Rapid detection, identification, and enumeration of Escherichia coli by fluorescence in situ hybridization using an array scanner

Review of microchip analytical methods for the determination of pathogenic Escherichia coli

Bacterial infections remain the principal cause of mortality worldwide, making the detection of pathogenic bacteria highly important, especially Escherichia coli (E. coli). Current E. coli detection methods are labour-intensive, time-consuming, or require expensive instrumentation, making it critical to develop new strategies that are sensitive and specific. Microchips are an automated analytical technique used to analyse food based on their separation efficiency and low analyte consumption, which make them the preferred method to detect pathogenic bacteria. This review presents an overview of microchip-based analytical methods for analysing E. coli, which were published in recent years. Specifically, this review focuses on current research based on microchips for the detection of E. coli and reviews the limitations of microchip-based methods and future perspectives for the analysis of pathogenic bacteria.

Photocatalytic Inactivation as a Method of Elimination of E. coli from Drinking Water

The presence of microorganisms, specifically the Escherichia coli, in drinking water is of global concern. This is mainly due to the health implications of these pathogens. Several conventional methods have been developed for their removal; however, this pathogen is still found in most drinking water. In the continuous quest for a more effective removal approach, photocatalysis has been considered as an alternative method for the elimination of pathogens including E. coli from water. Photocatalysis has many advantages compared to the conventional methods. It offers the advantage of non-toxicity and utilizes the energy from sunlight, thereby making it a completely green route. Since most photocatalysts could only be active in the ultraviolet region of the solar spectrum, which is less than 5% of the entire spectrum, the challenge associated with photocatalysis is the design of a system for the effective harvest and complete utilization of the solar energy for the photocatalytic process. In this review, different photocatalysts for effective inactivation of E. coli and the mechanism involved in the process were reviewed. Various strategies that have been adopted in order to modulate the band gap energy of these photocatalysts have been explored. In addition, different methods of estimating and detecting E. coli in drinking water were presented. Furthermore, different photocatalytic reactor designs for photocatalytic inactivation of E. coli were examined. Finally, the kinetics of E. coli inactivation was discussed.

Presence and Persistence of Salmonella in Water: The Impact on Microbial Quality of Water and Food Safety

Salmonella ranks high among the pathogens causing foodborne disease outbreaks. According to the Centers for Disease Control and Prevention, Salmonella contributed to about 53.4% of all foodborne disease outbreaks from 2006 to 2017, and approximately 32.7% of these foodborne Salmonella outbreaks were associated with consumption of produce. Trace-back investigations have suggested that irrigation water may be a source of Salmonella contamination of produce and a vehicle for transmission. Presence and persistence of Salmonella have been reported in surface waters such as rivers, lakes, and ponds, while ground water in general offers better microbial quality for irrigation. To date, culture methods are still the gold standard for detection, isolation and identification of Salmonella in foods and water. In addition to culture, other methods for the detection of Salmonella in water include most probable number, immunoassay, and PCR. The U.S. Food and Drug Administration (FDA) issued the Produce Safety Rule (PSR) in January 2013 based on the Food Safety Modernization Act (FSMA), which calls for more efforts toward enhancing and improving approaches for the prevention of foodborne outbreaks. In the PSR, agricultural water is defined as water used for in a way that is intended to, or likely to, contact covered produce, such as spray, wash, or irrigation. In summary, Salmonella is frequently present in surface water, an important source of water for irrigation. An increasing evidence indicates irrigation water as a source (or a vehicle) for transmission of Salmonella. This pathogen can survive in aquatic environments by a number of mechanisms, including entry into the viable but nonculturable (VBNC) state and/or residing within free-living protozoa. As such, assurance of microbial quality of irrigation water is critical to curtail the produce-related foodborne outbreaks and thus enhance the food safety. In this review, we will discuss the presence and persistence of Salmonella in water and the mechanisms Salmonella uses to persist in the aquatic environment, particularly irrigation water, to better understand the impact on the microbial quality of water and food safety due to the presence of Salmonella in the water environment.

