Development of a novel Trueperella pyogenes-specific PCR assay

Trueperella pyogenes is an opportunistic pathogen that causes a wide variety of purulent infections. We recently isolated a T. pyogenes strain unable to be identified by the previously reported T. pyogenes pyolysin gene (plo)-specific PCR from the lung of a sheep with astasia. Sequence comparison of plo among representative strains revealed several nucleotide substitutions in the primer-annealing regions. As such substitutions were considered to be a reason for the low PCR specificity, we designed novel primers in conserved regions of plo. Under optimized conditions, the novel primers precisely identified all T. pyogenes strains tested, and no products were generated from any other bacterial strains, suggesting the usefulness of the novel PCR assay for the diagnosis of T. pyogenes infections.

[Specific PCR method for identification of Trionycis Carapax and its preparation]

Trionycis Carapax is a commonly used animal medicine in Chinese medicine. It's difficult to identify Trionycis Carapax and its adulterants because of the loss of morphological characteristics after processing. To establish an efficient and stable method to identification Trionycis Carapax, this study combines SDS method with column purification to extract genomic DNA, uses universal primers for polymerase chain reaction (PCR) amplification and sequencing, and designs the specific primers based on the differences in the sequences of Pelodiscus sinensis and their adulterants. When the annealing temperature was 62 °C and the number of cycles was 35, the designed primer Biejia-272.F/R was used for PCR amplification and got optimum results. The crude drug and preparation of P. sinensis were all amplified to obtain a specific band of approximately 300 bp, while the adulterants showed no such a band. This method can be used as a rapid and accurate method to identify the authenticate of P. sinensis.

Specific PCR Identification between Peucedanum praeruptorum and Angelica decursiva and Identification between Them and Adulterant Using DNA Barcode

Background:

The traditional Chinese medicine (TCM) Qianhu and Zihuaqianhu are the dried roots of Peucedanum praeruptorum and Angelica decursiva, respectively. Since the plant sources of Qianhu and Zihuaqianhu are more complex, the chemical compositions of P. praeruptorum and A. decursiva are significantly different, and many adulterants exist because of the differences in traditional understanding and medication habits. Therefore, the rapid and accurate identification methods are required.

Objective:

The aim was to study the feasibility of using DNA barcoding to distinguish between Traditional Chinese medicine Qianhu (Peucedanum praeruptorum), Zihuaqianhu (Angelica decursiva), and common adulterants, based on internal transcribed spacer (ITS) sequences, as well as specific PCR identification between P. praeruptorum and A. decursiva.

Materials and Methods:

The ITS sequences of P. praeruptorum, A. decursiva, and adulterant were studied, and a phylogenetic tree was constructed. Based on the ITS barcode, the specific PCR primer pairs QH-CP19s/QH-CP19a and ZHQH-CP3s/ZHQH-CP3a were designed for P. praeruptorum and A. decursiva, respectively. The amplification conditions were optimized, and specific PCR products were obtained.

Results:

The results showed that the phylogenetic trees constructed using the BI and MP methods were consistent, and P. praeruptorum and A. decursiva sequence haplotypes formed their own monophyly. The experimental results showed that in PCR products, the target bands appeared in the genuine drug and not in the adulterant, which suggests the high specificity of the two primer pairs.

Conclusion:

The ITS sequence was ideal DNA barcode to identify P. praeruptorum, A. decursiva, and adulterant. The specific PCR is a quick and effective method to distinguish between P. praeruptorum and A. decursiva.

SUMMARY

Peucedanum praeruptorum and Angelica decursiva sequence haplotypes formed their own monophyly.

The ITS sequence was ideal DNA barcode to identify P. praeruptorum, A. decursiva, and adulterant.

Specific PCR is a quick and effective method to distinguish between P. praeruptorum and A. decursiva.

Abbreviations used: TCM: The traditional Chinese medicine, P.: Peucedanum, A.: Angelica, ITS: The internal transcribed spacer, PCR: Polymerase chain reaction, NCBI: National Center for Biotechnology Information, NI: Number of individuals, HN: Haplotype number; GAN: Gen Bank accession numbers, L.: Ligusticum, O.: Ostericum, A.: Angelica, P.: Pimpinella, BI: Bayesian inference, MP: Maximum parsimony, AIC: Akaike Information Criterion, MCMC: Markov Chains Monte Carlo, TBR: Tree bisection-reconnection, LPP: Length of PCR product, PRP: PCR reaction procedure, SNP: Single nucleotide polymorphisms, PP: Posterior probability, BS: Bootstrap.Qun Zhao

