Evaluation of Cobas Amplicor MTB test to detect Mycobacterium tuberculosis in pulmonary and extrapulmonary specimens

Tuberculosis (TB) is one of the major public health problems in the world. Effective control of TB depends on rapid and correct diagnosis and appropriate treatment. The aim of this study was to evaluate the performance of Cobas Amplicor MTB (CA-MTB) test for pulmonary and extrapulmonary specimens isolated in our laboratory. A total of 424 specimens obtained from the suspected TB patients from January 2003 to August 2004 were included in this study. All specimens (173 pulmonary and 251 extrapulmonary specimens) were processed, stained, cultured and assayed using the CA-MTB test for identification of Mycobacterium tuberculosis. The CA-MTB test results were compared to culture and acid-fast staining as gold standard. The sensitivity, specificity, positive and negative predictive values of CA-MTB were determined as 73%, 100%, 100%, and 97% for pulmonary specimens, and 45%, 100%, 100% and 96% for extrapulmonary specimens respectively. The sensitivity of the test for acid-fast bacilli (AFB) smear positive pulmonary and extrapulmonary specimens was 92% and 75%. These results indicate that the CA-MTB is a rapid test for detection of tuberculosis in pulmonary specimens, but does not perform well enough in extrapulmonary specimens.     

Detection of Candida antigen in bronchoalveolar lavage fluid

While bronchoalveolar lavage is frequently performed to evaluate immunocompromised hosts for infection, the significance of rare yeasts found on the cytologic examination of lavage fluid is unclear. This study used the latex agglutination method to test lavage fluids for Candida antigen to assess its usefulness in distinguishing Candida pneumonia from Candida colonization of the respiratory tract or oral contamination of the lavage specimen. Ninety-seven specimens from 87 patients were categorized on the basis of historical, microbiologic, cytologic and serologic data. Bronchoalveolar lavage fluids were positive for Candida antigen in 0 of 20 specimens from normal controls, 0 of 14 specimens from patient controls, 5 (36%) of 14 specimens from patients with Pneumocystis carinii pneumonia, 0 of 5 specimens from patients with gastrointestinal candidiasis, 0 of 9 specimens contaminated by oral-derived yeasts, 2 (10%) of 19 specimens from patients with probable Candida colonization and 15 (94%) of 16 specimens from patients with clinical and laboratory evidence of Candida pneumonia. We conclude that this test assists in the differentiation of Candida pneumonia from other situations in which yeasts are recovered by bronchoalveolar lavage.     

Anaerobic bacteria in clinical infections

The findings of 275 cultures from routine clinical specimens obtained from lesions in different sites of body, during a period of 11 months, are presented. The clinical specimens were obtained from surgical wounds, abdominal infections, orthopaedic operations, biliary tract infections and pleuropulmonary infections. The total number of positive cultures including both aerobes and anaerobes was 203 out of 275 (73.8%). Of the 38 cultures positive for anaerobes, 29 (76.3%) grew both aerobic and anaerobic bacteria, while in nine (23.7%) cultures only anaerobes were found. A total of 42 strains of anaerobic bacteria were isolated. The majority of them were found in clinical specimens obtained from abdominal infections (62%), while a low percentage (3.6%) was found in specimens from orthopaedic operations. Strains belonging to the genus Bacteroides were the most frequently isolated anaerobes, accounting for 35.7% of the total, followed by Clostridia 28.5%, Peptostreptococci 23.8% and Prevotella 12%.     

成人腹泻轮状病毒ELISA方法的建立和应用

本文通过特异性试验、阻断试验、交叉试验、敏感度试验和重复性试验,建立了成人腹泻轮状病毒一酶联免疫吸附试验法(ADRV—ELISA)。应用此法检测了全国20多个省区202份病人腹泻标本,检出率为91％。采用本ELISA、核酸电泳、电镜三种方法对48份病人腹泻标本进行了双盲法检测比较,结果三种方法的阳性检出率分别为100％、85.4％、56.25％(P<0.05)。实验结果表明,本ELISA应用于检测成人腹泻轮状病毒(ADRV),具有敏感度高。特异性强等优点。     

