Electronic microarray analysis of 16S rDNA amplicons for bacterial detection

Short-term effect of Eucalyptus plantations on soil microbial communities and soil-atmosphere methane and nitrous oxide exchange

Soil greenhouse gas (GHG) emissions are a significant environmental problem resulting from microbially-mediated nitrogen (N) and carbon (C) cycling. This study aimed to investigate the impact of Eucalyptus plantations on the structure and function of a soil microbial community, and how resulting alterations may be linked to GHG fluxes. We sampled and monitored two adjacent Eucalyptus plantations—a recently logged site that harbored new seedlings and an adult plantation—and compared them to a site hosting native vegetation. We used 16S rRNA gene sequencing and qPCR amplifications of key nitrogen and methane cycle genes to characterize microbial structure and functional gene abundance and compared our data with soil parameters and GHG fluxes. Both microbial community attributes were significantly affected by land use and logging of Eucalyptus plantations. The genes nosZ and archaeal amoA were significantly more abundant in native forest than in either young or old Eucalyptus plantations. Statistical analyses suggest that land use type has a greater impact on microbial community structure and functional gene abundance than Eucalyptus rotation. There was no correlation between GHG fluxes and shifts in microbial community, suggesting that microbial community structure and functional gene abundance are not the main drivers of GHG fluxes in this system.

Solid and Suspension Microarrays for Microbial Diagnostics

Advancements in molecular technologies have provided new platforms that are being increasingly adopted for use in the clinical microbiology laboratory. Among these, microarray methods are particularly well suited for diagnostics as they allow multiplexing, or the ability to test for multiple targets simultaneously from the same specimen. Microarray technologies commonly used for the detection and identification of microbial targets include solid-state microarrays, electronic microarrays and bead suspension microarrays. Microarray methods have been applied to microbial detection, genotyping and antimicrobial resistance gene detection. Microarrays can offer a panel approach to diagnose specific patient presentations, such as respiratory or gastrointestinal infections, and can discriminate isolates by genotype for tracking epidemiology and outbreak investigations. And, as more information has become available on specific genes and pathways involved in antimicrobial resistance, we are beginning to be able to predict susceptibility patterns based on sequence detection for particular organisms. With further advances in automated microarray processing methods and genotype-phenotype prediction algorithms, these tests will become even more useful as an adjunct or replacement for conventional antimicrobial susceptibility testing, allowing for more rapid selection of targeted therapy for infectious diseases.

Next revolution in the molecular theranostics of infectious diseases: microfabricated systems for personalized medicine

The molecular diagnosis of infectious diseases is currently going through a revolution sustained by the regulatory approval of amplification tests that have been shown to be equivalent or superior to existing gold standard methods. The recent approval of a microarray system for the pharmacogenomic profiling of cytochrome P450-mediated drug metabolism is paving the way to novel, rapid, sensitive, robust and economical microfabricated systems for point-of-care diagnostics, which are utilized closer and closer to the patient's bedside. These systems will enable the multiparametric genetic evaluation of several medical conditions, including infectious diseases. This forecoming revolution will position molecular theranostics in a broader integrated view of personalized medicine, which exploits genetic information from microbes and human hosts to optimize patient management and disease treatment.

A system to simultaneously detect tick-borne pathogens based on the variability of the 16S ribosomal genes

BACKGROUND

DNA microarrays can be used to quickly and sensitively identify several different pathogens in one step. Our previously developed DNA microarray, based on the detection of variable regions in the 16S rDNA gene (rrs), which are specific for each selected bacterial genus, allowed the concurrent detection of Borrelia spp., Anaplasma spp., Francisella spp., Rickettsia spp. and Coxiella spp.

METHODS

In this study, we developed a comprehensive detection system consisting of a second generation DNA microarray and quantitative PCRs. New oligonucleotide capture probes specific for Borrelia burgdorferi s.l. genospecies and Candidatus Neoehrlichia mikurensis were included. This new DNA microarray system required substantial changes in solution composition, hybridization conditions and post-hybridization washes.

