Impact of a Multipronged Approach to Reduce the Incidence of Clostridioides difficile Infections in Hospitalized Patients

BACKGROUND

Effective approaches to reduce Clostridioides difficile infections (CDI) in hospitalized patients are needed. We report data from 3 years preceding and 3 years following interventions that proved successful, with detailed analysis of all cases the first year after implementation.

METHODS

Interventions included a nursing protocol to identify cases present on admission by asking if the patient had 1 or more liquid stools in the last 24 hours, and a 2-step testing algorithm with samples positive by polymerase chain reaction (PCR) for the C. difficile toxin gene reflexing to an enzyme immunoassay (EIA) for the toxin antigen.

RESULTS

Healthcare-associated infections due to CDI fell from ∼160 in each of the preceding 3 years to <65 in each of the subsequent 3 years (P<0.001), while the ratio of observed-to-expected hospital-onset cases diminished to ∼0.50 (P<0.02). In the first year, 395 samples were PCR(+), but only 118 (29.9%) of these were EIA(+). 55 (46.6%) of the PCR(+)/EIA(+) samples were from hospital day 1 or 2 and classified as present on admission. The mean time from stool collection to report of PCR results was ∼7.5 hours, and the EIA took on average only 68 additional minutes to be reported.

CONCLUSIONS

The number of incident CDI cases can be dramatically decreased by implementing an admission screening question and a 2-step testing algorithm.

Customizing an Electronic Medical Record to Automate the Workflow and Tracking of an Antimicrobial Stewardship Program

Background

Documenting the actions and effects of an antimicrobial stewardship program (ASP) is essential for quality improvement and support by hospital leadership. Thus, our ASP tallies the number of charts reviewed, types of recommendations, how and to whom they were communicated, whether they were followed, and any effects on antimicrobial days of therapy. Here we describe how we customized the electronic medical record at our institution to facilitate our workflow and data analysis, while highlighting principles that should be adaptable to other ASPs.

Methods

The documentation system involves the creation of a novel and intuitive ASP form in each chart reviewed and 2 mutually exclusive tracking systems: 1 for active forms to facilitate the daily ASP workflow and 1 for finalized forms to generate cumulative reports. The ASP form is created by the ASP pharmacist, edited by the ASP physician, reopened by the pharmacist to assess whether the recommendation was followed and to quantify any antimicrobial days avoided or added, then reviewed and finalized by the ASP physician. Active forms are visible on a real-time “MPage,” whereas all finalized forms are compiled nightly into 65 informative tables and associated graphs.

Results and Conclusions

This system and its underlying principles have automated much of the documentation, facilitated follow-up of interventions, improved the completeness and validity of recorded data and analysis, enabled our ASP to expand its activities, and been associated with decreased antimicrobial usage, drug resistance, and Clostridioides difficile infections.

Severe Babesia microti Infection in an Immunocompetent Host in Pennsylvania

Babesiosis, due to infection by a tick-borne protozoan (predominantly Babesia microti in North America), is an emerging health risk that is expanding into new areas and may be unfamiliar to clinicians in locations not previously considered endemic. Manifestations of infection can range from asymptomatic to life threatening, with severe disease more likely in those who have had a splenectomy, are immunocompromised, have chronic medical conditions, or are over 50 years of age. In this article, we describe an elderly but otherwise healthy man from an area not generally considered endemic for babesiosis who presented with severe hemolysis, acute renal failure, and high-level Babesia microti parasitemia; serological results suggestive of possible coinfection by Borrelia burgdorferi (the agent of Lyme disease, which is carried by the same tick as is Babesia microti) also was found. This report highlights that severe babesiosis can occur in an apparently normal host and underscores the continued geographic expansion of this pathogen and the need for early recognition and therapy.

Building an Antimicrobial Stewardship Program: Cooperative Roles for Pharmacists, Infectious Diseases Specialists, and Clinical Microbiologists

Efforts to optimize the use of antimicrobial agents, referred to as antimicrobial stewardship programs (ASPs), are increasingly becoming part of the clinical enterprise at big and small hospitals. Such programs aim to achieve the synergistic goals of improving patient outcomes, limiting the unintended consequences of drug resistance and superinfections, and reducing health care expenditures. This article will review the need for antimicrobial stewardship and the key components of setting up a program; then, it will describe the ASP at one medical center to underscore how attention to acceptance by the clinical staff is crucial to changing the culture of antimicrobial use. Although the details may differ for each institution, the foundation of a successful stewardship program is support from hospital leadership and the cooperative interaction among the pharmacy, infectious diseases specialists, and clinical microbiologists.

Alternative nucleophilic substrates for the endonuclease activities of human immunodeficiency virus type 1 integrase

Retroviral integrase can use water or some small alcohols as the attacking nucleophile to nick DNA. To characterize the range of compounds that human immunodeficiency virus type 1 integrase can accommodate for its endonuclease activities, we tested 45 potential electron donors (having varied size and number or spacing of nucleophilic groups) as substrates during site-specific nicking at viral DNA ends and during nonspecific nicking reactions. We found that integrase used 22 of the 45 compounds to nick DNA, but not all active compounds were used for both activities. In particular, 13 compounds were used for site-specific and nonspecific nicking, 5 only for site-specific nicking, and 4 only for nonspecific nicking; 23 other compounds were not used for either activity. Thus, integrase can accommodate a large number of nucleophilic substrates but has selective requirements for its different activities, underscoring its dynamic properties and providing new information for modeling and understanding integrase.