Interaction of novel fluorescent nanoscale ionic silicate platelets with biomaterials for biosensors

The nano silicate platelets (NSPs) of 100 × 100 × 1 nm(3) in dimension were previously derived from the exfoliation of naturally occurring sodium montmorillonite clay, and their affinity to the surface of bacteria was revealed. The unique characteristics of ionic charges (≡Si-O-Na(+)) and the presence of siloxanol functionalities (≡Si-OH) allowed the organic modification of NSP to form NSP-tethering poly(hydroxyethyl methacrylate) (PHEMA) pendants through a sol-gel and living polymerization. By attaching nathphalimide-type fluorescence onto NSP-PHEMA, a new class of fluorescent organic-inorganic hybrid (NSP-PHEMA-HA), was prepared and its photoluminescence (PL) and bacterial trapping properties were characterized. The investigation of PL emission revealed that the fluorescent NSP hybrids could be used to detect bacteria and possess the potential for the biosensor applications.

PNA FISH: present and future impact on patient management

Inappropriate and inaccurate antimicrobial therapy can lead to adverse patient outcomes and also the development of antimicrobial resistance. Peptide nucleic acid (PNA) fluorescence in situ hybridization (FISH) gives rapid reporting with highly sensitive and specific results to clinicians within 3 h after blood cultures turn positive, thereby offering targeted therapeutics where necessary. It is simple to establish compared with real-time PCR and has resulted in significant cost savings for hospitals. PNA FISH is a promising future technology for the microbiology laboratory that will impact on patient management and clinical guidelines. This article will review the clinical data supporting these new technologies.

Peptide nucleic acid fluorescent in situ hybridization for hospital-acquired enterococcal bacteremia: delivering earlier effective antimicrobial therapy

Hospital-acquired vancomycin-resistant enterococcal bacteremia has been associated with increased hospital costs, length of stay, and mortality. The peptide nucleic acid fluorescent in situ hybridization (PNA FISH) test for Enterococcus faecalis and other enterococci (EFOE) is a multicolor probe that differentiates E. faecalis from other enterococcal species within 3 h directly from blood cultures demonstrating gram-positive cocci in pairs and chains (GPCPC). A quasiexperimental study was performed over two consecutive years beginning in 2005 that identified GPCPC by conventional microbiological methods, and in 2006 PNA FISH was added with a treatment algorithm developed by the antimicrobial team (AMT). The primary outcome assessed was the time from blood culture draw to the implementation of effective antimicrobial therapy before and after PNA FISH. The severity of illness, patient location, and empirical antimicrobial therapy were measured. A total of 224 patients with hospital-acquired enterococcal bacteremia were evaluated, with 129 in the preintervention period and 95 in the PNA FISH period. PNA FISH identified E. faecalis 3 days earlier than conventional cultures (1.1 versus 4.1 days; P < 0.001). PNA FISH identified Enterococcus faecium a median 2.3 days earlier (1.1 versus 3.4 days; P < 0.001) and was associated with statistically significant reductions in the time to initiating effective therapy (1.3 versus 3.1 days; P < 0.001) and decreased 30-day mortality (26% versus 45%; P = 0.04). The EFOE PNA FISH test in conjunction with an AMT treatment algorithm resulted in earlier initiation of appropriate empirical antimicrobial therapy for patients with hospital-acquired E. faecium bacteremia.

