Role of Gag mutations in PI resistance in the Swiss HIV cohort study: bystanders or contributors?

Background: HIV Gag mutations have been reported to confer PI drug resistance. However, clinical implications are still controversial and most current genotyping algorithms consider solely the protease gene for assessing PI resistance. Objectives: Our goal was to describe for HIV infections in Switzerland the potential role of the C-terminus of Gag (NC-p6) in PI resistance. We aimed to characterize resistance-relevant mutational patterns in Gag and protease and their possible interactions. Methods: Resistance information on plasma samples from 2004-12 was collected for patients treated by two diagnostic centres of the Swiss HIV Cohort Study. Sequence information on protease and the C-terminal Gag region was paired with the corresponding patient treatment history. The prevalence of Gag and protease mutations was analysed for PI treatment-experienced patients versus PI treatment-naive patients. In addition, we modelled multiple paths of an assumed ordered accumulation of genetic changes using random tree mixture models. Results: More than half of all PI treatment-experienced patients in our sample set carried HIV variants with at least one of the known Gag mutations, and 17.9% (66/369) carried at least one Gag mutation for which a phenotypic proof of PI resistance by in vitro mutagenesis has been reported. We were able to identify several novel Gag mutations that are associated with PI exposure and therapy failure. Conclusions: Our analysis confirmed the association of Gag mutations, well known and new, with PI exposure. This could have clinical implications, since the level of potential PI drug resistance might be underestimated.

Primary resistance to integrase strand-transfer inhibitors in Europe.

OBJECTIVES: The objective of this study was to define the natural genotypic variation of the HIV-1 integrase gene across Europe for epidemiological surveillance of integrase strand-transfer inhibitor (InSTI) resistance. METHODS: This was a multicentre, cross-sectional study within the European SPREAD HIV resistance surveillance programme. A representative set of 300 samples was selected from 1950 naive HIV-positive subjects newly diagnosed in 2006-07. The prevalence of InSTI resistance was evaluated using quality-controlled baseline population sequencing of integrase. Signature raltegravir, elvitegravir and dolutegravir resistance mutations were defined according to the IAS-USA 2014 list. In addition, all integrase substitutions relative to HXB2 were identified, including those with a Stanford HIVdb score ≥ 10 to at least one InSTI. To rule out circulation of minority InSTI-resistant HIV, 65 samples were selected for 454 integrase sequencing. RESULTS: For the population sequencing analysis, 278 samples were retrieved and successfully analysed. No signature resistance mutations to any of the InSTIs were detected. Eleven (4%) subjects had mutations at resistance-associated positions with an HIVdb score ≥ 10. Of the 56 samples successfully analysed with 454 sequencing, no InSTI signature mutations were detected, whereas integrase substitutions with an HIVdb score ≥ 10 were found in 8 (14.3%) individuals. CONCLUSIONS: No signature InSTI-resistant variants were circulating in Europe before the introduction of InSTIs. However, polymorphisms contributing to InSTI resistance were not rare. As InSTI use becomes more widespread, continuous surveillance of primary InSTI resistance is warranted. These data will be key to modelling the kinetics of InSTI resistance transmission in Europe in the coming years.

HIV-1 subtype is an independent predictor of reverse transcriptase mutation K65R in HIV-1 patients treated with combination antiretroviral therapy including tenofovir.

Subtype-dependent selection of HIV-1 reverse transcriptase resistance mutation K65R was previously observed in cell culture and small clinical investigations. We compared K65R prevalence across subtypes A, B, C, F, G, and CRF02_AG separately in a cohort of 3,076 patients on combination therapy including tenofovir. K65R selection was significantly higher in HIV-1 subtype C. This could not be explained by clinical and demographic factors in multivariate analysis, suggesting subtype sequence-specific K65R pathways.

Treatment with interleukin-18 binding protein ameliorates Toxoplasma gondii-induced small intestinal pathology that is induced by bone marrow cell-derived interleukin-18.

Peroral infection with Toxoplasma gondii results in a Th1-type immunopathology characterized by small intestinal necrosis and is dependent on IL-18. In the present study, we investigated whether treatment with IL-18 binding protein (IL-18bp) prevents ileal pathology. We observed increased expression of IL-18bp in intestinal biopsies of mice following infection. Whereas small intestines of control mice showed severe necrosis with complete destruction of the small intestinal architecture, mice treated with IL-18bp daily displayed only mild inflammatory changes including flattening of villi and edema in the space between the epithelium and lamina propria. Small intestinal parasite loads and concentrations of pro-inflammatory cytokines did not differ in control and IL-18bp-treated mice. Binding of IL-18 to immobilized IL-18bp revealed a remarkably slow dissociation rate, indicating high affinity. Using chimeric mice we observed that bone marrow-derived rather than stromal cells were the primary source of IL-18 that resulted in small intestinal pathology following peroral infection with T. gondii. In conclusion, the results presented here suggest that IL-18bp may be an effective and safe treatment for small intestinal inflammation. Antigen-presenting rather than epithelial cells appear to be the main source of IL-18 in T. gondii-induced small intestinal inflammation.

Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study).

OBJECTIVES: The EuResist expert system is a novel data-driven online system for computing the probability of 8-week success for any given pair of HIV-1 genotype and combination antiretroviral therapy regimen plus optional patient information. The objective of this study was to compare the EuResist system vs. human experts (EVE) for the ability to predict response to treatment. METHODS: The EuResist system was compared with 10 HIV-1 drug resistance experts for the ability to predict 8-week response to 25 treatment cases derived from the EuResist database validation data set. All current and past patient data were made available to simulate clinical practice. The experts were asked to provide a qualitative and quantitative estimate of the probability of treatment success. RESULTS: There were 15 treatment successes and 10 treatment failures. In the classification task, the number of mislabelled cases was six for EuResist and 6-13 for the human experts [mean±standard deviation (SD) 9.1±1.9]. The accuracy of EuResist was higher than the average for the experts (0.76 vs. 0.64, respectively). The quantitative estimates computed by EuResist were significantly correlated (Pearson r=0.695, P<0.0001) with the mean quantitative estimates provided by the experts. However, the agreement among experts was only moderate (for the classification task, inter-rater κ=0.355; for the quantitative estimation, mean±SD coefficient of variation=55.9±22.4%). CONCLUSIONS: With this limited data set, the EuResist engine performed comparably to or better than human experts. The system warrants further investigation as a treatment-decision support tool in clinical practice.

A protein antibiotic in the phage Qbeta virion: diversity in lysis targets.

A(2), a capsid protein of RNA phage Qbeta, is also responsible for host lysis. A(2) blocked synthesis of murein precursors in vivo by inhibiting MurA, the catalyst of the committed step of murein biosynthesis. An A(2)-resistance mutation mapped to an exposed surface near the substrate-binding cleft of MurA. Moreover, purified Qbeta virions inhibited wild-type MurA, but not the mutant MurA, in vitro. Thus, the two small phages characterized for their lysis strategy, Qbeta and the small DNA phage phiX174, effect host lysis by targeting different enzymes in the multistep, universally conserved pathway of cell wall biosynthesis.

The lysis protein E of phi X174 is a specific inhibitor of the MraY-catalyzed step in peptidoglycan synthesis.

Coliphage phi X174 encodes a single lysis protein, E, a 91-amino acid membrane protein. Dominant mutations have been isolated in the host gene mraY that confer E resistance. mraY encodes translocase I, which catalyzes the formation of the first lipid intermediate in bacterial cell wall synthesis, suggesting a model in which E inhibits MraY and promotes cell lysis in a manner analogous to cell wall synthesis inhibitors like penicillin. To test this model biochemically, we monitored the effect of E on cell wall synthesis in vivo and in vitro. We find that expression of Emyc, encoding an epitope-tagged E protein, from a multicopy plasmid inhibits the incorporation of [(3)H]diaminopimelic acid into cell wall and leads to a profile of labeled precursors consistent with MraY inhibition. Moreover, we find that membranes isolated after Emyc expression are drastically reduced in MraY activity, whereas the activity of Rfe, an enzyme in the same superfamily, was unaffected. We therefore conclude that E is indeed a cell wall synthesis inhibitor and that this inhibition results from a specific block at the MraY-catalyzed step in the pathway.

Purification and biochemical characterization of the lambda holin.

Holins are small phage-encoded cytoplasmic membrane proteins, remarkable for their ability to make membranes permeable in a temporally regulated manner. The purification of S105, the lambda holin, and one of the two products of gene S is described. Because the wild-type S105 holin could be only partially purified from membrane extracts by ion-exchange chromatography, an oligohistidine tag was added internally to the S105 sequence for use in immobilized metal affinity chromatography. An acceptable site for the tag was found between residues 94 and 95 in the highly charged C-terminal domain of S. This allele, designated S105H94, had normal lysis timing under physiological expression conditions. The S105H94 protein was overproduced, purified, and characterized by circular dichroism spectroscopy, which revealed approximately 40% alpha-helix conformation, consistent with the presence of two transmembrane helices. The purified protein was then used to achieve release of fluorescent dye loaded in liposomes in vitro, whereas protein from an isogenic construct carrying an S mutation known to abolish hole formation was inactive in this assay. These results suggest that S is a bitopic membrane protein capable of forming aqueous holes in bilayers.

