Advantages of peptide nucleic acid oligonucleotides for sensitive site directed 16S rRNA fluorescence in situ hybridization (FISH) detection of Campylobacter jejuni, Campylobacter coli and Campylobacter lari

Fluorescent In Situ Hybridization for the Detection of Intracellular Bacteria in Companion Animals

FISH techniques have been applied for the visualization and identification of intracellular bacteria in companion animal species. Most frequently, these techniques have focused on the identification of adhesive-invasive Escherichia coli in gastrointestinal disease, although various other organisms have been identified in inflammatory or neoplastic gastrointestinal disease. Previous studies have investigated a potential role of Helicobacter spp. in inflammatory gastrointestinal and hepatic conditions. Other studies evaluating the role of infectious organisms in hepatopathies have received some attention with mixed results. FISH techniques using both eubacterial and species-specific probes have been applied in inflammatory cardiovascular, urinary, and cutaneous diseases to screen for intracellular bacteria. This review summarizes the results of these studies.

Development of a Novel Peptide Nucleic Acid Probe for the Detection of Legionella spp. in Water Samples

Legionella are opportunistic intracellular pathogens that are found throughout the environment. The Legionella contamination of water systems represents a serious social problem that can lead to severe diseases, which can manifest as both Pontiac fever and Legionnaires' disease (LD) infections. Fluorescence in situ hybridization using nucleic acid mimic probes (NAM-FISH) is a powerful and versatile technique for bacterial detection. By optimizing a peptide nucleic acid (PNA) sequence based on fluorescently selective binding to specific bacterial rRNA sequences, we established a new PNA-FISH method that has been successfully designed for the specific detection of the genus Legionella. The LEG22 PNA probe has shown great theoretical performance, presenting 99.9% specificity and 96.9% sensitivity. We also demonstrated that the PNA-FISH approach presents a good signal-to-noise ratio when applied in artificially contaminated water samples directly on filtration membranes or after cells elution. For water samples with higher turbidity (from cooling tower water systems), there is still the need for further method optimization in order to detect cellular contents and to overcome interferents' autofluorescence, which hinders probe signal visualization. Nevertheless, this work shows that the PNA-FISH approach could be a promising alternative for the rapid (3-4 h) and accurate detection of Legionella.

The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection

Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

FISH Variants

FISH has gained an irreplaceable place in microbiology because of its ability to detect and locate a microorganism, or a group of organisms, within complex samples. However, FISH role has evolved drastically in the last few decades and its value has been boosted by several advances in signal intensity, imaging acquisitions, automation, method robustness, and, thus, versatility. This has resulted in a range of FISH variants that gave researchers the ability to access a variety of other valuable information such as complex population composition, metabolic activity, gene detection/quantification, or subcellular location of genetic elements. In this chapter, we will review the more relevant FISH variants, their intended use, and how they address particular challenges of classical FISH.

Identification of Campylobacter fetus by fluorescence in situ hybridization (FISH)

Two new DNA FISH-probes for Campylobacter fetus were designed, in silico checked for cross-reactions and successfully evaluated in a multi-centric approach with 41 Campylobacter fetus isolates including isolates of all three know subspecies: Campylobacter fetus ssp. fetus, Campylobacter fetus ssp. venerealis, and Campylobacter fetus ssp. testudinum and 40 strains of five non-target Campylobacter species.

Innovative Methods of Rapid Bacterial Quantification and Applicability in Diagnostics and in Implant Materials Assessment

In recent years, a variety of new technologies have been proposed that allow rapid qualitative and quantitative microbiological analyses. In this paper we discuss the urgent needs for reliable and rapid microbiological analytical techniques in different applicative fields involving the research, production and medical application of implant materials, and the potential benefits derived from the use of new methods for rapid bacterial quantification. Current compendial methods are easy to perform and have gained confidence over their long period of use, but the supplemental use of new technologies could represent real breakthroughs whenever sensitive and rapid responses are urgently required and not met by the tests currently in use. Overall, the new microbiological methods require critical evaluation depending on their specific type of application and they may still not be thought of as totally substitutive, but they certainly exhibit considerable potential for different areas of biomaterials, as well as for advanced therapy medicinal and tissue engineering treatments.

