was designed for rapid and reliable Escherichia coli (predominant BM pathogen) detection in various milk origins. The inherent surface void and pore morphology were physically optimized to augment the SERS effect using 4-aminothiphenol (4ATP) while achieving an enhancement factor >4.6 × 10⁷. An indirect immunoassay evaluated the residual unreacted antibodies using an optimized 4ATP/Ag-pSi SERS platform modified with secondary antibodies. Under optimized conditions, the porous substrate offered high sensitivity toward target bacteria detection of 3 CFU mL^-1 and linear response of 10¹-10⁵ CFU mL^-1. Moreover, the selectivity and specificity of the designed sensing platform were cross-validated against other interfering bacteria without compromising its performance efficiencies. Finally, the applicability of the developed system for real-life conditions was elucidated in different milk samples (bovine, goat, sheep) with recovery values of 78-115% compared to the conventional culture technique. Considering the complex media analysis, the miniaturized SERS platform is highly reliable, rapid and accurate that could be applicable for routine on-site analysis of various emerging pathogens relevant to BM management.

Recent Progress and Challenges on the Microfluidic Assay of Pathogenic Bacteria Using Biosensor Technology

Microfluidic technology is one of the new technologies that has been able to take advantage of the specific properties of micro and nanoliters, and by reducing the costs and duration of tests, it has been widely used in research and treatment in biology and medicine. Different materials are often processed into miniaturized chips containing channels and chambers within the microscale range. This review (containing 117 references) demonstrates the significance and application of nanofluidic biosensing of various pathogenic bacteria. The microfluidic application devices integrated with bioreceptors and advanced nanomaterials, including hyperbranched nano-polymers, carbon-based nanomaterials, hydrogels, and noble metal, was also investigated. In the present review, microfluid methods for the sensitive and selective recognition of photogenic bacteria in various biological matrices are surveyed. Further, the advantages and limitations of recognition methods on the performance and efficiency of microfluidic-based biosensing of photogenic bacteria are critically investigated. Finally, the future perspectives, research opportunities, potential, and prospects on the diagnosis of disease related to pathogenic bacteria based on microfluidic analysis of photogenic bacteria are provided.

Detection of Escherichia coli by Combining an Affinity-Based Method with Contactless Atmospheric Pressure Ionization Mass Spectrometry

Escherichia coli are common pathogens, whereas E. coli O157:H7 is the most notorious E. coli strain, owing to its high virulence that can cause serious adverse effects and death. E. coli contains abundant peroxidases. Thus, the presence of E. coli can be determined by mixing E. coli with its substrate such as 3,5,3′,5′ tetramethylbenzidines (TMB) for endogenous peroxidase reactions. Under the presence of a high concentration of E. coli, colorless TMB turned to bluish, owing to the generation of the complexity of TMB and its oxidized TMB. To further reduce the detectable cell concentration, we developed an affinity-based method combined with an endogenous peroxidase reaction and mass spectrometric detection to detect E. coli. Affinity probes (diameter: ~20 µm) modified with maltose were generated for the enrichment of E. coli from sample solutions. E. coli trapped by the affinity probes was reacted with TMB in the presence of hydrogen peroxide for endogenous peroxidase reactions. Contactless atmospheric pressure ionization mass spectrometry was used for the detection of the reaction product, oxidized TMB (TMB cationic radical), to indicate the presence of target bacteria. The results showed that the developed method can be used to rapidly determine the presence of E. coli from a sample solution based on the detection of the TMB cationic radicals. The lowest detectable concentration of our method against E. coli O157:H7 in buffers and in complex juice samples was as low as ~100 cfu mL−1.

Detection of bacteria using antimicrobial polymer derived via ring-opening metathesis (romp) pathway

There is growing interest in the detection of bacteria in consumables, for example, in the food and water sectors. In this study, the aim was to produce a polymer-based bacteria biosensor via ROMP (ring opening metathesis polymerization). In the first part of the study, block and random copolymers were synthesized, and their biocidal activities were tested on the glass surface. Interdigitated electrode arrays coated with the polymers possessing the highest activity were used to screen the affinity towards different bacterial strains by monitoring impedance variations in real-time. The polymer-coated electrode could detect gram-positive and gram-negative bacteria strains at a concentration of 107 cfu/mL. The results show that ROMP-based polymer offers bacterial detection and can be used in developing biosensor devices for efficiently detecting pathogenic bacteria.

