Microecological characterization of parasitic nematoda present in goats of arid zones of Venezuela

Goats from the Venezuelan northern arid zones were found infested by the following nematodes: Haemonchus contortus, Trichostrongylus axei, T. colubriformis, Cooperia curticei, Oesophagostomum columbianum, Skrjabinema ovis y Trichuris globulosa. The Shannon-Weaver index of diversity values oscillated between 0.045 and 1.73 bits (means = 1.16 +/- 0.24 bits). The maximum value of montly diversity ranged from 1 to 2.80 bits (means = 2.49 +/- 0.28 bits) and the equitability ranged from 0.045 to 0.67 (means = 0.44 +/- 0.09). Parasitic associations were found among 1) T. axei, T. colubriformis and H. contortus, 2) T. colubriformis, H. contortus and O. columbianum and 3) T. colubriformis, S. ovis and T. globulosa. The above results suggest that in months when the diversity index is close to the maximum value and the equitability index is near unity, wide spectrum antihelmintic treatment should be used for poly-parasitized animals.     

Distribution of nematode parasites of the digestive system in sheep (Ovis aries) and goats (Capra hircus) of the Piedmontese and Valdostano Alpine arc

A survey, carried out on gastro-intestinal nematodes of sheep and goats of Piemonte and of Valle d'Aosta (87 sheep and 12 goats) has shown the presence of the following species in sheep, Bunostomum trigonocephalum, Chabertia ovina, Cooperia curticei, Haemonchus contortus, Marshallagia marshalli, Nematodirus abnormalis, Nematodirus filicollis, Nematodirus helvetianus, Nematodirus spathiger, Oesophagostomum venulosum, Ostertagia circumcincta, Ostertagia lyrata, Ostertagia trifurcata, Skrjabinema ovis, Trichostrongylus axei, Trichostronglus colubriformis, Trichostronglus vitrinus, Trichuris ovis and Trichuris skrjabini; in goats, Bunostomum trigonocephalum, Chabertia ovina, Haemonchus contortus, Nematodirus filicollis, Nematodirus helvetianus, Oesophagostomum venulosum, Ostertagia circumcincta, Ostertagia ostertagi, Ostertagia trifurcata, Trichostrongylus axei, Trichostrongylus colubriformis and Trichostrongylus vitrinus. The percentage of each species in the two host is given in the text table.     

裸子植物DNA条形码ITS2高通用性引物的筛选

DNA条形码技术是利用标准DNA片段进行准确快速鉴定物种的一种方法,理想的DNA条形码片段应具有高通用性。虽然核糖体DNA内部转录间隔区II（ITS2）被建议作为种子植物有效的DNA条形码,但目前裸子植物还没有通用性高的引物可用。为获得高通用性的ITS2引物,本研究基于裸子植物55个属的5．8S基因的保守序列区设计了3个正向引物,与已有的ITS反向引物组合,组成了7对ITS2引物进行通用性的评价。选取了裸子植物8目、12科和40属的56个种用于本文的研究。引物组合5．8SR／ITS4、5．8SRa／ITS4和5．8SF2／S3R因为在科水平评价中通用性低或者产生的PCR产物有双带,因而排除在全部物种水平上进一步评价。其余4对引物（GYM-5．8SF1／ITS4、GYM-5．8SFl／S3R、GYM-5．8SF2／ITS4和S2F／S3R）在56个物种的PCR检测中,均有100％的扩增率。基于PCR产物的亮度、序列质量和正反向引物覆盖率的综合评价,建议引物GYM_5．8SF2／ITS4作为裸子植物条形码片段ITS2最好的通用引物。     

Cuticular carbohydrates of three nematode species and chemoreception by Trichostrongylus colubriformis

The cuticle of Haemonchus contortus, Nippostrongylus brasiliensis and Trichostrongylus colubriformis contained N-acetylgalactosamine and N-acetylglucosamine, based on the binding of fluorescein-labelled lectins. Binding of the lectins varied between the sexes and body regions of the nematodes. Treatment of male T. colubriformis with the lectin Lens culinaris agglutinin (LcA) reduced the feeding by helminths that was stimulated by histamine and the male's response to their female's pheromone, based on in vitro assays. Mannose residues may be involved in the helminth's chemoreceptors for feeding and sexual attraction, based on the specific binding of LcA.     

