Heterogeneous nuclear RNA-protein fibers in chromatin-depleted nuclei.

The heterogeneous nuclear RNA-protein (hnRNP) fibers in HeLa cell nuclei are visualized by a nuclear subfractionation technique which removes 96% of the chromatin in a single step and 99% in a two-step elution but leaves the bulk of the hnRNA complexed with the remnant nuclear structure or lamina. Both steady-state and newly synthesized (approximately 15-s label) hnRNA are associated with the remnant nuclei to about the same extent. This association does not appear to depend on the presence of chromatin and exists in addition to any possible association of hnRNP with chromatin itself. Electron microscopy of partially purified nuclear hnRNA complexes shows that the hnRNP fibers form a ribonucleoprotein network throughout the nucleus, whose integrity is dependent on the RNA. Autoradiography confirms that hnRNA is a constituent of the fibers. The RNA network visualized in these remnant nuclei may be similar to RNA networks seen in intact cells. The hnRNA molecules appear to be associated with the nuclear lamina, at least in part, by unusual hnRNA sequences. More than half of the recovered poly(A) and double-stranded hnRNA regions remains associated with the nuclear structures or the laminae after digestion with RNase and elution with 0.4 M ammonium sulfate. In contrast, the majority of oligo(A), another ribonuclease resistant segment, is released together with most of the partially digested but still acid-precipitable single-stranded hnRNA and the hnRNP proteins not eluted by the ammonium sulfate alone. These special RNA regions appear to be tightly bound and may serve as points of attachment of the hnRNA to nuclear substructures. It is suggested that hnRNA metabolism does not take place in a soluble nucleoplasmic compartment but on organized structures firmly bound to the nuclear structure.

Clinical utility of a quantitative polymerase chain reaction for diagnosis of cytomegalovirus disease in solid organ transplant patients.

BACKGROUND: Accurate and rapid diagnosis of human cytomegalovirus (HCMV) disease in solid organ transplant patients remains a challenge. We evaluated the clinical utility of a quantitative polymerase chain reaction (QPCR) method to diagnose transplant patients with HCMV disease. METHODS: A total of 429 plasma samples from 121 solid organ transplant patients were prospectively collected and evaluated for HCMV using a QPCR assay. To enhance the sensitivity of the QPCR assay, plasma samples were centrifuged in a manner designed to concentrate the virions before nucleic acid extraction. Quantitation was achieved by co-amplifying an internal quantitative standard (IS) that contained the same primer sequences as for HCMV. Polymerase chain reaction products were detected by hybridization to 96-well microtiter plates coated with either a HCMV- or an IS-specific probe. RESULTS: A total of 103 patients had all samples negative by QPCR. None of the 103 patients developed HCMV disease during the study. In contrast, 18 patients showed at least 1 sample positive by the QPCR assay, but only 8 of these developed HCMV disease. The mean viral load value for patients without HCMV disease was 93 viral copies (vc) per ml of plasma (range: 35-325 vc/ml plasma) and for the 8 patients with HCMV disease was 67,686 vc/ml plasma (range: 167-1,325,000 vc/ml plasma) (P<0.001). Using a cut-off value of 100 vc/ml plasma and clinical diagnosis of HCMV disease, the QPCR assay showed a sensitivity of 100% and specificity of 99.1%. CONCLUSION: HCMV viral load may be useful in the diagnosis of HCMV disease in solid organ transplant patients.

Characterization of serum neutralization response to the human immunodeficiency virus (HIV).