The cytopathology of bone marrow transplantation

Bone marrow transplantation (BMT) is an increasingly effective treatment for patients with hematologic disorders and malignant neoplasms. From 1975 to 1986, 1,457 specimens were obtained for cytologic evaluation from 328 of the 635 patients who received BMTs at Memorial Sloan-Kettering Cancer Center. These specimens consisted of 1,049 cerebrospinal fluids (CSFs) from 265 patients, 292 bronchoscopy specimens from 92 symptomatic patients and 116 other specimens (including brushings from the liver and gastrointestinal tract, sputa, urines and cervico-vaginal smears). CSF specimens examined before and after BMT from 80 (30%) patients showed an increased number of benign, nonepithelial cells, which were mainly lymphocytic or histiocytic in origin. Malignant cells were detected in CSF specimens from 44 (17%) patients. Bronchoscopy specimens from 3 patients had suspicious cells present; those from 27 patients contained opportunistic organisms. Atypical epithelial or lymphoreticular cells were seen in bronchial specimens from 49 patients. All cytologic findings were correlated with the pertinent clinical information as well as biopsy and autopsy material, including histopathologic evidence of graft-versus-host disease. Cytologic evaluation, especially of bronchial and CSF specimens, was useful in diagnosing the presence of malignant neoplasms, infectious organisms, inflammatory responses, reactive lesions and cellular atypia due to treatment.     

Cytologic findings in vitreous fluids. Analysis of 74 specimens

OBJECTIVE: To review the cytologic findings of vitreous specimens and propose a simplified approach to them. STUDY DESIGN: Seventy-four vitreous specimens from 60 patients obtained either during a pars plana vitrectomy or by vitreous aspiration were reviewed. Clinical correlation was obtained on all patients. RESULTS: Findings suggestive of a specific disorder were present in 30 specimens (41%); cytologic examination of the remaining 44 showed nonspecific changes. A lymphoproliferative disorder, the intraocular malignancy suspected most often in this series, was identified in eight specimens (11%). Large cell lymphomas were evident in 5 specimens, 2 specimens were suspicious for lymphoma, and 1 specimen was consistent with plasmacytoma. Twelve specimens (16%) contained hemorrhage. In rare instances, specific infectious agents, such as parasites (5%), bacteria (1%) and fungi (3%), could be identified. The diagnosis of viral infections required ancillary studies. Lens fragments were identified in four cases (5%), and a diagnosis of lens-induced endophthalmitis could be rendered in one case (1%). Changes consistent with sarcoidosis were present in 3% of cases. CONCLUSION: Based on this experience with vitreous specimens submitted for clinical reasons, we found that they could be divided into three broad diagnostic categories: inflammation/infection (54 specimens/41 patients), hemorrhage (12 specimens/12 patients) and malignancy (8 specimens/7 patients).     

Extraction of nuclear DNA from bone of skeletonized and fluid‐preserved museum specimens

Obtaining DNA sequences, particularly nuclear DNA, from museum specimens is challenging. We sequenced nuclear DNA from small bone fragments of skeletonized and fluid‐fixed museum specimens of squamate reptiles by using a forensic protocol developed for isolating DNA from human bones. The method yielded high quality nuclear DNA sequences from bones taken from 11 of 21 (52.4%) skeletonized or desiccated specimens, the oldest of which dated back to 1938, and 1 of 9 (11.1%) fluid‐preserved specimens, which was collected in 1957.     

Evaluation of rapid techniques for the detection of mycobacteria in sputum with scanty bacilli or clinically evident, smear negative cases of pulmonary and extra-pulmonary tuberculosis