Evaluation of a system to screen for stimulators of non-specific DNA nicking by HIV-1 integrase: application to a library of 50,000 compounds

BACKGROUND

In addition to activities needed to catalyse integration, retroviral integrases exhibit non-specific endonuclease activity that is enhanced by certain small compounds, suggesting that integrase could be stimulated to damage viral DNA before integration occurs.

METHODS

A non-radioactive, plate-based, solution phase, fluorescence assay was used to screen a library of 50,080 drug-like chemicals for stimulation of non-specific DNA nicking by HIV-1 integrase.

RESULTS

A semi-automated workflow was established and primary hits were readily identified from a graphic output. Overall, 0.6% of the chemicals caused a large increase in fluorescence (the primary hit rate) without also having visible colour that could have artifactually caused this result. None of the potential stimulators from this moderate-size library, however, passed a secondary test that included an inactive integrase mutant that assessed whether the increased fluorescence depended on the endonuclease activity of integrase.

CONCLUSIONS

This first attempt at identifying integrase stimulator compounds establishes the necessary logistics and workflow required. The results from this study should encourage larger scale high-throughput screening to advance the novel antiviral strategy of stimulating integrase to damage retroviral DNA.

A nonradioactive plate-based assay for stimulators of nonspecific DNA nicking by HIV-1 integrase and other nucleases

Retroviral integrase enzymes have a nonspecific endonuclease activity that is stimulated by certain compounds, suggesting that integrase could be manipulated to damage viral DNA. To identify integrase stimulator (IS) compounds as potential antiviral agents, we have developed a nonradioactive assay that is suitable for high-throughput screening. The assay uses a 49-mer oligonucleotide that is 5'-labeled with a fluorophore, 3'-tagged with a quencher, and designed to form a hairpin that mimics radioactive double-stranded substrates in gel-based nicking assays. Reactions in 384-well plates are analyzed on a real-time PCR machine after a single heat denaturation and subsequent cooling to a point between the melting temperatures of unnicked substrate and nicked products (no cycling is required). Under these conditions, unnicked DNA reforms the hairpin and quenches fluorescence, whereas completely nicked DNA yields a large signal. The assay was linear with time, stimulator concentration, and amount of integrase, and 20% concentrations of the solvent used for many chemical libraries did not interfere with the assay. The assay had an excellent Z' factor, and it reliably detected known IS compounds. This assay, which is adaptable to other nonspecific nucleases, will be useful for identifying additional IS compounds to develop the novel antiviral strategy of stimulating integrase to destroy retroviral DNA.

Identifying amino acid residues that contribute to the cellular-DNA binding site on retroviral integrase

Although retroviral integrase specifically trims the ends of viral DNA and inserts these ends into any sequence in cellular DNA, little information is available to explain how integrase distinguishes between its two DNA substrates. We recently described novel integrase mutants that were improved for specific nicking of viral DNA but impaired at joining these ends into nonviral DNA. An acidic or bulky substitution at one particular residue was critical for this activity profile, and the prototypic protein--Rous sarcoma virus integrase with an S124D substitution--was defective at nonspecifically binding DNA. We have now characterized 19 (including 16 new) mutants that contain one or more aspartic acid substitutions at residues that extend over the surface of the protein and might participate with residue 124 in binding cellular DNA. In particular, every mutant with an aspartate substitution at residue 98 or 128, similar to the original S124D protein, showed improved specific nicking of viral DNA but disturbed nonspecific nicking of nonviral DNA. These data describe a probable cellular-DNA binding platform that involves at least 5 amino acids, in the following order of importance: 124>128>(98, 125)>123. These experimental data are vital for new models of integrase and will contribute to identifying targets for the next generation of integrase inhibitors.

Retroviral integrases that are improved for processing but impaired for joining

Retroviral integrase specifically trims (or processes) the ends of retroviral DNA, then inserts (or joins) these ends into cellular DNA nonspecifically. We previously showed that Rous sarcoma virus integrase with a serine-to-aspartate substitution at amino acid 124 was markedly improved for processing but dramatically impaired for joining, making it the first mutant to separate the activities of integrase in this way. We now show that placing glutamic acid at this residue has the same effect, whereas asparagine or glutamine, which resemble aspartate and glutamate but without the negatively charged acid group, improved processing and impaired joining to a lesser extent. Placing aspartic acid at either of the adjacent residues 123 or 125 also had an intermediate effect. Thus, the charge, structure, and position of the substitution all contribute to the properties of the S124D protein. Infectivity of virions containing these mutations paralleled the in vitro findings, with substitutions having the greatest effect on joining completely blocking replication. Additional studies indicated the replication-defective viruses were blocked at integration and that the S124D protein is impaired at binding nonviral DNA. These functional, biochemical, and genetic data implicate this particular integrase residue as a key part of the binding site for cellular DNA.