Development of a new method based on unmodified gold nanoparticles and peptide nucleic acids for detecting bovine viral diarrhea virus-RNA

A simple colorimetric assay is presented for detecting bovine viral diarrhea virus (BVDV)-RNA based on aggregation of gold nanoparticles (AuNPs) in the presence of charge-neutral peptide nucleic acids (PNA). Free charge-neutral PNA oligomers tended to be adsorbed onto AuNPs and act as a coagulant, whereas hybridizing complementary RNA with PNA disrupted PNA-induced AuNP aggregation, and the NPs remained stable. However, non-complementary RNA did not have this effect, and PNA induced aggregation of the AuNPs that resulted in a color change of the reaction from red to blue. The label-free colorimetric assay developed was estimated to have a 10.48 ng/reaction BVDV-RNA detection limit for the visual assay and 1.05 ng/reaction BVDV-RNA using a spectrophotometer. Diagnostic sensitivity and specificity for the assay was in accordance with real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and nested RT-PCR results were 98 and 100%, respectively. Absorption of the 520/620 nm ratio was linear, along with an increase in the target RNA concentration of 1.64–52.4 ng/reaction (R² = 0.992), which showed a linear correlation for the quantitative assay. This study established a rapid visual label and enzyme-free diagnostic assay for detecting BVDV that is applicable in any clinical laboratory.

Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review

Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.

Molecular techniques for detecting and typing of bacteria, advantages and application to foodborne pathogens isolated from ducks

In recent times, several foodborne pathogens have become important and a threat to public health. Surveillance studies have provided data and a better understanding into the existence and spread of foodborne pathogens. The application of molecular techniques for detecting and typing of foodborne pathogens in surveillance studies provide reliable epidemiological data for tracing the source of human infections. A wide range of molecular techniques (including pulsed field gel electrophoresis, multilocus sequence typing, random amplified polymorphism deoxyribonucleic acid, repetitive extragenic palindromic, deoxyribonucleic acid sequencing, multiplex polymerase chain reaction and many more) have been used for detecting, speciating, typing, classifying and/or characterizing foodborne pathogens of great significance to humans. Farm animals including chickens, cattle, sheep, goats and pigs, and others (such as domestic and wild animals) have been reported to be primary reservoirs for foodborne pathogens. The consumption of contaminated poultry meats or products has been considered to be the leading source of human foodborne infections. Ducks like other farm animals are important source of foodborne pathogens and have been implicated in some human foodborne illnesses and deaths. Nonetheless, few studies have been conducted to explore the potential of ducks in causing foodborne outbreaks, diseases and its consequences. This review highlights some common molecular techniques, their advantages and those that have been applied to pathogens isolated from ducks and their related sources.

Cronobacter spp. in powdered infant formula

Cronobacter species are opportunistic pathogens, and a mortality rate of 40 to 80% is associated with infections. This pathogen can cause a range of serious diseases such as meningitis, septicemia, necrotizing enterocolitis, and brain abscesses and has been responsible for a variety of sequelae such as quadriplegia. Although Cronobacter can cause disease in both adults and infants, infant infections associated with powdered formula are the focus of this review. Since the first reported Cronobacter infection outbreak in 1958, powdered infant formula has been identified as a major source of these outbreaks, resulting in many recalls of powdered infant formula worldwide. This contamination has created an immense problem for the powdered infant formula industry. In this review, we discuss the taxonomy of Cronobacter species, the natural habitat of Cronobacter and its presence in foods, the physiology, pathogenicity, and virulence of Cronobacter species, and available detection methods. We also discuss reported cases of Cronobacter infection linked to powdered infant formula consumption and then focus specifically on the official World Health Organization guidelines for preparation of powdered infant formula.

Food analysis and food authentication by peptide nucleic acid (PNA)-based technologies

This tutorial review will address the issue of DNA determination in food by using Peptide Nucleic Acid (PNA) probes with different technological platforms, with a particular emphasis on the applications devoted to food authentication. After an introduction aimed at describing PNAs structure, binding properties and their use as genetic probes, the review will then focus specifically on the use of PNAs in the field of food analysis. In particular, the following issues will be considered: detection of genetically modified organisms (GMOs), of hidden allergens, of microbial pathogens and determination of ingredient authenticity. Finally, the future perspectives for the use of PNAs in food analysis will be briefly discussed according to the most recent developments.

