A PCR-based method for sex identification in Hippopotamus amphibius

Identification of the sex of aquatic mammals such as the hippopotamus (Hippopotamus amphibius) is difficult in the field. We have developed a PCR-based method for sex identification in the hippopotamus. This method amplifies a short fragment of the ZFX and ZFY genes from the X and Y chromosomes. The PCR products are then digested with the restriction endonuclease HaeIII. The method was verified using tissue samples taken from six captive animals in zoos. We then collected 54 tissue samples from free-ranging hippos in Kruger National Park, South Africa, using a biopsy dart and cross-bow. The PCR method correctly identified the sex of all individuals for whom the sex was known (either zoo animals, or those exhibiting clear behaviours or morphologies in the field). Field identification of the sex of other individuals was prone to error (6 of 22 misidentified, 27 %).     

Development of a PCR-based method for specific identification of genotypic markers of shiga toxin-producing Escherichia coli strains

A simple, rapid and specific PCR-based method for identification of shiga toxin-producing Escherichia coli (STEC) was developed. The procedure involves amplification of the E. coli-specific universal stress protein A (uspA) gene (uspa-PCR), with the primer pair described by other authors, which allows differentiation of E. coli (STEC and non-STEC) from other gram-negative bacteria followed by identification of the main genetic virulence traits of the uspA-positive isolates. For this purpose, two multiplex PCR assays, based on previously published primer sequences, were established. Assay 1 (mPCR-1) uses three primer pairs and detects the genes encoding O157 (rfb), enterohemolysin (ebly) and shiga toxin (stx), generating amplification products of 420, 534 and 230 bp, respectively. Assay 2 (mPCR-2) uses four primer pairs specific for rfb (E. coli O157), eaeA (intimin), stx1 and stx2 (shiga toxin 1 and 2, respectively), generating PCR amplicons of 420, 840, 348 and 584 bp, respectively. These two assays were validated by testing several E. coli reference strains and 202 previously characterized E. coli isolates originating from calves and from children, and 100% agreement with previous results was obtained. The method developed can be used for specific identification of STEC bacteria including those of the O157 serogroup.     

Characterization of multi-resistant Shigella species isolated from raw cow milk and milk products

This study was organized to investigate the prevalence, antibiotic and disinfectant resistance phenotypes and genotypes as well as plasmid profiles of Shigella species isolated from raw cow milk and milk products in Egypt. Genotypic analysis was performed to determine the presence of β-lactamase encoding genes (bla_TEM, bla_CTX-M, bla_OXA-1 and bla_SHV), tet(A) and qacE∆. Forty-two (7%) Shigella isolates (S. dysenteriae, S. flexneri, and S. sonnei) were recovered, with S. dysenteriae as the predominant type. Antibiotic sensitivity tests showed that 71.4% of Shigella isolates were resistant to three or more antibiotic classes (multidrug-resistant). High resistance rates were observed against tetracyclines (100%), ampicillin, amoxicillin-clavulanate (90.5%, each) and cefaclor (66.7%), while no resistance was detected against imipenem, sulfamethoxazole/trimethoprim, and azithromycin. Disinfectant susceptibility test of Shigella isolates revealed resistance to phenolic compound (vanillic acid), while 85.7% of the Shigella isolates were resistant to benzalkonium chloride. Uniplex PCR analysis declared the existence of β-lactamase encoding genes (bla_TEM in all isolates and bla_CTX-M in 28.6% of isolates) and, tet(A) in all isolates and 85.7% of the isolates were positive for qacE∆1, while all isolates were negative for bla_OXA-1 and bla_SHV. All Shigella extended spectrum β-lactamases (ESBL) producers (12, 100%) were positive for the bla_TEM, bla_CTX-M, and qacE∆1 genes. Furthermore, plasmid profiling revealed seven distinct plasmid patterns (P1–P7), ranging from 1.26 to 33.61 kb, among all the Shigella strains; S. dysenteriae exhibited the greatest variance. The co-transfer of β-lactamase genes (bla_TEM and bla_CTX-M) and qacE∆1 genes was observed by conjugation from all ESBL producers to a recipient strain. These findings indicate the emergence of Shigella species in Egypt that exhibited multi-resistance to either antibiotics (particularly ESBL producer strains) or disinfectants. Thus, the resistance of Shigella species should regularly be monitored and appropriate measures should be taken to manage this problem.     

猪胸膜肺炎放线杆菌血清型的PCR鉴定

据胸膜肺炎放线杆菌（Actinobacillus pleuropneumoniae,APP）生物I型各血清型之间外毒素（apx）基因组结构差异,参考GenBank上已发表的4种毒素（apxⅠ/apxⅡ/apxⅢ/apxⅣ）的核酸序列设计了6对特异性引物,对APP的12个血清型进行多重PCR扩增,得出不同的特异性的扩增片段,得以准确鉴定APP生物I型中的9种血清型,但其中血清型2和8,血清型5、9和11仍未能区分。     

Efficacy of the API Staph-Ident system for identification of Staphylococcus species from milk

A total of 524 staphylococcal isolates from bovine milk were identified, using the API Staph-Ident system and conventional biochemical methods. The API Staph-Ident system correctly identified 192 of 201 (95.5%) Staphylococcus aureus isolates, but was correct on only 23 of 323 (7.1%) non-S aureus isolates.     

