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PubMed2002

[Classification of genotyping hepatitis B virus with multiplex PCR].

OBJECTIVE: To establish a simple and practicable method to identify the different genotypes of hepatitis B virus (HBV). METHODS: Based on the alignment of 114 complete nucleotide sequence for HBV DNA of different genotypes, the specific sequence of each genotype was found. Six primer sets were designed for each of the six genotypes according to the genotype-specific sequence, and used separately for PCR. The genotype of HBV was identified according to the positive result of PCR. Three primer sets for B, C and D genotypes were added into a single tube for PCR reaction, and HBV was genotyped according to the length of the amplified DNA. RESULTS: There was no difference in the genotyping result of PCR by single or multiplex primers, which was identical to the PCR-RFLP method. CONCLUSIONS: This multiplex PCR method is simple, precise, sensitive, and easy to use.

DNA Primers↗
PubMed2000

[Using multiplex PCR for the detection of virulence genes in Escherichia coli O157:H7].

OBJECTIVE: To detect and characterize the virulence genes in E. coli O157:H7 isolated from various reservoir in six areas of Jiangsu province. METHOD: The virulence genes of Shiga-like toxin (SLT(1) and SLT(2)), intimin (eaeA) and hemolysin (hlyA) were chosen as the target genes and amplified in multiplex PCR assays. RESULTS: Of the eighty-five E. coli O157:H7 strains, the overall virulence gene prevalence was found to be 56.5% (48/85). The prevalence rates virulence genes of isolates from various areas were different from 0% up to 90.5%. It seemed to exist a relationship between the virulence gene prevalence and the level of incidence. In the areas where rates of incidence were divided into high, low, sporadic or zero, the prevalence rates were 85.7% (36/42), 52.6% (10/19) and 8.3% (2/24), respectively. The prevalence rates of isolates were also different from various reservoirs, decreasing by sheep, cattle, pig and poultry. One isolate from a rabbit was positive for SLT(2), eaeA and hly genes. Of forty-eight isolates carrying virulence genes, 38 (79.2%) had SLT(2), eaeA and hly genes, taking the dominate virulence gene pattern, 8 (16.6%) had all of the four virulence genes 2 (4.2%) had both SLT(2) and hly genes respectively. In addition, SLT(1) gene showed a lower prevalence, which was different from some findings abroad. CONCLUSION: Since virulence gene pattern of E. coli O157:H7 is an important molecular epidemiological marker, it can provide an useful information for epidemiologic studies, and helpful to the design of prevention and control strategies. For virulence gene detection, multiplex PCR seems to be a simple, rapid, specific and sensitive method.

Adhesins, Bacterial↗
PubMed2001

[A case of Churg-Strauss syndrome after corticosteroid withdrawal manifesting mononeuritis multiplex and gastrointestinal perforations].

We report a case of a 70-year-old man who developed Churg-Strauss syndrome (CSS), diagnosed by characteristic histological findings, clinical presentations of mononeuritis multiplex, and multiple small intestinal ulcers with perforations, after discontinuation of corticosteroid therapy. The patient had developed asthma at age of 45, treated with oral prednisolone (10-20 mg daily) from that time. At the age of 70 he developed pneumonia. The condition responded to antibiotics, and the corticosteroid was quickly tapered and discontinued. He was never given leukotriene receptor antagonists during the course of treatment. Approximately two weeks after discontinuation of steroid therapy, he developed severe abdominal pain and mononeuritis multiplex, confirmed by nerve conduction studies. Laboratory evaluation revealed an eosinophil count of 30,450/microliter, and P-antineutrophil cytoplasmic antibody (ANCA) was positive. An abdominal CT scan revealed free air in the abdominal cavity. Laparotomy revealed multiple small intestinal ulcers with perforations. Histologic examination of the intestine showed eosinophilic vasculitis and fibrinoid necrosis. Treatment with systemic corticosteroid (prednisolone 60 mg daily) led to a clinical improvement of neurological and gastroenterological deficits. The prednisolone dose was tapered to 20 mg daily without disease flares. Recently, there have been several reports of CSS that manifested after withdrawal of steroid therapy. CSS can be precipitated in patients with adult-onset, steroid-dependent bronchial asthma after corticosteroid withdrawal.