Fluorescence in situ hybridization method using a peptide nucleic acid probe for identification of Salmonella spp. in a broad spectrum of samples

A fluorescence in situ hybridization (FISH) method for the rapid detection of Salmonella spp. using a novel peptide nucleic acid (PNA) probe was developed. The probe theoretical specificity and sensitivity were both 100%. The PNA-FISH method was optimized, and laboratory testing on representative strains from the Salmonella genus subspecies and several related bacterial species confirmed the predicted theoretical values of specificity and sensitivity. The PNA-FISH method has been successfully adapted to detect cells in suspension and is hence able to be employed for the detection of this bacterium in blood, feces, water, and powdered infant formula (PIF). The blood and PIF samples were artificially contaminated with decreasing pathogen concentrations. After the use of an enrichment step, the PNA-FISH method was able to detect 1 CFU per 10 ml of blood (5 x 10(9) +/- 5 x 10(8) CFU/ml after an overnight enrichment step) and also 1 CFU per 10 g of PIF (2 x 10(7) +/- 5 x 10(6) CFU/ml after an 8-h enrichment step). The feces and water samples were also enriched according to the corresponding International Organization for Standardization methods, and results showed that the PNA-FISH method was able to detect Salmonella immediately after the first enrichment step was conducted. Moreover, the probe was able to discriminate the bacterium in a mixed microbial population in feces and water by counter-staining with 4',6-diamidino-2-phenylindole (DAPI). This new method is applicable to a broad spectrum of samples and takes less than 20 h to obtain a diagnosis, except for PIF samples, where the analysis takes less than 12 h. This procedure may be used for food processing and municipal water control and also in clinical settings, representing an improved alternative to culture-based techniques and to the existing Salmonella PNA probe, Sal23S10, which presents a lower specificity.

Development and application of a novel peptide nucleic acid probe for the specific detection of Cronobacter genomospecies (Enterobacter sakazakii) in powdered infant formula

Here, we report a fluorescence in situ hybridization (FISH) method for rapid detection of Cronobacter strains in powdered infant formula (PIF) using a novel peptide nucleic acid (PNA) probe. Laboratory tests with several Enterobacteriaceae species showed that the specificity and sensitivity of the method were 100%. FISH using PNA could detect as few as 1 CFU per 10 g of Cronobacter in PIF after an 8-h enrichment step, even in a mixed population containing bacterial contaminants.

DNA mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. The key step of FISH involves the detection of a nucleic acid region and as such, DNA molecules have typically been used to probe for the sequences of interest. However, since the turn of the century, an increasing number of laboratories have started to move on to the more robust DNA mimics methods, most notably peptide and locked nucleic acids (PNA and LNA). In this review, we will cover the state-of-the-art of the different DNA mimics in regard to their application as efficient markers for the presence of individual microbial cells, and consider their potential advantages and pitfalls. Available PNA probes are then reassessed in terms of sensitivity and specificity using rRNA databases. In addition, we also attempt to predict the applicability of DNA mimics in well-known techniques attempting to detect in situ low number of copies of specific nucleic acid sequences such as catalyzed reporter deposition (CARD) and recognition of individual genes (RING) FISH.

Detection of viable Yersinia pestis by fluorescence in situ hybridization using peptide nucleic acid probes

A successful method has been developed for the detection of live Yersinia pestis, the plague bacillus, which incorporates nascent RNA synthesis. A fluorescent in situ hybridization (FISH) assay using peptide nucleic acid (PNA) probes was developed specifically to differentiate Y. pestis strains from closely related bacteria. PNA probes were chosen to target high copy mRNA of the Y. pestis caf1 gene, encoding the Fraction 1 (F1) antigen, and 16S ribosomal RNA. Among Yersinia strains tested, PNA probes Yp-16S-426 and Yp-F1-55 exhibited binding specificities of 100% and 98%, respectively. Y. pestis grown in the presence of competing bacteria, as might be encountered when recovering Y. pestis from environmental surfaces in a post-release bioterrorism event, was recognized by PNA probes and neither hybridization nor fluorescence was inhibited by competing bacterial strains which exhibited faster growth rates. Using fluorescence microscopy, individual Y. pestis bacteria were clearly differentiated from competing bacteria with an average detection sensitivity of 7.9x10(3) cells by fluorescence microscopy. In the current system, this would require an average of 2.56x10(5) viable Y. pestis organisms be recovered from a post-release environmental sample in order to achieve the minimum threshold for detection. The PNA-FISH assays described in this study allow for the sensitive and specific detection of viable Y. pestis bacteria in a timely manner.