ATP regeneration by thermostable ATP synthase.

We investigated the possibility of using thermostable ATP synthase (TF(0)F(1)) for a new ATP regeneration method. TF(0)F(1) was purified from a thermophilic bacterium, PS3, and reconstituted into liposomes. ATP synthesis experiments showed that TF(0)F(1) liposomes could synthesize ATP in micromole concentrations by acid-base change. The acid-base change was repeated six times over an 11-day period with no detectable loss of activity at the reaction temperature (45 degrees C). Given these encouraging results, we conceptualized and modeled a system to synthesize ATP using ATP synthase with energy supplied by acid-base change. In this system, liposomes containing ATP synthase are immobilized on small glass spheres that facilitate separation of buffers from the liposomes after the acid-base change. Compared to an alternate system that uses membranes to separate the buffers from the liposomes, the glass spheres reduce inefficient mixing of acidic and basic buffers during the acid-base change. To increase the ATP synthesis yield, this system uses electrodialysis to regenerate a potassium gradient after the acid-base change. It also employs water-splitting electrodialysis to regenerate KOH and HCl required to adjust the pH of acidic and basic buffers. All reagents are recycled, so electrical energy is the only required input.

[Using the method of central relationship conflict topic in a study of the process and outcome of long-term inpatient group psychotherapy]. / Anwendung der Methode des Zentralen Beziehungskonfliktthemas (ZBKT) in einer Untersuchung zum Prozess und Ergebnis stationärer Langzeitgruppenpsychotherapie.

Within a research project dealing with the process and outcome of inpatient group psychotherapy, the core conflictual relationship theme method (CCRT) was used to determine if the central basic interpersonal problems of patients differ in comparison of individual pre- and postreatment sessions, if the CCRT determined at the beginning of treatment is related to outcome, and if there is a similarity between the CCRT from individual and group sessions. Comparisons of the CRRT(-components) from the beginning and the end of treatment (related to 19 patients) indicated marked changes on the levels of wishes and responses from others as well as "formal" changes of the narratives (temporal relations as well as the objects mentioned). The second part of the study (n = 26) revealed differences between subgroups determined on the basis of differential outcome measures with respect to the structure of their conflicts. The similarity of the CCRT from group and individual sessions which was studied for nine patients appeared to be moderate. The study revealed that the CCRT might need some minor revisions but appears to be an important method to thoroughly describe the effects of psychotherapies.

Threats, protests greet conference.

PIP: In preparation for the 1994 International Conference on Population and Development, Egypt has deployed 14,000 police to protect participants from threatened violence. The Vatican has joined forces with Muslim fundamentalists to condemn the conference as a vehicle for imposing Western ideals, particularly abortion, on Third world countries. In addition, the opposition is raising the specter of a descent of homosexuals onto Cairo and Muslim fundamentalists have threatened to murder Western representatives. A suit filed by Islamic lawyers, aimed at stopping the conference, failed. Sudan and Saudi Arabia plan to boycott the conference, and it remains uncertain whether Libya will be represented. Conference organizers have not been deterred by the threats and note that the controversy has drawn public attention to the central issues under debate.^ieng

U.S. tries to defuse abortion debate.

PIP: In an apparent attempt to defuse acrimony at the International Conference on Population and Development, underway in Cairo, the US delegation is softening its stance on abortion decriminalization. US Vice President Al Gore, the head of the delegation, has stated, "The United States does not seek to establish a new international right to abortion, and we do not believe that abortion should be encouraged as a method of family planning." The Vatican and Muslim fundamentalists remain concerned, however, that the Cairo gathering represents an opportunity for the US to impose its abortion rights agenda on other countries. The draft prepared for presentation to the conference makes no explicit mention of legal abortion. Rather, it advocates safe motherhood, complete reproductive health care, and fertility control-- phrases the Vatican insists mask an intent to promote the use of abortion for family planning.^ieng

Refugees, immigrants aggravate population controls.

