Evaluation of non-culture diagnosis of invasive meningococcal disease by polymerase chain reaction (PCR)

Antibiotic treatment prior to transport or admission to hospital has reduced the proportion of cases of invasive meningococcal disease (IMD) from which Neisseria meningitidis can be isolated by standard microbiological techniques. Identification of meningococci by polymerase chain reaction (PCR) was assessed in relation to microbiological diagnosis for cases over a 4-year period between 1998 and 2001. A screening assay for the IS1106 gene was used to detect meningococcal DNA and five additional assays for siaD and orf-2 genes were performed to determine the serogroup. PCR results were compared with results of bacteriological culture, other laboratory test results and clinical data. The sensitivity of the PCR assay for culture-confirmed cases was 98.5%. The specificity of the assay was 96% based on test results for patients from whom other bacteria were isolated, children with viral meningitis and afebrile negative controls. The siaD B/C/W-135 and Y as well as the orf-2 gene for serogroup A PCR assays were able to determine the serogroup for 75.2% of cases that were positive by PCR screening assay. When isolates from patients with IMD were tested by both agglutination and PCR, the results agreed in all cases. PCR is a useful tool for diagnosis of IMD when Gram stain and culture tests are negative due to antibiotic treatment prior to collection of samples for microbiological analyses.     

Isolation of a specific chromosomic DNA sequence of Bacillus anthracis and its possible use in diagnosis

Abstract A 277-bp long DNA fragment, Ba813, was isolated from an avirulent Bacillus anthracis strain 7700 genomic library. Two oligonucleotides derived from the Ba813 sequence were used as primers in polymerase chain reaction tests on genomic DNA from 28 Bacillus anthracis and from 33 heterologous bacteria strains. A specific, 152-bp long DNA fragment was amplified only when Bacillus anthracis DNA was used as the target. The amplified product was analysed by non-radioactive sandwich hybridisation in microtiter plates using two oligonucleotides. The capture oligonucleotide C1 was covalently linked onto aminated wells of microtiter plates. The detection oligonucleotide D3 was labelled with biotine. The hybrid molecules were detected by avidine conjugated with alkaline phosphatase and chromogenic substrate. Amplification of Ba813 sequence may provide the basis for rapid and reliable assay for the detection and identification of Bacillus anthracis .     

The polymerase chain reaction and hepatitis C virus diagnosis

Abstract: In the absence of tissue culture, electron microscopy or assays for viral antigen, the direct detection of hepatitis C virus (HCV) is by necessity dependent upon nucleic acid hybridisation methods. Of the available methods, amplification of HCV cDNA by polymerase chain reaction (PCR) commends itself by virtue of its extreme sensitivity and its consequent ability to detect the very low levels of HCV-RNA that are present in many clinical samples. In this review the development and evolution of PCR techniques for HCV detection are described and a number of clinical applications are considered in detail. The application include diagnosis of acute infection during the seronegative window period prior to the appearance of HCV antibodies, and diagnosis of HCV infection in the immunosuppressed. PCR also enables identification of chronic viraemic carrier state and it permits accurate monitoring of the antiviral effects of drugs such as interferon. Confirmation of the specificity HCV antibody assays and detection of HCV contamination of blood donations and blood products are other important areas in which PCR techniques have proved invaluable. In addition, PCR-based techniques underlie an increasing number of molecular epidemiological and genotyping studies and they are providing insights into the details of HCV cellular tropism and replication. A number of logistic problems and operational difficulties are also discussed. Despite these limitations it is concluded that PCR will continue to make significant contributions to both clinical practice and to our understanding of the basic biology of HCV infection.     

Determinants of short-run supply of small ruminants in Botswana

This study utilizes pooled agricultural region data for the 1982–1987 period to estimate the short-run supply of sheep and goats in Botswana. Elasticity estimates indicate that a 1% increase (decrease) in rainfall at year t leads to a 0.53% rise (fall) in goat marketing in year t+1, and that a 1% rise (fall) in goat population (inventory) leads to a 0.15% rise (fall) in goat sales. The sheep equation reveals that a 1% increase (decrease) in sheep inventory results in a 1.23% rise (fall) in the number of sheep marketed, and suggests that rainfall has no impact on sheep sales. It is argued that the inelastic response of goat sales to changes in goat inventory reinforces the general view that livestock in Botswana are treated as a store of wealth, rather than as primarily a commercial activity for generating cash incomes. This tendency seems to be reduced in the case of sheep, where an elastic response of sales to changes in sheep inventory is observed. Producer prices are found to have no impact on small ruminant sale. The lack of responsiveness of supply to prices may be revealing the existence of inadequate access by most producers to organized markets for small ruminants. It is further argued that without promoting the development of such markets, other developmental efforts, particularly those geared at improving farm-level productivity will yield no positive outcomes, as farmers lack the cash incentive to invest in improved management and husbandry practices.     