Research advances and applications of biosensing technology for the diagnosis of pathogens in sustainable agriculture

Plant diseases significantly impact the global economy, and plant pathogenic microorganisms such as nematodes, viruses, bacteria, fungi, and viroids may be the etiology for most infectious diseases. In agriculture, the development of disease-free plants is an important strategy for the determination of the survival and productivity of plants in the field. This article reviews biosensor methods of disease detection that have been used effectively in other fields, and these methods could possibly transform the production methods of the agricultural industry. The precise identification of plant pathogens assists in the assessment of effective management steps for minimization of production loss. The new plant pathogen detection methods include evaluation of signs of disease, detection of cultured organisms, or direct examination of contaminated tissues through molecular and serological techniques. Laboratory-based approaches are costly and time-consuming and require specialized skills. The conclusions of this review also indicate that there is an urgent need for the establishment of a reliable, fast, accurate, responsive, and cost-effective testing method for the detection of field plants at early stages of growth. We also summarized new emerging biosensor technologies, including isothermal amplification, detection of nanomaterials, paper-based techniques, robotics, and lab-on-a-chip analytical devices. However, these constitute novelty in the research and development of approaches for the early diagnosis of pathogens in sustainable agriculture.

Aptamer-based approaches for the detection of waterborne pathogens

Waterborne ailments pose a serious threat to public health and are a huge economic burden. Lack of hygiene in drinking and recreational water is the chief source of microbial pathogens in developing countries. Poor water quality and sanitation account for more than 3.4 million deaths a year worldwide. This has urged authorities and researchers to explore different avenues of pathogen detection. There is a growing demand for rapid and reliable sensor technologies, in particular those that can detect in situ and perform in harsh conditions. Some of the major waterborne pathogens include Vibrio cholerae, Leptospira interrogans, Campylobacter jejuni, Shigella spp., enterotoxigenic Escherichia coli, Clostridium difficile, Cryptosporidium parvum, Entamoeba histolytica, and Hepatitis A virus. While conventional methods of pathogen detection like serodiagnosis and microbiological methods have been superseded by nucleic acid amplification methods, there is still potential for improvement. This review provides an insight into aptamers and their utility in the form of aptasensors. It discusses how aptamer-based approaches have emerged as a novel strategy and its advantages over more resource-intensive and complex biochemical approaches.

PCR-Based Direct Detection of Streptococcus uberis from Subclinical and Clinical Dairy Cattle Milk Samples

Streptococcus uberis is one of the leading causes worldwide of mastitis in the dairy industry, with the most likely sources of infection attributed to environmental reservoirs such as contaminated bedding materials. Early detection of those cases most likely to progress to clinical disease would lead to improved animal welfare, a critical component of overall health and productivity. A multiplex PCR-based diagnostic test was developed for detection of S. uberis directly from milk and targeting two genes previously identified as important for intramammary colonisation and persistence in dairy cattle. Results indicated the threshold for detection directly from milk was 20,000 CFU/ml and this was achieved without the need for preenrichment. In addition, S. uberis could be identified from milk samples collected during intramammary challenge studies, prior to clinical signs of infection and at much lower detection limits. The PCR test developed for confirmation of the presence of S. uberis directly from infected milk has potential value as a diagnostic test to identify early infection and/or to confirm that antibiotic therapy has been successful.

Antibiogram and beta-lactamase genes among cefotaxime resistant E. coli from wastewater treatment plant

BACKGROUND

The World Health Organization (WHO) recently classified Enterobacteriaceae resistance to third-generation cephalosporin into the group of pathogens with critical criteria for future research.

METHODS

A study to assess the antibiogram and beta-lactamase genes among the cefotaxime resistant E. coli (CREc) from a South African wastewater treatment plant (WWTP) was conducted using standard phenotypic and molecular biology characterization methods.

RESULTS

Approximate total E. coli (TEc) concentration (log₁₀ CFU/mL) ranged between 5.7 and 6.8 among which cefotaxime resistant E. coli were between 1.8 and 4.8 (log₁₀ CFU/mL) for cefotaxime antibiotic concentration of 4 and 8 mg/L in the influent samples. Effluent samples, heavily influenced by the chlorination had only 0.3 log₁₀ CFU/mL of TEc. Fifty-one cefotaxime resistant isolates were selected out of an overall of 75 isolates, and subjected to a new round of testing, with a follow up of 36 and 48 isolates for both colistin and gentamicin, respectively as guided by initial results. Selected CREc exhibited resistance to amoxicillin-clavulanic acid (35.3%; n = 51), colistin sulphate (76.5%; n = 36), ciprofloxacin (47.1%; n = 51), gentamicin (87.5%; n = 48) and intermediate-resistance to meropenem (11.8%; n = 51). Extended spectrum-beta-lactamase genes detected, viz.: bla_CTX-M (52.6%; n = 38) and bla_TEM (84.2%; n = 38) and concurrent bla_CTX-M + bla_TEM (36.8%; n = 38), but no bla_SHV was detected. Carbapenem resistance genes, blaKPC-2 (15.8%; n = 38), blaOXA-1 (57.9%; n = 38), blaNDM-1 (15.8%; n = 38) were also detected. Approximately, 10.5 - 36.8% (n = 38) co-occurrence of two or more beta-lactamase genes was detected in some isolates. Out of the selected number (n = 30), 7(23.3%) were enterotoxigenic E. coli (ETEC), 14 (46.7%) were Enteroaggregative E. coli (EAEC), but no enteropathogenic E. coli (EPEC) was detected.