Centrifugation of bacterial cells on slide surface improves the spatial distribution, cell recovery and reduces the time of enumeration for fluorescence in situ hybridization

Fluorescence in situ hybridization (FISH), which is used for the enumeration of bacteria in various ecosystems including the human intestinal tract, has several limitations. One of the major problems encountered is the uneven distribution of bacterial cells on the slide surface, which increases the coefficient of variation between repetitions and thereby increase the time required for enumeration. In order to improve the spatial distribution, we designed a centrifugation device, which allows the direct centrifugation of bacterial cells onto the slide surface. Another problem is the loss of bacterial cells during the hybridization procedure. This leads to an underestimation of the true cell numbers in the sample. To overcome this problem we tested the use of silanized or chrome gelatine coated slides. Our study indicates that the use of the centrifugation device in conjunction with chrome gelatine coated slides highly improves the quality of enumeration data obtained by manual and automated microscopic counting and shortens the time of analysis.

Development and application of a novel peptide nucleic acid probe for the specific detection of Helicobacter pylori in gastric biopsy specimens

In this work, a fluorescence in situ hybridization (FISH) method for the rapid detection of Helicobacter pylori using a novel peptide nucleic acid (PNA) probe is reported. Laboratory testing with several different bacterial species, including other Helicobacter spp., has shown that this probe is highly specific for H. pylori strains. In addition, the PNA FISH method has been successfully adapted for detection of the pathogen in paraffin-embedded gastric biopsy specimens.

Antisense PNA accumulates in Escherichia coli and mediates a long post-antibiotic effect

Antisense agents that target growth-essential genes display surprisingly potent bactericidal properties. In particular, peptide nucleic acid (PNA) and phosphorodiamidate morpholino oligomers linked to cationic carrier peptides are effective in time kill assays and as inhibitors of bacterial peritonitis in mice. It is unclear how these relatively large antimicrobials overcome stringent bacterial barriers and mediate killing. Here we determined the transit kinetics of peptide-PNAs and observed an accumulation of cell-associated PNA in Escherichia coli and slow efflux. An inhibitor of drug efflux pumps did not alter peptide-PNA potency, indicating a lack of active efflux from cells. Consistent with cell retention, the post-antibiotic effect (PAE) of the anti-acyl carrier protein (acpP) peptide-PNA was greater than 11 hours. Bacterial cell accumulation and a long PAE are properties of significant interest for antimicrobial development.

PNA-based probe for quantitative chemiluminescent in situ hybridisation imaging of cellular parvovirus B19 replication kinetics

To allow the ultrasensitive localization and the quantitative detection of parvovirus B19 nucleic acids in single infected cells at various times post-infection, a peptide nucleic acid (PNA)-based in situ hybridisation (ISH) assay with chemiluminescent detection has been developed. The assay is based on the use of a biotin-labelled PNA probe detected by a streptavidin-linked alkaline phosphatase and a chemiluminescent dioxetane phosphate derivative substrate. The luminescent signal was quantified and imaged with an ultrasensitive nitrogen-cooled CCD camera connected to an epifluorescence microscope. The assay was used to analyze the parvovirus B19 infection process in cell cultures and to quantify the amount of viral nucleic acids at different times after infection. The chemiluminescent ISH-PNA assay is characterized by high resolution providing a sharp localization of B19 nucleic acids within single cells, with higher sensitivity with respect to conventional colorimetric ISH detection. Thanks to the high detectability and wide linear range of chemiluminescence detection, an objective evaluation of the percentage of infected cells, which reached its maximum at 24 h after infection, following a B19 virus infectious cycle could be accurately evaluated. Chemiluminescence detection also allowed the quantitative analysis of viral nucleic acids at the single-cell level, showing a continuous increase of the content of viral nucleic acids in infected cells with time after infection. The developed chemiluminescent ISH-PNA assay could thus represent a potent tool for the assessment of viral infections and for the quantitative evaluation of the virus nucleic acid load of infected cells in virus studies and diagnostics.

Survival of Mycobacterium avium, Legionella pneumophila, Escherichia coli, and caliciviruses in drinking water-associated biofilms grown under high-shear turbulent flow