Mutations in Ovis aries TMEM154 are associated with lower small ruminant lentivirus proviral concentration in one sheep flock

Small ruminant lentivirus (SRLV), also called ovine progressive pneumonia virus or maedi‐visna, is present in 24% of US sheep. Like human immunodeficiency virus, SRLV is a macrophage‐tropic lentivirus that causes lifelong infection. The production impacts from SRLV are due to a range of disease symptoms, including pneumonia, arthritis, mastitis, body condition wasting and encephalitis. There is no cure and no effective vaccine for preventing SRLV infection. However, breed differences in prevalence and proviral concentration indicate a genetic basis for susceptibility to SRLV. Animals with high blood proviral concentration show increased tissue lesion severity, so proviral concentration represents a live animal test for control post‐infection in terms of proviral replication and disease severity. Recently, it was found that sheep with two copies of TMEM154 haplotype 1 (encoding lysine at position 35) had lower odds of SRLV infection. In this study, we examined the relationship between SRLV control post‐infection and variants in two genes, TMEM154 and CCR5, in four flocks containing 1403 SRLV‐positive sheep. We found two copies of TMEM154 haplotype 1 were associated with lower SRLV proviral concentration in one flock (P < 0.02). This identified the same favorable diplotype for SRLV control post‐infection as for odds of infection. However, frequencies of haplotypes 2 and 3 were too low in the other three flocks to test. The CCR5 promoter deletion did not have consistent association with SRLV proviral concentration. Future work in flocks with more balanced allele frequencies is needed to confirm or refute TMEM154 association with control of SRLV post‐infection.     

Identification of specific gene sequences in preimplantation embryos by genomic amplification: detection of a transgene

Endogenous and foreign DNA sequences can be detected in an extremely small number of cells via sequence amplification in vitro. The polymerase chain reaction (PCR) technique applied in multiple cycles allows the amplification of specific short regions of the genome to levels that can be detected by DNA blotting techniques. Cow and mouse blastocysts were analyzed by PCR for the presence of an endogenous singlecopy gene or an integrated foreign gene. The endogenous single-copy gene encoding the beta chain of bovine luteinizing hormone was detectable in cow blastocysts and in purified bovine genomic DNA representing as few as 25 cells. To determine whether exogenous genes (transgenes) can be detected in preimplantation embryos, transgenic male mice hemizygous for the prokaryotic gene encoding neomycin resistance were bred to nontransgenic females, and the resulting blastocysts were analyzed. The neo gene was detected in approximately half of the embryos. The capability to identify specific gene sequences in a limited number of embryonic cells affords investigators the opportunity to study genetics in early development.     

Zika病毒感染的实验室诊断

Zika病毒是一种新现虫媒黄病毒,近期在美洲暴发流行,并有向全球扩散的趋势,已成为国际关注的突发公共卫生事件。Zika病毒感染的临床诊断主要依据实验室检测结果。本文就Zika病毒的核酸检测、抗原和抗体检测、病毒分离鉴定等方面进行综述。     

安徽省不同人群及各型肝炎患者庚型肝炎病毒感染检测分析

应用酶联免疫试验（ＥＩＡ）和逆转录套式聚合酶链反应（ＲＴ－ｎＰＣＲ）对１００ 例一般人群、３８５例献血员、５４ 例血液透析患者、７２ 例乙型肝炎、４１ 例丙型肝炎２７ 例非甲－戊型肝炎患者进行检测。结果抗－ＨＧＶ 阳性率分别为２．００％ 、７．５３％ 、２７．７８％ 、１８．０６％ 、１９．５１％ 和１４．８１％ ;抗－ＨＧＶ 阳性者中ＨＧＶＲＮＡ 阳性率分别为１００．００％ 、６２．０７％ 、６６．６７％ 、６９．２３％ 、７５．００％ 和 １００．００％ ,提示本地区不同人群存在ＨＧＶ 感染。献血员、血透患者、乙型肝炎、丙型肝炎、非甲－戊型肝炎患者的ＨＧＶ 感染率显著高于一般人群,提示献血员,血透患者及ＨＢＶ、ＨＣＶ 感染者是ＨＧＶ 感染的高危人群。ＨＧＶ 常与ＨＢＶ 或ＨＣＶ 重叠／联合感染,也可单独感染。抗－ＨＧＶ 阳性者中ＨＧＶ ＲＮＡ 阳性率为８３．８２％ ,提示抗－ＨＧＶＥＩＡ 可用于ＨＧＶ 感染的检测。ＡＬＴ 正常和异常献血员中抗－ＨＧＶ 阳性率无显著性差异。     