Evaluation of broad-spectrum anthelmintic activity in a novel assay against Haemonchus contortus, Trichostrongylus colubriformis and T. sigmodontis in the gerbil Meriones unguiculatus

The gerbil Meriones unguiculatus, infected with three species of nematodes, each located in a separate part of the gastrointestinal tract, provided a reliable laboratory assay for the evaluation of broad-spectrum anthelmintic activity. Gerbils harbouring 6-day-old infections of Haemonchus contortus, Trichostrongylus colubriformis and T. sigmodontis were given selected broad-spectrum anthelmintics by gavage. Three benzimidazoles, thiabendazole, oxfendazole and albendazole, a tetrahydropyrimidine, morantel, an imidazothiazole, levamisole hydrochloride, a macrocyclic lactone, ivermectin and an experimental natural product, paraherquamide, were active against all three nematodes at various dosages. Trichostrongylus colubriformis was most sensitive to levamisole hydrochloride, morantel, thiabendazole and paraherquamide whereas ivermectin, oxfendazole and albendazole were more effective against H. contortus. All compounds were active against the caecal nematode T. sigmodontis although it was less sensitive than T. colubriformis. Haemonchus contortus was more sensitive than T. sigmodontis to all anthelmintics tested except thiabendazole.     

Efficacy of p-Toluoyl chloride phenylhydrazone against gastrointestinal helminths in ovines.

A new anthelmintic candidate, p-toluoyl chloride phenlylhydrazone, was administered to lambs in a paste formulation. The efficacy of this drug was determined at dose rates of 20, 30, 40, and 50 mg of active ingredient per kilogram of body weight. Helminths expelled by these dosages included Haemonchus contortus, Ostertagia circumcicta, Trichostrongylus colubriformis, T. axei, Nematodirus filicollis, Cooperia curticei, Strongyloides papillosus, Oesophagostomum columbianum, Bunostomum trigoncephalum, Chabertia ovina, Moniezia expansa, and M. benedeni.     

Diversity of benzimidazole-resistance alleles in populations of small ruminant parasites

The resistance of gastro-intestinal nematodes of small ruminants (sheep and goat) to benzimidazole anthelmintic drugs seems to be linked primarily to a single mutation in the isotype 1 beta-tubulin gene. This study was carried out to investigate the origin and diversity of benzimidazole-resistance alleles in trichostrongylid nematodes. We sequenced a 550 bp fragment of the isotype 1 beta-tubulin gene from several benzimidazole-resistant Teladorsagia circumcincta populations isolated from dairy goat farms in the central and south-western France. We also sequenced the same beta-tubulin fragment from Trichostrongylus colubriformis and Haemonchus contortus populations in south-western France. We found eight benzimidazole-resistance alleles in all T. circumcincta populations studied, six in H. contortus populations, and only one in T. colubriformis populations. In most cases, only one benzimidazole-resistance allele was present in T. circumcincta and H. contortus populations, but two alleles were found in a fewer number of them. Some T. circumcincta populations shared the same benzimidazole-resistance allele whereas some others had a specific benzimidazole-resistance allele. Similar findings were obtained for H. contortus. As no parasites are introduced once the flock of dairy goat farms has been constituted, these data indicate for the three studied species that rare pre-existing benzimidazole-resistance alleles already present before the isolation of populations had been selected. On the other hand, the fact that some benzimidazole-resistance alleles were specific to one population of T. circumcincta or H. contortus, seems to be in agreement with the hypothesis of the selection of spontaneous mutations. Thus, the origin of benzimidazole-resistance alleles in trichostrongylid nematodes seems to involve primarily the selection of rare alleles and possibly of spontaneous mutations.     

Rapid genotyping by MALDI-monitored nuclease selection from probe libraries

Data on five single-nucleotide polymorphisms (SNPs) per gene are estimated to allow association of disease risks or pharmacogenetic parameters with individual genes. Efficient technologies for rapidly detecting SNPs will therefore facilitate the mining of genomic information. Known methods for SNP analysis include restriction-fragment-length polymorphism polymerase chain reaction (PCR), allele-specific oligomer hybridization, oligomer-specific ligation assays, minisequencing, direct sequencing, fluorescence-detected 5'-exonuclease assays, and hybridization with PNA probes. Detection by mass spectrometry (MS) offers speed and high resolution. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) can detect primer extension products, mass-tagged oligonucleotides, DNA created by restriction endonuclease cleavage, and genomic DNA. We have previously reported MALDI-TOF-monitored nuclease selections of modified oligonucleotides with increased affinity for targets. Here we use nuclease selections for genotyping by treating DNA to be analyzed with oligonucleotide probes representing known genotypes and digesting probes that are not complementary to the DNA. With phosphodiesterase I, the target-bound, complementary probe is largely refractory to nuclease attack and its peak persists in mass spectra (Fig. 1A). In optimized assays, both alleles of a heterozygote were genotyped with six nonamer DNA probes (> or = 125 fmol each) and asymmetrically amplified DNA from exon 10 of the cystic fibrosis transmembrane regulatory gene (CFTR).     