CONCLUSION

Resistance to cefotaxime and the presence of a wide range of beta-lactamase genes exposed the potential risks associated with these pathogens via occupational and domestic exposure during the reuse of treated wastewater.

Low concentration E. coli O157:H7 bacteria sensing using microfluidic MEMS biosensor

This paper reports the design, fabrication, and testing of a microfluidic MEMS biosensor for rapid sensing of low concentration Escherichia coli O157:H7. It consists of a specially designed focusing and sensing region, which enables the biosensor to detect low concentration of bacterial cells. The focusing region consists of a ramped vertical electrode pair made of electroplated gold along with tilted thin film finger pairs (45°) embedded inside a microchannel. The focusing region generates positive dielectrophoresis force, which moves the cells towards the edges of the tilted thin film electrode fingers, located at the center of the microchannel. The fluidic drag force then carries the focused cells to the sensing region, where three interdigitated electrode arrays (IDEAs) with 30, 20, and 10 pairs, respectively, are embedded inside the microchannel. This technique resulted in highly concentrated samples in the sensing region. The sensing IDEAs are functionalized with the anti-E. coli antibody for specific sensing of E. coli 0157:H7. As E. coli binds to the antibody, it results in an impedance change, which is measured across a wide frequency range of 100 Hz-10 MHz. The biosensor was fabricated on a glass substrate using the SU8 epoxy resist to form the microchannel, gold electroplating to form the vertical focusing electrode pair, a thin gold film to form the sensing electrode, the finger electrodes, traces and bonding pads, and polydimethylsiloxane to seal the device. The microfluidic impedance biosensor was tested with various low concentration bacterial samples and was able to detect bacterial concentration, as low as 39 CFU/ml with a total sensing time of 2 h.

Advanced DNA-Based Point-of-Care Diagnostic Methods for Plant Diseases Detection

Diagnostic technologies for the detection of plant pathogens with point-of-care capability and high multiplexing ability are an essential tool in the fight to reduce the large agricultural production losses caused by plant diseases. The main desirable characteristics for such diagnostic assays are high specificity, sensitivity, reproducibility, quickness, cost efficiency and high-throughput multiplex detection capability. This article describes and discusses various DNA-based point-of care diagnostic methods for applications in plant disease detection. Polymerase chain reaction (PCR) is the most common DNA amplification technology used for detecting various plant and animal pathogens. However, subsequent to PCR based assays, several types of nucleic acid amplification technologies have been developed to achieve higher sensitivity, rapid detection as well as suitable for field applications such as loop-mediated isothermal amplification, helicase-dependent amplification, rolling circle amplification, recombinase polymerase amplification, and molecular inversion probe. The principle behind these technologies has been thoroughly discussed in several review papers; herein we emphasize the application of these technologies to detect plant pathogens by outlining the advantages and disadvantages of each technology in detail.

Molecular biological tools applied for identification of mastitis causing pathogens

The molecular diagnostic tools became the gold standard of mastitis diagnosis in the last few years. They enable rapid, qualitative, quantitative and large scale diagnosis. In addition to their role in diagnosis, they can identify pathogens at the subspecies level which is necessary for the epidemiological studies. They are increasingly used in mastitis control programs through identification of suitable candidates for vaccine production and through the selection of mastitis resistant cattle breeds. The present molecular techniques are continuously improved and new techniques are developed in order to provide higher sensitivity and specificity and to minimize the costs. The present work aims to provide an overview of the modern molecular tools, discuss why they replaced the traditional tools and became the new gold standard in mastitis diagnosis through comparing both traditional and molecular tools, explore the prospective of the molecular diagnostic techniques in mastitis diagnosis and control and to explore new horizons of using molecular assays in near future.