To determine the clinical significance of human neutralizing antibodies to the human immunodeficiency virus (HIV), we measured serum neutralization in patients with different clinical outcomes following HIV infection. Serum neutralization titers ranged from less than 1:5 to 1:100. The neutralization response after HIV infection appeared slow, with neutralization titers remaining low, at or below 1:5, at 7 months following seroconversion. Comparison of 78 HIV seropositive subjects with AIDS, AIDS-related complex, or no symptoms failed to reveal any significant differences in titer which correlated with clinical status. However, a greater proportion of AIDS patients with Kaposi's sarcoma (11/12) had neutralization titers of 1:20 or greater than did AIDS patients with opportunistic infections (2/11). Serum samples were analyzed by Western blot for their reactivity to specific viral proteins. Clinical status could not be predicted by a particular serological profile. However, sera which reacted with the HIV major envelope glycoprotein gp120 tended to have higher neutralization titers, suggesting that gp120 may be a target of anti-HIV neutralizing antibody in man.

Superiority of conventional culture technique over rapid detection of group A Streptococcus by optical immunoassay.

An optical immunoassay (OIA) has been reported to be more sensitive than conventional culture for the detection of Group A Streptococcus, eliminating the need for culture. We attempted to confirm the sensitivity and specificity through a laboratory quantitation study and a clinical trial. OIA did not detect Group A Streptococcus below 10(5) colony forming units (CFU). Culture detected Streptococcus to 10(2) CFU from the inoculated swab. In the clinical study, throat swabs were obtained from 77 patients in an outpatient clinic. Compared with culture, the sensitivity of OIA was 78% and the specificity was 90%. These results demonstrate that OIA was less sensitive than culture in seeded experiments and missed 22% of positives in clinical practice. Our study, contrary to previous reports, suggests that OIA is not sensitive enough to be used as the sole assay for Group A Streptococcus pharyngitis.

The use of mucolysed induced sputum for the identification of pulmonary pathogens associated with human immunodeficiency virus infection.

We describe a system for diagnosis of pulmonary disease in the human immunodeficiency virus-infected patient using induced sputum and other diagnostic procedures. This system has been successfully used at San Francisco (Calif) General Hospital for more than 2 years. It utilizes outpatient facilities and reduces the need for bronchoscopy. Sputum induced by inhalation of 3% saline mist, mucolysed, concentrated by centrifugation, and stained by a rapid modified Giemsa stain was the first diagnostic specimen examined in 404 episodes of suspected human immunodeficiency virus-associated pulmonary disease in 358 patients. Pneumocystis carinii was found in 222 (55%) sputum specimens. In 118 episodes in which the sputum did not contain P carinii, bronchoscopy with transbronchial biopsy and/or bronchoalveolar lavage was performed and P carinii was found in 50 (42%). These 118 bronchoscopy results, as well as evaluation of the subsequent clinical course of those patients who accounted for 64 episodes of lung disease and who did not have bronchoscopy following examination of nondiagnostic induced sputum, indicated a range of sensitivity for detection of P carinii in induced sputum of 74% to 77% and a negative predictive value of 58% to 64%. Mycobacteria were recovered from 11 (6%) of the induced sputum and 6 (12%) of the bronchoscopic specimens containing P carinii. However, only oral or environmental fungi were recovered from P carinii-containing induced sputum or bronchoscopic specimens. For those patients in whom P carinii was not detected, only the bronchoscopic specimens were cultured for Mycobacteria and fungi. Potentially pathogenic Mycobacteria and fungi were recovered from 16 (23.5%) and 34 (50%), respectively, of these P carinii-negative specimens. Analysis of these results, obtained under routine practice conditions, indicates that bronchoscopy should be reserved for those patients whose induced sputum examinations do not show P carinii and that mycobacterial and fungal cultures be performed only on bronchoscopic specimens in which P carinii is not detected.

Detection and clinical significance of extended-spectrum beta-lactamases in a tertiary-care medical center.