The objective of the current study was to compare two rapid methods, the BBL Mycobacteria Growth Indicator Tube (MGIT TM) and Biotec FASTPlaque TB TM (FPTB) assays, with the conventional L?wenstein-Jensen (LJ) media assay to diagnose mycobacterial infections from paucibacillary clinical specimens. For evaluation of the clinical utility of the BBL MGIT TM and FPTB assays, respiratory tract specimens (n = 208), with scanty bacilli or clinically evident, smear negative cases and non-respiratory tract specimens (n = 119) were analyzed and the performance of each assay was compared with LJ media. MGIT and FPTB demonstrated a greater sensitivity (95.92% and 87.68%), specificity (94.59% and 98.78%), positive predictive value (94.91% and 99.16%) and negative predictive value (96.56% and 90.92%), respectively, compared to LJ culture for both respiratory tract and non-respiratory tract specimens. However, the FPTB assay was unable to detect nontuberculous mycobacteria and few Mycobacterium tuberculosis complex cases from paucibacillary clinical specimens. It is likely that the analytical sensitivity of FPTB is moderately low and may not be useful for the direct detection of tuberculosis in paucibacillary specimens. The current study concluded that MGIT was a dependable, highly efficient system for recovery of M. tuberculosis complexes and nontuberculous mycobacteria from both respiratory and non-respiratory tract specimens in combination with LJ media.     

Detection of viral agents in fecal specimens of monkeys with diarrhea

BACKGROUND: Diarrheal disease is a major cause of morbidity and mortality in humans and animals, including non human primates. While the diagnostics for gastrointestinal bacterial and parasitic pathogens and their etiological role in disease are well established, little is known about the epidemiology, prevalence and role of viral agents in diarrheal illness among monkeys. METHODS: We collected fecal specimens from monkeys with diarrhea that were housed in two primate colonies, the Institute of Laboratory Animal Sciences, Beijing, China and the Yerkes National Primate Research Center, Georgia, USA. We screened these fecal specimens for rotaviruses and enteric adenoviruses 40/41 by using commercial EIA kits (Rotaclone and Adenoclone), enteroviruses by RT-PCR and Southern blot hybridization, and picobirnaviruses by polyacrylamide gel electrophoresis and silver staining. Some of the specimens were examined by EM for coronaviruses and noroviruses. RESULTS: Of the 92 specimens from China, we found 63 (68%) positive for viruses, including enteroviruses (52%), enteric adenoviruses (21%), rotaviruses (20%), and picobirnaviruses (2%). Coronaviruses were detected in some specimens. Mixed infection of two or more viral agents was seen in 23 (25%) specimens. In the US collection, we detected enteroviruses and enteric adenoviruses in 76% (45/59) and 14% (7/50) of the specimens, respectively. Electron microscopy showed norovirus-like particles in some specimens from both colonies. CONCLUSIONS: Our findings indicate endemic infections with enteric viruses in monkeys of both colonies. The availability of new simian rotaviruses, enteric adenoviruses, enteroviruses, and coronaviruses and the discovery of noroviruses and picobirnaviruses may allow us to develop better diagnostics for these agents and determine which of these agents are clearly associated with gastroenteritis in monkeys.     

Murine cytomegalovirus gene amplification and culture after submaxillary salivary gland biopsy.

An important target tissue for murine cytomegalovirus (CMV) infection is the submaxillary salivary gland. Submaxillary salivary gland biopsy specimens from BALB/c mice latently infected with murine CMV were examined for murine CMV DNA by in vitro enzymatic amplification using the polymerase chain reaction preceding oligonucleotide hybridization. The amplified sequence was a 152-base pair segment from within the immediate early gene of murine CMV. Biopsy and whole gland specimens from acutely infected BALB/c mice and latently infected, immunosuppressed BALB/c mice were compared for active murine CMV infection. After acute infection with murine CMV, virus was recovered in all cultures of both biopsy and whole salivary gland specimens but from none of the latently infected animals. Reactivated virus was detected by culture of both biopsy (90%) and whole salivary gland specimens (100%) from latently infected mice that received antithymocyte serum. Viral nucleic acid was detected in 90% of biopsy specimens from latently infected animals. Hence, active murine CMV infection can be detected in biopsy specimens from mice with acute and reactivated infection and murine CMV DNA can be amplified and detected in salivary gland biopsy specimens from latently infected animals. Biopsy of this or other target tissues can be useful for obtaining tissue for viral studies where the survival of the animal is important and it is useful to distinguish latent from acute or reactivated infection.     