Animal species identification in food products: evolution of biomolecular methods

Species identification in food has increasingly acquired importance due to public health, economic and legal concerns. Traditional methods have relied on the identification of morphological traits, but this does not lead to accurate identification of those species used in many types of processed food. As a result, laboratory techniques have been devised using electrophoretic and immunological methods focussing on protein profiles and, more recently, biomolecular techniques have been developed. However, these techniques also present problems and difficulties, especially in the case of matrices that are heterogeneous or have been subjected to severe treatments during processing.     

Characterization of rDNA sequences from Syphacia obvelata, Syphacia muris, and Aspiculuris tetraptera and development of a PCR-based method for identification

To differentiate the morphologically similar pinworms of the common laboratory rodents, such as Syphacia obvelata and Syphacia muris, we amplified and sequenced the region spanning the internal transcribed spacer 1 (ITS-1), 5.8S gene, and ITS-2 of the ribosomal DNA followed by designing of species-specific primers for future use in the identification of the worms. It was observed that S. obvelata, S. muris and Aspiculuris tetraptera can be differentiated from each other based on their rDNA sequences. This is the first report of the ITS-1, 5.8S, and ITS-2 of the rDNA of the three aforementioned rodent pinworm species. The use of restriction endonucleases, AluI or RsaI, further allowed the delineation of the three species. Moreover, we also constructed species-specific primers that were designed for unique regions of the ITS-2 of the three species. This approach allowed their specific identification with no amplicons being amplified from heterogenous DNA samples, and sequencing confirmed the identity of the sequences amplified. Thus, the use of these specific primers along with PCR-RFLP can serve as useful tools for the identification of pinworms in rats, mice, and wild rodents.     

A TaqMan real-time PCR-based assay for the identification of Fasciola spp

Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts.     

Detection of staphylococcal enterotoxins in milk and milk products

For food evaluation the determination of the number of Staphylococcus aureus (hereinafter S. aureus) colonies is insufficient in view of present scientific knowledge. The results, advantages and shortcomings of diagnostic methods are demonstrated on an example of three methods of detection of staphylococcal enterotoxins in milk and milk products. 133 strains were investigated by the method of biotyping of S. aureus strains. Four strains of S. aureus were included in biotype A, seven xin-producing strains were isolated seventeen times by detection of 96 S. aureus strains were not included in any biotype, the other strains belonged to biotypes C and E. This method can be used as an auxiliary method of evaluation of foods containing S. aureus bacteria. The agar-gel precipitation method of enterotoxin detection in isolated strains of S. aureus has just restricted validity. The enteroto-strains. The main shortcoming of this method is a fact that the result concerning the isolated strains need not be identical with the result of enterotoxin detection in food. Direct assays of staphylococcal enterotoxins in milk and milk products using an enzymoimmunological method seem to be the most promising, mainly due to their high sensitivity (0.0001-0.001 micrograms.ml1-) and other advantages. Positive and negative results are presented on an example of two model trials with winter sheep milk cheese.     

Determination of donor-type chimerism using a semi-quantitative PCR-based method in a canine model for bone marrow transplantation

Dogs are used in preclinical transplantation models to study methods of allogeneic bone marrow transplantation (BMT). The evaluation of chimerism is of major significance for the investigation of graft-vs.-host (GvH) and host-vs.-graft (HvG) reactions. To detect and quantitate male donor cells after a sex-mismatched (male to female) allogeneic BMT, we established a semi-quantitative polymerase chain reaction (PCR) assay. Based on the canine Y-chromosome sex-determining region (Sry) sequence, we designed primer specific for the detection of male DNA and optimised PCR conditions and cycle numbers. Artificial mixtures of male and female leukocytes were used to analyse the sensitivity of the assay. To validate our established method, we determined the percentage of chimerism in three transplanted female dogs. Under optimised conditions, the established PCR assay specifically detected male cells down to 0.01%, which corresponds to 0.1ng of transplanted male DNA. The percentage of chimerism could be quantitated either by agarose gel analysis or Southern blot analysis. Using our assay, we could confirm the percentage of chimerism in blood samples of three transplanted female canines, previously determined by karyotype analysis as 0, 100 and 100%, respectively. The established semi-quantitative PCR assay offers a quick, simple, accurate and sensitive way of evaluating and quantitating the percentage of chimerism in a sex-mismatched canine BMT model.     