Aged↗
PubMed2002

Characterization and validation studies of powerPlex 2.1, a nine-locus short tandem repeat (STR) multiplex system and penta D monoplex.

In order to increase the power of discrimination for human identification purposes, a nine-locus short tandem repeat (STR) multiplex, the GenePrint PowerPlex 2.1 system (PowerPlex 2.1) developed by Promega Corporation and a separate pentanucleotide-repeat locus, Penta D, were tested. This megaplex system includes the highly polymorphic loci FGA, TPOX, D8S1179, vWA, Penta E, D18S51, D21S11, TH01, and D3S1358 and may be used in combination with the eight-locus STR multiplex, the GenePrint PowerPlex 1.1 system (PowerPlex 1.1) that has been previously developed. Three of the loci, TPOX, TH01 and vWA, have been included in both systems for quality control purposes. As with PowerPlex 1.1, PowerPlex 2.1 is also based on a two-color detection of fluorescent-labeled DNA products amplified by polymerase chain reaction (PCR) and provides a valuable tool for accurate and rapid allele determination. The primer sequences used in the PowerPlex 2.1/Penta D system are also presented in this report. To meet the "Quality Assurance Standards for Forensic DNA Testing Laboratories" (FBI), we tested the efficiency and reproducibility of the PowerPlex 2.1/PentaD system by several validation studies that were conducted as a joint project among seven laboratories. Validation tests included concordance studies, sensitivity, and species specificity determination, as well as performance in forensic and environmentally impacted samples. The results produced from these tests demonstrated the consistency and reliability of the PowerPlex 2.1/Penta D system.

Animals↗
PubMed2002

Validation of a 16-locus fluorescent multiplex system.

STR multiplexes have been indispensable for the efficient genotyping of forensic samples. The PowerPlex 16 System contains the coreCODIS loci, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, THOI, TPOX, vWA, the sex determinant locus, amelogenin, and two pentanucleotide STR loci, Penta D and Penta E. This multiplex satisfies the locus requirements for most national databases and is the most efficient currently available system due to its single PCR amplification. To provide the groundwork for judicial acceptance, including the publication of primer sequences, and to evaluate laboratory-to-laboratory variation, a developmental validation for casework on this commercially available system was performed in 24 laboratories and produced the following conclusions. Amplification was reliable on a variety of thermal cyclers and product could be analyzed on either an ABI PRISM 310 Genetic Analyzer or an ABI PRISM 377 DNA Sequencer. Genotyping using single source samples was consistent between 0.25 and 2 ng of input DNA template with a few laboratories obtaining complete genotypes at 0.0625 ng. However, heterozygote allele imbalance (<60% peak height balance) caused by stochastic effects was observed at a rate of 13% with 0.125 ng DNA and 22% at 0.0625 ng DNA. Mixture analyses were done using a total of 1 ng of DNA template. Most alleles were detected in mixtures of 4 to 1 and some minor alleles were detected in mixtures of 19 to 1. Optimum amplification cycle number was dependent on the sensitivity of the detection instrument used and could also be adjusted to accommodate larger amounts of DNA on solid supports such as FTA paper. Reaction conditions including volume, annealing temperature, and concentrations of primer, AmpliTaq Gold, and magnesium were shown to be optimal yet robust enough to withstand moderate variations without affecting genotype analysis. Environmental, matrix and standard source analyses revealed an ability to obtain complete genotypes in all sample types except those exposed to 80 degrees C for 12-48 days. Finally, comparison of genotype results from the PowerPlex 16 System with other commercially available systems on non-probative reference and forensic samples showed consistent results.

Alleles↗
PubMed2002

Recovery of genomic DNA from archived PCR product mixes for subsequent multiplex amplification and typing of additional loci: forensic significance for older unsolved criminal cases.

A method for genomic DNA recovery from different types of PCR product mixes suitable for multiplex amplification and typing using the Profiler Plus STR typing system has been investigated. The application of this method is of significance in cases where the original DNA samples have been exhausted due to repeated typing analyses in an effort to maximize their evidentiary value. Such cases typically involve samples analyzed using the available DNA typing systems of the time which gave a markedly lower power of discrimination, either alone or in combination, compared to that of modern multiplex STR typing systems. It was found that an effective method for recovering genomic DNA from HLA-DQA1 +PM and CTT triplex amplification mixes, suitable for reproducible achievement of the complete Profiler Plus profile, involved the use of Amicon Microcon-100 microconcentrators. Interestingly, this method was not required to achieve the complete nine STR profile using D1S80 amplification mixes.