The prevalence of extended-spectrum beta-lactamase (ESBL)-mediated resistance remains unknown for most hospitals, and national guidelines for testing and reporting ESBL-mediated resistance have not yet been developed. We undertook a study to determine the prevalence of ESBLs and the clinical need for testing in our tertiary-care medical center. Members of the family Enterobacteriaceae isolated over a 6-month period for which ceftazidime or ceftriaxone MICs were greater than 1 microg/ml were tested for production of ESBLs by the double-disk synergy method. Approximately 1.5% of isolates of the family Enterobacteriaceae (50 of 3,273), which were isolated from 1.2% of patients (23 of 1,844), were found to express ESBLs. ESBL-producing strains included eight different species and were isolated from patients located throughout the hospital, including outpatient clinics. By using the interpretive guidelines of the National Committee for Clinical Laboratory Standards, 26 to 39% of the isolates would have been reported to be susceptible to ceftazidime, depending upon the routine susceptibility method used. However, tests with cefpodoxime found all of the ESBL-producing strains to be resistant or intermediate. Nine patients infected with ESBL-producing isolates were treated with therapy which included an expanded-spectrum cephalosporin. Seven were cured. The deaths of the other two patients were not attributed to bacterial resistance missed by routine susceptibility testing. These observations suggest that in our tertiary-care medical center, it may not be clinically necessary or cost-effective at this time to institute additional testing on a routine basis to detect ESBL production in all clinical isolates of the family Enterobacteriaceae.

Mutagenesis during in vitro DNA synthesis.

The error frequency of in vitro DNA synthesis using a natural DNA template has been measured with a biological assay for nucleotide substitutions. phiX174 DNA containing an amber mutation was copied in vitro by Escherichia coli DNA polymerase I, and the reversion frequency of the progeny DNA was determined by transfection of E. coli spheroplasts. E. coli polymerase I makes less than 1 mistake at the am3 locus for every 7700 nucleotides incorporated under standard reaction conditions. Substitution of Mn2+ for Mg2+ and unequal concentrations of deoxynucleoside triphosphate substrates raises this mutation frequency to greater than 1 in 1000. Thus, E. coli DNA polymerase I can copy natural DNA templates with high fidelity and its accuracy can be affected by alterations in reaction conditions.

Cytomegalovirus antibody in the elderly.

Presence of cytomegalovirus (CMV) specific immunoglobulin M (IgM) is generally considered strong evidence of current or recent CMV infection. Sera from 110 elderly individuals (age range 61-100 years) were compared with sera from 87 younger individuals (age range 16-47 years). Prevalence of CMV IgM was found to be 30% in the older group (mean age 83 years) and only 6% in the younger group (mean age 29 years). In spite of increased CMV antibody levels, none of the elderly individuals were symptomatic. Viral cultures of urine from 72 elderly individuals were negative for CMV. These results suggest that the presence of CMV-specific IgM must be interpreted with caution in an elderly population.

Mycobacterium xenopi infection masquerading as pulmonary tuberculosis in two patients infected with the human immunodeficiency virus.

Mycobacterium xenopi infections have rarely been reported among patients infected with the human immunodeficiency virus (HIV). We recently treated two HIV-infected men, neither of whom had a history of pulmonary disease or AIDS-defining conditions, and who had M. xenopi lung infections. Both patients presented with night sweats, cough, and pleuritic chest pain. Chest radiographs showed an upper-lobe nodule in the first patient and a perihilar cavitary infiltrate in the second patient. Both patients were initially believed to have pulmonary tuberculosis and were treated accordingly; however, only M. xenopi grew on cultures of multiple respiratory specimens. This diagnosis was confirmed by cultures of biopsied lung tissue from the first patient and of fluid from a peritracheal abscess in the second patient. Both patients' clinical conditions improved after multidrug therapy (isoniazid, rifampin, pyrazinamide, ethambutol, and ciprofloxacin in the first case; isoniazid, rifampin, and pyrazinamide in the second case). The second patient's condition improved despite in vitro resistance of his isolate to isoniazid and rifampin.

Enhanced analytical sensitivity of a quantitative PCR for CMV using a modified nucleic-acid extraction procedure.