Diagnostic Value of the Amplicor PCR Assay for Initial Diagnosis and Assessment of Treatment Response for Pulmonary Tuberculosis

We evaluated the Amplicor PCR assay as an initial diagnostic tool on the basis of clinical diagnosis, and assessed this assay as a follow-up test for patients with pulmonary tuberculosis during chemotherapy. Of the 208 specimens from 155 patients who were bacteriologically and/or clinically diagnosed with active tuberculosis before chemotherapy, 144 were Amplicor PCR-positive (sensitivity, 69.2%), which was equal to the results of culturing. Among 89 specimens which showed positive results by smear and culturing, the Amplicor PCR assay detected 87 (97.8%), whereas among 55 specimens which showed smear-negative but culture-positive results, the Amplicor PCR assay detected 46 (83.6%)(P = 0.003). No false positive results were found in the two systems (specificity, 100%, 120/120). The Amplicor PCR assay was also evaluated as a follow-up test using 926 specimens from 207 patients receiving active tuberculosis chemotherapy. Among 433 specimens which showed Amplicor-PCR positive, 222 (51.3%) were culture-negative. On the other hand, among 233 culture-positive specimens, only 12 (5.2%) were Amplicor PCR-negative. Therefore, this assay is useful for the rapid diagnosis of tuberculosis. The duration of Amplicor PCR-positive after culture-negative conversion was significantly associated with the presence of cavitary lesion, smear-positive specimens before treatment, and smear-positive specimens with negative cultures during chemotherapy.     

Anti-HIV testing by automated systems

The accuracy and ease of use of three automated test systems (Behring Opus, Boehringer Mannheim ES300 and bioMerieux Vidas) and their associated assays (Opus HIV 1 + 2, Enzymun-Test Anti-HIV 1 + 2 and Vidas HIV 1 + 2) for the detection of anti HIV-1 and anti HIV-2 in human serum and plasma were investigated by testing them against a panel of 364 well-characterised specimens. The panel included specimens confirmed to contain anti HIV-1 (n = 65) and anti HIV-2 (n = 25), specimens collected during HIV-1 seroconversion (n = 40), specimens (n = 116) which had given spurious reactions in a variety of anti-HIV screening assays, specimens from patients infected with anti HTLV-I (n = 18) and specimens from unselected blood donors (n = 100). Excluding the seroconversion specimens, all three assays were 100% sensitive. Observed specificities ranged from 98.3% to 99.6%. For the seroconversion specimens the Vidas HIV 1 + 2 was the most sensitive overall. All three assays were as sensitive and specific as most of the conventional anti-HIV enzyme immunoassays currently available. The Opus and Vidas systems would be convenient for clinical laboratories handling small to medium numbers of specimens per day. The Boehringer Mannheim ES300 is designed for larger scale use and required more familiarisation.     

Incorporating historical museum specimens into molecular systematic and conservation genetics research

We successfully amplified mitochondrial DNA (mtDNA) and microsatellites from historical museum specimens of lizards and frogs dating from 1894 through to 1998. Ancient DNA techniques were used to extract whole genomic DNA from a number of different tissues, including liver, leg muscle and toe clips, followed by standard polymerase chain reaction techniques for amplification. We had a 78% success rate amplifying mtDNA from 14 museum specimens and a 57% success rate amplifying microsatellite markers for seven museum specimens. Our study demonstrates the feasibility of incorporating historical museum specimens into molecular systematic and conservation genetic studies.     

Coli-aerogenes Bacteria on Plants

S ummary . Specimens of plant foliage and flowers collected in the region of Attica from various situations and geographical regions were examined over a period of 13 months for the presence of coli-aerogenes bacteria able to grow at 37°. Twenty-five (12.2%) of 204 specimens carried coli-aerogenes bacteria of which Escherichia coli type I was isolated from 12 (5.8%). Coli-aerogenes bacteria were seldom isolated from plants grown in uninhabited areas, and they occured more frequently during summer and autumn.
Vegetables and fruits sold in the central market of Athens are frequently contaminated with coli-aerogenes bacteria. Of 76 specimens of vegetables examined 66 (86.8%) were positive for coli-aerogenes bacteria, and 17 (22.3%) for E. coli type I. The figures from 41 specimens of fruits were 26 (65.8%) and 4 (9.7%), respectively.     