Adult↗
PubMed2002

Comparison of multiplex PCR, and an immunochromatographic method sensitivity for the detection of Escherichia coli O157:H7 in minced beef.

In this study, the sensitivities of multiplex PCR and an immuno-chromatographic methods to detect Escherichia coli O157:H7 in minced beef were compared. The detection of Escherichia coli O157:H7 in minced beef inoculated with 1-100 cells of this bacterium was possible after enrichment of culture and subsequent analysis by either of the two methods. Enrichment conditions were eight hours of incubation at 37 degrees C or 42 degrees C in a non-selective medium (Buffered Peptone Water). Multiplex PCR analysis was performed using three primer sets with analysis by gel electrophoresis. The Quix immuno-chromatographic assay which is a new kit being marketed by New Horizons Diagnostics, Columbia, MD, was used for immunological analysis of the enriched broths.The sensitivity of both tests was similar. The results depended on the concentration of the specific bacterium in the culture since the influence of the proportion of other bacteria to the E. coli O157:H7 was not observed. The data suggests that either method or used together, when coupled with an enrichment technique, could provide a rapid mean to detect the presence of this pathogen in minced meat samples.

Animals↗
PubMed2001

Multidrug-resistant Salmonella typhimurium and Salmonella enteritidis identified by multiplex PCR from animals.

Antibiotic resistance in Salmonella enteritidis and S. typhimurium, one of most frequent etiologic pathogens of food-borne bacterial gastroenteritidis in humans, is a serious health problem worldwide. Fifteen and 22 each of S. enteritidis and S. typhimurium were isolated from animals from 1983 to 1999 in Korea and tested for their antibiotic resistance patterns and phage types. S. enteritides isolates were highly resistant to sulfonamides (86.7%) and four of them (26.6%) showed multiple antibiotic resistance. The most frequent phage type (PT) of S. enteritids was PT1 (33.3%) even though none of them had multiple antibiotic resistance. S. typhimurium isolates were highly resistant to streptomycin, sulfonamides, and tetracycline, 100%, 95.5%, and 86.4% respectively. The incidence of multiple antibiotic resistance of S. typhimurium isolates was extremely high (100%) comparing to S. enteritidis isolates (26.7%). Two of the five ACSSuT type S. typhimurium isolates, resistant to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline, were phage type DT104. All S. typhimurium isolates were sensitive to florfenicol. For the rapid detection of multiple antibiotic resistant S. enteritidis and S. typhimurium isolates, particularly ACSSuT type S. typhimurium DT104, antibiotic resistance genes, cmlA/tetR, PSE-1, and TEM, and Salmonella spp. Specific gene, SipB/C, were amplified using four pairs of primers in hot-started multiplex polymerase chain reaction. Two Korean isolates of S. typhimurium DT104 showed TEM amplicons instead of PSE-1 for the ampicillin resistance. The multiplex PCR used in this study was useful in rapid detection of ACSSuT type S. typhimurium and identification of b-lactamase gene distribution among Salmonella isolates.

Animals↗
PubMed1998

[Detection of hepatitis C virus and hepatitis G virus RNA by multiplex reverse transcription-polymerase chain reaction and microtiter plate reverse hybridization].

Multiplex reverse transcription-polymerase chain reaction for the simultaneous detection of HCV and HGV RNA has been established, in which primers were deduced from high conservative region of HCV and HGV and PCR amplicons were detected by microtiter plate reverse hybridization with HCV or HGV specific probe. Sequence analyses showed that amplicons of HCV were 93.1%-94.1% and 92.5%-93.7% of nucleotide homology compared with Takamizawa and Choo, and amplicons of HGV were 90.7%-92.5%, 92.0%-92.1% and 94.3%-94.5% of nucleotide homology with Simons, Linnen and Chang. The detective sensitivity was 100 times over that of electrophoretic assay with single amplification. CVs of HCV and HGV were 8.9% and 9.8%, respectively, and the optimal concentration of NaOH for hybridization was 0.1-0.15 mol/L. The optimal time for hybridization was 30-50 minutes. The results of detection with multiplex PCR showed the presence of infection with HCV or HGV alone and coinfection with both % them.

