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PubMed2001

Quality control of PCR primers used in multiplex STR amplification reactions.

Reliable amplification of short tandem repeat (STR) DNA markers with the polymerase chain reaction (PCR) is dependent on high quality PCR primers. The particular primer combinations and concentrations are especially important with multiplex amplification reactions where multiple STR loci are simultaneously copied. Commercially available kits are now widely used for STR amplification and subsequent DNA typing. We present here the use of high performance liquid chromatography (HPLC) and time-of-flight mass spectrometry (TOF-MS) methods for characterization of commercially available STR kits.

Chromatography, High Pressure Liquid↗
PubMed2002

Distribution of alleles of 15 STR loci of the Powerplex 16 Multiplex system in four predominant population groups of South India.

Allele distribution of the 15 STR loci of Powerplex 16 Multiplex System were studied in four predominant population groups of South India for evaluating their significance in human identification and population study: Iyengar Brahmin (65), Gowda (59), Lingayat (98) and Muslim (45) from the state of Karnataka. The loci analyzed are--D3S1358, THOI, D2ISI I, D18S51, D5S818, Penta E, D13S317, D7S820, D16S539, CSFIPO, Penta D, vWA, D8S179, TPOX and FGA. Out of 15 STR loci Penta D and D18S51 were found highly polymorphic in the studied populations.

Alleles↗
PubMed2002

A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers.

A multiplex polymerase chain reaction (PCR) assay capable of simultaneously amplifying 20 Y chromosome short tandem repeat (STR) markers has been developed to aid human identity testing and male population studies. These markers include all of the Y STRs that make up the "extended haplotype" used in Europe (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAII) plus additional polymorphic Y STRs (DYS437, DYS438, DYS439, DYS447, DYS448, DYS388, DYS426, GATA A7.1, and GATA H4). Primers for the markers DYS385, DYS389, and YCAII target duplicated regions of the Y chromosome and thus can provide two polymorphic peaks for each respective primer set. This Y STR 20plex, which utilizes 34 different PCR primers, is the first to include a simultaneous amplification of all the markers within the European "minimal" and "extended" haplotypes. Relative primer positions are compared between the newly developed primers described here and previously published ones. Efforts were made to avoid X chromosome homology in the primer design as well as close packing of PCR product size ranges in order to keep all alleles less than 350 bp through careful examination of known allele ranges. Haplotype comparisons between the 20plex and a commercially available kit found excellent agreement across the 76 samples in the Y chromosome consortium panel.

Alleles↗
PubMed2004

Allele distribution of 15 PCR-based loci in the Rwanda Tutsi population by multiplex amplification and capillary electrophoresis.

A genetic study of 15 autosomal STRs is carried out (D2S1338, D3S1358, D5S818, D7S820, D8S1 79, D13S317, D16S359, D18S51, D19S433, D21S11, CSF1PO, FGA, TPOX, THO1, VWA) in a sample of unrelated Tutsis. The molecular phenotypes were determined by means of multiplex strategies (AmpFlSTR Identifiler PCR Amplification Kit, Applied Biosystems) followed by capillary electrophoresis.

DNA Fingerprinting↗
PubMed1997

Multiplexing of Y chromosome specific STRs and performance for mixed samples.

A combination of four Y-specific polymorphic STR loci was amplified simultaneously using fluorescently labeled primers. Multiplex conditions required optimization to eliminate constant bands and amplification products for female DNA. A series of experiments was carried out for mixtures of DNA from two males, and from male and female individuals for the Y-specific STRs and an autosomal locus. For the male/male mixtures amplified with the Y specific system, and amplified for an autosomal locus, the minor component in the mixture could only be identified up to a ratio of 1:10, 1:50 respectively. In male/female DNA mixtures the Y STR alleles could be identified for the highest ratio tested, 400 pg male in DNA in 800 ng female DNA which amounts to a ratio of 1:2000.

Alleles↗
PubMed1997

Development of guidelines to designate alleles using an STR multiplex system.

We have carried out extensive validation of a multiplex system of 6 STR loci and the Amelogenin sex test to investigate the following characteristics: relative peak areas of heterozygote peaks; non-specific artefacts; stutters caused by slippage of the Taq enzyme; pull-up (an electronic artefact often associated with software). The purpose of this paper is to demonstrate how interpretation guidelines can be formulated by experimentation and analysis using casework samples. Automation allows data relating to band position (in base pairs), peak area and peak height to be easily collected and manipulated in spreadsheets or computer programs. This paves the way to designing expert systems to carry out the interpretative process.