Genetic Identification of Members of the Genus Corynebacterium at Genus and Species Levels with 16S rDNA-Targeted Probes

16S rRNA gene-targeted probes were designed for the identification of corynebacteria at the genus and species levels. The genus-specific probe hybridized all clinically important members of the genus Corynebacterium and could distinguish them from other coryneform bacteria and phylogenetically related high G + C% gram-positive bacteria, including Actinomyces, Rhodococcus, Gordona, Nocardia, Streptomyces, Brevibacterium and Mycobacterium. The species-specific probes for C. jeikeium and C. diphtheriae could differentiate these two species from other members of this genus. The probes were used to select corynebacteria among gram-positive clinical isolates which had been tentatively identified as corynebacteria by biochemical tests. We screened 59 strains with the genus-specific probe; 51 strains hybridized to the genus-specific probe, 8 did not. Of the 51 strains that hybridized to the genus-specific probe, 1 hybridized to the C. diphtheriae species probe and 13 hybridized to the C. jeikeium species probe. The 8 strains that did not hybridize to the genus probe were further characterized by analyzing cell wall diaminopimelic acid and partial 16S rRNA sequencing. The results indicated that these strains were distributed in the genera Arthrobacter and Brevibacterium.     

牙龈卟啉菌特异性克隆探针的筛选

目的 从牙龈卟啉菌47A－1的基因文库中筛选出特异性片段,制备成特异性克隆探针,方法 将牙龈卟啉菌47A－1基因文库中的重组质粒大量扩增和纯化,采用地高辛标记法制备成探针,与口腔中14种常见细菌DNA进行杂交鉴定,检测其特异性,从中筛选出对牙龈叶卟啉菌具有特异性的克隆探针。结果 重组质粒pZJ1与牙龈卟啉菌47A－1杂交,而与其它细菌DNA均不杂交,包括牙龈卟啉菌ATCC33277和W83。结论 重组质粒pZJI可制备成高特异笥克隆探针。     

Multiple resistance to anthelmintics by Haemonchus contortus and Trichostrongylus colubriformis in sheep in Brazil

The objective of this study was to determine the level of resistance of Haemonchus contortus and Trichostrongylus colubriformis in sheep to levamisole, albendazole, ivermectin, moxidectin, closantel and trichlorfon. The parasites were isolated from sheep naturally infected by gastrointestinal nematodes and were then kept in monospecifically-infected lambs for production of infective larvae (L3) of both species. Forty-two lambs, at three months of age, were simultaneously artificially infected with 4000 L3 of H. contortus and 4000 L3 of T. colubriformis. The animals were allocated into seven groups with six animals each that received one of the following treatments: Group 1--control, no treatment; Group 2--moxidectin (0.2mg/kg body weight (BW)); Group 3--closantel (10mg/kg BW); Group 4--trichlorfon (100mg/kg BW); Group 5--levamisole phosphate (4.7 mg/kg BW); Group 6--albendazole (5.0mg/kg BW); and Group 7--ivermectin (0.2mg/kg BW). Nematode fecal egg counts (FEC) were carried out on the day of treatment and again at 3, 7, 10 and 14 days post-treatment. On the same occasions, composite fecal cultures were prepared for each group for production of L3, which were identified into genus. The animals were sacrificed for worm counts at 14 days after treatment. The efficacy of each treatment was calculated from the arithmetic mean of the FEC or worm burden of the treated group, compared with the values of the control group. Only trichlorfon and moxidectin treatments resulted in a significant reduction of H. contortus recorded at necropsy (73% and 45% respectively). Moxidectin reduced T. colubriformis worm burdens by 82% and albendazole by 19%. All other anthelmintics resulted in no significant reduction in the numbers of worms found at necropsy. In conclusion, the isolates of H. contortus and T. colubriformis showed multiple resistance to all groups of anthelmintics tested. This is the first report, based on the controlled efficacy test, to show resistance of T. colubriformis to macrocyclic lactones in Brazil.     

Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species

DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.     

