Daniel M. Jenkins

Detection of Ralstonia solanacearum by Loop-Mediated Isothermal Amplification

Ralstonia solanacearum is a pathogenic bacterium that causes wilt in over 200 plant species. Here we report a rapid and sensitive detection of R. solanacearum using an isothermal method for copying DNA known as loop-mediated amplification (LAMP). A set of four primers was designed to replicate the gene coding for the flagellar subunit, fliC, and conditions for detection were optimized to complete in 60 min at 65 degrees C. Magnesium pyrophosphate resulting from the amplification reaction could be detected optically as an increase in the solution turbidity, and the DNA products spread in a reproducible ladder-like banding pattern after electrophoresis in an agarose gel. Replication of the fliC gene was detected only from R. solanacearum. The detection limit of this LAMP assay was between 10(4) to 10(6) colony forming units/ml, and the technique may be useful for developing rapid and sensitive detection methods for the R. solanacearum pathogen in soil and water.

Phylogeny and classification of Dickeya based on multilocus sequence analysis.

Bacterial heart rot of pineapple reported in Hawaii in 2003 and reoccurring in 2006 was caused by an undetermined species of Dickeya. Classification of the bacterial strains isolated from infected pineapple to one of the recognized Dickeya species and their phylogenetic relationships with Dickeya were determined by a multilocus sequence analysis (MLSA), based on the partial gene sequences of dnaA, dnaJ, dnaX, gyrB and recN. Individual and concatenated gene phylogenies revealed that the strains form a clade with reference Dickeya sp. isolated from pineapple in Malaysia and are closely related to D. zeae; however, previous DNA-DNA reassociation values suggest that these strains do not meet the genomic threshold for consideration in D. zeae, and require further taxonomic analysis. An analysis of the markers used in this MLSA determined that recN was the best overall marker for resolution of species within Dickeya. Differential intraspecies resolution was observed with the other markers, suggesting that marker selection is important for defining relationships within a clade. Phylogenies produced with gene sequences from the sequenced genomes of strains D. dadantii Ech586, D. dadantii Ech703 and D. zeae Ech1591 did not place the sequenced strains with members of other well-characterized members of their respective species. The average nucleotide identity (ANI) and tetranucleotide frequencies determined for the sequenced strains corroborated the results of the MLSA that D. dadantii Ech586 and D. dadantii Ech703 should be reclassified as Dickeya zeae Ech586 and Dickeya paradisiaca Ech703, respectively, whereas D. zeae Ech1591 should be reclassified as Dickeya chrysanthemi Ech1591.

Handheld device for real-time, quantitative, LAMP-based detection of Salmonella enterica using assimilating probes.

A simple handheld instrument was designed to enable real-time detection of the LAMP reaction in a standard PCR tube using newly described assimilating probes as sequence-specific reporter molecules. The system was validated using DNA isolated from Salmonella enterica, demonstrating accurate temperature control with little power and little overshoot of setpoint temperatures, with rapid and accurate detection often in less than 30 min and within 20 min for reactions with high (>10(5)) genome copy numbers. The system could be used for quantitative determination of pathogen DNA, with a limit of detection of about 15 genome copies in purified DNA or 25 cells in DNA extracts from chicken rinsate--comparable to values obtained when running the same reaction on a commercial benchtop real-time PCR instrument. Positive classification of standards nominally containing a single genome equivalent was demonstrated, and no false positives were reported. Detection of S. enterica in rinsate from a contaminated chicken sample required 48 h enrichment prior to the LAMP reaction or plating on semi-selective media. The new system demonstrates a major compelling advantage of the LAMP reaction, in that it may be enabled in simple, low-power, handheld devices without sophisticated custom miniaturized disposables. This new diagnostic system is especially promising for on-site diagnostics in the food and agricultural industries where laboratory space is often primitive if it is available at all.