Alleles↗
PubMed1998

Fluorescent multiplex analysis of nine STR loci: Spanish population data.

A total of 171 Caucasians living in Andalucia (southern Spain) have been typed for nine short tandem repeat (STR) loci by multiplex PCR amplification using a commercially available kit (Profiler Plus; Perkin-Elmer, Norwalk, CT, USA) and semi-automatic electrophoresis (ABI Prism 377 DNA Sequencer, Applied Biosystems, Foster City, CA, USA). The kit enables typing of the STR loci D3S1358, VWA, FGA, D5S818, D13S317, D7S820, D8S1179, D21S11, and D18S51. All loci, except D7S820, meet Hardy-Weinberg equilibrium. Because of the large number of loci that can be analyzed, the power of discrimination (PD) is greater than 0.99999, and the probability of exclusion (PE) reaches 0.99991 in our population sample.

Alleles↗
PubMed1991

A screening for dystrophin gene deletions in Japanese patients with Duchenne/Becker muscular dystrophy by the multiplex polymerase chain reaction.

A new screening method involving the multiplex polymerase chain reaction was developed to detect dystrophin gene deletions in Japanese patients with Duchenne and Becker muscular dystrophy (DMD/BMD). Eleven exonic regions including deletion "hot spots" were analyzed. Gene deletions were found in 33% of 92 unrelated Japanese patients, mainly in the central portion (exons 43-52) and at the 5' end (exons 1-17). This is a useful laboratory test for the rapid genetic diagnosis of DMD/BMD.

Asian People↗
PubMed1985

CT-scanning of skeletal muscle in arthrogryposis multiplex congenita.

CT-scanning of skeletal muscles was performed on 14 patients with arthrogryposis multiplex congenita (AMC), according to an eight-slice protocol. Adipose tissue replacement and atrophy of muscles was found in six patients with neurogenic or myopathic origin of AMC, associated with severe muscle weakness. In the remaining patients with other forms of AMC, in which muscle weakness was less marked or absent, muscular CT-scanning was normal. It is stated that muscular CT-scanning is not a routine investigation in a screening procedure of all cases of AMC. However, CT-scanning appears to be useful in cases of severe AMC with associated muscle weakness in detecting the neurogenic and myopathic forms. It also facilitates the selection of a suitable site for EMG and biopsy and may provide important information for orthopaedic management.

Adolescent↗
PubMed1998

Discrimination among Pediocin AcH/PA-1 producer strains by comparison of pedB and pedD amplified genes and by multiplex PCR assay.

Pediococcus acidilactici, Pediococcus parvulus and Lactobacillus plantarum pediocin AcH/PA-1 produces strains were studied with the aim to investigate their common genetic pediocin determinant using pedA, pedB, pedC and pedD gene-targeted PCR assay. Single Strand Conformation Polymorphism and restriction analysis of pedA and pedC amplified fragments from the three different species did not show any differences in sequence while these analysis carried out on pedB and pedD amplified fragments highlighted differences related to the three species analyzed harboring these plasmid encoded genes. Furthermore different multiplex PCR assay using IdhD, pedA and pedD as target genes were developed to clearly identify the pediocin AcH/PA-1 producer strains and to obtain the simultaneous identification of the P. acidilactici strains.

Bacteriocins↗
PubMed2000

Performance of a multiplex PCR for the determination of Haemophilus influenzae capsular types in the clinical microbiology laboratory.

To improve tools for the surveillance of invasive H. influenzae in the context of the drastic decrease of type b infections following the implementation of vaccination, a two-step PCR technique was developed to detect the capsule and type specific regions of H. influenzae. The technique of Falla et al (1994) was modified to amplify in a first step the capsule and type b regions by multiplex PCR. For non-b capsulated strains, the type a, c, d, e, and f loci were afterward detected simultaneously by an optimized touch-down PCR technique. An internal control of extraction and amplification (16S rDNA) was included for both PCR techniques. Overall, this technique was shown to perform as efficiently or better than the slide agglutination without risks of interpretation errors. Of the 138 H. influenzae strains tested, seven that had given doubtful results by the agglutination technique were unequivocally typed by PCR.