PIP: The UN Conference on Population and Development in Cairo in 1994 will discuss the pressure of population growth, the increase in the numbers of refugees, and labor migration between developing and developed countries. Population movement has been estimated as 1/50 in the world, regardless of reason. The impact of movement can be to augment a declining work force or to strain resources in poor countries, such as Zaire or Thailand. Rich countries may also respond with resentment and political turmoil, as is currently occurring in Germany. The tendency is to respond after the fact. Rwanda could be used as an example of a country with population pressure on land resources, which has exacerbated ethnic conflict. If the world in 1994 shows this pattern, the concern is that the future prospects are likely to reflect even greater turmoil and migration. The number of refugees has already increased from 2.5 million in 1970 to 20 million today. The head of the UN Commission on Refugees views the end of the Cold War as responsible for exposed and heightened ethnic and tribal rivalry. Migration movement is viewed as the desire for an improvement in quality of life. Significant shifts are to developed countries such as the US, Canada, Australia, and New Zealand. The 1994 UN Plan of Action offers concrete recommendations about mass movements. Recommendations are made to assure host country's assurances of protection in work and safety for migrants, removal of restrictive banking practices that impede monetary transfers between countries, and arrangements for temporary migration. Host countries are urged to provide assistance for return migration. Rights and equal treatment with nationals should be extended to longterm migrants. Each country has a right to enact migration restrictions. Smuggling of immigrants should be stopped through international cooperation. Countries of origin have a responsibility to readmit nationals rejected by other countries. There are few recommendations for dealing with migration related to fear for one's life. Many countries are not open to offers of political asylum, when there are so many seekers and there is misuse of asylum procedures. Refugee solutions should reflect the underlying conditions of war and famine.^ieng

Focus of population conference is turning to women.

PIP: The empowerment of women is emerging as a central theme at the 1994 International Conference on Population and Development. A representative of the United Nations Development Fund for Women, Roxanna Carrillo, notes, "For the first time, the United Nations and the world is now working with women. Every single population policy in the last 30 years has failed because it wasn't done with participation of women." Concern has been expressed, however, that this emphasis on women's issues will shift attention from broader population issues and alienate participants from male-dominated Third World countries. Muslim Fundamentalists, for example, believe that all family planning decisions should be made by the husband. Even if a women's agenda is adopted, female delegates face the task of ensuring that governments follow though on its implementation.^ieng

Differential expression of the cytotoxic and hemolytic activities of the ApxIIA toxin from Actinobacillus pleuropneumoniae.

The ApxIIA protein secreted from Actinobacillus pleuropneumoniae is both hemolytic and cytotoxic. However, when the cloned apxII operon is expressed in Escherichia coli, two forms of the ApxIIA protein can be recovered. Toxin which remains intracellular has hemolytic and cytotoxic activities, while toxin that is secreted is cytotoxic with little or no hemolytic activity. This indicates that the cytotoxicity of ApxIIA is independent of its hemolytic activity.

Efficacy of Pasteurella haemolytica subunit antigens in a goat model of pasteurellosis.

The effectiveness of Pasteurella haemolytica biovar A, serovar 1 (Ph1) subunit vaccines was tested in goats, using challenge exposure by transthoracic injection. Twenty-two weanling male Spanish goats were randomly allotted to 4 groups. Six goats were given 2 transthoracic injections into the lung 18 days apart with live Ph1 impregnated in agar beads (positive controls). Six goats were not given injections (negative controls). Five goats were given 2 transthoracic injections into the lung 18 days apart with 4.6 mg of cytotoxin in agar beads. The remaining 5 goats were given 2 IM injections, 18 days apart, into the thigh with 4.6 mg of cytotoxin emulsified in incomplete Freund's adjuvant. Twenty-four days after the second injection, all goats were challenge-exposed to live Ph1 by transthoracic injection into the lung, and 4 days later, all goats were euthanatized and necropsied. Serum neutralizing anticytotoxin titer was measured throughout the experiment. Mean volume of consolidated lung tissue was 0.38 cm3 for the positive control group, 32 cm3 for the negative control group; 19 cm3 for the cytotoxin-lung group; and 88 cm3 for the cytotoxin-adjuvant-IM group. Only the positive control group was protected from Ph1 challenge exposure. The Ph1 cytotoxin subunit vaccine alone appeared to be ineffective, and the anticytotoxin titer was not correlated with protection. In a separate trial, 32 weanling male Spanish goats were randomly allotted to 5 groups. Each was given 2 transthoracic injections into the lung 22 days apart. Six goats were given Ph1 cytotoxin impregnated into agar beads; 6 were given Ph1 lipopolysaccharide impregnated in agar beads; 6 were given Ph1 capsule impregnated in agar beads. Six goats were given agar beads only (negative controls), and 6 were given live Ph1 impregnated into agar beads (positive controls). Twenty days after the second injection, all goats were challenge-exposed to live Ph1 by transthoracic injection into the lung, and 4 days later, all goats were euthanatized and necropsied. Mean volume of consolidated lung tissue was 0.14 cm3 for the positive control group, 7.59 cm3 for the negative control group, 11.21 cm3 for the cytotoxin group, 10.19 cm3 for the lipopolysaccharide group, and 1.6 cm3 for the capsule group. Again, only injection of live Ph1 (positive controls) induced solid protection; however, the capsule subunit vaccine induced partial protection against challenge exposure in this trial. Lipopolysaccharide and cytotoxin subunit vaccines were ineffective in protecting goats against challenge exposure with live Ph1.