Accurate and rapid diagnosis of CMV disease in immunocompromised individuals remains a challenge. Quantitative polymerase chain reaction (QPCR) methods for detection of CMV in peripheral blood mononuclear cells (PBMC) have improved the positive and negative predictive value of PCR for diagnosis of CMV disease. However, detection of CMV in plasma has demonstrated a lower negative predictive value for plasma as compared with PBMC. To enhance the sensitivity of the QPCR assay for plasma specimens, plasma samples were centrifuged before nucleic-acid extraction and the extracted DNA resolubilized in reduced volume. Optimization of the nucleic-acid extraction focused on decreasing or eliminating the presence of inhibitors in the pelleted plasma. Quantitation was achieved by co-amplifying an internal quantitative standard (IS) with the same primer sequences as CMV. PCR products were detected by hybridization in a 96-well microtiter plate coated with a CMV or IS specific probe. The precision of the QPCR assay for samples prepared from untreated and from pelleted plasma was then assessed. The coefficient of variation for both types of samples was almost identical and the magnitude of the coefficient of variations was reduced by a factor of ten if the data were log transformed. Linearity of the QPCR assay extended over a 3.3-log range for both types of samples but the range of linearity for pelleted plasma was 20 to 40,000 viral copies/ml (vc/ml) in contrast to 300 to 400,000 vc/ml for plasma. Thus, centrifugation of plasma before nucleic-acid extraction and resuspension of extracted CMV DNA in reduced volume enhanced the analytical sensitivity approximately tenfold over the dynamic range of the assay.

Comparative evaluation of three products for the detection of Borrelia burgdorferi antibody in human serum.

Eighty human serum specimens tested concomitantly by immunoblot and an enzyme-linked immunosorbent assay developed jointly at the University of Connecticut School of Medicine and the Connecticut Agricultural Experiment Station were used to evaluate three commercially available diagnostic products for Lyme borreliosis. The sources of the kits were Hillcrest Biologicals, Cypress, Calif.; Whittaker Bioproducts, Walkersville, Md.; and Cambridge Bioscience, Worcester, Mass. When compared with Western blot analysis, the sensitivities and specificities, respectively, for the diagnostic assays were as follows: Hillcrest Biologicals, 93 and 75%; Whittaker Bioproducts, 73 and 100%; Cambridge Bioscience, 89 and 100%; and University of Connecticut School of Medicine, 96 and 92%.

Mycobacterium xenopi: innocent bystander or emerging pathogen?

Mycobacterium xenopi is a recognized cause of smoldering pulmonary disease in patients with chronic lung disease. This organism is frequently isolated from respiratory specimens from individuals infected with human immunodeficiency virus (HIV) and is often considered nonpathogenic. Cases of pulmonary and disseminated M. xenopi disease have been described in patients with HIV infection and other immunodeficiencies. Many physicians are unaware of the clinical significance of M. xenopi isolation. Whether this organism represents a commensal or a pathogen capable of causing considerable morbidity and mortality is not fully understood. In this study, we investigated the clinical significance of M. xenopi isolation and explored the clinical spectrum of M. xenopi disease. Clinical illness occurred both in elderly people with chronic lung disease and in young individuals with HIV infection. The repeated isolation of M. xenopi in association with pulmonary lesions suggests significant infection and mandates further workup and therapy.

Infidelity of DNA synthesis as related to mutagenesis and carcinogenesis.

An assay system has been developed for measuring the fidelity of DNA synthesis in vitro by using synthetic polynucleotide templates and purified DNA polymerases. Nearest-neighbor analysis of the synthesized product indicates that noncomplementary nucleotides are incorporated as single base substitutions. The accuracy of DNA synthesis can be decreased by (1) prior alkylation of the template, (2) increasing the relative concentration of incorrect nucleotides, and (3) addition of specific metal salts to the reaction mixture. As an initial evaluation of the utility of this system, the effects of 31 metal salts on the fidelity of DNA synthesis have been determined. The results indicate that potential metal mutagens and/or carcinogens may be detected by measuring alterations in the fidelity of DNA synthesis.