MANOMETRIC BIOSENSOR FOR ON-LINE MEASUREMENT OF MILK UREA

Performance of a prototype sensor for on-line measurement of urea in milk during milking was evaluated. The sensor was based on a manometric assay of the carbon dioxide generated by the enzymatic hydrolysis of urea. Temperature compensation of the sensor was described briefly, and was shown to be effective. The calibration of the sensor was described and resulted in a standard calibration error of about 0.15 mM of urea. The standard error of the sensor in milk was shown to be about 0.25 mM (given a physiological range of about 2-7 mM in cow milk). The sensor was simple, inexpensive, suffered from no interferences in raw milk, and completed a measurement cycle in about 5 min (less than the time to milk a typical cow). A custom made sampling device, whereby milk was passively collected from the milk line under vacuum, was shown to collect an ample volume within 10 s to run a test with the sensor. No measurable bubbles or foam were introduced from the sampling mechanism so that the milk sampled was not diminished in density compared to samples taken by other methods.

In silico genomic subtraction guides development of highly accurate, DNA-based diagnostics for Ralstonia solanacearum race 3 biovar 2 and blood disease bacterium

New rapid diagnostic methods are urgently needed to discriminate the quarantine pathogen Ralstonia solanacearum (Rs) race 3 biovar 2 (R3B2) from other populations of Rs that lack the adaptation to cause bacterial wilt disease in temperate regions. We used an in silico bioinformatic approach to identify several genome sequences potentially specific to R3B2 strains. Primer sets were designed to PCR-amplify sequences in these regions, and four sets were ultimately shown to be >99% accurate for detection of R3B2 strains. On the basis of these results, several primers were designed to enable development of a loop-mediated isothermal amplification assay that was rapid, technologically simple, and essentially 100% accurate for identification of R3B2 when applied to a comprehensive collection of geographically diverse Rs strains. We fortuitously found that a sequence in one of the “R3B2-specific” regions has ~90% identity to a sequence present in strains of the blood disease bacterium (BDB), a member of the Rs species complex that infects banana. Alignments of these sequences allowed design of a second PCR primer set that proved 100% accurate for identification of BDB strains when tested on the 22 BDB strains available to us. These results demonstrate the power of in silico genomic subtraction for rapid identification of population-specific DNA sequences and for the development of simple, reliable detection methods for Rs subpopulations.

Adaptation of a manometric biosensor to measure glucose and lactose

A manometric sensor previously developed to measure urea was modified to measure glucose and lactose through enzymatic oxidation. Change in pressure in an enclosed cavity was correlated to the depletion of oxygen resulting from the enzymatic oxidation of glucose or lactose. The response of the sensor was linear and could be made adjustable over a large range by adjusting the amount of sample loaded into the fixed volume reactor. Because of the slow mutarotation of glucose, the oxidation of glucose was not allowed to proceed to completion. Therefore, the precision of the sensor (approximately 0.2 mM in a range from 0 to 5 mM) was limited by variations in the oxidation rate of glucose by glucose oxidase. Because the assay for lactose measured glucose subsequent to the hydrolysis of lactose by beta-galactosidase, the same degree of precision was observed in lactose. Milk lactose, typically at concentrations of about 150 mM, was estimated using the lactose assay after first diluting the samples. For many fluids such as milk, the use of manometric sensors for oxidizable substrates may be preferable to optical and electrochemical methods because they are robust and suffer a low degree of optical and chemical interferences. Glucose and lactose are representative of many important oxidizable substrates, which may be determined in this manner, many of which do not suffer from limitations caused by mutarotation. In theory, detection limits less than 1 microM may be achieved using these methods.

Real-Time Duplex Applications of Loop-Mediated AMPlification (LAMP) by Assimilating Probes

Isothermal nucleic-acid amplification methods such as Loop-Mediated isothermal AMPlification (LAMP) are increasingly appealing alternatives to PCR for use in portable diagnostic system due to the low cost, weight, and power requirements of the instrumentation. As such, interest in developing new probes and other functionality based on the LAMP reaction has been intense. Here, we report on the development of duplexed LAMP assays for pathogen detection using spectrally unique Assimilating Probes. As proof of principle, we used a reaction for Salmonella enterica as a model coupled with a reaction for λ-phage DNA as an internal control, as well as a duplexed assay to sub-type specific quarantine strains of the bacterial wilt pathogen Ralstonia solanacearum. Detection limits for bacterial DNA analyzed in individual reactions was less than 100 genomic equivalents in all cases, and increased by one to two orders of magnitude when reactions were coupled in duplexed formats. Even so, due to the more robust activity of newly available strand-displacing polymerases, the duplexed assays reported here were more powerful than analogous individual reactions reported only a few years ago, and represent a significant advance for incorporation of internal controls to validate assay results in the field.