Tunable Bacterial Agglutination and Motility Inhibition by Self-Assembled Glyco-Nanoribbons

We explored a method of controlling bacterial motility and agglutination by using self-assembled carbohydrate-coated beta-sheet nanoribbons. To this aim, we synthesized triblock peptides that consist of a carbohydrate, a polyethylene glycol (PEG) spacer, and a beta-sheet-forming peptide. An investigation into the effect of PEG-spacer length on the self-assembly of the triblock peptides showed that the PEG should be of sufficiently length to stabilize the beta-sheet nanoribbon structure. It was found that the stabilization of the nanoribbon led to stronger activity in bacterial motility inhibition and agglutination, thus suggesting that antibacterial activity can be controlled by the stabilization strategy. Furthermore, another level of control over bacterial motility and agglutination was attained by co-assembly of bacteria-specific and -nonspecific supramolecular building blocks. The nanoribbon specifically detected bacteria after the encapsulation of a fluorescent probe. Moreover, the detection sensitivity was enhanced by the formation of bacterial clusters. All these results suggest that the carbohydrate-coated beta-sheet nanoribbons can be developed as promising agents for pathogen capture, inactivation, and detection, and that the activity can be controlled at will.

Development of a base stacking hybridization-based microarray method for rapid identification of clinical isolates

A base stacking hybridization-based microarray method was developed for rapid identification of clinical isolates within 2 h. The oligonucleotide probe sequences for species or genus-level identification were targeted against ribosomal RNA. Isolates were lysed and directly hybridized to the microarray-bound capture probes without conventional DNA or RNA isolation and prior polymerase chain reaction amplification. Five bacterial species encountered frequently in the clinical setting, Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae, and one genus Enterococcus, could be discriminated by the microarray-based assay. Identification by this method matched biochemical identification for 150 of 152 clinical strains. This base-stacking hybridization microarray offers a simple, fast (</=2 h), and accurate identification of bacterial cultures and is a potential tool for routine clinical diagnosis.

Quantitative, longitudinal profiling of the primate fecal microbiota reveals idiosyncratic, dynamic communities

We used slot blot hybridization, quantitative polymerase chain reaction (qPCR), and flow cytometry microarrays to quantify specific 16S rDNAs in weekly fecal specimens from four monkeys housed in a research vivarium for periods ranging from five to 8 months. Even in these uniformly housed and fed animals the gut microbiota is idiosyncratic, very dynamic on short timescales, and shows significant positive and negative correlations among some bacteria as well as responses to heavy metal exposure. The relative quantification (fmol targets per total fmol bacterial 16S rDNA) afforded by flow cytometry microarrays agreed well with the absolute quantification (nanogram of target DNA per nanogram of fecal DNA) afforded by slot blots and qPCR. We also noted strengths and weaknesses in inter-method comparisons for DNA-based quantification of these complex bacterial communities.

Nucleic acid-based methods for the detection of bacterial pathogens: Present and future considerations for the clinical laboratory

BACKGROUND

Recent advances in nucleic acid-based methods to detect bacteria offer increased sensitivity and specificity over traditional microbiological techniques. The potential benefit of nucleic acid-based testing to the clinical laboratory is reduced time to diagnosis, high throughput, and accurate and reliable results.

METHODS

Several PCR and hybridization tests are commercially available for specific organism detection. Furthermore, hundreds of nucleic acid-based bacterial detection tests have been published in the literature and could be adapted for use in the clinical setting. Contamination potential, lack of standardization or validation for some assays, complex interpretation of results, and increased cost are possible limitations of these tests, however, and must be carefully considered before implementing them in the clinical laboratory.

CONCLUSIONS

A major area of advancement in nucleic acid-based assay development has been for specific and broad-range detection of bacterial pathogens.

Let them fly or light them up: matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry and fluorescence in situ hybridization (FISH)