Detection Methodologies for Pathogen and Toxins: A Review

Pathogen and toxin-contaminated foods and beverages are a major source of illnesses, even death, and have a significant economic impact worldwide. Human health is always under a potential threat, including from biological warfare, due to these dangerous pathogens. The agricultural and food production chain consists of many steps such as harvesting, handling, processing, packaging, storage, distribution, preparation, and consumption. Each step is susceptible to threats of environmental contamination or failure to safeguard the processes. The production process can be controlled in the food and agricultural sector, where smart sensors can play a major role, ensuring greater food quality and safety by low cost, fast, reliable, and profitable methods of detection. Techniques for the detection of pathogens and toxins may vary in cost, size, and specificity, speed of response, sensitivity, and precision. Smart sensors can detect, analyse and quantify at molecular levels contents of different biological origin and ensure quality of foods against spiking with pesticides, fertilizers, dioxin, modified organisms, anti-nutrients, allergens, drugs and so on. This paper reviews different methodologies to detect pathogens and toxins in foods and beverages.

Isolation, Biochemical and Molecular Identification, and In-Vitro Antimicrobial Resistance Patterns of Bacteria Isolated from Bubaline Subclinical Mastitis in South India

Buffaloes are the second largest source of milk. Mastitis is a major impediment for milk production, but not much information is available about bubaline mastitis, especially subclinical mastitis. The aim of this study was to (a) investigate the application of various tests for the diagnosis of bubaline subclinical mastitis, (b) identify the major bacteria associated with it, and (c) evaluate the antibiotic resistance pattern of the bacteria. To this end, 190 quarter milk samples were collected from 57 domesticated dairy buffaloes from organized (64 samples) and unorganized (126 samples) sectors. Of these, 48.4%, 40.0%, 45.8%, 61.1%, and 61.6% were positive for subclinical mastitis by somatic cell count, electrical conductivity, California mastitis test, bromothymol blue test, and N-acetyl glucosaminidase test, respectively. As compared to the gold standard of somatic cell count, California mastitis test performed the best. However, a combination of the two methods was found to be the best option. Microbiological evaluation, both by biochemical methods as well as by monoplex and multiplex polymerase chain reaction, revealed that coagulase-negative staphylococci were the most predominant (64.8%) bacteria, followed by streptococci (18.1%), Escherichia coli (9.8%) and Staphylococcus aureus (7.3%). Most of the pathogens were resistant to multiple antibiotics, especially to β-lactam antibiotics. We propose that California mastitis test be combined with somatic cell count for diagnosis of subclinical mastitis in domestic dairy buffaloes. Further, our results reveal high resistance of the associated bacteria to the β-lactam class of antibiotics, and a possible major role of coagulase-negative staphylococci in causing the disease in India.

Advantages and limitations of potential methods for the analysis of bacteria in milk: a review

Contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. HACCP principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. Milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers, manufacturers and regulatory agencies. Due to the availability of numerous methods used for analysing the microbial quality of milk in literature and differences in priorities of stakeholders, it is sometimes confusing to choose an appropriate method for a particular analysis. The objective of this paper is to review the advantages and disadvantages of selected techniques that can be used in the analysis of bacteria in milk. SSC, HRMA, REP, and RAPD are the top four techniques which are quick and cost-effective and possess adequate discriminatory power for the detection and profiling of bacteria. The following conclusions were arrived at during this review: HRMA, REP and RFLP are the techniques with the most reproducible results, and the techniques with the most discriminatory power are AFLP, PFGE and Raman Spectroscopy.

Multiple antibiotic resistance indexing of Escherichia coli to identify high-risk sources of faecal contamination of water

We evaluated the antibiogram profile of Escherichia coli (n = 300) isolated from selected rivers in Osun State, Nigeria. The identities of the E. coli isolates were confirmed by polymerase chain reaction (PCR) technique. Susceptibility of the isolates to 20 antibiotics conventionally used in clinical cases was assessed in vitro by the standardized agar disc-diffusion method. All the isolates were susceptible to imipenem, meropenem, amikacin and gatilofloxacin. The isolates were variously susceptible to the other antibiotics as follows: ciprofloxacin (96 %), kanamycin (95 %), neomycin (92 %), streptomycin (84 %), chloramphenicol (73 %), nalidixic acid (66 %), nitrofurantoin (64 %), gentamycin (63 %), doxycycline (58 %), cefepime (57 %), tetracycline (49 %) and cephalothin (42 %). The multiple antibiotic resistance indexing ranged from 0.50 to 0.80 for all the sampling locations and exceeded the threshold value of 0.2, suggesting the origin of the isolates to be of high antimicrobial usage. Our findings signify an increase in the incidence of antimicrobial resistance of E. coli towards conventionally used antibiotics necessitating proper surveillance programmes towards the monitoring of antimicrobial resistance determinants in water bodies.