A substitution in rous sarcoma virus integrase that separates its two biologically relevant enzymatic activities

Retroviral integrase prepares viral DNA for integration by removing 2 nucleotides from each end of unintegrated DNA in a reaction referred to as processing. However, it has been known since the processing assay was first described that avian integrases frequently nick 3 nucleotides, as well as 2 nucleotides, from viral DNA ends when reaction mixtures contain Mn2+. We now report that specificity for the biologically relevant "-2" site is enhanced when the serine at amino acid 124 of Rous sarcoma virus (RSV) integrase is replaced by alanine, valine, glycine, lysine, or aspartate. The protein with a serine-to-aspartate substitution exhibited especially high fidelity for the correct site, as evidenced by a ratio of -2 nicks to -3 nicks that was more than 40-fold greater than that for the wild-type enzyme in reactions with Mn2+. Even with Mg2+, the substituted proteins exhibited greater specificity than the wild type, especially the S124D protein. Moreover, this protein was more efficient than the wild type at processing viral DNA ends. Unexpectedly, however, the S124D protein was significantly impaired at catalyzing the insertion of viral DNA ends in reactions with Mn2+ and joining was undetectable in reactions with Mg2+. Thus, the S124D protein has separated the processing and joining activities of integrase. Similar results were found for human immunodeficiency virus integrase with the analogous substitution. No proteins with comparable properties have been described. Moreover, RSV virions containing integrase with the S124D mutation were unable to replicate in cell cultures. Together, these data suggest that integrase has evolved to have submaximal processing activity so that it can also catalyze DNA joining.

An amino acid in the central catalytic domain of three retroviral integrases that affects target site selection in nonviral DNA

Integrase can insert retroviral DNA into almost any site in cellular DNA; however, target site preferences are noted in vitro and in vivo. We recently demonstrated that amino acid 119, in the alpha2 helix of the central domain of the human immunodeficiency virus type 1 integrase, affected the choice of nonviral target DNA sites. We have now extended these findings to the integrases of a nonprimate lentivirus and a more distantly related alpharetrovirus. We found that substitutions at the analogous positions in visna virus integrase and Rous sarcoma virus integrase changed the target site preferences in five assays that monitor insertion into nonviral DNA. Thus, the importance of this protein residue in the selection of nonviral target DNA sites is likely to be a general property of retroviral integrases. Moreover, this amino acid might be part of the cellular DNA binding site on integrase proteins.

Characteristics of bulimic patients whose parents do or do not abuse alcohol

OBJECTIVES

This study attempts to understand the effects of a parental history of alcohol abuse on the psychopathology and symptoms of bulimia nervosa (BN).

METHOD

The study involved 121 female BN patients consecutively admitted to the Eating Disorders Unit of the University Hospital of Bellvitge. The sample was divided post hoc into two subgroups on the basis of the presence (PAA, n=25) or not of parental abuse of alcohol (NPAA, n=96). All of the patients fulfilled the DSM-IV criteria for BN.

EVALUATION

The assessment measures were the Eating Attitudes Test (EAT-40), the Eating Disorders Inventory (EDI), the Bulimic Investigatory Test Edinburgh (BITE), the Body Shape Questionnaire (BSQ) and Beck Depression Inventory (BDI), as well as clinical and psychopathological variables.

RESULTS AND CONCLUSIONS

Only 7.4% of the patients reported current alcohol abuse and this correlated positively with the presence of other impulsive behaviours (p<0.001). Furthermore, PAA was observed in 20.7% of cases. When the PAA and NPAA subgroups were compared, no significant differences were found in the symptomatological or psychopathological variables, but the PAA group showed more frequent parental obesity (p<0.001) and its members lived less frequently with their parents (p<0.001). The results of this study suggest that there is little correlation between parental abuse of alcohol and the severity of BN.

Activity of HIV-1 integrases recovered from subjects with varied rates of disease progression

We recently described 102 HIV-1 integrase sequences that were amplified from blood cells or plasma obtained up to 18 years ago from 5 hemophiliacs who later died of AIDS and 5 hemophiliacs subsequently classified as slow or nonprogressors ( J Acquir Immune Defic Syndr Hum Retrovirol 1998;19:99-110). Although the region of the HIV-1 genome that encodes integrase was highly conserved, none of the deduced protein sequences of the patient-derived enzymes matched that of the clade B consensus or standard laboratory integrases. To test the hypothesis that the activity of HIV-1 integrases prevalent within an infected person contributes to the rate of disease progression, we have now expressed and purified these proteins and compared them in various assays. Most of the 75 unique full-length integrase proteins from the 102 clones were enzymatically active. Comparison of proteins derived from samples obtained soon after infection showed that the specificity and extent of viral DNA processing and the amount of DNA joining (the two biologically relevant activities of integrase) did not differ between the two groups of patients. In addition, the relative usage of alternative nucleophiles for processing and the amount of nonspecific nicking catalyzed by the proteins were indistinguishable between the patient groups. Although the patient-derived enzymes often exhibited different patterns of target site preferences compared with the laboratory integrase, there was no correlation with clinical course. Thus, the activities of HIV-1 integrases prevalent within these infected individuals, at least as reflected by standard assays, did not influence or predict the rate of disease progression.