Development of Candida-Specific Real-Time PCR Assays for the Detection and Identification of Eight Medically Important Candida Species

Culture-based identification methods have been the gold standard for the diagnosis of fungal infection. Currently, molecular technologies such as real-time PCR assays with short turnaround time can provide desirable alternatives for the rapid detection of Candida microbes. However, most of the published PCR primer sets are not Candida specific and likely to amplify DNA from common environmental contaminants, such as Aspergillus microbes. In this study, we designed pan-Candida primer sets based on the ribosomal DNA-coding regions conserved within Candida but distinct from those of Aspergillus and Penicillium. We demonstrate that the final two selected pan-Candida primer sets would not amplify Aspergillus DNA and could be used to differentiate eight medically important Candida pathogens in real-time PCR assays based on their melting profiles, with a sensitivity of detection as low as 10 fg of Candida genomic DNA. Moreover, we further evaluated and selected species-specific primer sets covering Candida albicans, Candida glabrata, Candida tropicalis, and Candida dubliniensis and show that they had high sensitivity and specificity. These real-time PCR primer sets could potentially be assembled into a single PCR array for the rapid detection of Candida species in various clinical settings, such as corneal transplantation.

Isolation and identification of Pseudomonas syringae facilitated by a PCR targeting the whole P. syringae group

We present a reliable PCR-based method to avoid the biases related to identification based on the conventional phenotypes currently used in the identification of Pseudomonas syringae sensu lato, a ubiquitous environmental bacterium including plant pathogens. We identified a DNA target suitable for this purpose by applying a comparative genomic pipeline to Pseudomonas genomes. We designed primers and developed PCR conditions that led to a clean and strong PCR product from 97% of the 185 strains of P. syringae strains tested and gave a clear negative result for the 31 non-P. syringae strains tested. The sensitivity of standard PCR was determined with pure strains to be 10(6) bacteria mL(-1) or 0.4 ng of DNA μL(-1). Sensitivity could be improved with the touchdown method. The new PCR-assisted isolation of P. syringae was efficient when deployed on an environmental sample of river water as compared to the isolation based on phenotypes. This innovation eliminates the need for extensive expertise in isolating P. syringae colonies, was simpler, faster and very reliable. It will facilitate discovery of more diversity of P. syringae and research on emergence, dispersion and evolution to understand the varied functions of this environmental bacterium.

Piceirhiza bicolorata- the ectomycorrhizal expression of the Hymenoscyphus ericae aggregate?

The mycobionts of Piceirhiza bicolorata, a distinct ectomycorrhizal morphotype of conifers and hardwoods, have been identified by internal transcribed spacer 1 (ITS1) nuclear ribosomal DNA (rDNA) sequence comparison of the fungi involved. Samples of Piceirhiza bicolorata were obtained from seedlings of Picea abies, Pinus sylvestris, Betula pubescens, Populus tremula, Quercus robur and Salix phylicifolia. In an initial screening, the fungus amplified with universal ITS primers from ectomycorrhizal root samples of P. bicolorata shared approx. 95% ITS1 sequence identity with the ericoid mycorrhizal fungus Hymenoscyphus ericae. A total of 77 out of 88 (= 87.5%) DNA samples (i.e. 52/56 root samples and 25/32 axenic culture isolates) of P. bicolorata were successfully amplified with a taxon-selective primer designed for exclusive amplification of H. ericae-like strains. Forty-seven amplicons were sequenced, yielding 15 different ITS1 genotypes that differed by 1-14 nucleotide character state changes. An inferred ITS1 phylogeny (maximum parsimony) showed that a single major evolutionary lineage of P. bicolorata embraced the historically important H. ericae isolates in a 100% bootstrap-supported clade. The 15 P. bicolorata genotypes were positioned in four subclades, roughly corresponding to morphological groups of P. bicolorata isolates observed in axenic culture. Culture isolates of H. ericae and P. bicolorata share some common morphological features including slow, dense growth and formation of short aerial hyphal aggregates. Our results suggest that members of the H. ericae aggregate participate in the formation of the distinct ectomycorrhizal morphotype P. bicolorata. This opposes the widely accepted discrimination of ericoid and ectomycorrhizal mycobionts of the boreal forest ecosystem. The high prevalence of the P. bicolorata morphotype on pioneer seedlings of P. sylvestris, B. pubescens and S. phylicifolia at a copper mine spoil was remarkable. Hypotheses of possible nutrient mobilization and detoxification potentials of the fungal associates of P. bicolorata are discussed. We hypothesize that ericoid and ectomycorrhizal plants may share mycobionts of the H. ericae aggregate.