Detection of E. coli O157:H7 and Shigella dysenteriae toxins in clinical samples by PCR-ELISA

Shiga toxin producing bacteria are potential causes of serious human disease such as hemorrhagic colitis, severe inflammations of ileocolonic regions of gastrointestinal tract, thrombocytopenia, septicemia, malignant disorders in urinary ducts, hemolytic uremic syndrome (HUS). Shiga toxin 1 (stx1), shiga toxin 2 (stx2), or a combination of both are responsible for most clinical symptoms of these diseases. A lot of methods have been developed so far to detect shiga toxins such as cell culture, ELISA, and RFPLA, but due to high costs and labor time in addition to low sensitivity, they have not received much attention. In this study, PCR-ELISA method was used to detect genes encoding shiga toxins1 and 2 (stx1 and stx2). To detect stx1 and stx2 genes, two primer pairs were designed for Multiplex-PCR then PCR-ELISA. PCR products (490 and 275, respectively) were subsequently verified by sequencing. Sensitivity and specificity of PCR-ELISA method were determined by using genome serial dilution and Enterobacteria strains. PCR-ELISA method used in this study proved to be a rapid and precise approach to detect different types of shiga toxins and can be used to detect bacterial genes encoding shiga toxins.

NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification

Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications.

Limit of detection of genomic DNA by conventional PCR for estimating the load of Staphylococcus aureus and Escherichia coli associated with bovine mastitis

Detection of mastitis-associated bacteria can be accomplished by culturing or by molecular techniques. On the other hand, rapid and inexpensive methods to enumerate bacterial load without culturing can be better achieved by molecular methods. Staphylococcus aureus and Escherichia coli are the predominant bacterial pathogens associated with bovine mastitis. Here, we describe the application of conventional PCR for the limit of detection (LOD) of genomic DNA of S. aureus and E. coli based on single-copy genes. The selected genes were thermonuclease (nuc), aureolysin (aur), and staphopain A (scpA) for S. aureus and β-D-glucuronidase A (uidA), cytochrome d oxidase (cyd), and rodA (a gene affecting cell shape and methicillin sensitivity) for E. coli. The LOD was 5.3, 15.9, and 143 pg for aur, nuc, and scpA genes, corresponding to S. aureus genomic copies of 1.75 × 10(3), 5.16 × 10(3), and 4.71 × 10(4), respectively. The LOD was 0.45, 12.3 and 109 pg for uidA, rodA and cyd genes, corresponding to E. coli genome copies of 8.91 × 10(1), 2.43 × 10(3), and 2.16 × 10(4), respectively. Application of uidA and aur PCRs to field strains revealed that as low as approximately 100 genome copies of E. coli and 1000-10,000 copies of S. aureus could be detected. This study is the first to report LOD of genomic DNA using conventional PCR for aur and scpA genes of S. aureus, and rodA and cyd genes of E. coli. The results should be useful for developing assays to assess bacterial load in milk and to determine the load that contributes to subclinical or clinical mastitis.

Application of PCR-ELISA in molecular diagnosis

Polymerase chain reaction-enzyme linked immunosorbent assay (PCR-ELISA) is an immunodetection method that can quantify PCR product directly after immobilization of biotinylated DNA on a microplate. This method, which detects nucleic acid instead of protein, is a much more sensitive method compared to conventional PCR method, with shorter analytical time and lower detection limit. Its high specificity and sensitivity, together with its semiquantitative ability, give it a huge potential to serve as a powerful detection tool in various industries such as medical, veterinary, and agricultural industries. With the recent advances in PCR-ELISA, it is envisaged that the assay is more widely recognized for its fast and sensitive detection limit which could improve overall diagnostic time and quality.