Use of patient-derived human immunodeficiency virus type 1 integrases to identify a protein residue that affects target site selection

To identify parts of retroviral integrase that interact with cellular DNA, we tested patient-derived human immunodeficiency virus type 1 (HIV-1) integrases for alterations in the choice of nonviral target DNA sites. This strategy took advantage of the genetic diversity of HIV-1, which provided 75 integrase variants that differed by a small number of amino acids. Moreover, our hypothesis that biological pressures on the choice of nonviral sites would be minimal was validated when most of the proteins that catalyzed DNA joining exhibited altered target site preferences. Comparison of the sequences of proteins with the same preferences then guided mutagenesis of a laboratory integrase. The results showed that single amino acid substitutions at one particular residue yielded the same target site patterns as naturally occurring integrases that included these substitutions. Similar results were found with DNA joining reactions conducted with Mn(2+) or with Mg(2+) and were confirmed with a nonspecific alcoholysis assay. Other amino acid changes at this position also affected target site preferences. Thus, this novel approach has identified a residue in the central domain of HIV-1 integrase that interacts with or influences interactions with cellular DNA. The data also support a model in which integrase has distinct sites for viral and cellular DNA.

Nucleophile selection for the endonuclease activities of human, ovine, and avian retroviral integrases

Retroviral integrases catalyze four endonuclease reactions (processing, joining, disintegration, and nonspecific alcoholysis) that differ in specificity for the attacking nucleophile and target DNA sites. To assess how the two substrates of this enzyme affect each other, we performed quantitative analyses, in three retroviral systems, of the two reactions that use a variety of nucleophiles. The integrase proteins of human immuno- deficiency virus type 1, visna virus, and Rous sarcoma virus exhibited distinct preferences for water or other nucleophiles during site-specific processing of viral DNA and during nonspecific alcoholysis of nonviral DNA. Although exogenous alcohols competed with water as the nucleophile for processing, the alcohols stimulated nicking of nonviral DNA. Moreover, different nucleophiles were preferred when the various integrases acted on different DNA targets. In contrast, the nicking patterns were independent of whether integrase was catalyzing hydrolysis or alcoholysis and were not influenced by the particular exogenous alcohol. Thus, although the target DNA influenced the choice of nucleophile, the nucleophile did not affect the choice of target sites. These results indicate that interaction with target DNA is the critical step before catalysis and suggest that integrase does not reach an active conformation until target DNA has bound to the enzyme.

Subterminal viral DNA nucleotides as specific recognition signals for human immunodeficiency virus type 1 and visna virus integrases under magnesium-dependent conditions

Many reports describe the characteristics of susceptible viral DNA substrates to various retroviral integrases during in vitro reactions in which manganese serves as the divalent cation cofactor for site-specific nicking. However, manganese is known to alter the specificity of some endonucleases and magnesium may be the divalent cation used during retroviral integration in vivo. To address these concerns, we identified conditions under which the integrases of human immunodeficiency virus type 1 and visna virus were optimally active with magnesium (the first time such activity was shown for visna virus integrase) and used these conditions to test the susceptibility of a series of oligodeoxynucleotide substrates. The data show that two base pairs immediately internal to the conserved CA dinucleotide near the termini of retroviral DNA are selectively recognized by the two integrases and that the final six base pairs of viral DNA contain sufficient sequence information for specific recognition and cleavage by each enzyme. The results validate the importance of the subterminal viral DNA positions even in the presence of magnesium and identify viral DNA positions that functionally interact with integrase. The data obtained under magnesium-dependent conditions, which were obtained with substrates containing single and multiple base-pair substitutions and two different retroviral integrases, are consistent with those previously obtained with manganese. Thus, the large body of manganese-dependent data identifying terminal viral DNA positions that are important in substrate recognition by various integrases likely reflects interactions that are biologically relevant.

Mapping target site selection for the non-specific nuclease activities of retroviral integrase

To identify the parts of retroviral integrase that interact with its DNA substrates, we compared the patterns of target site usage by chimeric enzymes and protein fragments in assays that reveal integrase's non-specific nuclease activities. The central region of 12 chimeric proteins between the human immunodeficiency virus type 1 and visna virus integrases was found to be responsible for selecting non-viral target DNA sites when small alcohols provide the attacking nucleophilic OH group during non-specific alcoholysis assays. Testing deletion derivatives of the integrase protein in this assay, which has similarities to the DNA joining reaction that occurs during retroviral integration, defined a smaller central domain that is sufficient for activity. Thus, this core domain likely contains both the host DNA site and the nucleophile site. Surprisingly, the region of integrase responsible for selecting non-viral target DNA sites when the viral DNA end is the attacking nucleophile could not similarly be mapped with the standard oligonucleotide joining assay. We therefore tested the proteins in a more sensitive assay that displays preferred sites of viral DNA insertion in a plasmid DNA target. All 12 chimeras yielded novel patterns compared with the wild-type enzymes in this assay, although local insertion patterns indicated that the central domain plays an important role in target site selection. Together, these data suggest that other protein regions must be involved when the attacking nucleophilic group is provided by viral DNA. Because specific recognition of viral DNA ends was previously mapped to the central domain, two different regions of integrase must interact with retroviral DNA.

