Molecular Methods For Rapid Identification Research Articles

Multiple DNA Markers for Identification of Xanthomonas arboricola pv. juglandis Isolates and its Direct Detection in Plant Samples.

Xanthomonas arboricola pv. juglandis (Xaj) is the etiological agent of walnut (Juglans regia L.) bacterial blight (WBB), and has been associated to other walnut emerging diseases, namely brown apical necrosis (BAN) and vertical oozing canker (VOC), altogether severely affecting the walnut production worldwide. Despite the research efforts carried out to disclose Xaj genetic diversity, reliable molecular methods for rapid identification of Xaj isolates and culture-independent detection of Xaj in infected plant samples are still missing. In this work, we propose nine novel specific DNA markers (XAJ1 to XAJ9) selected by dedicated in silico approaches to identify Xaj isolates and detect these bacteria in infected plant material. To confirm the efficacy and specificity of these markers, dot blot hybridization was carried out across a large set of xanthomonads. This analysis, which confirmed the pathovar specificity of these markers, allowed to identify four broad-range markers (XAJ1, XAJ4, XAJ6, and XAJ8) and five narrow-range markers (XAJ2, XAJ3, XAJ5, XAJ7, and XAJ9), originating 12 hybridization patterns (HP1 to HP12). No evident relatedness was observed between these hybridization patterns and the geographic origin from which the isolates were obtained. Interestingly, four isolates that clustered together according the gyrB phylogenetic analysis (CPBF 1507, 1508, 1514, and 1522) presented the same hybridization pattern (HP11), suggesting that these nine markers might be informative to rapidly discriminate and identify different Xaj lineages. Taking into account that a culture-independent detection of Xaj in plant material has never been described, a multiplex PCR was optimized using markers XAJ1, XAJ6, and XAJ8. This triplex PCR, besides confirming the dot blot data for each of the 52 Xaj, was able to detect Xaj in field infected walnut leaves and fruits. Altogether, these nine Xaj-specific markers allow conciliating the specificity of DNA-detection assays with typing resolution, contributing to rapid detection and identification of potential emergent and acutely virulent Xaj genotypes, infer their distribution, disclose the presence of this phytopathogen on potential alternative host species and improve phytosanitary control.

The evaluation of different molecular methods for rapid identification of non-tuberculous Mycobacterium

Objective To evaluate three molecular methods for rapid identification of nontuberculous Mycobacterium(NTM).Methods Forty-one clinical NTM isolates were collected and 16S rRNA gene sequencing was used as the standard method for NTM identification.Meanwhile,the restriction fragment length polymorphism of hsp65 PCR-RFLP and hsp65 gene sequencing were used to identify NTM strains and compared with 16S rRNA gene sequencing.Results The results of 16S rRNA sequencing showed that there were nine Mycobacterium chelonae complex strains,seven Mycobacteriumfortuitum strains,seven Mycobacterium intracellulare strains,three Mycobacterium avium strains,three Mycobacterium kansasii complex strains, three Mycobacterium smegmatis strains, three Mycobacterium terrae strains, two Mycobacterium phlei strains,two Mycobacterium nonchromogenicum strains,one Mycobacterium scrofulaceum strain and one Mycobacterium arupense strain.Compared with 16S rRNA gene sequencing,hsp65 PCR-RFLP could identify nine Mycobacterium chelonae complexes and three Mycobacterium kansasii complexes to subspecies Mycobacterium abscessus and Mycobacterium kansasii,respectively; One Mycobacterium fortuitum strain and one Mycobacterium nonchromogenicum strain were different from 16S rRNA gene sequencing results ,but other isolates were the same.The coincidence was 95.1%.By hsp65 gene sequencing,only one identification of Mycobacterium hiberniae strain was different from 16S rRNA gene sequencing and the coincidence was 97.6%.And hsp65 gene sequencing could further identify nine Mycobacterium chelonae complexes and three Mycobacterium kansasii complexes to subspecies Mycobacterium abscessus and Mycobacterium kansasii,respectively.Conclusions All three molecular methods can identify NTM strains rapidly.Compared with 16S rRNA gene sequencing,hsp65 gene sequencing and hsp65 PCR-RFLP are easier to identify clinical common NTM strains(such as Mycobacterium kansasii and Mycobacterium abscessus),and can be widely used in clinical practice. Key words: Mycobacterium; RNA,ribosomal,16S; Bacterial proteins; Heat-shock proteins; Polymerase chain reaction; Polymorphism,restriction fragment length

The Application of Mitochondrial DNA Cytochrome Oxidase II Gene for the Identification of Forensically Important Blowflies in Western China

Blowflies found on human corpses are important for the estimation of the postmortem interval and other questions of forensic relevance. Some of these species are difficult to differentiate morphologically, and therefore a molecular method was elaborated for species identification. Here, we describe a molecular method for rapid identification of these insects. Specific insect DNA fragments were amplified using the polymerase chain reaction, followed by direct DNA sequencing of the amplification products. Analysis of the cytochrome oxidase II sequences revealed abundant phylogenetically informative nucleotide substitutions that could identify blowfly species to species group. In contrast, because of the low level of sequence divergence of sister species, the data could not distinguish among taxa from the same species group, ie, the species within the Lucilia sericata and Lucilia cuprina groups. The molecular data support the existing species group separation of the taxa within the Calliphora. Because of the speed and accuracy of current nucleotide sequencing technology and the abundant apomorphic substitutions available from mtDNA sequences, this approach enables quick identification of species used for estimation of postmortem interval.

A DNA-Based Approach to the Identification of Insect Species Used for Postmorten Interval Estimation

Insect larvae found on a corpse can be used for estimating postmortem intervals. Here, we describe a molecular method for rapid identification of these insects. Specific insect DNA fragments were amplified using the polymerase chain reaction (PCR), followed by direct DNA sequencing of the amplification products. We sequenced 2300 base pairs of mitochondrial DNA from each of three blowfly species: Phormia regina, Phaenicia sericata and Lucilia illustris. All three species are important in forensic entomology. We found 118 nucleotide differences between the L. illustris and P. sericata sequences, 186 between L. illustris and P. regina, and 192 between P. sericata and P. regina. Based on these abundant DNA sequence differences, we can unambiguously identify the immature larval stages of these insects. These DNA sequence differences were also used to predict species-specific, diagnostic restriction sites in the amplified DNA, and these predictions were verified by digestion with nine restriction enzymes. The DNA sequences reported here encode the mitochondrial COI, COII and tRNA-leucine genes.