RESULTS

This second generation chip displayed high specificity and sensitivity. The specificity of the capture probes was tested by hybridizing the DNA microarrays with Cy5-labeled, PCR-generated amplicons encoding the rrs genes of both target and non-target bacteria. The detection limit was determined to be 10(3) genome copies, which corresponds to 1-2 pg of DNA. A given sample was evaluated as positive if its mean fluorescence was at least 10% of the mean fluorescence of a positive control. Those samples with fluorescence close to the threshold were further analyzed using quantitative PCRs, developed to identify Francisella spp., Rickettsia spp. and Coxiella spp. Like the DNA microarray, the qPCRs were based on the genus specific variable regions of the rrs gene. No unspecific cross-reactions were detected. The detection limit for Francisella spp. was determined to be only 1 genome copy, for Coxiella spp. 10 copies, and for Rickettsia spp., 100 copies.

CONCLUSIONS

Our detection system offers a rapid method for the comprehensive identification of tick-borne bacteria, which is applicable to clinical samples. It can also be used to identify both pathogenic and endosymbiontic bacteria in ticks for eco-epidemiological studies, tick laboratory colony testing, and many other applications.

Implementation of random bacterial genomic DNA microarray chip (RBGDMC) for screening of dominant bacteria in complex cultures

The random bacterial genomic DNA microarray chip (RBGDMC), which was fabricated using random genomic DNA fragments obtained from the fragmentation of bacterial genome by using four different pairs of restriction enzymes, was found to discriminate bacterial species in the same genus and resulted in the determination of dominant bacteria in enriched cultures. The identification of a dominant bacterial species was successfully conducted in the co-culture of three different bacteria using the RBGDMC. In addition, the analysis of the chip data could confirm if any of the selected bacteria is the most abundant or if some bacteria were enriched and became the dominant species within the consortium after the samples were prepared from the repeated cultures of real sludge in a complex medium. This study shows the successful implementation of the RBGDMC for the identification and monitoring of dominant bacteria in complex environmental bacterial communities simply without any PCR amplification of the target nucleic acids.

Basic concepts of microarrays and potential applications in clinical microbiology

The introduction of in vitro nucleic acid amplification techniques, led by real-time PCR, into the clinical microbiology laboratory has transformed the laboratory detection of viruses and select bacterial pathogens. However, the progression of the molecular diagnostic revolution currently relies on the ability to efficiently and accurately offer multiplex detection and characterization for a variety of infectious disease pathogens. Microarray analysis has the capability to offer robust multiplex detection but has just started to enter the diagnostic microbiology laboratory. Multiple microarray platforms exist, including printed double-stranded DNA and oligonucleotide arrays, in situ-synthesized arrays, high-density bead arrays, electronic microarrays, and suspension bead arrays. One aim of this paper is to review microarray technology, highlighting technical differences between them and each platform's advantages and disadvantages. Although the use of microarrays to generate gene expression data has become routine, applications pertinent to clinical microbiology continue to rapidly expand. This review highlights uses of microarray technology that impact diagnostic microbiology, including the detection and identification of pathogens, determination of antimicrobial resistance, epidemiological strain typing, and analysis of microbial infections using host genomic expression and polymorphism profiles.

Design and validation of a microarray for detection, hemagglutinin subtyping, and pathotyping of avian influenza viruses

Continuing threats of devastating outbreaks in poultry and of human infections caused by highly pathogenic avian influenza virus (HPAIV) H5N1 emphasize the need for the further development of rapid and reliable methods of virus detection and characterization. Here we report on the design and comprehensive validation of a low-density microarray as a diagnostic tool for the detection and typing of avian influenza virus (AIV). The array consists of one probe for the conserved matrix gene and 97 probes targeting the HA(0) cleavage-site region. Following fragment amplification by a generic PCR approach, the array enables AIV detection, hemagglutinin (HA) subtyping, and pathotyping within a single assay. For validation, a panel of 92 influenza A viruses which included 43 reference strains representing all 16 HA subtypes was used. All reference strains were correctly typed with respect to their HA subtypes and pathotypes, including HPAIV H5N1/Asia, which caused outbreaks in Germany in 2006 and 2007. In addition, differentiation of strains of the Eurasian and North American lineages of the H5 and H7 subtypes was possible. The sensitivity of the microarray for the matrix gene is comparable to that of real-time reverse transcription-PCR (RT-PCR). It is, however, 10- to 100-fold lower than that of real-time RT-PCR with respect to HA subtyping and pathotyping. The specificity of the array was excellent, as no pathogens relevant for differential diagnosis yielded a positive reaction. Validation with field samples included 19 cloacal swab specimens from wild and domestic birds. Influenza A virus was verified in all samples, whereas the HA subtypes could be determined for 14 samples. The results demonstrate that the microarray assay described complements current methods and can accelerate the diagnosis and characterization of AIV.