DNA Probes↗
PubMed2001

[Genetic studies of 13 loci in Guangdong Han population by two multiplex PCR systems and its forensic application].

OBJECTIVE: The genetic studies of 13 short tandem repeats(STRs) loci in two multiplex amplification systems were carried out on Chinese Han population in Guangdong. METHODS: DNA samples from 328 unrelated individuals were screened. The 13 loci were D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX and CSF1PO. The PCR products were analyzed and genotyped by ABI 377-96 Sequencer. RESULTS: The combined power of discrimination (DP) was 0.999999999999993 and the combined paternity of exclusion(PE) was 99.999%. These 13 loci met the Hardy-Weinberg expectations. CONCLUSION: The two multiplex amplification systems were very useful in forensic case investigation.

Asian People↗
PubMed2003

Development and validation of a multiplexed Y-chromosome STR genotyping system, Y-PLEX 6, for forensic casework.

A Y-chromosome multiplex polymerase chain reaction (PCR) amplification kit, known as Y-PLEX 6, has been developed for use in human identification. The Y-PLEX 6 kit enables simultaneous amplification of six polymorphic short tandem repeat (STR) loci located on the non-recombinant region of the human Y-chromosome. These loci are: DYS393, DYS19, DYS38911, DYS390, DYS391, and DYS385. Our studies show that as little as 0.2 ng of template DNA can be used for analysis. The specificity of the amplification reaction enabled analysis of male DNA in a male:female DNA mixture at a ratio of 1:125. Among the six Y-STR loci, the maximum mean stutter percentage was 11.9 for allele at DYS38911 locus. Attempts at amplification of DNA from various animal sources revealed that the Y-PLEX 6 primers are human specific. Details of the development of the kit, generation and description of the allelic ladders, and validation of the multiplex PCR are presented. In addition, Y-STR allele and haplotype frequencies in three populations have been investigated. The data indicate that results obtained using the Y-PLEX 6 kit are robust, sensitive, and reliable and can be used in human forensic and male lineage identification cases.

Animals↗
PubMed2002

Identification of Escherichia coli O157:H7 by multiplex PCR with primers specific to the hlyA, eaeA, stx1, stx2, fliC and rfb genes.

Escherichia coli O157:H7 can cause fatal diseases such as hemolytic-uremic syndrome and thrombotic thrombocytopenic purpura. The early symptoms of E. coli O157:H7 infection are similar to those of infection with other gastrointestinal bacteria, so the availability of a rapid and precise method to identify E. coli O157:H7 is important for early recognition. We report a multiplex polymerase chain reaction (PCR) with primers to detect the presence of the E. coli O157:H7 genes hlyA, which produces enterohemolysin, eaeA (intimin), stx1 (Shiga-like toxin I), stx2 (Shiga-like toxin II), fliC (flagella H-antigen), and rfb (surface O-antigen). The technique improves specificity compared to general PCR when used with > or = 10(3) CFU/assay. Specificity was examined using 32 E. coli O157:H7 strains from the USA, Japan, Canada and Taiwan, all of which were positive for hlyA, eaeA, fliC, rfb, and stx1 and/or stx2. Thirty-five non-O157 enterovirulent E. coli strains, two Shigella sp strains, and two Salmonella sp strains were also examined and none gave the positive gene expression results described above. This multiplex PCR was highly specific in identifying E. coli O157 and was more useful than general PCR in early clinical detection of this pathogen.

Bacterial Proteins↗
PubMed2002

Detection of Escherichia coli O157:H7 in raw meat by immunomagnetic separation and multiplex PCR.