Substrate recognition by retroviral integrases

Substrate recognition by the retroviral IN enzyme is critical for retroviral integration. To catalyze this recombination event, IN must recognize and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity. Although particular sequences at the viral DNA termini are recognized by IN, many host DNA sequences can serve as the target for integration. Over the last decade, both in vitro and in vivo data have contributed to our understanding of how IN recognizes its substrates. This review provides an overview of the sequence and structure requirements for recognition of viral and host DNA by different retroviral INs and discusses recent progress in mapping protein domains involved in these interactions.

Engagement and outcome in the treatment of bulimia nervosa: first phase of a sequential design comparing motivation enhancement therapy and cognitive behavioural therapy

Despite the major advances in the development of treatments for bulimia nervosa, drop-outs and a lack of engagement in treatment, continue to be problems. Recent studies suggest that the transtheoretical model of change may be applicable to bulimia nervosa. The aim of this study was to examine the roles of readiness to change and therapeutic alliance in determining engagement and outcome in the first phase of treatment. One hundred and twenty five consecutive female patients meeting DSM-IV criteria for bulimia nervosa took part in a randomised controlled treatment trial. The first phase of the sequential treatment compared four sessions of either cognitive behavioural therapy (CBT) or motivational enhancement therapy (MET) in engaging patients in treatment and reducing symptoms. Patients in the action stage showed greater improvement in symptoms of binge eating than did patients in the contemplation stage. Higher pretreatment scores on action were also related to the development of a better therapeutic alliance (as perceived by patients) after four weeks. However, pretreatment stage of change did not predict who dropped out of treatment. There were no differences between MET and CBT in terms of reducing bulimic symptoms or in terms of developing a therapeutic alliance or increasing readiness to change. The results suggest that the transtheoretical model of change may have some validity in the treatment of bulimia nervosa although current measures of readiness to change may require modification. Overall, readiness to change is more strongly related to improvement and the development of a therapeutic alliance than the specific type of treatment.

Analysis of a large collection of natural HIV-1 integrase sequences, including those from long-term nonprogressors

A large collection of natural HIV-1 integrase (IN) sequences has not previously been described. We reasoned that analysis of such sequences would address whether natural variation of HIV-1 IN contributes to the pathogenesis of AIDS and might also identify amino acid residues important for IN function. Sequences encoding HIV-1 IN were amplified from cryopreserved lymphocytes or plasma obtained at different times from 10 hemophilia patients who had been observed for up to 17 years. The region of the HIV-1 genome that encodes the 288-amino acid IN protein was sequenced from a total of 102 clones; information was obtained for 99.97% of 29,478 amino acid positions. Phylogenetic analysis indicated that patient samples were unique. Interpatient nucleic acid distances ranged from 0.8% to 4.9%, highlighting the tight conservation of this genomic region. No major differences were found between DNA and RNA or between early and late time points from the same patient. Significantly, no amino acid changes that might account for the variable rate of disease progression between patients were evident. Only one amino acid substitution involved a highly conserved residue known to be important for enzymatic activity. However, several interesting amino acid substitutions were noted, including residues within the C-terminal region of the protein for which sequence comparisons between animal retroviruses have not been very informative. These results should encourage the pursuit of anti-integrase therapies, especially inasmuch as the apparent biologic constraints on the IN sequence may deter the development of drug resistance.

Mapping viral DNA specificity to the central region of integrase by using functional human immunodeficiency virus type 1/visna virus chimeric proteins

We previously described the construction and analysis of the first set of functional chimeric lentivirus integrases, involving exchange of the N-terminal, central, and C-terminal regions of the human immunodeficiency virus type 1 (HIV-1) and visna virus integrase (IN) proteins. Based on those results, additional HIV-1/visna virus chimeric integrases were designed and purified. Each of the chimeric enzymes was functional in at least one oligonucleotide-based IN assay. Of a total of 12 chimeric IN proteins, 3 exhibit specific viral DNA processing, 9 catalyze insertion of viral DNA ends, 12 can reverse that reaction, and 11 are active for nonspecific alcoholysis. Functional data obtained with the processing assay indicate that the central region of the protein is responsible for viral DNA specificity. Target site selection for nonspecific alcoholysis again mapped to the central domain of IN, confirming our previous data indicating that this region can position nonviral DNA for nucleophilic attack. However, the chimeric proteins created patterns of viral DNA insertion distinct from that of either wild-type IN, suggesting that interactions between regions of IN influence target site selection for viral DNA integration. The results support a new model for the functional organization of IN in which viral DNA initially binds nonspecifically to the C-terminal portion of IN but the catalytic central region of the enzyme has a prominent role both in specific recognition of viral DNA ends and in positioning the host DNA for viral DNA integration.