Applications of PCR-based tools for detection and identification of animal trypanosomes: a review and perspectives

This paper aims to review the applications of the polymerase chain reaction (PCR) for the detection and identification of trypanosomes in animals. The diagnosis of trypanosomes, initially based on microscopic observations and the host range of the parasites, has been improved, since the 1980s, by DNA-based identification. These diagnostic techniques evolved successively through DNA probing, PCR associated to DNA probing, and currently to PCR alone. Several DNA sequences have been investigated as possible targets for diagnosis, especially multi-copy genes such as mini-exon, kinetoplastid mini-circles, etc., but the most favoured target is the nuclear satellite DNA of mini-chromosomes, which presents the advantages, and the drawbacks, of highly repetitive short sequences (120-600 bp). Several levels of specificity have been achieved from sub-genus to species, sub-species and even types. Random priming of trypanosome DNA has even allowed "isolate specific" identification. Other work based on microsatellite sequences has provided markers for population genetic studies. For regular diagnosis, the sensitivity of PCR has increased with the advancement of technologies for sample preparation, to reach a level of 1 trypanosome/ml of blood, which has brought to field samples a sensitivity two to three times higher than microscopic observation of the buffy coat. Similarly, PCR has allowed an increase in the specificity and sensitivity of diagnosis in vectors such as tsetse flies. However, because of the diversity of Trypanosoma species potentially present in a single host, PCR diagnosis carried out on host material requires several PCR reactions; for example, in cattle, up to five reactions per sample may be required. Research is now focusing on a diagnosis based on the amplification of the internal transcribed spacer-1 (ITS-1) of ribosomal DNA which presents the advantages of being a multi-copy locus (100-200), having a small size (300-800 bp), which varies from one taxon to another but is conserved in size in a given taxon. This may lead to the development of a multi-species-specific diagnostic protocol using a single PCR. By reducing the cost of the PCR diagnosis, this technique would allow a greater number of field samples to be tested in epidemiological studies and/or would increase the variety of Trypanosoma species that could be detected. Further investigations are required to develop and optimise multi-species-specific diagnostic tools for trypanosomes, which could also serve as a model for such tools in other pathogens.     

Improved rapid and efficient method for Staphylococcus aureus DNA extraction from milk for identification of mastitis pathogens

A rapid and efficient DNA extraction method was developed for detecting mastitis pathogens in milk. The first critical step involved cell wall disruption by bead-beating, as physical disruption using beads was more effective for DNA extraction from Gram-positive bacteria, such as Staphylococcus aureus, than enzymatic disruption using proteinase K. The second critical step involves the use of acetic acid and ammonium sulfate in the purification process, as these reagents effectively and efficiently remove the lipids and proteins in milk. Using these methods, DNA suitable for loop-mediated isothermal amplification was obtained within 30 min. Also, the rapid and sensitive detection of S. aureus in milk was possible at levels as low as 200 cfu/ml.     

Detection of classical enterotoxins and identification of enterotoxin genes in Staphylococcus aureus from milk and dairy products

Milk and dairy products are frequently contaminated with enterotoxigenic Staphylococcus aureus, which is often involved in staphylococcal food poisoning. The distribution of genes encoding staphylococcal enterotoxins (SE) in S. aureus isolated from bovine, goat, sheep and buffalo milk and dairy products was verified by the presence of the corresponding SE production. A total of 112 strains of S. aureus were tested for SE production by immuno-enzymatic (SEA-SEE) and reversed passive latex agglutination (SEA-SED) methods, while multiplex-PCR was applied for SE genes (sea, sec, sed, seg, seh, sei, sej and sel). Of the total strains studied, 67% were detected to have some SE genes (se), but only 52% produced a detectable amount of the classic antigenic SE types. The bovine isolates frequently had enterotoxin SEA, SED and sej, while SEC and sel predominated in the goat and sheep strains. The results demonstrated (i) marked enterotoxigenic S. aureus strain variations, in accordance with strain origin and (ii) the two methods resulted in different information but concurred on the risk of foodstuff infection by S. aureus.     

The significance of mycotoxin assimilation for the contamination of milk and milk products

The two possible pathways contaminating milk and milk products with mycotoxins are either the secretory or post-secretory route. The latter is of only little importance due to cooling conditions in production and storage. A secretory contamination can only occur with such mycotoxins, which undergo no complete degradation through their passage into the milk. From the mycotoxins, present in cow's feed; virtually only aflatoxin B1 yields a milkborne metabolite, the aflatoxin M1. The carry over rate is low (2 +/- 1%), but can be enhanced by polyhalogenated biphenyls, also present in the forage. Under normal conditions, however, this enhancement will not be measurable due to low equimolar concentrations of both reactants. The aflatoxin M1 content in herd's bulk milk depends exclusively on the content of the precursor aflatoxin B1 in the ration of the cow and is with less than 10 ng/kg fairly low at present in the Federal Republic of Germany. A careful supervision of the imported feed ingredients for mixed feed, however, will ensure to keep those batches out of dairy cow feeding which exceed a certain level of aflatoxin. The legal threshold is 10 micrograms/kg, being even too high to ensure a milk containing less than 10 ng/kg under high energy feeding conditions. The discussed thresholds for aflatoxin M1 in milk are 50 and 10 ng/kg resp., the latter value is scheduled for milk used in infant nutrition. To keep this low concentration the intake of aflatoxin B1 must be less than 2 micrograms/kg of the daily ration.