This review focuses on clinical bacteriology and by and large does not cover the detection of fungi, viruses or parasites. It discusses two completely different but complementary approaches that may either supplement or replace classic culture-based bacteriology. The latter view may appear provocative in the light of the actual market penetration of molecular genetic testing in clinical bacteriology. Despite its elegance, high specificity and sensitivity, molecular genetic diagnostics has not yet reached the majority of clinical laboratories. The reasons for this are manifold: Many microbiologists and medical technologists are more familiar with classical microbiological methods than with molecular biology techniques. Culture-based methods still represent the work horse of everyday routine. The number of available FDA-approved molecular genetic tests is limited and external quality control is still under development. Finally, it appears difficult to incorporate genetic testing in the routine laboratory setting due to the limited number of samples received or the lack of appropriate resources. However, financial and time constraints, particularly in hospitals as a consequence of budget cuts and reduced length of stay, lead to a demand for significantly shorter turnaround times that cannot be met by culture-dependent diagnosis. As a consequence, smaller laboratories that do not have the technical and personal equipment required for molecular genetic amplification techniques may adopt alternative methods such as fluorescence in situ hybridization (FISH) that combines easy-to-perform molecular hybridization with microscopy, a technique familiar to every microbiologist. FISH is hence one of the technologies presented here. For large hospital or reference laboratories with a high sample volume requiring massive parallel high-throughput testing we discuss matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) of nucleic acids, a technology that has evolved from the post-genome sequencing era, for high-throughput sequence variation analysis (1, 2).

PNA Technology

Peptide nucleic acids (PNA) are deoxyribonucleic acid (DNA) mimics with a pseudopeptide backbone. PNA is an extremely good structural mimic of DNA (or of ribonucleic acid [RNA]), and PNA oligomers are able to form very stable duplex structures with Watson-Crick complementary DNA and RNA (or PNA) oligomers, and they can also bind to targets in duplex DNA by helix invasion. Therefore, these molecules are of interest in many areas of chemistry, biology, and medicine, including drug discovery, genetic diagnostics, molecular recognition, and the origin of life. Recent progress in studies of PNA properties and applications is reviewed.

Molecular biology and DNA microarray technology for microbial quality monitoring of water

Public concern over polluted water is a major environmental issue worldwide. Microbial contamination of water arguably represents the most significant risk to human health on a global scale. An important challenge in modern water microbial quality monitoring is the rapid, specific, and sensitive detection of microbial indicators and waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. Rapid microbiological analyses and detection of rare events in water systems are important challenges in water safety assessment since culture methods present serious limitations from both quantitative and qualitative points of view. To circumvent lengthy culture methods, newer enzymatic, immunological, and genetic methods are being developed as an alternative. DNA microarray technology is a new and promising tool that allows the detection of several hundred or even thousands DNA sequences simultaneously. Recent advances in sample processing and DNA microarray technologies provide new perspectives to assess microbial water quality. The aims of this review are to (1) summarize what is currently known about microbial indicators, (2) describe the most important waterborne pathogens, (3) present molecular methods used to monitor the presence of pathogens in water, and (4) show the potential of DNA microarrays in water quality monitoring.

Enumeration of viable E. coli in rivers and wastewaters by fluorescent in situ hybridization

A combination of direct viable count (DVC) and fluorescent in situ hybridization (FISH) procedures was used to enumerate viable Escherichia coli in river waters and wastewaters. A probe specific for the 16S rRNA of E. coli labeled with the CY3 dye was used; enumeration of hybridized cells was performed by epifluorescence microscopy. Data showed that the method was able to accurately enumerate a minimum of 3000 viable E. coli among a large number of non-fecal bacteria. When applied to river water and wastewater samples, the DVC-FISH method gave systematically higher E. coli counts than a reference culture-based method (miniaturized MPN method). The ratio between both counts (DVC-FISH/MPN) increased with decreasing abundance of culturable E. coli indicating that the proportion of viable but non-culturable (VBNC) E. coli (detectable by the DVC-FISH procedure and not by a culture-based method) was higher in low contaminated environments. We hypothesized that the more stressing conditions, i.e. nutritional stress and sunlight effect, met in low contaminated environments were responsible for the larger fraction of VBNC E. coli. A survival experiment, in which sterile mineral water was inoculated with a pure E. coli strain and incubated, confirmed that stressing conditions induced the apparition of non-culturable E. coli detectable by the DVC-FISH procedure. The analysis of the E. coli concentration along a Seine river longitudinal profile downstream a large input of fecal bacteria by a WWTP outfall showed an increasing fraction of VBNC E. coli with increasing residence time of the E. coli in the river after release. These data suggest that the DVC-FISH method is useful tool to analyze the dynamics of fecal bacteria in river water.