Influence of subterminal viral DNA nucleotides on differential susceptibility to cleavage by human immunodeficiency virus type 1 and visna virus integrases

A comparison of the extents of site-specific cleavage of U5 and U3 viral DNA termini by the integrases of human immunodeficiency virus type 1 and visna virus guided the quantitative testing of oligonucleotide substrates containing specific base substitutions. The simultaneous exchange of positions 5 and 6 between U3 substrates switched the patterns of differential susceptibility to the two integrases. The activity of visna virus integrase was more dependent on the identity of position 5 adjacent to the invariant CA bases than on position 6, whereas human immunodeficiency virus type 1 integrase appeared to interact even more critically with position 6. Although the paired natural substrates of most lentiviral integrases match at positions 7 and 8, these bases were not important for susceptibility of U5 substrates. In fact, the final six U5 positions contained all of the sequence information necessary for susceptibility. These results suggest that constraints other than integration influence the terminal inverted repeats of retroviral DNA.

Nonspecific alcoholysis, a novel endonuclease activity of human immunodeficiency virus type 1 and other retroviral integrases

Retroviral integrase (IN) exhibits a previously unrecognized endonuclease activity which we have termed nonspecific alcoholysis. This action occurred at every position in nonviral DNA sequences except those near 5' ends and is clearly distinguished from, and was not predicted by, the site-specific alcoholysis activity previously described for IN at the processing site near viral DNA termini. The integrases of human immunodeficiency virus type 1, visna virus, and Rous sarcoma virus exhibited different target site preferences in this new assay. The isolated central domain of human immunodeficiency virus type 1 IN preferred the same sites as the full-length protein. Nonspecific alcoholysis may provide insights into the structure and function of IN and other endonucleases and suggests that stimulators of some activities possessed by retroviral enzymes should be sought as antiviral agents.

Issues and concerns associated with different risk models for eating disorders

OBJECTIVE

The present paper examines issues and concerns associated with different risk models in identifying individuals who may be vulnerable for eating disorders.

METHOD

Studies were located by computerized search and the authors' knowledge of the literature. For the purposes of this paper, different risk models are grouped according to three types of sample selection criteria: exposure to environmental pressures toward thinness, parental psychopathology, and intraindividual characteristics. Intraindividual characteristics were subdivided into biological and behavior vulnerability markers, and within the behavior risk approach, symptom and nonsymptom risk models were further identified.

RESULTS

Our literature review indicates that risk research on eating disorders is still in its formative years. More well-planned prospective risk studies are needed.

CONCLUSIONS

Among these risk models, the nonsymptom risk approach, which defines risk on the basis of nonsymptom vulnerability markers, represents one of the more promising avenues for future risk research and deserves further exploration.

Mapping domains of retroviral integrase responsible for viral DNA specificity and target site selection by analysis of chimeras between human immunodeficiency virus type 1 and visna virus integrases

Human immunodeficiency virus type 1 (HIV-1) and visna virus integrases were purified from a bacterial expression system and assayed on oligonucleotide substrates derived from each terminus of human immunodeficiency virus type 1 and visna virus linear DNA. Three differences between the proteins were identified, including levels of specific 3'-end processing, patterns of strand transfer, and target site preferences. To map domains of integrase (IN) responsible for viral DNA specificity and target site selection, we constructed and purified chimeric proteins in which the N-terminal, central, and C-terminal regions of these lentiviral integrases were exchanged. All six chimeric proteins were active for disintegration, demonstrating that the active site in the central region of each chimera maintained a functional conformation. Analysis of endonucleolytic processing activity indicated that the N terminus of IN does not contribute to viral DNA specificity; this function must reside in the central region or C terminus of IN. In the viral DNA integration assay, chimeric proteins gave novel patterns of strand transfer products which did not match that of either wild-type IN. Thus, target site selection with a viral DNA terminus as nucleophile could not be mapped to regions of IN defined by these boundaries and may involve interactions between regions. In contrast, when target site preferences were monitored with a new assay in which glycerol stimulates IN-mediated cleavage of nonviral DNA, chimeras clearly segregated between the two wild-type patterns. Target site selection for this nonspecific alcoholysis activity mapped to the central region of IN. This report represents the first detailed description of functional chimeras between any two retroviral integrases.

Human immunodeficiency virus type 1 quantitative cell microculture as a measure of antiviral efficacy in a multicenter clinical trial

A quantitative cell microculture assay (QMC) was used to measure the human immunodeficiency virus type 1 (HIV-1) peripheral blood mononuclear cell (PBMC)-associated titer in 109 subjects rolled in an open-label phase I/II study of didanosine monotherapy or combination therapy with zidovudine. The titer was inversely correlated with CD4+ cell count at baseline (r = .37, P = .001). After 12 weeks of therapy, subjects showed a significant decreases in virus titer and those with the highest baseline virus titers had the greatest increase in CD4+ cell number (r = .430, P = .002). The QMC assay was more sensitive (98%) for assessing the antiretroviral effect of therapy than was immune complex-dissociated HIV p24 antigen (32%) or plasma culture (3.4%). Estimated sample sizes for phase I/II clinical trials were derived using the within-subject QMC SD of .72 log10 infectious units per 10(6) PMBC.