A Species-Specific Polymerase Chain Reaction Assay for Rapid and Sensitive Detection of <Emphasis Type="Italic">Colletotrichum</Emphasis><Emphasis Type="Italic">capsici</Emphasis>

Colletotrichum capsici is an important fungal species that causes anthracnose in many genera of plants causing severe economic losses worldwide. A primer set was designed based on the sequences of the ribosomal internal transcribed spacer (ITS1 and ITS2) regions for use in a conventional PCR assay. The primer set (CcapF/CcapR) amplified a single product of 394 bp with DNA extracted from 20 Mexican isolates of C. capsici. The specificity of primers was confirmed by the absence of amplified product with DNA of four other Colletotrichum species and eleven different fungal genera. This primer set is capable of amplifying only C. capsici from different contaminated tissues or fungal structures, thereby facilitating rapid diagnoses as there is no need to isolate and cultivate the fungus in order to identify it. The sensitivity of detection with this PCR method was 10 pg of genomic DNA from the pathogen. This is the first report of a C. capsici-specific primer set. It allows rapid pathogen detection and provides growers with a powerful tool for a rational selection of fungicides to control anthracnose in different crops and in the post-harvest stage.     

Genomic RFLP Analysis of Meloidogyne arenaria Race 2 Populations

Traditional morphological methods of Meloidogyne identification have been unsuccessful in distinguishing three South Carolina, USA Meloidogyne arenaria race 2 populations—Govan, Pelion, and Florence. These populations differ greatly in reproductive rate and aggressiveness on soybean hosts. Total genomic DNA from eggs of each population was digested with the restriction endonuclease Eco RI and Southern hybridization analyses were performed with single-copy and interspersed multi-copy cloned probes. Probes were isolated from a genomic library of Eco RI, M. arenaria DNA fragments cloned into pUC8. One probe, designated pE1.6A, when hybridized to Southern blots of M. arenaria genomic DNAs, displayed an interspersed repetitive pattern, and the RFLPs distinguished the Govan population from the Pelion and Florence populations. Another clone, pE6.0A, carrying moderately repeated sequences, distinguished the Pelion and Florence isolates. This communication demonstrates the utility of genomic RFLP analysis for distinguishing populations of the same race within the same species. To test the possible utility of these moderately repeated sequence probes for detecting the presence of nematode DNA in DNA samples from roots inoculated with varying numbers of nematodes, dot blot hybridization analyses were performed. It is possible to detect as few as 30 nematodes per root sample with these cloned probes.     

IDENTIFICATION OF ALEXANDRIUM (DINOPHYCEAE) SPECIES USING PCR AND rDNA-TARGETED PROBES

A PCR (polymerase chain reaction)-based assay for the detection of Alexandrium species in cultured samples using rDNA-targeted probes was developed. The internal transcribed spacers 1 and 2 (ITS1 and ITS2) and the 5.8S ribosomal RNA gene (rDNA) from cultured isolates of A. tamarense (Lebour) Taylor, A. catenella (Whedon et Kofoid) Balech, A. fundyense Balech and A. lusitanicum Balech were amplified using PCR and sequenced. Sequence comparisons showed that the 5.8S and ITS1-ITS2 regions contain sequences specific for the Alexandrium genus, especially at the 3' end of the 5.8S coding region. PCR primers and a radioactive ³²P-labeled DNA probe were devised for this region. The cross-reactivity of the PCR primers and probe was tested against cultured isolates of Alexandrium and other dinoflagellates and diatoms. All the Alexandrium isolates screened reacted toward the genus-specific probe; in contrast, the other groups of microalgae (dinoflagellates and diatoms) did not react with the probe. Furthermore, the PCR amplification technique combined with the use of the rDNA-target probe allowed us to develop a method for the detection of Alexandrium cells in cultured samples. This PCR method might offer a new approach for the identification and enumeration of the HAB (harmful algal bloom) species present in natural phytoplankton populations.     

How quantitative is quantitative PCR with respect to cell counts?