Loop-Mediated Amplification of the Clavibacter michiganensis subsp. michiganensis micA Gene Is Highly Specific

Loop-mediated amplification (LAMP) was used to specifically identify Clavibacter michiganensis subsp. michiganensis, causal agent of bacterial canker of tomato. LAMP primers were developed to detect micA, a chromosomally stable gene that encodes a type II lantibiotic, michiganin A, which inhibits growth of other C. michiganensis subspecies. In all, 409 bacterial strains (351 C. michiganensis subsp. michiganensis and 58 non-C. michiganensis subsp. michiganensis) from a worldwide collection were tested with LAMP to determine its specificity. LAMP results were compared with genetic profiles established using polymerase chain reaction (PCR) amplification of seven genes (dnaA, ppaJ, pat-1, chpC, tomA, ppaA, and ppaC). C. michiganensis subsp. michiganensis strains produced eight distinct profiles. The LAMP reaction identified all C. michiganensis subsp. michiganensis strains and discriminated them from other C. michiganensis subspecies and non-Clavibacter bacteria. LAMP has advantages over immunodiagnostic and other molecular detection methods because of its specificity and isothermal nature, which allows for easy field application. The LAMP reaction is also not affected by as many inhibitors as PCR. This diagnostic tool has potential to provide an easy, one-step test for rapid identification of C. michiganensis subsp. michiganensis.

Detection of Ralstonia solanacearum in natural substrates using phage amplification integrated with real-time PCR assay

A sensitive, selective, and rapid protocol for detecting Ralstonia solanacearum from soil and plant tissues was developed based on the integration of the rapid self-replicating ability of bacteriophages with quantitative PCR (q-PCR). Six bacteriophages were isolated and selected for their ability to specifically infect and lyse R. solanacearum. Sixty-three strains of R. solanacearum and 72 isolates of other bacterial species were tested for their susceptibility to the bacteriophages. Based on the large host range and observed replication speed and reproductive burst sizes in ginger infecting R. solanacearum strain GW-1, phage M_DS1 was selected for the development of the phage-based indirect assay. With primers based on the phage genome, the protocol was used to detect R. solanacearum from a number of substrates. In pure R. solanacearum cultures, the protocol consistently detected approximately 3.3 CFU/ml after an hours incubation with 5.3x10(2) PFU/ml M_DS1. We used the protocol to confirm the presence of the pathogen in infected potted ginger plants, detecting levels near 10(2) CFU/g in 0.1 g of leaf tissue and levels near 10(3) CFU/ml in drainage water from the pots. In soils emended with the bacteria, we observed detection limits down to approximately 10(2) CFU/g.

Non-Instrumented Nucleic Acid Amplification (NINA) for Rapid Detection of Ralstonia solanacearum Race 3 Biovar 2.

We report on the use of a non-instrumented device for the implementation of a loop-mediated amplification (LAMP) based assay for the select-agent bacterial-wilt pathogen Ralstonia solanacearum race 3 biovar 2. Heat energy is generated within the device by the exothermic hydration of calcium oxide, and the reaction temperature is regulated by storing latent energy at the melting temperature of a renewable lipid-based engineered phase-change material. Endpoint detection of the LAMP reaction is achieved without opening the reaction tube by observing the fluorescence of an innovative FRET-based hybridization probe with a simple custom fluorometer. Non-instrumented devices could maintain reactions near the design temperature of 63°C for at least an hour. Using this approach DNA extracted from the pathogen could be detected at fewer than ten copies within a 25 μL reaction mix, illustrating the potential of these technologies for simple, powerful agricultural diagnostics in the field. Furthermore, the assay was just as reliable when implemented in a tropical environment at 31°C as it was when implemented in an air-conditioned lab maintained at 22°C, illustrating the potential value of the technology for field conditions in the tropics and subtropics.