Surface-conjugated antimicrobial peptide leucocin a displays high binding to pathogenic gram-positive bacteria

Leucocin A, a representative class IIa bacteriocin, is a ribosomally synthesized antimicrobial peptide (AMP) that displays potent activity against specific gram-positive bacteria. The antibacterial activity of such peptides is preceded by the binding event that can be utilized for studying specific peptide-bacteria interactions. In this study, 37-residue Leucocin A (LeuA) was synthesized using solid-phase peptide synthesis and covalently immobilized on gold substrates from either the N- or C-terminal. Both the peptide monolayers on gold substrates were incubated separately with five strains of gram-positive bacteria and displayed differential binding to different strains with highest binding to pathogenic Listeria monocytogenes . The C-terminally immobilized LeuA showed higher bacterial binding compared to the N-terminally attached LeuA. The full length immobilized LeuA (37-residue) was active as well as displayed higher bacterial binding (73 ± 6 bacteria/100 μm(2)) compared to 24-residue inactive LeuA fragment (40 ± 8 bacteria/100 μm(2)) from the C-terminal region. The high and specific bacterial binding ability of LeuA functionalized surfaces support the potential use of class IIa bacteriocins in antimicrobial peptide-based diagnostic platforms.

Impedimetric detection of pathogenic Gram-positive bacteria using an antimicrobial peptide from class IIa bacteriocins

Real-time, label-free detection of Gram-positive bacteria with high selectivity and sensitivity is demonstrated using an interdigitated impedimetric array functionalized with naturally produced antimicrobial peptide from class IIa bacteriocins. The antimicrobial peptide, leucocin A, was chemically synthesized and covalently immobilized on interdigitated gold microelectrodes via the interaction between the C-terminal carboxylic acid of the peptide and free amines of a preattached thiolated linker. Exposing the peptide sensor to various concentrations of Gram-positive bacteria generated reproducible impedance spectra that detected peptide-bacteria interactions at a concentration of 1 cell/μL. The peptide sensor also selectively detected Listeria monocytogenes from other Gram-positive strains at a concentration of 10(3) cfu mL(-1). The study highlights that short peptide ligands from bacteriocin class offer high selectivity in bacterial detection and can be used in developing a robust, portable biosensor device to efficiently detect pathogenic Gram-positive bacteria in food samples.

Construction of nanoantennas on the bacterial outer membrane

A simple and highly sensitive detection of pathogenic bacteria is achieved by utilizing gold nanoparticles as an optical antenna.

Detection of Escherichia coli O157:H7 using immunomagnetic separation and mPCR in Turkish foods of animal origin

The present study was conducted to investigate the presence of Escherichia coli O157:H7 in food samples of animal origin and to detect its virulence genes by immunomagnetic separation technique and multiplex PCR (mPCR). A total of 500 samples (consisting of diced meat, minced meat, burger, raw cow's milk and raw cow's milk cheese) were analysed. Escherichia coli O157:H7 was detected in 5 (1%) of 500 analysed samples including two diced meat, one minced meat and two raw-milk cheese. None of the burger samples tested contained E. coli O157:H7. Three isolates obtained from minced and diced meat were found to carry stx1 , stx2 , hlyA and eaeA genes whereas two isolates from raw-milk cheese were found to harbour the stx1 , eaeA and hlyA genes. The results of this study suggest that raw meat and raw-milk cheese tested could pose public health problems in consumers with regard to their virulence factors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Escherichia coli (E. coli) O157:H7 is an important human pathogen. Escherichia coli 0157:H7 infections have been associated with consumption of uncooked meat and meat products, as well as unpasteurized dairy products. This study demonstrated that without specific tests for E. coli virulence factors raw meat and raw-milk cheese could pose public health problems to Turkish consumers.

Detection of Escherichia coli, Salmonella species, and Vibrio cholerae in tap water and bottled drinking water in Isfahan, Iran

BACKGROUND

The quality of drinking water has an important role in human infection and disease. This study was aimed at comparing polymerase chain reaction and culture in detecting Escherichia coli, Salmonella species and Vibrio cholera in tape water and bottled drinking water in various seasons in Isfahan province, Iran.

METHODS

A total of 448 water samples from tap water and bottled mineral water were taken over 6 months, from July 2010 to December 2010, and after filtration, samples were examined by culture and polymerase chain reaction methods for detection of Escherichia coli, Salmonella species, and Vibrio cholerae.

RESULTS

The culture method showed that 34 (7.58%), 4 (0.89%) and 3 (0.66%) of all 448 water samples were positive for Escherichia coli, Salmonella species, and Vibrio cholera, respectively. The uidA gene from Escherichia coli, IpaB gene from Salmonella species, and epsM gene from Vibrio cholera were detected in 38 (26.38%), 5 (3.47%), and 3 (2.08%) of 144 tap-water samples, respectively. Escherichia coli was detected in 8 (2.63%) of 304 samples of bottled drinking water from 5 companies. The water of southern part of Isfahan and company 5 had the highest prevalence of bacteria. The Escherichia coli water contamination was significantly higher (P < 0.05) in the hot seasons (July-August) than cold (November-December) seasons and in company 5 than other companies. There were significant differences (P < 0.05) for the prevalence of bacteria between the tap waters of southern part and tap waters of central part of Isfahan.