New techniques in rapid viral diagnosis

Abstract The development of new diagnostic techniques in immunology and molecular biology during the last two decades has opened up new possibilities for rapid viral diagnosis. Solid phase immunoassays for antigen and antibody detection are now widely used in diagnostic settings. Several novel techniques have been introduced and have led to commercially available tests. Diagnostic methods using nucleic acid amplification procedures are already applied in research laboratories and will be commercialized soon. Biosensor-based diagnostic techniques have the potential of generating a result nearly instantaneously and it has become possible to monitor kinetic processes. Automatization and simplified procedures are needed to allow diagnostic tests to be performed soon after the sample has been obtained from the patient. In order to evaluate the new procedures and avoid false results, rigorous quality control in diagnostic virology will have to be instituted.     

An IS900-like sequence found in a Mycobacterium sp. other than Mycobacterium avium subsp. paratuberculosis

The insertion sequence IS900 has been considered specific for Mycobacterium avium subsp. paratuberculosis (M. paratuberculosis) and has, therefore, been used as the target gene for diagnostic PCR of M. paratuberculosis. From a healthy dairy cow we have isolated and characterised a mycobacterium harbouring one copy of a sequence with 94% identity to IS900 at the nucleic acid level. The isolate was shown to be related to Mycobacterium cookii, as assessed by 16S rRNA sequencing. Strong amplifications were obtained with several PCR primers described for detection of IS900. This finding shows the need of alternative PCR systems based on other genes than IS900 to confirm the presence of M. paratuberculosis.     

Direct quantification of polymerase chain reaction fragments using field-amplified sample injection in capillary zone electrophoresis for gene dosage estimation

To assess gene dosages for clinical application, especially for prognostication of cancer, we developed a direct quantification method for polymerase chain reaction products. We report on an application of field amplified sample injection (FASI) to capillary zone electrophoresis which allows the quantification of PCR products without sample preparation. Using an external standard and UV detection for the quantification of DNA, a low coefficient of variation has been obtained. Overall, the described method provides a fast and easy tool for PCR product quantification in clinical laboratories.     

Epidemiology and risk factors associated with Anaplasma marginale infection of cattle in Peninsular Malaysia

Bovine anaplasmosis is a major concern to cattle farming in most parts of the world. Anaplasmosis negatively impacts the profitability of cattle farming by reducing the production, reproduction, and draft ability of cattle. Here, we report results from a one-year cross sectional study to determine the epidemiology and the risk factors for Anaplasma marginale infection of cattle in Peninsular Malaysia. Examination of one thousand and forty five blood samples of apparently healthy cattle from forty-three farms in all the states of Peninsular Malaysia by polymerase chain reaction (PCR) assay revealed an overall prevalence of A. marginale infection of cattle of 72.6%, showing high endemicity of this heamoprotozoan among cattle in the country. Cattle breeds, production type, herd owner, herd size, management system, farm size, farm age, prophylactic treatment against blood parasites, presence of ticks, frequency of deticking, zones, closeness to forest, closeness to waste area, closeness to human settlement and closeness to body of water were the risk factors significantly associated (P?<?0.05) with the detection of A. marginale in cattle. Results of this first molecular study on the epidemiology and risk factors for A. marginale infection of cattle from all the states of Peninsular Malaysia suggest policies and strategies for the prevention and control of the parasite to improve profitability of cattle farming in the country.     

Evaluation of the presence of equine viral herpesvirus 1 (EHV-1) and equine viral herpesvirus 4 (EHV-4) DNA in stallion semen using polymerase chain reaction (PCR)