Most of the bacteria in drinking water distribution systems are associated with biofilms. In biofilms, their nutrient supply is better than in water, and biofilms can provide shelter against disinfection. We used a Propella biofilm reactor for studying the survival of Mycobacterium avium, Legionella pneumophila, Escherichia coli, and canine calicivirus (CaCV) (as a surrogate for human norovirus) in drinking water biofilms grown under high-shear turbulent-flow conditions. The numbers of M. avium and L. pneumophila were analyzed with both culture methods and with peptide nucleic acid fluorescence in situ hybridization (FISH) methods. Even though the numbers of pathogens in biofilms decreased during the experiments, M. avium and L. pneumophila survived in biofilms for more than 2 to 4 weeks in culturable forms. CaCV was detectable with a reverse transcription-PCR method in biofilms for more than 3 weeks. E. coli was detectable by culture for only 4 days in biofilms and 8 days in water, suggesting that it is a poor indicator of the presence of certain waterborne pathogens. With L. pneumophila and M. avium, culture methods underestimated the numbers of bacteria present compared to the FISH results. This study clearly proved that pathogenic bacteria entering water distribution systems can survive in biofilms for at least several weeks, even under conditions of high-shear turbulent flow, and may be a risk to water consumers. Also, considering the low number of virus particles needed to result in an infection, their extended survival in biofilms must be taken into account as a risk for the consumer.

Pathogen detection: A perspective of traditional methods and biosensors

The detection of pathogenic bacteria is key to the prevention and identification of problems related to health and safety. Legislation is particularly tough in areas such as the food industry, where failure to detect an infection may have terrible consequences. In spite of the real need for obtaining analytical results in the shortest time possible, traditional and standard bacterial detection methods may take up to 7 or 8 days to yield an answer. This is clearly insufficient, and many researchers have recently geared their efforts towards the development of rapid methods. The advent of new technologies, namely biosensors, has brought in new and promising approaches. However, much research and development work is still needed before biosensors become a real and trustworthy alternative. This review not only offers an overview of trends in the area of pathogen detection but it also describes main techniques, traditional methods, and recent developments in the field of pathogen bacteria biosensors.

Campylobacter in waterfowl and aquatic environments: incidence and methods of detection

Campylobacters are emerging as one of the most significant causes of human infections worldwide, and the role that waterfowl and the aquatic environment have in the spread of disease is beginning to be elucidated. On a world scale campylobacters are possibly the major cause of gastrointestinal infections. Campylobacters are common commensals in the intestinal tract of many species of wild birds, including waterfowl. They are also widely distributed in aquatic environments where their origins may include waterfowl as well as sewage effluents and agricultural runoff. Campylobacters have marked seasonal trends. In temperate aquatic environments they peak during winter, whereas spring-summer is the peak period for human infection. Campylobacter species may survive, and remain potentially pathogenic, for long periods in aquatic environments. The utility of bacterial fecal indicators in predicting the presence of campylobacters in natural waters is questionable. Viable but nonculturable Campylobacter cells may occur, but whether they have any role in the generation of outbreaks of campylobacteriosis is unclear. The routine detection of Campylobacter spp. in avian feces and environmental waters largely relies on conventional culture methods, while the recognition of a particular species or strain is based on serotyping and increasingly on molecular methods. Thus, PCR combined with selective enrichment enhances the detection of campylobacters in water and feces, while DNA sequencing facilitates recognition of particular species and strains.

Simple detection of small amounts of Pseudomonas cells in milk by using a microfluidic device

AIMS

Flow cytometry offers rapid and reliable analyses of bacteria in milk. However, a flow cytometer is relatively expensive and operation is rather complicated for an unskilled operator. We applied flow cytometry using a microfluidic device (on-chip flow cytometry) in detection of small amounts of milk-spoiling bacteria.

METHODS AND RESULTS

Pseudomonas cells in milk were in situ hybridized with Cy5-labelled probe specific for Pseudomonas spp. under optimized condition. Numbers of Pseudomonas cells in the stationary phase and in the starved state determined by on-chip flow cytometry were compared with those determined by conventional plate counting, and on-chip flow cytometry detected targeted cells in milk that were undetectable as colony forming units(CFU) on Standards Methods Agar.

CONCLUSIONS

The contamination in milk with fewer than 10 CFU ml(-1) of targeted cells in starved state was detectable with simple procedure (0.5 h milk-clearing, 1 h fixation, 2 h hybridization and 0.5 h on-chip flow cytometry following 12 h enrichment of cells).

SIGNIFICANCE AND IMPACT OF THE STUDY

On-chip flow cytometry following fluorescence in situ hybridization could be applicable to simple detection of milk-spoiling bacteria.