Quantitative diagnostic PCR systems based upon rDNA targeted primer and probe combinations were developed for the detection of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas alcaligenes, enterococci, Staphylococcus aureus, and Staphylococcus epidermidis. Primers and probes were designed in silico using the ARB software package (TU Munich) in combination with Primer Design software of PE Applied Biosystems. Purified genomic DNA or bacterial cells of target and reference organisms were used for the evaluation of the PCR assays applying the TaqMan technique on an ABI PRISM TM 7700 Sequence Detection System (PE Applied Biosystems). Sensitive, reliable and reproducible quantification of target rDNA could be achieved applying primer-probe combinations that mediate in vitro amplification of DNA fragments smaller than 100 base pairs. Large amounts of non target DNA (1 mg per sample) remarkably affected the quantification potential of the approach resulting in an underestimation of the amounts of target DNA. One of the principal goals was to use quantitative PCR to study the correlation of gene and cell numbers depending on the growth behavior of target organisms and to explore the potential to estimate cell numbers from target DNA quantification. A clear correlation of rDNA quantification and bacterial growth was observed, however, cell numbers cannot directly be estimated from quantitative PCR data, given that the cellular genome content varies with the growth phase of the organisms. In the case of Escherichia coli the cell numbers which could be assigned to a certain number of rDNA targets varied reasonably depending upon the growth phase of batch cultures.     

Large restriction fragments containing poly-TG are highly polymorphic in a variety of vertebrates.

Southern blots of genomic DNA from a variety of species digested by restriction endonucleases having a four-bp specificity, were probed with a bovine genomic clone consisting of seven tandem poly-TG stretches separated by a 29bp linker sequence. Highly variable DNA 'fingerprint' patterns were obtained in chicken, sheep, and horse, moderately variable DNA 'fingerprints' in mouse and man, and a monomorphic pattern in Drosophila. In chicken, horse and man a (TG)10 synthetic oligonucleotide probe gave results identical to those given by the bovine probe. Furthermore, in chicken the DNA fingerprint variation showed typical Mendelian inheritance and differed from the fingerprints obtained with Jeffreys 33.6 and M13 minisatellite probes. Thus, for a variety of vertebrate species, poly-TG-containing probes can uncover useful genetic variation.     

Use of a novel multiplex probe array for rapid identification of <Emphasis Type="Italic">Mycobacterium</Emphasis> species from clinical isolates

Conventional identification of mycobacteria is based on the analysis of their phenotypic and biochemical characteristics after culture; thus this method is time-consuming, laborious, and is not always conclusive. Developing a fast and accurate method for rapid identification of Mycobacterium species is in urgent need for early diagnosis of mycobacteriosis and effective patient management. In this study, an efficient and affordable novel multiplex probe array which allows simultaneous identification of 15 medically important mycobacterial species was developed. A pair of genus-specific primers and a set of genus- and species-specific probes were designed according to the conserved and polymorphic regions of the 16S rRNA gene, internal transcribed spacer (ITS) sequence, and 23S rRNA gene of mycobacteria. This probe array was applied for the identification of 78 clinical mycobacterial isolates recovered from Henan, China. The results showed that the specificity and sensitivity of the probe array were 100% for both genus-specific probe and Mycobacterium tuberculosis complex-specific probe. Among 52 isolates of nontuberculous mycobacteria, 43 isolates (82.7%) can be rapidly identified to the species level. Genetic variability of 16S-23S rRNA gene ITS region in M. avium, M. intracellulare, M. chelonae, M. abscessus and M. fortuitum were analyzed. With the accumulation of the sequences of ITS identified and further optimization of probes, the multiplex probe array has the potential to be developed into a practical tool for rapid and accurate identification of mycobacterial species in clinical laboratory.     

Investigation of intestinal nematode responses to naphthalophos and pyrantel using a larval development assay.

Responses of several nematode species to naphthalophos and pyrantel/levamisole were examined using a larval development assay in order to determine the potential of this assay for detection of resistance. Haemonchus contortus and Ostertagia circumcincta showed concentration-dependent responses to naphthalophos, however, the assay was unsuitable for Trichostrongylus colubriformis due to the low toxicity of the drug to the larval stages of this nematode. Measurement of concentration-dependent response to pyrantel in susceptible T. colubriformis was limited by a reduced toxicity against larvae at high drug concentrations, resulting in a parabolic response with a development-inhibition maxima of less than 100%. This limits the usefulness of the assay to detect pyrantel resistance in this species as the presence of a small resistant fraction in a field isolate may be indistinguishable from the parabolic susceptible response. On the other hand, responses of susceptible T. colubriformis to levamisole, and susceptible H. contortus to pyrantel and levamisole showed 100% development inhibition over a range of drug concentrations, indicating that the appearance of a resistant fraction in a field population would be readily discernible from the susceptible response, allowing resistance detection for these drug/parasite combinations. This study has highlighted the varied suitability of the larval development assay technique for resistance detection with different combinations of drugs and parasite species.