In the horse, the risk of excretion of two major equine pathogens (equine herpesvirus types 1 (EHV-1) and 4 (EHV-4)) in semen is unknown. The objective of our study was to assess the possible risks for the horizontal transmission of equine rhinopneumonitis herpesviruses via the semen and the effect of the viruses on stallion fertility.Samples of stallion semen (n = 390) were gathered from several different sources. Examination of the semen involved the detection of viral DNA using specific PCR. The mean fertility of the stallions whose sperm tested positive for viral DNA and the mean fertility of stallions whose sperm did not contain viral DNA, were compared using the Student's t-test.EHV-4 viral DNA was not detected in any of the semen samples. EHV-1 DNA was identified in 51 of the 390 samples, (13%). One hundred and eighty-two samples came from 6 studs and there was significant difference (p < 0.05) among the proportion of stallions whose semen tested positive for viral DNA from 0 to 55% between the studs.There was a significant difference (p < 0.014) between the fertility of stallions whose semen tested positive for viral DNA and those whose semen was free from viral DNA. The stallions that excreted the EHV-1 virus in their semen appeared to be more fertile than the non-excretors, but this difference was in fact related to the breeding technique since higher proportion of excretors were found among those whose semen was used fresh rather than preserved by cooling or freezing.In conclusion, this study suggests that the EHV-1 virus may be transmitted via the semen at mating or by artificial insemination as demonstrated with other herpes viruses in other species.     

脂阿拉伯甘露糖联合38kD蛋白在结核病诊断中的应用

本研究旨在评价脂阿拉伯甘露糖(LAM)联合38kD蛋白的混合抗原在结核病血清学诊断中的应用价值。选取128例活动性结核病患者(活动性肺结核107例,肺外结核21例)、51例潜伏性结核感染者和68例健康对照者的血清,检测抗LAM和38kD混合抗原的IgG抗体(LAM-38kD-IgG)。结果显示,LAM-38kD-IgG检测的总敏感度为46.88%,特异度为98.53%,阳性预测值为98.36%,阴性预测值为49.63%。其中肺结核组敏感度为46.73%,肺外结核组敏感度为47.62%(P0.05);初治组为45.54%,复治组为51.85%(P0.05)。涂片阳性肺结核组敏感度为52.54%,高于涂片阴性组(39.58%),但差异无统计学意义(P0.05)。LAM-38kD-IgG检测在对照组中的特异度为98.53%。其特异度远高于结核菌素试验(TST)的41.46%(P0.01)。LAM-38kD-IgG水平与结核病病情有一定的相关性。结果提示,应用LAM和38kD混合抗原的酶联免疫吸附试验(ELISA)在诊断活动性结核病方面具有中等敏感度、极高特异度及阳性预测值,不仅可与结核病的其他诊断方法联用以提高诊断的准确性,而且特别适用于细菌学检查阴性结核病和肺外结核病的诊断。     

Setting up equine embryo gender determination by preimplantation genetic diagnosis in a commercial embryo transfer program

Preimplantation genetic diagnosis (PGD) allows identifying genetic traits in early embryos. Because in some equine breeds, like Polo Argentino, females are preferred to males for competition, PGD can be used to determine the gender of the embryo before transfer and thus allow the production of only female pregnancies. This procedure could have a great impact on commercial embryo production programs. The present study was conducted to adapt gender selection by PGD to a large-scale equine embryo transfer program. To achieve this, we studied (i) the effect on pregnancy rates of holding biopsied embryos for 7 to 10 hours in holding medium at 32 °C before transfer, (ii) the effect on pregnancy rates of using embryos of different sizes for biopsy, and (iii) the efficiency of amplification by heating biopsies before polymerase chain reaction. Equine embryos were classified by size (≤300, 300–1000, and >1000 μm), biopsied, and transferred 1 to 2 or 7 to 10 hours after flushing. Some of the biopsy samples obtained were incubated for 10 minutes at 95 °C and the rest remained untreated. Pregnancy rates were recorded at 25 days of gestation; fetal gender was determined using ultrasonography and compared with PGD results. Holding biopsied embryos for 7 to 10 hours before transfer produced pregnancy rates similar to those for biopsied embryos transferred within 2 hours (63% and 57%, respectively). These results did not differ from pregnancy rates of nonbiopsied embryos undergoing the same holding times (50% for 7–10 hours and 63% for 1–2 hours). Pregnancy rates for biopsied and nonbiopsied embryos did not differ between size groups or between biopsied and nonbiopsied embryos within the same size group (P > 0.05). Incubating biopsy samples for 10 minutes at 95 °C before polymerase chain reaction significantly increased the diagnosis rate (78.5% vs. 45.5% for treated and nontreated biopsy samples respectively). Gender determination using incubated biopsy samples matched the results obtained using ultrasonography in all pregnancies assessed (11/11, 100%); untreated biopsy samples were correctly diagnosed in 36 of 41 assessed pregnancies (87.8%), although the difference between treated and untreated biopsy samples was not significant. Our results demonstrated that biopsied embryos can remain in holding medium before being transferred, until gender diagnosis by PGD is complete (7–10 hours), without affecting pregnancy rates. This simplifies the management of an embryo transfer program willing to incorporate PGD for gender selection, by transferring only embryos of the desired sex. Embryo biopsy can be performed in a clinical setting on embryos of different sizes, without affecting their viability. Additionally, we showed that pretreating biopsy samples with a short incubation at 95 °C improved the overall efficiency of embryo sex determination.     