The application of peptide nucleic acid probes for rapid detection and enumeration of eubacteria, Staphylococcus aureus and Pseudomonas aeruginosa in recreational beaches of S. Florida

A novel chemiluminescent in situ hybridization technique using peptide nucleic acids (PNA) was adapted for the detection of bacteria in beach sand and recreational waters in South Florida. The simultaneous detection and enumeration of eubacteria and the novel indicators, Staphylococcus aureus and Pseudomonas aeruginosa, was achieved within 6-8 h of processing. Following 5 h of incubation on TSA, soybean peroxidase-labeled peptide nucleic acid probes (Boston Probes, Boston, MA) targeting species-specific 16S rRNA sequences of P. aeruginosa and S. aureus were used to hybridize microcolonies of the target species in-situ. In addition, a universal probe for 16S rRNA sequences was used to target the eubacteria. Probes were detected after a light generating reaction with a chemiluminescent substrate and their presence recorded on Polaroid film. The probes showed limited cross-reactivity with mixed indigenous bacteria extracted from seawater and sand by shaking with phosphate-buffered saline (PBS). Specificity and cross-reactivity was tested on the reference bacterial genera Pseudomonas, Staphylococcus, Vibrio, Shigella, Salmonella, Acinetobacter, Enterobacter, Escherichia and Citrobacter. These tests confirmed that the probes were specific for the microorganisms of interest and were unaffected by high salt levels. The results of the PNA chemiluminescent in situ hybridization were compared with traditional plate count methods (PCM) for total 'freshwater' eubacteria, S. aureus and P. aeruginosa. Counts of eubacteria and S. aureus were comparable with numbers obtained from traditional plate counts but levels of P. aeruginosa were higher with PNA than with PCM. It is possible that PNA is more sensitive than PCM because it can detect microcolonies on the agar surface that never fully develop with the plate count method. We conclude that the in situ hybridization technique used here represents an important potential tool for the rapid monitoring of novel indicator organisms in beaches and recreational waters.

Seven-hour fluorescence in situ hybridization technique for enumeration of Enterobacteriaceae in food and environmental water sample

AIMS

A fluorescent in situ hybridization (FISH) technique using an Enterobacteriaceae-specific probe (probe D) to target 16S rRNA was improved in order to enumerate, within a single working day, Enterobacteriaceae present in food and environmental water samples.

METHODS AND RESULTS

In order to minimize the time required for the FISH procedure, each step of FISH with probe D was re-evaluated using cultured Escherichia coli. Five minutes of ethanol treatment for cell fixation and hybridization were sufficient to visualize cultured E. coli, and FISH could be performed within 1 h. Because of the difficulties in detecting low levels of bacterial cells by FISH without cultivation, a FISH technique for detecting microcolonies on membrane filters was investigated to improve the bacterial detection limit. FISH with probe D following 6 h of cultivation to grow microcolonies on a 13 mm diameter membrane filter was performed, and whole Enterobacteriaceae microcolonies on the filter were then detected and enumerated by manual epifluorescence microscopic scanning at magnification of x100 in ca 5 min. The total time for FISH with probe D following cultivation (FISHFC) was reduced to within 7 h. FISHFC can be applied to enumerate cultivable Enterobacteriaceae in food (above 100 cells g-1) and environmental water samples (above 1 cell ml-1).

CONCLUSIONS

Cultivable Enterobacteriaceae in food and water samples were enumerated accurately within 7 h using the FISHFC method.

SIGNIFICANCE AND IMPACT OF THE STUDY

A FISHFC method capable of evaluating Enterobacteriaceae contamination in food and environmental water within a single working day was developed.