Comparison of Dermatophyte PCR Kit with Conventional Methods for Detection of Dermatophytes in Skin Specimens

The laboratory diagnosis of dermatophytosis is usually based on direct microscopic examination and culturing of clinical specimens. A commercial polymerase chain reaction kit (Dermatophyte PCR) has had favorable results when used for detection of dermatophytes and identification of Trichophyton rubrum in nail specimens. This study investigated the efficacy of the Dermatophyte PCR kit for detecting dermatophytosis in 191 hair or skin specimens from patients with suspected dermatophytosis. PCR was positive for 37 % of samples, whereas 31 and 39 % of the specimens were positive by culturing and direct microscopy, respectively. The sensitivity, specificity, positive predictive value, and negative predictive value for PCR analysis were 83, 84, 71, and 91 %, respectively. The sensitivity of the PCR test was higher in specimens obtained from skin (88 %) than in those obtained from hair (58 %), while the specificity remained almost the same (84 and 86 % for skin and hair, respectively). Our results show that the Dermatophyte PCR kit is a promising diagnostic tool for detection of dermatophytosis in skin samples, providing clinicians with a rapid diagnosis.     

Biological collections in an ever changing world: Herbaria as tools for biogeographical and environmental studies

Plant specimens stored in herbaria are being used as never before to document the impacts of global change on humans and nature. However, published statistics on the use of biological collections are rare, and ecologists lack quantitative data demonstrating the relevance to science of herbarium specimens. I found 382 studies with original data that used herbarium specimens to document biogeographical patterns or environmental changes. Most studies are less than 10 years old, and only 1.4% of the herbarium specimens worldwide have been used to answer biogeographical or environmental questions. The vast majority (82%) of papers dealt with vascular plants, but some studies also used bryophytes, lichens, seaweeds and fungi. The herbarium specimens were collected from all continents, but most of the studies used specimens from North America (40% of studies) or Europe (28%). Many types of researches (conservation, plant disease, plant invasion, pollution, etc.) can be conducted using herbarium specimens. Climate change, and especially phenological reconstructions, are clearly emerging research topics. By group, small herbaria (<100,000 specimens) are consulted as often as very large herbaria (>1,000,000 specimens) for biogeographical and environmental research, but in most cases, only large facilities provide specimens collected worldwide. The median number of specimens per study in papers using computerized collections (15,295) was much higher than for papers that did not include electronic data (226). The use of molecular analyses to investigate herbarium specimens is still relatively unexplored, at least from biogeographical and environmental points of view. Combined with recently developed procedures to correct biases, herbarium specimens might provide in the near future exciting additional spatio-temporal insights that are currently unimaginable.     

Value and Interpretation of Serological Tests for the Diagnosis of Cryptococcosis

MAXIMAL SEROLOGICAL DIAGNOSIS OF CRYPTOCOCCOSIS MAY BE ACCOMPLISHED THROUGH THE CONCURRENT USE OF THREE TESTS: the latex agglutination (LA) test for cryptococcal antigen, and the indirect fluorescent antibody (IFA) and tube agglutination (TA) tests for Cryptococcus neoformans antibodies. These tests were applied to 141 serum and cerebral spinal fluid specimens from 66 culturally proven cases of cryptococcosis and to 42 sera from normal subjects and from patients with other systemic mycotic diseases. The LA test was sensitive and completely specific; of the sera from proven cases, 55% were positive. With the TA test, 37% of the specimens were positive and the test was highly specific. With the IFA test, 38% of the specimens were positive and the test appears to be the least specific of the three. Cross-reactions were most evident with blastomycosis and histoplasmosis case sera. When the three tests were used concurrently, 87% of the cryptococcosis case specimens were positive and permitted a presumptive diagnosis of C. neoformans infections in 61 (92%) of the 66 patients whose specimens were examined.     