Evaluation of in situ methods used to detect Mycobacterium avium subsp. paratuberculosis in samples from patients with Crohn's disease

In common with other diagnostic tests, detection of mycobacteria in tissue by microscopic examination is susceptible to spectrum bias. Since Crohn's disease is defined by the absence of detectable pathogenic organisms, the use of in situ techniques to search for Mycobacterium avium subsp. paratuberculosis in Crohn's disease samples requires validation of methods in a paucibacillary setting. To generate paucibacillary infection, C57BL/6 mice were artificially infected with Mycobacterium avium subsp. paratuberculosis strain K10 and M. tuberculosis H37Rv, yielding tissues harboring fewer than one bacillus per oil immersion field. Serial sections of organs were then studied by cell wall-based staining techniques (Ziehl-Neelsen and auramine rhodamine) and nucleic acid-based staining techniques (in situ hybridization [ISH] and indirect in situ PCR [IS PCR]). Microscopic examination and measurement of morphometric parameters of bacilli revealed that for all methods, Mycobacterium avium subsp. paratuberculosis bacilli were observed to be shorter, smaller, and less rod shaped than M. tuberculosis bacilli. Ziehl-Neelsen, auramine rhodamine stains, ISH targeting rRNA, and IS-PCR targeting the IS900 element afforded comparable sensitivities, but for all methods, visualization of individual bacterial forms required magnification x1,000. Auramine rhodamine staining and IS-PCR generated positive signals in negative controls, indicating the nonspecificity of these assays. Together, our results indicate that detection of Mycobacterium avium subsp. paratuberculosis bacilli in tissue requires oil immersion microscopy, that rRNA-ISH provides sensitivity and specificity comparable to those of Ziehl-Neelsen staining, and that the microscopic detection limit for Mycobacterium avium subsp. paratuberculosis in tissue is governed more by bacterial burden than by staining method.

Targeting species-specific low-affinity 16S rRNA binding sites by using peptide nucleic acids for detection of Legionellae in biofilms

Using fluorescence in situ hybridization to detect bacterial groups has several inherent limitations. DNA probes are generally used, targeting sites on the 16S rRNA. However, much of the 16S rRNA is highly conserved, with variable regions often located in inaccessible areas where secondary structures can restrict probe access. Here, we describe the use of peptide nucleic acid (PNA) probes as a superior alternative to DNA probes, especially when used for environmental samples. A complex bacterial genus (Legionella) was studied, and two probes were designed, one to detect all species and one targeted to Legionella pneumophila. These probes were developed from existing sequences and are targeted to low-binding-affinity sites on the 16S rRNA. In total, 47 strains of Legionella were tested. In all cases, the Legionella spp. PNA probe labeled cells strongly but did not bind to any non-Legionella species. Likewise, the specific L. pneumophila PNA probe labeled only strains of L. pneumophila. By contrast, the equivalent DNA probes performed poorly. To assess the applicability of this method for use on environmental samples, drinking-water biofilms were spiked with a known concentration of L. pneumophila bacteria. Quantifications of the L. pneumophila bacteria were compared using PNA hybridization and standard culture methods. The culture method quantified only 10% of the number of L. pneumophila bacteria found by PNA hybridization. This illustrates the value of this method for use on complex environmental samples, especially where cells may be in a viable but noncultivable state.

Peptide nucleic acid-based in situ hybridization assay for detection of parvovirus B19 nucleic acids

BACKGROUND

Peptide nucleic acid (PNA) molecules are known to bind complementary nucleic acid sequences with a much stronger affinity and with more stable binding than DNA or RNA molecules. We chose parvovirus B19, which is diagnosed by detection of nucleic acids by in situ hybridization assay (ISH) and/or PCR, as an experimental model to develop an ISH assay that uses biotinylated PNA probes to detect viral genome in clinical specimens.

METHODS

We first optimized the PNA-ISH assay on B19-infected and mock-infected UT-7/EpoS1 cells and then tested the assay on archival B19 specimens and on consecutive specimens. All data were compared with data obtained with a standardized DNA-based ISH assay and confirmed by a PCR-ELISA.

RESULTS

PNA-ISH detected B19 genome in a higher number of B19-infected UT-7/EpoS1 cells and with a more defined localization of viral nucleic acids than the standardized DNA-ISH assay. Moreover, PNA-ISH was able to detect B19 genome in all positive archival samples, whereas DNA-ISH failed in 5 samples. PNA-ISH detected more positive samples than DNA-ISH when consecutive specimens were analyzed, and a close agreement was found with PCR-ELISA results.

CONCLUSIONS

The PNA-ISH assay had sensitivity and specificity comparable to a PCR assay and was more practical and quicker to perform than standard hybridization assays. The assay may be a suitable diagnostic test for the detection of viral nucleic acids in clinical specimens.