The aim of this research was to elaborate fast and sensitive method ofdetection of E. coli O157:H7 in food samples. Raw ground meat obtained from retail was artificially inoculated with low numbers of E. coli O157:H7. 18 h enrichment culture allowed pathogenic bacteria to multiply to the levels detectable in multiplex PCR. Immunomagnetic separation with magnetic beads coated with an antibody against E. coli O157:H7 were used to concentrate target bacteria and to separate PCR inhibitors. A portion of the bacterial suspension was used in a multiplex PCR to amplify eae (attaching and effacing) gene, stx (shiga toxin) genes and 90 kbp plasmid. The sensitivity of E. coli O157:H7 detection method was shown to be 1 cfu per 25 g of food sample. The total analysis can be completed within 24 h, whilst traditional methods involves enrichment, direct plating and confirmation tests with entire time at least 3 days.

Animals↗
PubMed2003

[Restoration of elbow joint flexion by transfer of the pectoralis major muscle in patients with arthrogryposis multiplex congenita. Part II. Results of electromyographic and histologic examinations].

PURPOSE OF THE STUDY: In the framework of a prospective study on transposition of the m. pectoralis major according to Clark in patients with type I arthrogryposis multiplex congenita, electromyography was carried out in order to determine pre-operative states of the elbow joint flexors and m. pectoralis major and then the post-operative electric activity of a transposed muscle and to correlate changes with clinical findings. Histological examination was performed to reveal changes in muscle morphology and to complete a comprehensive assessment of muscle transposition. MATERIAL AND METHODS: Electromyography was carried out on nine upper limbs of five pediatric patients aged 4.3 to 8.9 years. Using a needle electrode, activities of the elbow flexors (m. biceps and m. brachialis), m. pectoralis major, m. triceps brachii and m. deltoideus were examined. In the post-operative period, activity was repeatedly measured in both the transposed and non-transposed parts of the m. pectoralis major. In one patient, histological examination of muscle tissue was performed at 26 months after transposition; light microscopy of paraffin-mounted sections stained with hematoxylin-eosin was used. RESULTS: Out of seven arms examined by electromyography before muscle transfer, six showed complete and one incomplete atrophy of the m. biceps brachii and m. brachialis. The m. pectoralis major had a five- to four-degree electric activity, which provided enough strength for transposition. Post-operative examination revealed changes leading to re-innervation of the transposed muscle, which corresponded to a partial denervation of the muscle followed by repair of innervation. None of the muscles was markedly atrophic due to denervation. In muscles with a higher electric activity, clinical outcomes were better, although electric activity always slightly exceeded clinical activity. In terms of electric activity, the transposed muscle was stabilized a year after surgery. Non-transposed parts of the muscle were not damaged by the surgical procedure, as shown by electromyography. Histological examination showed the muscle at a state of partial atrophy but with signs of ongoing regeneration of muscle fibers. DISCUSSION: No data on examination of the electric activity of the m. pectoralis major following its transposition in patients with arthrogryposis multiplex congenita have been reported in the literature. Electromyography in this study proved useful for providing information on the electric activity of a muscle before transposition and on contractility of the muscle after surgery; it also allowed us to distinguish between a mechanical failure of transfer and muscle atrophy due to neurogenic or vascular causes. All transposed muscles that were examined revealed changes indicating a minimum denervation followed by re-innervation. This finding was confirmed by the results of histological examination. CONCLUSIONS: Electromyography showed that the electric activity of a transposed muscle corresponded to the clinical presentation of this muscle and thus became an indispensable part of both pre- and post-operative examination. Both electromyographic and histological examination confirmed the applicability of the treatment described here.

Arthrogryposis↗
PubMed2003

[Detection of 29 types of fusion gene in leukemia by multiplex RT-PCR].

OBJECTIVE: To analyze the fusion genes derived from 29 types of chromosome structural aberrations in children with leukemia. METHODS: Bone marrow samples from 191 children with leukemia were analyzed with a novel multiplex nested RT-PCR. RESULTS: Of the 191 leukemic samples, 86 (45.0%) carried 14 types of fusion genes including SIL/TAL1, MLL/AF1q, E2A/PBX1, MLL/AF6, AML1/ETO, MLL/AF9, TEL/ABL, BCR/ABL, MLL/AF10, dupMLL, MLL/ENL, TEL/AML1, PML/RARalpha and CBFbeta/MYH11. The activation of oncogene HOX11 was detected in 31 cases, with or without other chromosome aberrations in 15 (7.8%) and 16 cases (8.4%), respectively. CONCLUSION: This multiplex nested RT-PCR reaction could screen 29 types of chromosome structural aberrations at the same time. It may be helpful for the detection of minimal residual diseases after chemotherapy and bone marrow transplantation.