CONCLUSIONS

This study showed that the polymerase chain reaction assays can be an extremely accurate, fast, safe, sensitive and specific approach to monitor drinking water quality from purification facilities and bottled water companies. Also, our study confirmed the presence of Escherichia coli, Salmonella species, and Vibrio cholerae as water-borne pathogens in tap water and bottled drinking water of Isfahan, Iran. The present study showed the important public health problem in Isfahan, Iran.

Development of SCAR primers based on a repetitive DNA fingerprint for Escherichia coli detection

The present study aimed to use enterobacterial repetitive intergenic consensus (ERIC) fingerprints to design SCAR primers for the detection of Escherichia coli. The E. coli strains were isolated from various water sources. The primary presumptive identification of E. coli was achieved using MacConkey agar. Nineteen isolates were selected and confirmed to be E. coli strains based on seven biochemical characteristics. ERIC-PCR with ERIC 1R and ERIC 2 primers were used to generate DNA fingerprints. ERIC-PCR DNA profiles showed variant DNA profiles among the tested E. coli strains and distinguished all E. coli strains from the other tested bacterial strains. A 350 bp band that predominated in five E. coli strains was used for the development of the species-specific SCAR primers EC-F1 and EC-R1. The primers showed good specificity for E. coli, with the exception of a single false positive reaction with Sh. flexneri DMST 4423. The primers were able to detect 50 pg and 10(0) CFU/ml of genomic DNA and cells of E. coli, respectively.

Screening of peptides bound to breast cancer stem cell specific surface marker CD44 by phage display

CD44, a cancer-associated membrane glycoprotein involved in cell adhesion and tumor progression, has been implicated as a cancer stem cell antigen in several cancers including breast cancer. If the detection sensitivity of CD44 as an early marker for cancer could be improved, this would have important clinical applications. As compared with early stage treatments of other kinds of cancer, treatment of breast cancer is more likely to results in positive outcomes, so this early detection is crucial. Therefore, CD44 is a potential diagnostic target for cancer detection. Herein, we have used a peptide library to screen novel diverse peptides that bind to CD44 with high affinity and characterized the specific binding of these peptides. Our work provides a basis to develop novel diagnostic peptides which may replace antibodies as CD44 detection probes.

Raman spectroscopy as a potential tool for detection of Brucella spp. in milk

Detection of Brucella, causing brucellosis, is very challenging, since the applied techniques are mostly time-demanding and not standardized. While the common detection system relies on the cultivation of the bacteria, further classical typing up to the biotype level is mostly based on phenotypic or genotypic characteristics. The results of genotyping do not always fit the existing taxonomy, and misidentifications between genetically closely related genera cannot be avoided. This situation gets even worse, when detection from complex matrices, such as milk, is necessary. For these reasons, the availability of a method that allows early and reliable identification of possible Brucella isolates for both clinical and epidemiological reasons would be extremely useful. We evaluated micro-Raman spectroscopy in combination with chemometric analysis to identify Brucella from agar plates and directly from milk: prior to these studies, the samples were inactivated via formaldehyde treatment to ensure a higher working safety. The single-cell Raman spectra of different Brucella, Escherichia, Ochrobactrum, Pseudomonas, and Yersinia spp. were measured to create two independent databases for detection in media and milk. Identification accuracies of 92% for Brucella from medium and 94% for Brucella from milk were obtained while analyzing the single-cell Raman spectra via support vector machine. Even the identification of the other genera yielded sufficient results, with accuracies of >90%. In summary, micro-Raman spectroscopy is a promising alternative for detecting Brucella. The measurements we performed at the single-cell level thus allow fast identification within a few hours without a demanding process for sample preparation.

Electron beam lithography designed silver nano-disks used as label free nano-biosensors based on localized surface plasmon resonance

We present a label-free, optical nano-biosensor based on the Localized Surface Plasmon Resonance (LSPR) that is observed at the metal-dielectric interface of silver nano-disk arrays located periodically on a sapphire substrate by Electron-Beam Lithography (EBL). The nano-disk array was designed by finite-difference and time-domain (FDTD) algorithm-based simulations. Refractive index sensitivity was calculated experimentally as 221-354 nm/RIU for different sized arrays. The sensing mechanism was first tested with a biotin-avidin pair, and then a preliminary trial for sensing heat-killed Escherichia coli (E. coli) O157:H7 bacteria was done. Although the study is at an early stage, the results indicate that such a plasmonic structure can be applied to bio-sensing applications and then extended to the detection of specific bacteria species as a fast and low cost alternative.