Overexpression of HER2/neu oncoprotein in cytologic specimens

OBJECTIVE: To assess the rate of HER2/neu overexpression in cytologic specimens by immunocytochemistry (ICC) and compare these results in matched surgical specimens by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), when available. STUDY DESIGN: All cytologic specimens processed for HER2/neu evaluation by ICC (72 cases) and available corresponding histologic specimens (16 cases) were retrieved from our files. ICC was applied to previously Papanicolaou stained, routine fine needle aspirations specimens (64 cases) and cytocentrifuged, alcohol-fixed, fluid specimens (8 cases). FISH was performed on 6 histologic specimens. RESULTS: Overexpression of HER2/neu was seen in 7/22 breast cancers (31.8%), 3/18 pulmonary adenocarcinomas (16.6%), 2/5 colorectal adenocarcinomas (40%), 1/2 adenocarcinomas of the biliary system (50%), 1/3 thyroid papillary carcinomas (33.3%) and 1/3 prostate adenocarcinomas (33.3%). Sixteen cases had IHC in matched histologic specimens: 14 (87.5%) cases were concordant (11 negative and 3 positive in both specimens), 1 case was negative in the cytologic specimen and positive in the histologic specimen (with no amplification by FISH), and 1 case was positive in the cytologic specimen and negative in the histologic specimen (not informative by FISH). CONCLUSION: Our data suggest that overexpression of HER2/neu oncoprotein can be successfully detected in routine cytologic specimens, providing a simple, fast and cost-effective method of selecting patients for specific treatment.     

从急性腹泻儿童中检出的人博卡病毒2型的研究

为了调查北京地区急性腹泻患儿中人博卡病毒2型（HBoV2）的流行情况并了解这一病毒的基因组特征,本研究收集2010年11月至2011年10月到首都儿科研究所附属儿童医院门诊就诊的急性腹泻患儿的粪便标本553例,采用荧光实时PCR进行HBoV2 DNA的检测。选择2例病毒载量较高的阳性标本进行HBoV2各基因片段的扩增并测序。将所测到的序列进行拼接后得到完整的基因组序列并与GenBank中的相关序列进行比较分析。结果显示,553例粪便标本中共检出HBoV2阳性标本15例,阳性率为2.7%;各年龄组中,3~6月龄患儿中的HBoV2 DNA阳性检出率最高（4.1%）;所检年度中,7月份阳性检出率最高（7.0%）;15例HBoV2检测阳性的患儿年龄均在2岁以下,其中4例患儿同时检出了诺如病毒,3例患儿同时检出了轮状病毒,1例检出了腺病毒。经测序得到两株接近完整的HBoV2基因组序列BJQ19和BJQ390;序列分析表明,这两株序列的同源性为99.2%,与GenBank中的FJ375129同源性最高,分别为99.1%和99.2%,为典型的HBoV2。上述结果表明,北京地区部分儿童的急性腹泻可能与HBoV2感染相关,且HBoV2感染在低年龄组儿童中更为常见。     

Predictive value of the acid fast smear for detection of Mycobacterium tuberculosis in respiratory specimens in a reference center of HIV/AIDS in Rio de Janeiro, Brazil

In order to evaluate the predictive value of acid fast bacilii (AFB) smear for the diagnosis of Mycobacterium tuberculosis in respiratory specimens in a setting with a high prevalence of AIDS and an unknown prevalence of nontuberculous mycobacteria (NTM), we retrospectively examined specimens cultured for mycobacteria between 1 September 1993 and 30 September 1994 and medical records of patients with positive culture in a General Hospital, AIDS reference in Rio de Janeiro, Brazil. Seventy three per cent (1517/2077) of samples were respiratory specimens and mycobacteria were recovered from 20.6% (313/1517) of these. M. tuberculosis was identified in 94.2% (295/313) and NTM in 5.8% (18/313). The yield of positive AFB smear and of positive culture was 6.1% (93/1517) and 20.6% (313/1517), respectively. The positive predictive value (PPV) of AFB for M. tuberculosis was 98.4% in expectorated sputum and 96.4% in bronchoalveolar lavage. Forty four percent (130/295) of specimens with positive culture for M. tuberculosis and 66.7% (12/18) for NTM were from patients HIV positive. The conclusion was that in our study population, the PPV of AFB for M. tuberculosis in respiratory specimens was high and the prevalence of NTM was low despite the high prevalence of HIV positive.