In vitro activities of purified visna virus integrase

Although integration generally is considered a critical step in the retrovirus life cycle, it has been reported that visna virus, which causes degenerative neurologic disease in sheep, can productively infect sheep choroid plexus cells without detectable integration. To ascertain whether the integrase (IN) of visna virus is an inherently defective enzyme and to create tools for further study of integration of the phylogenetically related human immunodeficiency virus type 1 (HIV-1), we purified visna virus IN by using a bacterial expression system and applied various in vitro oligonucleotide-based assays to studying this protein. We found that visna virus IN demonstrates the full repertoire of in vitro functions characteristic of retroviral integrases. In particular, visna virus IN exhibits site-specific endonuclease activity following the invariant CA found two nucleotides from the 3' ends of viral DNA (processing activity), joins processed oligonucleotides to various sites on other oligonucleotides (strand transfer or integration activity), and reverses the integration reaction by resolving a complex that mimics one end of viral DNA integrated into host DNA (disintegration activity). In addition, although it has been reported that purified HIV-1 IN cannot specifically nick visna virus DNA ends, purified visna virus IN does specifically process and integrate HIV-1 DNA ends.

Hepatobiliary infections caused by Haemophilus species

Haemophilus species are rarely associated with hepatobiliary infections. We report a case of hepatic abscess caused by Haemophilus paraphrophilus and review the English-language literature for reports of infections of the liver and biliary system caused by Haemophilus species. Most patients identified had predisposing conditions. The pathogenesis of hepatobiliary infections due to Haemophilus species may involve ascending spread from the gastrointestinal tract or hematogenous seeding following oropharyngeal colonization.

High incidence of bronchospasm with regular administration of aerosolized pentamidine

A systematic evaluation of changes in pulmonary status by objective spirometric assessment and subjective rating using visual analog scale was performed in a cohort of 134 patients receiving aerosolized pentamidine (AP) for the prevention of Pneumocystis carinii pneumonia. Significant bronchospasm defined as greater than or equal to 15 percent reduction in the forced expiratory volume in 1 s was noted in 26 of 100 (26 percent) of patients receiving AP alone. Despite the use of salbutamol (albuterol) as concurrent aerosolized treatment in 34 subjects, bronchospasm developed in 9 of 34 (26 percent) of the patients. The subjective respiratory status rating scale was found to be unreliable in correctly predicting the development of bronchospasm. We conclude that a high incidence of bronchospasm is present in patients receiving regular AP administration using an ultrasonic nebulizer as studied, and concurrent administration of salbutamol is not fully protective of this acute adverse pulmonary reaction.

Overlapping retrovirus U5 sequence elements are required for efficient integration and initiation of reverse transcription

A secondary structure in the 5' noncoding region of avian retrovirus RNA, called the U5-leader stem, was shown previously to have a role in initiation of reverse transcription (D. Cobrinik, L. Soskey, and J. Leis, J. Virol. 62:3622-3630, 1988). We now show that an additional RNA secondary structure near the U5 terminus, called the U5-IR stem, is also important for reverse transcription. Mutations that disrupt the U5-IR stem cause a replication defect associated with both a decrease in synthesis of viral DNA in infected cells and a decrease in initiation of reverse transcription in melittin-permeabilized virions. Structure-compensating base substitutions in the U5-IR restore reverse transcription efficiency. In viral DNA, U5-IR sequences are included in the U5 terminal region that functions as a viral integration donor site. When base substitutions are introduced into these sequences, a reduced efficiency of integration in vitro and in vivo is observed. These observations indicate that U5-IR sequences have a structural role in reverse transcription of viral RNA and a sequence-specific role in the integration of viral DNA.

A covalent complex between retroviral integrase and nicked substrate DNA

Purified retroviral integrase (IN) from avian sarcoma-leukosis viruses can appropriately process the termini of linear viral DNA, cleave host DNA in a sequence-independent manner, and catalyze integrative recombination; an exogenous source of energy is not required for these reactions. Using DNA substrates containing radioactive phosphate groups, we demonstrate that IN becomes covalently joined to the new 5' phosphate ends of DNA produced at sites of cleavage. Most of the phosphodiester linkages between IN and DNA involve serine, but some involve threonine. Computer-assisted alignment of 80 retroviral and retrotransposon IN sequences identified one serine that is conserved in all of these proteins and three less-conserved threonine residues. These results identify candidate active-site residues and provide support for the participation of a covalent IN-DNA intermediate in retroviral integration.