Use of DNA and peptide nucleic acid molecular beacons for detection and quantification of rRNA in solution and in whole cells

DNA and peptide nucleic acid (PNA) molecular beacons were successfully used to detect rRNA in solution. In addition, PNA molecular beacon hybridizations were found to be useful for the quantification of rRNA: hybridization signals increased in a linear fashion with the 16S rRNA concentrations used in this experiment (between 0.39 and 25 nM) in the presence of 50 nM PNA MB. DNA and PNA molecular beacons were successfully used to detect whole cells in fluorescence in situ hybridization (FISH) experiments without a wash step. The FISH results with the PNA molecular beacons were superior to those with the DNA molecular beacons: the hybridization kinetics were much faster, the signal-to-noise ratio was much higher, and the specificity was much better for the PNA molecular beacons. Finally, it was demonstrated that the combination of the use of PNA molecular beacons in FISH and flow cytometry makes it possible to rapidly collect quantitative FISH data. Thus, PNA molecular beacons might provide a solution for limitations of traditional FISH methods, such as variable target site accessibility, poor sensitivity for target cells with low rRNA content, background fluorescence, and applications of FISH in microfluidic devices.

Direct detection and identification of African trypanosomes by fluorescence in situ hybridization with peptide nucleic acid probes

We have developed a rapid and easy to perform fluorescence in situ hybridization test that allows specific identification of trypanosomes from the subgenus Trypanozoon, using peptide nucleic acid probes. Probes were designed to target subgenus-specific sequences on the multiple-copy 18S rRNA, greatly facilitating the detection of a single trypanosome.

PNA for rapid microbiology

The acceptance of rRNA sequence diversity as a criterion for phylogenetic discrimination heralds the transition from microbiological identification methods based on phenotypic markers to assays employing molecular techniques. Robust amplification assays and sensitive direct detection methods are rapidly becoming the standard protocols of microbiology laboratories. The emergence of peptide nucleic acid (PNA) from its status as an academic curiosity to that of a promising and powerful molecular tool, coincides with, and complements, the transition to rapid molecular tests. The unique properties of PNA enable the development of assay formats, which go above and beyond the possibilities of DNA probes. PNA probes targeting specific rRNA sequences of yeast and bacteria with clinical, environmental, and industrial value have recently been developed and applied to a variety of rapid assay formats. Some simply incorporate the sensitivity and specificity of PNA probes into traditional methods, such as membrane filtration and microscopic analysis; others involve recent techniques such as real-time and end-point analysis of amplification reactions.

Identification of indicator microorganisms using a standardized PNA FISH method

A standardized fluorescent in situ hybridization (FISH) method using Peptide Nucleic Acid (PNA) probes for analysis of gram-negative and gram-positive bacteria, as well as yeast, has been developed. Fluorescently labeled PNA probes targeting specific rRNA sequences of Escherichia coli, Pseudomonas aeruginosa, Staphyloccocus aureus, Salmonella were designed, as well as PNA probes targeting eubacteria and eucarya. These PNA probes were evaluated by PNA FISH using 27 bacterial and 1 yeast species, representing both phylogenetically closely related species, as well as species important to both clinical and industrial settings. The S. aureus and P. aeruginosa PNA probes did not cross react with any of the organisms tested, whereas the E. coli PNA probe, as expected from sequence data, also detected Shigella species. The Salmonella PNA probe reacted with all of the 13 Salmonella strains, representing the 7 subspecies of Salmonella, however, it is also complementary to a few other bacterial species. The eubacteria- and eucarya-specific PNA probes detected all bacterial species and one yeast species, respectively. The general applicability of the PNA FISH method made simultaneous identification of multiple species, both gram-negative and gram-positive, in a mixed population an attractive possibility never accomplished using DNA probes. Four color images using differently labeled PNA probes showed simultaneous identification of E. coli, P. aeruginosa, S. aureus and Salmonella, thereby demonstrating the potential of multiplex FISH for various diagnostic applications within both clinical and industrial microbiology.