Split hybridisation probes for electrochemical typing of single-nucleotide polymorphisms

This paper describes the development of a highly selective single-nucleotide polymorphisms (SNPs) typing method based on the use of split hybridisation probes and demonstrates the concept through the electrochemical analysis of single-base mutations in actual patient samples. The requirement that two probes hybridised adjacent to one another to allow for stabilisation (via base-stacking) and binding of the allele-specific oligonucleotide (ASO), imparted highly stringent selectivity criteria to the assay. Simple rules for tuning the characteristics of such stacking/ASO probe pairs and achieve full mismatch discrimination at ambient conditions (with no need to strictly control the temperature) are provided. All genotyping experiments were indeed performed at room temperature, using the planar surface of disposable probe-modified gold electrodes as the genosensing platform. The ability to detect nanomolar amounts of a synthetic target even within a vast excess of single-base substituted sequences gave strong evidence of the specificity of the split probes assay. Proving the general validity of this genotyping approach, application of the analytical pathway was further demonstrated for clinical targets (amplified from the human TP53 gene) whose mutational site was poorly accessible, being part of a thermodynamically stable hairpin. In combination with use of auxiliary oligonucleotides (which restored the availability of each pre-defined hybridisation site), the assay demonstrated the ability to fully discriminate single-base mutations with detection limits in the high picomolar range (total analysis time: 60 min). Our specific probe design, hybridisation and signal transduction paths make the analytical process remarkably simple, relatively low cost and, thus, well suited for low throughput analysis of clinically relevant samples.

BioMEMS -Advancing the Frontiers of Medicine

Biological and medical application of micro-electro-mechanical-systems (MEMS) is currently seen as an area of high potential impact. Integration of biology and microtechnology has resulted in the development of a number of platforms for improving biomedical and pharmaceutical technologies. This review provides a general overview of the applications and the opportunities presented by MEMS in medicine by classifying these platforms according to their applications in the medical field.

The use of transcriptomic biomarkers for personalized medicine

Microarrays are a high throughput technology that allows the quantification of tens of thousands of RNA transcripts in a single reaction. This new technology offers the promise of comprehensive study of disease at a genomic level, potentially identifying novel molecular abnormalities, developing novel clinical biomarkers, and investigating drug efficacy. The ability to develop a molecular profile corresponding to a therapeutic effect is the basis for the concept of drug repositioning. With regard to prediction of clinical events, microarray technology has the potential to contribute to the development of sophisticated new biomarkers useful as predictors of disease etiology, outcome, and responsiveness to therapy-so-called personalized medicine. Currently progress in the field is hampered by a degree of skepticism about the reliability of microarray data and its relevance for clinical applications. Here we discuss possible pitfalls of transcriptomic analysis, review current developments in the cardiovascular area and address the use of transcriptomics for clinical applications.

Detection of bacteria associated with harmful algal blooms from coastal and microcosm environments using electronic microarrays

With the global expansion of harmful algal blooms (HABs), several measures, including molecular approaches, have been undertaken to monitor its occurrence. Many reports have indicated the significant roles of bacteria in controlling algal bloom dynamics. Attempts have been made to utilize the bacteria/harmful algae relationship in HAB monitoring. In this study, bacterial assemblages monitored during coastal HABs and bacterial communities in induced microcosm blooms were investigated. Samples were analysed using denaturing gradient gel electrophoresis (DGGE) of the 16S rRNA gene. DGGE bands with peculiar patterns before, during, and after algal blooms were isolated and identified. Probes for six ribotypes representing organisms associated with Chatonella spp., Heterocapsa circularisquama, or Heterosigma akashiwo were used for analysis on NanoChip electronic microarray. In addition, a new approach using cultured bacteria species was developed to detect longer (533 bp) polymerase chain reaction-amplified products on the electronic microarray. The use of fluorescently labelled primers allowed the detection of individual species in single or mixed DNA conditions. The developed approach enabled the detection of the presence or absence and relative abundance of the HAB-related ribotypes in coastal and microcosm blooms. This study indicates the ability of electronic microarray platform to detect or monitor bacteria in natural and induced environments.

Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted

Hybridization of rRNAs to microarrays is a promising approach for prokaryotic and eukaryotic species identification. Typically, the amount of bound target is measured by fluorescent intensity and it is assumed that the signal intensity is directly related to the target concentration. Using thirteen different eukaryotic LSU rRNA target sequences and 7693 short perfect match oligonucleotide probes, we have assessed current approaches for predicting signal intensities by comparing Gibbs free energy (ΔG°) calculations to experimental results. Our evaluation revealed a poor statistical relationship between predicted and actual intensities. Although signal intensities for a given target varied up to 70-fold, none of the predictors were able to fully explain this variation. Also, no combination of different free energy terms, as assessed by principal component and neural network analyses, provided a reliable predictor of hybridization efficiency. We also examined the effects of single-base pair mismatch (MM) (all possible types and positions) on signal intensities of duplexes. We found that the MM effects differ from those that were predicted from solution-based hybridizations. These results recommend against the application of probe design software tools that use thermodynamic parameters to assess probe quality for species identification. Our results imply that the thermodynamic properties of oligonucleotide hybridization are by far not yet understood.

Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization

Different labeling methods were studied to compare various approaches to the preparation of labeled target DNA for microarray experiments. The methods under investigation included a post-PCR labeling method using the Klenow fragment and a DecaLabel DNA labeling kit, the use of a Cy3-labeled forward primer in the PCR, generating either double-stranded or single-stranded PCR products, and the incorporation of Cy3-labeled dCTPs in the PCR. A microarray that had already been designed and used for the detection of microorganisms in compost was used in the study. PCR products from the organisms Burkholderia cepacia and Staphylococcus aureus were used in the comparison study, and the signals from the probes for these organisms analyzed. The highest signals were obtained when using the post-PCR labeling method, although with this method, more non-specific hybridizations were found. Single-stranded PCR products that had been labeled by the incorporation of a Cy3-labeled forward primer in the PCR were found to give the next highest signals upon hybridization for a majority of the tested probes, with less non-specific hybridizations. Hybridization with double-stranded PCR product labeled with a Cy3-labeled forward primer, or labeled by the incorporation of Cy3-labeled dCTPs resulted in acceptable signal to noise ratios for all probes except the UNIV 1389a and Burkholderia genus probes, both located toward the 3' end of the 16S rRNA gene. The comparison of the different DNA labeling methods revealed that labeling via the Cy3-forward primer approach is the most appropriate of the studied methods for the preparation of labeled target DNA for our purposes.

Recent developments in bio-molecular electronics techniques for food pathogens

Food borne illnesses contribute to the majority of infections caused by pathogenic microorganisms. Detection of these pathogens originating from different sources has led to increased interest of researchers. New bio-molecular techniques for food pathogen detection are being developed to improve the sensor characteristics such as sensitivity, reusability, simplicity and economic viability. Present article deals with the various methods of food pathogen detection with special emphasis on bio-molecular electronics techniques such as biosensors, microarrays, electronic nose, and nano-materials based methods.

An electronic DNA microarray technique for detection and differentiation of viable Campylobacter species

An electronic oligonucleotide microarray technique was developed for detection and differentiation of the viable Campylobacter species, C. jejuni, C. coli, and C. lari. This development consisted of four major components: identification of single nucleotide polymorphisms (SNPs) within the hsp60 gene as species markers, design of fluorescently labelled SNP-based reporters, development of an electronic microarray detection, and application of the integrated technique to analysis of Campylobacter species in food samples. A unique capability of this technique is the specific detection of viable cells and not dead ones. This is achieved by using mRNA of the 60 kDa heat-shock protein as the viability marker. The identification of two unique SNPs closely located at positions 291 and 294 of the hsp60 gene enabled the differentiation of the three Campylobacter species. This technique was able to detect as few as two viable Campylobacter cells. The analysis of 19 blind Campylobacter samples showed 100% agreement with their identities obtained using pulsed-field gel electrophoresis. The analysis of six chicken samples revealed the presence of C. coli in one of the samples.

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.