The avian retroviral integration protein cleaves the terminal sequences of linear viral DNA at the in vivo sites of integration

The purified integration protein (IN) of avian myeloblastosis virus is shown to nick double-stranded oligodeoxynucleotide substrates that mimic the ends of the linear form of viral DNA. In the presence of Mg2+, nicks are created 2 nucleotides from the 3' OH ends of both the U5 plus strand and the U3 minus strand. Similar cleavage is observed in the presence of Mn2+ but only when the extent of the reaction is limited. Neither the complementary strands nor sequences representing the termini of human immunodeficiency virus type 1 DNA were cleaved at analogous positions. Analysis of a series of substrates containing U5 base substitutions has defined the sequence requirements for site-selective nicking; nucleotides near the cleavage site are most critical for activity. The minimum substrate size required to demonstrate significant activity corresponds to the nearly perfect 15-base terminal inverted repeat. This in vitro activity of IN thus produces viral DNA ends that are joined to host DNA in vivo and corresponds to an expected early step in the integrative recombination reaction. These results provide the first enzymatic support using purified retroviral proteins for a linear DNA precursor to the integrated provirus.

Serious infectious complications of corticosteroid therapy for COPD

We report seven elderly patients with COPD who developed serious infectious complications during prolonged treatment with high doses of corticosteroids. Infections included invasive pulmonary aspergillosis, Herpes simplex stomatitis and esophagitis, cytomegalovirus pneumonia, bacterial sepsis, fungemia and meningitis due to Cryptococcus neoformans. Each of the three patients who developed invasive aspergillus pneumonia died. The efficacy of prolonged therapy with high doses of corticosteroids in patients with COPD is not proven. These cases illustrate the potential for serious infections in patients with COPD treated with corticosteroids.

Properties of avian sarcoma-leukosis virus pp32-related pol-endonucleases produced in Escherichia coli

The gag-pol precursor protein of the avian sarcoma-leukosis virus is processed into three known pol-encoded mature polypeptides; the 95- and 63-kilodalton (kDa) beta and alpha subunits, respectively, of reverse transcriptase and the 32-kDa pp32 protein. The pp32 protein possesses DNA endonuclease activity and is produced from the precursor by two proteolytic cleavage events, one of which removes 4.1 kDa of protein from the C terminus. A 36-kDa protein (p36pol) which retains this C-terminal segment is detectable in small quantities in virions. We have constructed Escherichia coli plasmid clones that express the C-terminal domains of pol corresponding to pp32 and p36. These proteins have been purified by column chromatographic methods to near homogeneity. No significant differences could be detected in the enzymatic properties of the bacterially produced p32pol and p36pol proteins. Both possess DNA endonuclease activity and, like the pp32 protein isolated from virions, can cleave near the junction of two tandem avian sarcoma-leukosis virus long terminal repeats in double-stranded supercoiled DNA substrates. In the presence of Mg2+, both p32pol and viral pp32 cleave either strand of DNA 2 nucleotides 5' to the junction.

Molluscum contagiosum and the acquired immunodeficiency syndrome: clinical and immunological details of two cases

We report here the clinical and immunological findings in two patients with molluscum contagiosum poxvirus infection and the acquired immunodeficiency syndrome (AIDS). These cases support earlier evidence that the molluscum contagiosum virus may act as cases support earlier evidence that the molluscum contagiosum virus may act as an opportunistic pathogen. There is now evidence that members of all five families of double stranded DNA-containing human viruses have been associated with unusual clinical manifestations in AIDS patients, and the significance of DNA virus infections in patients with AIDS is discussed.

Defective postbinding lysis underlies the impaired natural killer activity in factor VIII-treated, human T lymphotropic virus type III seropositive hemophiliacs

We investigated the diminished natural killer (NK) activity in human T lymphotropic virus type III (HTLV-III) seropositive hemophiliacs. Despite normal percentages of NK cells, lymphocytes from five hemophiliacs showed impaired NK activity against K-562 tumor cells in 4-h chromium release microcytotoxicity assays. For example, at an effector-to-target cell ratio of 10:1, cells from patients caused 21.7 +/- 2.5% lysis of tumor targets compared with 47.9 +/- 5.1% lysis by cells from controls (mean +/- SEM, P less than 0.005). Cells from patients were as cytotoxic in 18 h as were cells from controls in 4 h. Binding to tumor targets was not impaired since 11.0 +/- 1.5% of cells from patients and 11.1 +/- 1.3% of cells from controls bound to K-562 cells. Patients' binding cells, however, showed defective killing of attached tumor cells at all time points tested from 0 to 18 h. At 4 h, for example, patients' cells had lysed 10.9 +/- 2.1% of attached tumor cells compared with 26.3 +/- 3.3% lysis by controls' cells (P less than 0.005). The percentage of lymphocytes which were active NK cells (i.e., cells that bound and lysed a tumor cell) was always lower for patients than for controls (1.17 +/- 0.25% vs. 2.82 +/- 0.33%, P less than 0.005). Two methods for estimating recycling of effector cells against multiple target cells demonstrated that active NK cells from patients could recycle as well as those from controls (approximately 3-4 times in 4 h). Mixing experiments showed no evidence for cellular suppression of NK activity. The lytic function of NK cells from HTLV-III seropositive hemophiliacs is thus heterogeneous. This is characterized by a defect in post-binding lysis, with relative sparing of binding capability and recycling capacity.