ATP-Binding Cassette Transporters↗
PubMedDate not supplied

Development of a ceuE-based multiplex polymerase chain reaction (PCR) assay for direct detection and differentiation of Campylobacter jejuni and Campylobacter coli in Thailand.

A novel ceuE-based multiplex PCR system was developed as an efficient diagnostics test to detect and differentiate C. jejuni and C. coli. There is no cross reactivity between C. jejuni and C. coli. In addition, the assay does not produce a positive signal from other enteric bacteria including Salmonella, Shigella and Escherichia coli strains. Campylobacter detection sensitivity was determined to be equivalent to previously reported PCR for other enteric bacteria. We also noticed that silicon dioxide extraction can improve Campylobacter detection sensitivity from infected stool samples. It was demonstrated that the PCR assay developed in this study had a much better Campylobacter detection rate than the traditional culturing method (77% versus 56%). However, we also identified small numbers of culture positive stools (8%, or 16 out of 202 samples) that did not yield PCR positive results for Campylobacter. These PCR negative/culture positive stools were proven to be inhibitory to PCR amplification.

Bacterial Proteins↗
PubMed2001

Effect of routine use of a multiplex PCR for detection of vanA- and vanB- mediated enterococcal resistance on accuracy, costs and earlier reporting.

A multiplex PCR (MPCR) for detection of vanA-and vanB-mediated resistance to vancomycin was optimized and adapted for use in the routine microbiology laboratory. Consecutive specimens (1196) submitted for vancomycin resistant Enterococci (VRE) surveillance were processed by clinical technologists on Bile Esculin Azide Agar containing 6 mg/L vancomycin (BEAA/Vanco6) plates and 466 showing black colony growth were processed by conventional biochemical testing (CBT) and by MPCR. CBT identified 208 VRE positives. MPCR detected 205 of the CBT- positives plus an additional 10. Analysis of the discordant specimens determined that 5 CBT- negative/MPCR-positive specimens also contained Enterococci with vanC resistance, 3 CBT-positive/MPCR-negative specimens were true positives, and 5 CBT-negative/MPCR-positive specimens occurred due to technical error. The sensitivity and specificity of MPCR were 98.4% and 96.1%. MPCR identifications of VRE were achieved approximately 48 h earlier than CBT and at 60% of the costs.

Bacterial Proteins↗
PubMed2002

Simultaneous detection of the mecA and ileS-2 genes in coagulase-negative staphylococci isolated from Brazilian hospitals by multiplex PCR.

Coagulase-negative Staphylococcus spp. (CNS) has been associated with primary bloodstream infections and implanted medical devices. Its importance is increasing due to the acquisition of resistance to oxacillin (Oxa) and, recently, resistance to mupirocin (Mup). Mupirocin, a topical antimicrobial, has been used in the prevention of staphylococci catheter colonization. Susceptibility to Oxa and Mup was analyzed by different testing methods in clinical CNS isolates. Among 112 CNS strains, 69 (61.6%) were Oxa(R) by the disk diffusion (DD) method and 72 (64.2%) grew on the oxacillin agar screen plate. S. epidermidis and S. haemolyticus presented high rates of oxacillin resistance, 75.4% and 96.1%, respectively. Twenty four (21.4%) strains were Mup(R) by the DD test and 21 of them (87.5%) were identified as S. epidermidis. The detection of the mecA and ileS-2 genes, determined by multiplex-PCR, showed that 72 (64.2%) CNS strains possessed the mecA gene, while 16 (14.3%) possessed the ileS-2 gene. Fifteen of these strains presented the two resistance genes simultaneously. The isolates containing the ileS-2 gene presented a minimum inhibitory concentration (MIC) >1024 microg/mL in the E-test, while low-level mupirocin resistance (MICs of 12-16 microg/mL) was observed in those strains without ileS-2. The resistances to high and low levels of mupirocin could not be distinguished when the DD test was used. The analysis of the Mup(R) S. epidermidis strains by Pulsed Field Gel Electrophoresis showed that 17 (80.9%) strains belonged to one of two patterns (A and B), which have been shown to be prevalent in hospitals in Rio de Janeiro. This report showed that the PCR method for detection of oxacillin and mupirocin resistance in CNS is necessary to determine accurate rates of these resistance, and will can help in the staphylococcal infections prevention and control policies in Brazil.