Carbohydrate-based label-free detection of Escherichia coli ORN 178 using electrochemical impedance spectroscopy

A label-free biosensor for Escherichia coli (E. coli) ORN 178 based on faradaic electrochemical impedance spectroscopy (EIS) was developed. α-Mannoside or β-galactoside was immobilized on a gold disk electrode using a self-assembled monolayer (SAM) via a spacer terminated in a thiol functionality. Impedance measurements (Nyquist plot) showed shifts due to the binding of E. coli ORN 178, which is specific for α-mannoside. No significant change in impedance was observed for E. coli ORN 208, which does not bind to α-mannoside. With increasing concentrations of E. coli ORN 178, electron-transfer resistance (R(et)) increases before the sensor is saturated. After the Nyquist plot of E. coli/mixed SAM/gold electrode was modeled, a linear relationship between normalized R(et) and the logarithmic value of E. coli concentrations was found in a range of bacterial concentration from 10(2) to 10(3) CFU/mL. The combination of robust carbohydrate ligands with EIS provides a label-free, sensitive, specific, user-friendly, robust, and portable biosensing system that could potentially be used in a point-of-care or continuous environmental monitoring setting.

SERS-based sandwich immunoassay using antibody coated magnetic nanoparticles for Escherichia coli enumeration

A method combining immunomagnetic separation (IMS) and surface-enhanced Raman scattering (SERS) was developed to enumerate Escherichia coli (E. coli). Gold-coated magnetic spherical nanoparticles were prepared by immobilizing biotin-labeled anti-E. coli antibodies onto avidin-coated magnetic nanoparticles and used in the separation and concentration of the E. coli cells. Raman labels have been constructed using rod shaped gold nanoparticles coated with 5,5-dithiobis-(2-nitrobenzoic acid) (DTNB) and subsequently with a molecular recognizer. Then DTNB-labeled gold nanorods were interacted with gold-coated magnetic spherical nanoparticle-antibody-E. coli complex. The capture efficiency and calibration graphs were obtained and examined in different E. coli concentrations (10(1)-10(7) cfu mL(-1)). The correlation between the concentration of bacteria and SERS signal was found to be linear within the range of 10(1)-10(4) cfu mL(-1) (R(2) = 0.992). The limit of detection (LOD) and limit of quantification (LOQ) values of the developed method were found to be 8 and 24 cfu mL(-1), respectively. The selectivity of the developed immunoassay was examined with Enterobacter aerogenes, Enterobacter dissolvens, and Salmonella enteriditis which did not produce any significant response. The ability of the immunoassay to detect E. coli in real water samples was also investigated and the results were compared with the experimental results from plate-counting methods. There was no significant difference between the methods that were compared (p > 0.05). This method is rapid and sensitive to target organisms with a total analysis time of less than 70 min.

Electrical detection of pathogenic bacteria via immobilized antimicrobial peptides

The development of a robust and portable biosensor for the detection of pathogenic bacteria could impact areas ranging from water-quality monitoring to testing of pharmaceutical products for bacterial contamination. Of particular interest are detectors that combine the natural specificity of biological recognition with sensitive, label-free sensors providing electronic readout. Evolution has tailored antimicrobial peptides to exhibit broad-spectrum activity against pathogenic bacteria, while retaining a high degree of robustness. Here, we report selective and sensitive detection of infectious agents via electronic detection based on antimicrobial peptide-functionalized microcapacitive electrode arrays. The semiselective antimicrobial peptide magainin I--which occurs naturally on the skin of African clawed frogs--was immobilized on gold microelectrodes via a C-terminal cysteine residue. Significantly, exposing the sensor to various concentrations of pathogenic Escherichia coli revealed detection limits of approximately 1 bacterium/μL, a clinically useful detection range. The peptide-microcapacitive hybrid device was further able to demonstrate both Gram-selective detection as well as interbacterial strain differentiation, while maintaining recognition capabilities toward pathogenic strains of E. coli and Salmonella. Finally, we report a simulated "water-sampling" chip, consisting of a microfluidic flow cell integrated onto the hybrid sensor, which demonstrates real-time on-chip monitoring of the interaction of E. coli cells with the antimicrobial peptides. The combination of robust, evolutionarily tailored peptides with electronic read-out monitoring electrodes may open exciting avenues in both fundamental studies of the interactions of bacteria with antimicrobial peptides, as well as the practical use of these devices as portable pathogen detectors.