Adolescent↗
PubMedDate not supplied

Bacteriology of chronic maxillary sinusitis and normal maxillary sinuses: using culture and multiplex polymerase chain reaction.

BACKGROUND: Although many investigations have been performed on bacteriology of chronic sinusitis and normal sinuses, there still is much discussion. Also a new bacterial agent, Alloiococcus otitidis determined in the nasopharynx and middle ear specimens can be thought as a causative agent of sinusitis. METHODS: The bacteriology of chronic maxillary sinusitis and maxillary sinuses with normal radiogram and endoscopic findings were studied by culture methods for aerobic and anaerobic bacteria. Multiplex polymerase chain reaction (PCR) was used to investigate four bacteria in study and control groups. There were 27 specimens in the study group and 28 specimens in the control group. RESULTS: In the study group, the bacteria commonly isolated were Staphylococcus aureus (11.1%), alpha-hemolytic streptococci (11.1%), Streptococcus pneumoniae (11.1%), Haemophilus influenzae (7.4%), coagulase-negative staphylococci (7.4%), and anaerobes (33.3%). Coagulase-negative staphylococci (14.3%), alpha-hemolytic streptococci (10.7%), and anaerobes (35.7%) were isolated also in the control group. PCR was used to investigate S. pneumoniae, H. influenzae, Moraxella catarrhalis, and A. otitidis in the study and control groups. None of these bacteria was determined in the control group whereas detection rates of these bacteria in the study group were 11.1, 11.1, 3.7, and 7.4%, respectively. It should be considered that PCR yielded faint amplification band for A. otitidis. CONCLUSION: Using multiplex PCR can help to increase detection rates of bacterial etiology. Healthy sinuses are not sterile. A. otitidis may be one of the pathogens causing sinusitis.

Adult↗
PubMed2003

Single tube multiplex PCR detection of 27 cystic fibrosis mutations and 4 polymorphisms using neonatal blood samples collected on Guthrie cards.

In response to recommendations for cystic fibrosis (CF) carrier screening of the American College of Medical Genetics/American College of Obstetrics and Gynecology (ACMG/ACOG), we evaluated a commercial kit for mutation panel testing (Roche CF Gold Linear Array Panel). This kit tests for 25 CF mutations and 4 polymorphisms; it comprises an analyte specific reagent for single tube multiplex polymerase chain reaction (PCR) amplification and subsequent allele specific oligonucleotide (ASO) hybridization. Neonatal whole blood samples collected on Guthrie card filter paper served as the DNA source. Following a wash step to remove whole blood PCR inhibitors, multiplex PCR amplification could be performed either on DNA that was heat extracted from Guthrie cards or directly on the filter paper matrix itself. In 13 CF patient samples, the CF mutation results obtained with this kit agreed completely with those obtained from a reference laboratory that performs an 87 CF mutation panel. The kit was reliable, despite the small sample size (3 mm diameter punch of the Guthrie card), the presence of PCR inhibitors in whole blood, and protracted storage of blood samples (up to 9 yr at room temperature). The kit was convenient, cost competitive, and practical for use in a small CF screening laboratory.

Alleles↗
PubMed1992

Dystrophin gene deletion in Chinese Duchenne/Becker muscular dystrophy patients via multiplex DNA amplification.

Duchenne/Becker muscular dystrophy (DMD/BMD) is a progressive muscle-wasting disease. The dystrophin gene responsible for the disease is the largest human gene ever cloned and is prone to gross gene deletion in two "hot spot" regions. Using nine pairs of oligonucleotide primers deduced from the two regions, we have screened 23 unrelated Chinese DMD/BMD patients by multiplex polymerase chain reaction. Nine (39%) patients were noted to have gene deletion, one in the 5' terminus and eight in the distal half of the gene. The incidence is similar to that reported in other large series mainly on Caucasian patients. The "hot-spot" regions also seem to be present in Chinese patients. Multiplex gene amplification for deletion analysis is useful in the diagnosis of patients with neuromuscular diseases and is an important aid in the prenatal diagnosis and genetic counseling of at-risk families.

Base Sequence↗