Bacterial Proteins↗
PubMed2002

Mupirocin resistance in methicillin-resistant Staphylococcus aureus clinical isolates in a Spanish hospital. Co-application of multiplex PCR assay and conventional microbiology methods.

A total of 1785 Staphylococcus aureus clinical isolates were collected in our hospital during 1998 (526), 1999 (564) and 2000 (695). Among them, one hundred and thirty (39, 33 and 58, respectively) were phenotypically assigned as methicillin-resistant Staphylococcus aureus (MRSA); sixteen of these isolates (3, 2 and 11, respectively) were detected as highly mupirocin-methicillin resistant Staphylococcus aureus (MMRSA). In this work, our goal was to characterize MRSA and MMRSA clinical isolates by co-application of phenotypic and genotypic methods in order to determine the MMRSA incidence in our hospital during the period 1998-2000. With this purpose we compared and integrated the results obtained using conventional microbiology methods with those obtained using a multiplex polymerase chain reaction (PCR) assay. Our results showed a good complementation between these two approximations to determine the incidence of MMRSA clinical isolates and permitted to estimate that such incidence increased from 7.7% in 1998 to 19% in 2000.

Bacterial Proteins↗
PubMedDate not supplied

An assessment of a multiplex PCR assay for differentiating clinically important mycobacteria based on pncA gene variation.

The pncA genes in mycobacteria are responsible for the production of pyrazinamidase (PZase). In Mycobacterium tuberculosis, PZase hydrolyses pyrazinamide (PZA) to pyrazonic acid, a compound that possesses bactericidal activity against tubercle bacilli. Nucleotide sequences of pncA genes found within mycobacteria where aligned in an effort to ascertain the significance of any variability in sequence. Three sets of primers (one degenerate and five consensus sequences) were designed and employed in a multiplex PCR assay to amplify the pncA region in seven clinically common mycobacteria. The banding patterns generated from each species in conjunction with PZase activity tests demonstrated that the mycobacterial species examined could be clearly identified and differentiated from one another. Although not yet tested with clinical isolates, the combination of these two assays has provided a promising discriminatory tool for the identification of commonly encountered clinical mycobacteria species.

Amidohydrolases↗
PubMed2003

A strategy based on 5' nuclease multiplex PCR to detect enterotoxin genes sea to sej of Staphylococcus aureus.

We describe the development of a strategy based on 5' nuclease multiplex PCR for the rapid detection of nine enterotoxin genes (sea, seb, sec, sed, see, seg, seh, sei, sej) of Staphylococcus aureus. The genotyping scheme consists in identifying these nine enterotoxin genes by three 5' nuclease Triplex-PCR assays. The strategy was evaluated using a collection of S. aureus reference strains previously examined with conventional PCR assays, and by testing previously characterized food S. aureus field strains. The 5' nuclease Triplex-PCR assays correctly detected the se genes in all the reference strains. In tests with field strains there was generally excellent agreement with the results obtained by conventional PCR, except for some strains harbouring variant se genes. The detection limits of the Triplex-PCR assays evaluated using fivefold dilution of recombinant plasmids for each se gene ranged from 16 to 2000 copies of target se genes in the PCR tube. The 5' nuclease Triplex-PCR assays developed are fast and specific, and provide a useful diagnostic tool for the detection and genotyping of se genes. The development of this method is an improvement that should facilitate epidemiological investigations of staphylococcal food poisoning outbreaks.

Base Sequence↗
PubMed1995

A multiplex polymerase chain reaction for distinguishing Mycobacterium tuberculosis from Mycobacterium tuberculosis complex.

A multiplex polymerase chain reaction has been developed which is able to distinguish Mycobacterium tuberculosis from other members of the M. tuberculosis complex. The assay is based on the simultaneous amplification of two different targets: a 396bp region from the mtp40 species-specific gene sequence of M. tuberculosis and a 245bp fragment from the M. tuberculosis complex insertion sequence IS986. Results have been obtained for 54 mycobacterial strains including five non-M. tuberculosis complex isolates. All 49 strains of the M. tuberculosis complex were positive for IS986 but only the 27 M. tuberculosis isolates were positive for both IS986 and mtp40.

Base Sequence↗