Evaluation of three serological tests for detection of anti-candidal antibodies in diagnosis of invasive candidiasis

Immunoblot detection of antibody against 47 KD cytoplasmic antigen ofCandida albicans was evaluated in diagnosis of invasive candidiasis and compared to whole cell agglutination and gel diffusion tests for detection of anticandidal antibody in 64 patients. The patients included 17 with culture proved candidemia, 34 with significant candiduria (more than 10,000 colony forming units per ml of urine) and 13 with nonsignificant candiduria. Antibody against 47 KD antigen was found to be the best indicator for diagnosis of invasive candidiasis even in patients with malignancy. The sensitivity of this procedure was 82.4%, specificity 86.7%, positive predictive value 77.8%, negative predictive value 89.7% and efficacy 85.1%. The gel diffusion procedure lacked in sensitivity whereas whole cell agglutination lacked in specificity. Detection of antibody against 47 KD antigen proved to be a valuable adjunct in the diagnosis of invasive candidiasis.     

Fast classification of plant-associated bacteria in the Xanthomonas genus

Abstract A rapid method for identifying Xanthomonas bacteria was developed, based on specific PCR amplification. In all Xanthomonas pathovars tested, a single 16S rDNA fragment of 480 bp was produced. Phytobacteria from other genera showed other fragment patterns on agarose gel electrophoresis. This Xanthomonas identification system was used to screen Xanthomonas -related organisms, newly isolated phytobacteria and bacterial populations in wheat seed extracts.     

False positive diagnosis of meningococcal infection by the IS1106 PCR ELISA

At a time when optimal case ascertainment for meningococcal infection is a high priority, the need for non-culture case confirmation, in particular by DNA amplification, is seen as being of vital importance to assist contact management and cluster recognition. A solution hybridisation assay with colorimetric microtitre plate detection (polymerase chain reaction-enzyme-linked immunosorbent assay (PCR ELISA)) has been developed using the multicopy insertion sequence IS1106 which had reportedly achieved a specificity of 100% and was described as being meningococcal specific. This PCR ELISA assay was evaluated on specimens from over 5000 patients at the national Meningococcal Reference Unit (MRU) between late 1995 and early 1997 and was found to be highly sensitive. Insertion sequences, however, are genetically mobile with the ability to spread between species and even genera. During the evaluation period of the IS1106 PCR ELISA a number of false positives proved to be caused by organisms other than N. meningitidis were recorded resulting in the withdrawal of this assay as a front line screening assay for routine confirmation of meningococcal infection.     

肺炎克雷伯菌耐药性与I类整合子关系的研究

目的检测I类整合子在肺炎克雷伯菌临床分离株中的分布,分析整合子对细菌耐药性的影响。方法采用K—B纸片扩散法对127株肺炎克雷伯菌临床分离株进行药敏试验;并用WHONET5．6软件分析菌株药敏情况;采用聚合酶链反应（PCR）分析127株肺炎克雷伯菌株的I类整合子。并对I类整合子阳性株与阴性株的耐药性进行对比分析。结果127株菌中有53株（41．70％）含有I类整合子,I类整合子阳性菌株对氨基糖苷类、喹诺酮类及大多数B一内酰胺类的耐药率高于整合子阴性的菌株。结论I类整合子在肺炎克雷伯菌临床分离株存在较广,含有I类整合子的肺炎克雷伯菌更易获得耐药性。     

PCR法快速检测临床标本中结核杆菌DNA

应用聚合酶链反应（ＰＣＲ）快速检测临床标本（脑脊液、胸水、腹水、血、痰液）中的结核杆菌ＤＮＡ,特异性扩增片段１２３ｂｐ,为结核杆菌的特异性重复序列ＩＳ６１１０部分基因。ＰＣＲ检测人型结核杆菌的敏感性达１０ｆｇＤＮＡ。临床标本的ＰＣＲ检测阳性率（２３．３％）明显高于抗酸染色涂片（２．９％）和细菌培养（５．７％）的阳性率（Ｐ〈０．０５）。通过设立对照系统及对扩增产物酶切分析,表明该法无假阴性结果（特异