Cloning, sequencing and expression of a Pasteurella haemolytica A1 gene encoding a PurK-like protein.

A membrane protein antigen of Pasteurella haemolytica A1 encoded on the recombinant plasmid pYFC13 is isolated and characterized. Nucleotide sequence analysis of the insert DNA in pYFC13 identified the gene mpa1, which codes a protein of approximately 45 kDa without signal sequence. The deduced amino acids from the DNA sequence are homologous to Bacillus subtilis PurK by 29.4%; to Schizosaccharomyces pombe Pur6 by 29.34%, to Saccharomyces cerevisiae Pur6 by 25.867%; and to E. coli PurK by 25.223% identity, respectively. The purK and pur6 from these organisms are responsible for the activity of 5'-phosphoribosyl- 5-amino-4-imidazole carboxylase which is involved in de novo purine biosynthesis. The protein was over-expressed in E. coli by its own promoter. The antigen we designated as Mpa1, could be localized to the cytoplasmic membrane of both P. haemolytica A1 and E. coli TB1 harbored pYFC13. The Mpa1 was antigenic in rabbit and in cattle since both animals produced antibody against this protein.

Characterization of a neutralizing monoclonal antibody to Pasteurella haemolytica leukotoxin.

Six hybridoma clones producing monoclonal antibodies (MAbs) reactive with Pasteurella haemolytica A1 leukotoxin were derived from mice immunized with leukotoxin excised from sodium dodecyl sulfate-polyacrylamide gels. Of the six MAbs, only one, Ltx-2, neutralized leukotoxin in a BL-3 cell cytotoxicity assay. MAb Ltx-2 blocked association of A1 leukotoxin to BL-3 cells, as measured by flow cytometric analysis. The epitope recognized by Ltx-2 was localized to the carboxyl half of the native protein, between residues 450 and 939, by Western immunoblot analysis of CNBr fragments. Further analysis with leukotoxin deletion proteins indicated either that the Ltx-2-reactive epitope was localized in the carboxyl portion of the leukotoxin between amino acids 768 and 939 or that this region influences MAb recognition of the epitope. MAb Ltx-2 was tested for neutralizing activity against leukotoxin produced by P. haemolytica serotypes 1 through 12. The MAb neutralized leukotoxin produced by all of the A biotype isolates (serotypes 1, 5, 6, 7, 8, 9, and 12), with the exception of serotype A2, but did not neutralize any T biotype leukotoxin tested (T3, T4, or T10). The results indicate that MAb Ltx-2 neutralizes leukotoxin by interfering with target cell association and that the MAb-specific epitope is either not present or not critical for function in the leukotoxin produced by P. haemolytica serotypes A2, T3, T4, and T10.

Characterization of plasmids with antimicrobial resistant genes in Pasteurella haemolytica A1.

Two R plasmids, pYFC1 and pYFC2, from Pasteurella haemolytica A1 encoding sulfonamide, streptomycin (pYFC1), and ampicillin (pYFC2) resistances have been characterized by restriction endonuclease digestions, subcloning or DNA sequencing. pYFC1 consists of 4225 bp and is 51.9% in AT content. Physical mapping indicated a highly conserved region of restriction sites among pYFC1, RSF1010, pGS05, pFM739, pHD148 and pGS03B. pYFC1 encoded a dihydropteroate synthase (29.8 kDa), and streptomycin kinase (29.6 kDa) which is homologous in nucleotide sequences or deduced amino acid sequence to that encoded by a broad-host range IncQ plasmid RSF1010. Based on the primary structure of pYFC1, the sulfonamide and streptomycin genes are derived from the same ancestor of RSF1010. pYFC2 is similar to the plasmid from P. haemolytica LNPB51 isolated in France by partial restriction enzyme mapping. pYFC1 and pYFC2 have the same size of 4.2 kbp.